On episode #185 of the science show This Week in Virology, Vincent visits with members of the Department of Microbiology and Immunology at Northwestern University School of Medicine to discuss their work on herpesviruses and parainfluenzaviruses.

You can find TWiV #185 at www.twiv.tv.

On episode #184 of the science show This Week in Virology, Vincent, Rich, and Alan consider how to reform the scientific enterprise to make it more effective and robust.

You can find TWiV #184 at www.twiv.tv.

The retrovirus XMRV does not cause prostate cancer or chronic fatigue syndrome – that hypothesis was disproved by the finding that the virus was produced in the laboratory in the 1990s by passage of a prostate tumor in nude mice. A trio of new papers on the virus attempt to address questions about the serological detection of XMRV in prostate cancer, and further emphasize that XMRV is not a human pathogen.

Absence of XMRV and Closely Related Viruses in Primary Prostate Cancer Tissues Used to Derive the XMRV-Infected Cell Line 22Rv1. The human cell line 22Rv1, which was established from a human prostate tumor (CWR22), produces infectious XMRV. It was previously shown that DNA from various passages of the prostate tumor in nude mice (called xenografts), did not contain XMRV, but cells from the mice do contain two related proviruses called PreXMRV-1 and PreXMRV-2 which recombined to form XMRV between 1993-1996. In a new study samples of the original prostate tumor CWR22 were examined for the presence of XMRV or related viruses. PCR assays targeting the viral gag, pol, and env sequences failed to provide evidence of XMRV in CWR22 tissue. These assays could detect endogenous murine leukemia virus DNA in mouse DNA, indicating that the CWR22 tumor contained neither XMRV nor related viruses. In addition, no XMRV sequences were detected when sections from the CWR22 tumor were examined by in situ hybridization. The same assay previously detected XMRV sequences in stromal cells of prostate tumors. The authors conclude that “Our findings conclusively show an absence of XMRV or related viruses in prostate of patient CWR22, thereby strongly supporting a mouse origin of XMRV.”

An important question not addressed by this study is why XMRV was originally detected in multiple prostate tumors obtained from patients at the Cleveland Clinic. The authors seem to be working on this problem, as they state that “…the sequence of XMRV present in 22Rv1 cells is virtually identical with XMRV cloned using human prostate samples, thus suggesting laboratory contamination with XMRV nucleic acid from 22Rv1 cells as the source. Further experiments designed to confirm or refute this hypothesis are currently underway.”

No biological evidence of XMRV in blood or prostatic fluid from prostate cancer patients. Samples from individuals with prostate cancer were tested for the presence of infectious XMRV and for antibodies against the virus. Neither infectious virus nor antibodies were detected in blood plasma (n = 29) or prostate secretions (n = 5). Among these were five specimens that had previously tested positive for XMRV DNA, including two from the original study. The authors conclude that the results “support the conclusion from other studies that XMRV has not entered the human population”.

Susceptibility of human lymphoid tissue cultured ex vivo to Xenotropic murine leukemia virus-related virus (XMRV) infection. Although XMRV is not known to cause human disease, whether it has to potential to do so is unknown. The virus can infect a variety of cultured human cells including peripheral blood mononuclear cells and neuronal cells. In this study the authors placed human tonsillar tissue in culture and infected it with XMRV. Proviral (integrated) DNA could be detected in the cells several weeks after infection and virus particles were released into the medium. However these released viruses could not infect fresh tonsillar tissue, possibly due to modification by innate antiviral restriction factors such as APOBEC, which is known to inhibit XMRV infectivity.

Based on their findings the authors conclude that “laboratories working with XMRV producing cell lines should be aware of the potential biohazard risk of working with this replication-competent retrovirus”.

It is clear that XMRV does not cause chronic fatigue syndrome; the original findings of Lombardi and colleagues linking the virus to this disease have been retracted by the journal. However there are still two papers in the literature that report the presence of XMRV in prostate – the original XMRV discovery paper and one from Ila Singh’s laboratory. In both papers XMRV detection in tissues was accomplished by using serological procedures. Based on the papers summarized here, the assays did not detect XMRV – but a satisfactory explanation for the positive signals has not yet been provided.

On episode #33 of the science show This Week in Microbiology, Vincent, Michael, and Ivo review the requirement for segmented, filamentous bacteria for the induction of a specific type of helper T cell in the gut.

You can find TWiM #33 at microbeworld.org/twim.

On episode #183 of the science show This Week in Virology, Connor Bamford joins the TWiV team to discuss bats as hosts for major mammalian paramyxoviruses.

You can find TWiV #183 at www.twiv.tv.

On episode #182 of the science show This Week in Virology, Michael Imperiale joins the TWiV crew to discuss the recently published influenza H5N1 transmission paper and how it was viewed by the NSABB.

You can find TWiV #182 at www.twiv.tv.

On episode #32 of the science show This Week in Microbiology, Vincent, Elio and Michael speak with Rosie Redfield about her evidence that a bacterium cannot grow on arsenic instead of phosphorus.

If you only listen to one episode of TWiM all year, make it this one – Rosie is terrific!

You can find TWiM #32 at microbeworld.org/twim.

One of two papers on avian influenza H5N1 virus that caused such a furor in the past six months was published today in the journal Nature. I have read it, and I can assure you that the results do not enable the construction of a deadly biological weapon. Instead, they illuminate important requirements for the airborne transmission of influenza viruses among ferrets. Failure to publish this work would have compromised our understanding of influenza viral transmission.

The paper from Kawaoka’s group focuses on the viral hemagglutinin (HA) protein, an important determinant of whether influenza viruses can infect birds or mammals. In the image, the HA is shown as blue ‘spikes’ on the virion surface; a single HA molecule is shown at right. Avian influenza viruses prefer to attach to cells via a specific form of sialic acid that differs from the form bound by mammalian influenza viruses. This difference in receptor preference is one reason why avian influenza viruses do not transmit among mammals.

Kawaoka’s group used a random mutagenesis and selection approach to identify amino acid changes in the avian H5 HA protein that allow it to bind human receptors. These changes are located around the sialic acid binding pocket in the HA head (figure). Some of the amino acid changes were previously known, but there are also some new ones reported, expanding our understanding of how the HA binds sialic acids. Some of the HA amino acid changes allow virus binding to ciliated epithelial cells of the human respiratory tract (wild type H5 HA cannot). All of this is important new information.

The H5 HA genes with these amino acid changes were then substituted for the HA gene in a 2009 H1N1 pandemic virus, and this reassortant virus was inoculated intranasally into ferrets. The viruses did not replicate well in the ferret trachea, but viruses recovered from the animals contained a new change in the HA protein that improves replication. This change (asparagine to aspartic acid at amino acid 158) is known to prevent attachment of a sugar group to the HA and enhance binding to human receptors. Viruses with this change probably have a replicative advantage in ferrets.

A reassortant virus with HA amino acid changes N158D/N224K/Q226L transmitted through the air to 2 of 6 ferrets. Viruses recovered from one of the animals contained a new change in the HA protein, T318I. A virus with four amino acid changes in the H5 HA (N158D/N224K/Q226L/T318I) replicates well in ferrets and transmits efficiently, although the infection is not lethal.

Even more interesting are the results of experiments to understand how these HA amino acid changes affect viral transmission. The N224K/Q226L amino acid changes that shift the HA from avian to human receptor specificity reduce the stability of the HA protein. The N158D and T318I changes, which were selected in ferrets, restore stability of the HA.

There are three key questions concerning this work that must be answered.

Would an H5N1 virus with the changes N158D/N224K/Q226L/T318I transmit among humans? Probably not. The virus tested by the authors derived 7 of 8 RNA segments from a human H1N1 strain, which is well adapted for human transmission. It is likely that changes in other avian influenza viral proteins would be needed for human transmission. It might also be that entirely different changes in the H5 HA are required for transmission in humans compared with ferrets.

Is this information useful for the surveillance of circulating H5N1 strains; specifically, would the emergence of these HA changes signify a virus with pandemic potential? I don’t believe so. These are mutations that enhance the transmission of H5 viruses in ferrets, and their effect in humans is unknown. Ferret transmission experiments are not meant to be predictive of what might occur in humans.

If these results are not predictive of what might happen in humans, why were these experiments done? (to paraphrase Laurie Garret at the New York Academy of Sciences Meeting on Dual Use Research). A substantial portion of this work goes far beyond surveillance of H5N1 strains: it provides a mechanistic framework for understanding what regulates airborne transmission of avian H5 influenza viruses. In the Kawaoka study, amino acid changes that improve the stability of the HA protein were selected for during replication and transmission of the H5 viruses in ferrets. In other words, stability of the HA protein is an important property that allows efficient airborne transmission among ferrets. Additional experiments can now be designed to extend this idea. If such stabilizing changes can be shown to be important for transmission of human strains, then they might be a valuable marker of influenza transmission.

The Kawaoka paper is a significant piece of work that substantially advances our understanding of what viral properties control airborne transmission of influenza viruses. To view it as enabling construction of a bioweapon is highly speculative and fundamentally incorrect.

M. Imai, T. Watanabe, M. Hatta, S.C. Das, M. Ozawa, K. Shinya, G. Zhone, A. Hanson, H. Katsura, S. Watanabe, C. Li, E. Kawakami, S. Yamada, M. Kiso, Y. Suzuki, E.A. Maher, G. Neumann, Y. Kawaoka. 2012. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets.   doi: 10.1038/nature10831.

Nearly four months ago I stood at the front of a crowded classroom at Columbia University and began teaching the third year of my undergraduate virology course. Twice a week we discussed the basic principles of virology, including how virions are built, how they replicate, and how they cause disease. Yesterday was the 26th and last lecture in the course, entitled “H5N1″. In this lecture we covered the recent controversy over the publication of results on adapting avian influenza H5N1 viruses to transmit by the airborne route among ferrets. Fittingly, one of the two papers in question will be published tomorrow.

Each lecture in my virology course has been recorded as a videocast and is available at the course website, at iTunes University, or on Vimeo. Eighty-seven Columbia University undergraduates registered for the course in 2012, but over 14,000 individuals have subscribed to virology W3310 through iTunes University. I believe that it is important that the general public understand as much as possible about viruses, so they can participate in the debate about issues that impact them, such as XMRV or H5N1. It is my goal to be Earth’s virology professor.

I am sure that the students were perplexed when I took their photo before the first lecture. Little did they know that they were about to take a very different science course, one taught by a professor who uses social media (blogs, podcasts, twitter) to teach the subject both in and out of the classroom. As one student wrote to me yesterday:

I wish that every professor I had had such passion and energy and a TWiV-like blog/show so I could be updated on all the big science gossip/news to complement my in-class knowledge! I can’t recount how many times I told my non-science friends about TWiV as an exhibit to prove that science is cool and important. Thank you for being passionate scientists that made me want to study science (and be super nerdy but connected to the world) in the first place.

I would like to thank all the students of virology in and out of the classroom for their enthusiasm and their willingness to learn a complex subject. Virology will be offered again in the spring of 2013, and you can be reassured that it will be different. My course, like viruses, is continually evolving.

On episode #181 of the science show This Week in Virology, Vincent, Rich, and Kathy discuss Cotia virus, a new poxvirus, Orf virus infections associated with handling goats and lamb, and the innate immune response to prions.

You can find TWiV #181 at www.twiv.tv.

Science magazine will be conducting a live chat on whether some scientific research is too dangerous to publish, and how governments are getting involved in regulating such studies. It will be moderated by Science writer David Malakoff and will include Gregory Viglianti of Boston University School of Medicine.

The live chat begins at 3 PM EST on Thursday, 26 April at this link.

A dairy cow in California is the fourth known American case of mad cow disease, which is caused by prions, infectious agents composed only of protein (the story hit the press the day after my lecture on this type of illness). Unlike viruses, prions have no nucleic acid and no protective coat. But virologists know all about them because, as Stanley Prusiner once said, there was a time when only virologists believed that they existed.

Prions are found in mammals and in fungi, but only in mammals are they infectious and pathogenic. All mammals make normal forms of the prion protein (PrP^c) which is found in many tissues including the nervous system. The pathogenic form, called PrP^Sc, is a structurally altered form of PrP^c. The PrP^Sc protein, named after the first prion disease studied, scrapie in sheep, causes PrP^c to undergo a structural transformation to the pathogenic form. The PrP^Sc protein becomes deposited in amyloid fibrils in the brain, leading to neurodegenerative diseases known as transmissible spongiform encephalopathies (TSE), after the sponge-like appearance of the brain observed in afflicted animals (image).

There are three different ways to acquire a TSE. One is by infection: a human consumes meat that contains PrP^Sc, or receives a corneal transplant from a donor with an undiagnosed TSE . The PrP^Sc proteins make their way to the brain where they cause the host’s PrP^c to misfold and become the pathogenic PrP^Sc. The more PrP^Sc that is made, the more the normal PrP^c is converted to the pathogenic form. After an incubation period of many years, the host develops an invariably fatal neurodegenerative disease characterized by dementia in humans. There is also a familial form, in which mutations in the gene encoding PrP^c are inherited; these cause the PrP^c protein to misfold to form the pathogenic form. In the sporadic form PrP^c spontaneously converts to PrP^Sc without any known mutation or infection.

TSEs occur in different forms with varied symptoms and pathology. There are TSEs of humans (Creutzfeld-Jacob disease, fatal familial insomnia, Gerstmann-­Sträussler syndrome, Kuru) cows (bovine spongiform encephalopathy or mad cow disease), sheep and goats (scrapie), deer, elk, and moose (chronic wasting disease), and of a variety of other mammals.

This brings us back to the mad American cow, the first in the US since 2006. It died on a dairy farm and was tested for BSE as are 40,00o other cows each year in this country. The reason why this is big news is that back in the 1990s there was an outbreak of human TSE in the United Kingdom caused by consuming beef from animals with BSE. The cows acquired BSE by being fed processed animal byproducts as protein supplements, which unknowingly contained pathogenic prions. Bt the time the disease was detected in cows, contaminated meat had already entered the human food chain. Cows are routinely tested for BSE precisely to avoid a similar outbreak of human TSE.

The dead cow apparently had atypical BSE – that is, it was not a consequence of eating contaminated meat and it was not an inherited disease. Atypical BSE is caused by strains of prions distinct from other forms. This is good news because it means that the feed that the cow was receiving was not contaminated with pathogenic prions. Furthermore, the cow was not destined for meat production; it was a dairy cow that had died and was selected for random sampling.

Could the milk produced by this cow and consumed by humans pose a risk for transmission of a TSE to humans? It is known that ewes with scrapie shed infectious and pathogenic prions in their milk. However cows with BSE have  much less PrP^Sc accumulation in peripheral tissues, and in particular lymphoid tissues which include the mammary glands. It seems unlikely that cow milk contains prions, but it is a question worth revisiting. Pathogenic prions are highly resistant to heat, ultraviolet irradiation and other extreme conditions, so would certainly survive the pasteurization process.

On episode #180 of the science show This Week in Virology, Vincent, Alan, and Rich review association of an interferon-induced protein with severe influenza, and stabilization of HCV RNA by a microRNA.

You can find TWiV #180 at www.twiv.tv.

When my laboratory discovered the cell receptor for poliovirus in 1989, many new research directions were suddenly revealed – such as creating a mouse model for poliomyelitis. One application we did not think of was to use the receptor to screen samples of drinking water for the presence of viruses.

Contamination of the water supply with fecal material can lead to the presence of enteric viruses, which constitute a public health risk. A variety of methods have been developed to screen for viruses in water samples using cell culture or nucleic acid detection techniques. Because the numbers of human viruses in water samples are low, a concentration step must usually be included. These are typically laborious and costly, and innovative improvements are needed. Enter CD155, the cellular receptor for poliovirus, which the authors used as a model for developing a new way to concentrate viruses from water samples.

Viral receptors, which are present on the surface of susceptible cells, are very efficient at capturing viral particles. Why not put these receptors on the surface of bacteria, where they can bind to viruses? Concentrating the viruses would then be a simple matter of centrifuging the bacteria from the water sample. This concept was tested by using poliovirus and the poliovirus receptor.

For this method to work, the viral receptor protein must be present on the surface of bacteria (Figure). To accomplish this goal, an artificial gene was made which codes for the poliovirus receptor protein fused to the ice nucleation protein (INP) gene. This protein is normally present on the surface of the bacterium Pseudomonas syringae.

When the PVR-INP gene was expressed in E. coli, the fusion protein was located to the surface of the bacteria, where it could bind poliovirus. The recovery efficiency was then tested by adding poliovirus to tap water, saline, and samples from several local rivers. The engineered bacteria were added to the poliovirus-laced waters and mixed for 20-60 minutes. The bacteria were then removed by low speed centrifugation, and the viral titers in the cell and in the liquid sample were determined by plaque assay. The recovery of infectious virus ranged from 99% (saline samples) to 75% (river water).

These findings demonstrate that recombinant bacterial cells can be used to capture virus particles in different types of water samples. Compared with other water concentration methods, centrifugation is inexpensive and easy. Whether or not this assay is sensitive enough to detect low levels of viruses in drinking water and other samples must still be determined.

In a way it is fitting that bacteria have been used to capture poliovirus. After all, poliovirus initially replicates in the gastrointestinal tract, where the microbial flora (including E. coli) helps the virus invade the host.

Abbaszadegan M, Alum A, Abbaszadegan H, Stout V. 2011. Cell surface display of poliovirus receptor on Escherichia coli, a novel method for concentrating viral particles in water. Appl Envir Micro 77:5141–5148.

On episode #31 of the science show This Week in Microbiology, Vincent, Jo, and Michael discuss an archetypal protein transport system in bacterial outer membranes, and evidence that gut microbial enterotypes might not fall into defined groups.

You can find TWiM at microbeworld.org/twim.

On episode #179 of the science show This Week in Virology, Gertrud joins the TWiVoners to review how dengue virus infection of mosquitoes alters blood feeding behavior, and gene therapy as practiced by parasitoid wasps.

You can find TWiV #179 at www.twiv.tv.

Influenza H5N1 virus frightens many because of the widely quoted case fatality ratio of >50%, which is based on the number of deaths among the fewer than 600 cases confirmed by the World Health Organization. Such fear is misguided, because it is likely that the fatality ratio is far lower. For example, studies of >7,000 healthy individuals have revealed that about 0.5% of them carry antibodies to the virus in their blood, indicating that mild or asymptomatic infections do occur. T-lymphocytes that recognize influenza H5N1 virus have now been detected in a high-risk cohort of individuals in Vietnam, providing additional evidence for asymptomatic human infections.

Viral infection of a healthy host usually leads to the production of both antibodies and lymphocytes. Antibodies generally bind to virus particles in the blood and at mucosal surfaces, blocking the spread of infection. In contrast, T-cells recognize and kill infected cells. The presence of specific antibodies has historically been used as an indicator of viral infection, partly due to the simplicity of the assay. In practice, dilutions of patient sera can be mixed with infectious virus to measure its ability to block infection (virus neutralization or hemaggultination-inhibition), or used to detect antibodies to viral proteins (ELISA or western blot).

Another option for assessing previous viral infection is to determine whether virus-specific T-cells are present. In the past this type of assay has been difficult to carry out with large numbers of samples, but technical advances have now made it possible to do population screens for T-cell responses. In the current study, peripheral blood mononuclear cells (which contain T-lymphocytes and other blood cells) were obtained from patients and placed in culture. Next, pools of overlapping peptides that span most of the influenza viral proteins were added to the cells. These peptides were derived from influenza H5N1, H3N2, and H1N1 proteins. When T-cells recognize a peptide (via the T-cell receptor that recognizes the peptide presented by another cell type; see figure), the cells respond by producing interferon gamma, which can be readily measured.

The Vietnamese patients used for this study were part of a rural community where human and avian infections with influenza H5N1 had been previously documented. Twenty-four of of 747 individuals had evidence for the presence of T-cells that recognize peptides from the H5 HA more strongly than peptides from H3 or H1 HA. Another 111 samples had T-cells that react with H5, H1, and H3 peptides. If all positive patient samples (those lead to production of interferon gamma) are included, then one can conclude that 20% of the patients respond to H5 peptides. Control samples (n=271) were obtained from two individuals in Vietnam and the United Kingdom who are not believed to have been exposed to H5N1 virus. None of these had H5N1-specific T-cell responses.

Curiously, only four subjects had both antibody and T-cell responses to H5N1 virus. The timing of sample acquisition with respect to infection is likely to be important for detecting responses. For example, antibody to H5N1 virus may not be detected earlier than 3 weeks after onset of disease, and T-cell responses may wane with time. It is also possible that abortive H5n1 infections in humans may lead to production of T-cells but not antibodies, as is seen in some individuals infected with HIV-1.

On episode #178 of the science show This Week in Virology, the TWiValians meet up with Tyler Sharp for a discussion on the Epidemic Intelligence Service and controlling dengue.

You can find TWiV #178 at www.twiv.tv.

On episode #169 of This Week in Virology we had a good discussion about how to read a scientific paper. Many individuals have asked about making this into a separate audio file, so here it is.

Click the arrow above to play, or right-click this link to download our thoughts on how to read a scientific paper (22 MB .mp3, 30 minutes).

Epidemiologist Michael Walsh has shared a PowerPoint presentation on this topic (482 KB PowerPoint file).

On episode #30 of the science show This Week in Microbiology, Vincent, Elio, and Michael review how a toxin from Burkholderia pseudomallei inhibits protein synthesis, and the role of the gut microbiome in modulating insulin resistance in mice lacking an innate immune sensor.

You can find TWiM #30 at microbeworld.org/twim.

This past February I was interviewed by the Australian Broadcasting Company on the topic of the Fouchier and Kawaoka experiments on avian influenza virus H5N1. The video, Building the Perfect Bug, has been released by Journeyman Pictures and includes interviews with S.T. Lai, Laurie Garrett, Michael Osterholm, and Ron Fouchier (transcript available). It is far too alarmist for my taste, but both sides of the issue are represented.

The video includes sequences of me working in the cell culture laboratory. Note that I did wear a tie for my interview while Michael Osterholm did not.

On episode #38 of the science show This Week in Parasitism, Vincent and Dickson tackle the backlog of listener email, then consider the life cycle and pathogenesis of Trichomonas vaginalis, the flagellated protozoan transmitted by sexual contact.

You can find TWiP #38 at microbeworld.org/twip.

On episode #177 of the science show This Week in Virology, Vincent, Connor Bamford, Wendy Barclay, and Ron Fouchier discussed avian influenza H5N1 transmission experiments in ferrets and novel bunyaviruses at the 2012 Spring Conference of the Society for General Microbiology in Dublin, Ireland.

You can find TWiV #177 at www.twiv.tv.

The National Science Advisory Board for Biosecurity (NSABB) has re-examined two manuscripts on the transmissibility of influenza H5N1 virus in ferrets:

After careful deliberation, the NSABB unanimously recommended that this revised Kawaoka manuscript should be communicated in full. The NSABB also recommended, in a 12 to 6 decision, the communication of the data, methods, and conclusions presented in this revised Fouchier manuscript.

The NSABB reached this decision using ‘analytical tools that it previously developed for considering the risks and benefits associated with the communication of dual use research of concern.

Apparently information communicated in revised versions of the Fouchier and Kawaoka manuscripts changed the Board’s risk/benefit calculation:

The data described in the revised manuscripts do not appear to provide information that would immediately enable misuse of the research in ways that would endanger public health or national security.

New evidence has emerged that underscores the fact that understanding specific mutations may improve international surveillance and public health and safety.

This decision (full text here) is welcome, although I wonder how the manuscripts have been ‘revised’ – were data added or removed? Furthermore, why does the NSABB now feel that the results do not endanger public health, and can be used to improve international surveillance? These arguments have been made previously but the NSABB discounted them.

I look forward to publication of the Fouchier and Kawaoka findings and a comprehensive discussion of how they influence influenza H5N1 transmission in ferrets.

Update: According to the New York Times, the chair of the NSABB said “the new decision was not a reversal, because the revised manuscripts were so different from the originals. Had these versions been presented originally, the board would not have recommended withholding any details”.

Did the authors remove data from the manuscripts, or just clarify them?

Update 2. According to Kawaoka, quoted in the The Chronicle of Higher Education, the revisions of his manuscript “provided a more in-depth explanation of the significance of the findings to public health and a description of the laboratory biosafety and biosecurity.” His paper, he added, would contain descriptions of all the mutations that enhanced transmission of the virus, the very data that initially concerned the board.” Furthermore, Ron Fouchier wrote to me in an email that “the manuscripts will indeed be published in full.” All this is very good news.

I just returned from Dublin where I was honored to receive the Peter Wildy Prize for Microbiology Education from the Society for General Microbiology. This prize is awarded annually for an outstanding contribution to microbiology education, including university teaching, education of the general public, school pupils or professional groups.

Below is a video of my acceptance talk. Thanks to Chris Condayan of ASM for the excellent split-screen recording.

While at the SGM meeting in Dublin I recorded TWiV 177 with Connor Bamford, Wendy Barclay, Richard Elliott and Ron Fouchier. Audio and video will be posted on 1 April 2012.

On episode #176 of the podcast This Week in Virology, Vincent, Alan, and Rich answer listener email about MS, CFS, EBV, B cells, virii, influenza B, scientific papers, and more.

You can find TWiV #176 at www.twiv.tv.

Some viruses that infect bacteria (bacteriophages) deliver their DNA into the host cell with an amazing injection machine. The tailed bacteriophages (such as T4, illustrated) store their DNA in a capsid attached to a long tail tube that is surrounded by a sheath. At the bottom of the tube is a baseplate with a spike in the center. When the baseplate contacts the host cell, the sheath contracts, driving the spike into the cell membrane. The viral DNA travels down the tube and enters the cell through the opening produced by the spike. The structure of the spike has now been determined, providing insight into how it makes a hole in the cell membrane.

Structures of the spike from P2, a well studied virus of E. coli, and the choleraphage phi92 were determined.  The spikes are built from three copies of a single protein (trimers). The trimers are indeed shaped like spikes: they are wider at one end and taper to a rather sharp tip (figure at right). The bulk of the spike is made up of alternating beta-strands which form a corkscrew-like beta-helix. The sharp tip is composed of three beta-hairpins which the authors say “come together like petals in a flower bud”.

An interesting feature on the interior of the spike tip are three pairs of histidine residues that hold a single iron atom (figure at left). The authors believe that the iron helps the trimers form by keeping the protein chains in register, and also provides increased strength to the tip. The latter would be important as it pierces the cell membrane. This idea could be tested by changing one or more histidines to another amino acid so that iron cannot be held in the tip.

To verify that these structures are those of the spike that is attached to the baseplate, the authors solved the structure of the phage particle by cryo-electron microscopy and image reconstruction. The image clearly shows the spike protruding from the base plate (figure below). The structures of the spike proteins solved by X-ray crystallography could then be computationally fitted in the correct location in the cryo-EM image of the baseplate.

These structures support the idea that the spike is a rigid needle that pierces the bacterial membrane and forms a channel through which the DNA can pass. An interesting question is how the DNA gets past the spike, which plugs the end of the tail tube. The authors believe that the spike is loosely attached to the tube and might be easily dissociated once it passes through the cell membrane. The spike of phage T4 can be dissociated at low pH, a condition that is found in the periplasm, the space between the inner and outer bacterial membranes.

There are distinct signatures of the spike structure that can be identified in proteins of other contractile injection systems, including diverse bacteriophages. They can also be found in bacterial type VI secretion systems, which are membrane complexes used to transport proteins outside of the cell. Once evolution builds a useful machine, it is often put to many diverse uses.

 
Browning, C., Shneider, M., Bowman, V., Schwarzer, D., & Leiman, P. (2012). Phage Pierces the Host Cell Membrane with the Iron-Loaded Spike Structure, 20 (2), 326-339 DOI: 10.1016/j.str.2011.12.009

On episode #29 of the podcast This Week in Microbiology, Vincent and Stanley review how a phage pierces the cell membrane with an iron-loaded spike, and two programmed cell death systems in E. coli.

You can find TWiM #29 at microbeworld.org/twim.

Join us for a live-streaming episode of This Week in Virology from the Society for General Microbiology 2012 Spring Conference in Dublin, Ireland. My guests for this special episode are Connor Bamford, Wendy Barclay, Richard Elliott, and Ron Fouchier.  Watch the live stream below which starts on Monday, 26 March at 3:30 PM GMT (10:30 AM EST | 7:30 AM PST). If you have questions during the broadcast you can tweet them using the #TWiV hash tag.

You can use www.everytimezone.com to calculate when the live streams will start in your area.

If you are using an iOS device, you will not be able to see the live stream below as it is flash encoded.

On episode #175 of the podcast This Week in Virology, Vincent, Alan, and Matt discuss herpes simplex encephalitis in children with innate immune deficiency, and the local response to microneedle-based influenza skin immunization.

You can find TWiV #175 at www.twiv.tv.

A consequence of the recent warm weather in the northeastern United States is the emergence of crocuses, an event that I documented at the TWiV Facebook page. A reader replied that it reminded her of the highly valued tulips with beautiful variegations produced by viruses.

In 17th-century Holland patterned tulips such as the Semper Augustus (image) were of enormous value, with single bulbs selling for 3000 guilders or more (about $1600 US today). The intricate lines and flame-like streaks produced stunning effects. We now know that these colorful patterns are caused by infection with potyviruses, which are filamentous plant viruses with positive-strand RNA genomes. The specific viruses involved are tulip-breaking virus, tulip top-breaking virus, tulip bandbreaking virus, and Rembrandt tulip-breaking virus. Lilies may also be patterned by infection with Lily mottle virus. These viruses infect the bulb and cause the single color to break, leading to bars, stripes, streaks, featherings or flame-like effects of different colors on the petals. These effects are caused by altered distribution of pigments in the petal caused by virus replication.

Unfortunately, infection with tulip-breaking viruses is not benign: with successive generations the bulb shrinks until it can no longer flower. For this reason most of the lines of broken tulips, including Semper Augustus, no longer exist. These viruses still circulate globally, transmitted by aphids. Because infection can cause costly damage to tulips, precautions must be taken to minimize spread. Contemporary variegated tulips such as Rem’s Sensation are produced by breeding, not virus infection.

It is spring break for students at Columbia University, which means that my annual virology course is one lecture past the halfway point. The first eleven lectures addressed basic aspects of viral replication in cell culture, including virus entry into cells, genome replication, and assembly. From this point onwards we will be discussing viral infection of a host, including pathogenesis, immunity, immunization, antivirals, and evolution.

All my virology lectures are available as videocasts (slides and audio) either at the course website, or at the new iTunes University.

On episode #174 of the podcast This Week in Virology, Vincent, Alan, and Rich consider whether pet dogs might transmit human noroviruses, and an RNA virus microRNA that might be involved in oncogenesis.

You can find TWiV #174 at www.twiv.tv.

On episode #173 of the podcast This Week in Virology, the TWiVites discuss seroevidence for human infection with avian influenza H5N1, and the discovery of a new influenza virus in Guatemalan bats.

You can find TWiV #173 at www.twiv.tv.

Ron Fouchier has discussed his influenza H5N1 transmission experiments in ferrets at an ASM Biodefense Conference, clarifying several assumptions about the transmissibility of the virus in this animal model.

Two different influenza H5N1 strains were used for Fouchier’s experiments: a wild type virus, and a mutated virus (we’ll call it mutH5N1). He did not reveal the nature of the mutations in this virus but from previous reports they consist of changes introduced into the viral HA protein to allow binding to sialic acid receptors in the avian respiratory tract, and other changes selected during passage in ferrets.

Ferrets are housed in neighboring cages separated by steel grids to allow free air flow between cages. The cages are placed in a class 3 biosafety hood within a BSL3+ facility. A ferret in one cage is inoculated intranasally with virus, and then ferrets in neighboring cages are assayed for presence of virus in the respiratory tract. When ferrets are inoculated with wt H5N1 virus, viral replication ensues in the respiratory tract, but the virus is not transmitted to animals in neighboring cages. When ferrets are inoculated with mutH5N1, the virus is transmitted to 3/4 ferrets in neighboring cages. If the mutH5N1 virus is recovered from these animals and used to infect new ferrets, it is then transmitted to 2/2 ferrets in neighboring cages. The results are summarized in the following figure:

Fouchier concluded that this work identified the mutations that are needed for H5 transmission between ferrets.

Next Fouchier indicated that because the work has not yet been published, and the press has ‘picked up on it’, there are many misconceptions about what can or cannot be concluded. For example, it has been suggested that this virus would spread ‘like wildfire’ if it were to get out of his facility. He presented data indicating that this would not be the case. Although his results demonstrate aerosol transmission of H5N1 among ferrets, the assay is not quantitative, and therefore the efficiency of transmission cannot be deduced. He showed results of ferret transmission studies using the 2009 H1N1 pandemic influenza virus strain. This virus spreads to all ferrets by aerosol and replicates to high titers in the respiratory tract. In comparison, the mutH5N1 virus does not transmit to all ferrets, virus titers are lower, and shedding does not begin until later in infection. He concluded that the mutH5N1 virus does not transmit among ferrets as does a pandemic or seasonal influenza virus.

The second misconception that he addressed is that the mutH5N1 virus would be highly lethal. He showed the results of experiments demonstrating that when ferrets are inoculated intranasally with high doses of mutH5N1 virus, only 1/8 animals show signs of disease. In contrast, 2 of 2 ferrets developed disease when inoculated in the same way with wild type H5N1 virus. When the mutH5N1 virus is transmitted to ferrets via aerosol, none of the recipient animals develop disease. Only when the mutH5N1 virus is delivered to the lower respiratory tract of ferrets by intratracheal intubation does the virus cause disease in 6 of 6 animals.

Finally, Fouchier showed that pre-exposure of ferrets to seasonal influenza virus protects them from disease caused by H5N1 viruses. These findings are summarized on the following figure.

After this presentation Dr. Anthony Fauci, head of the National Institute of Allergy and Infectious Disease, said that “There is a gross, pervasive misunderstanding out there,” and recommended that the data be re-examined by the NSABB.

The data presented by Fouchier appear to be at odds with the conclusions of the NSABB to redact publication. They are also not consistent with statements made by Fouchier and others to Science magazine in November 2011. For example, Fouchier called mutH5N1 ”probably one of the most dangerous viruses you can make”, and Paul Keim, head of the NSABB, said ”I can’t think of another pathogenic organism that is as scary as this one.”

Update: Here is what Fouchier said about his work at the Malta meeting in September 2011, as reported by New Scientist. The article begins with the statement:

…five mutations in just two genes have allowed the virus to spread between mammals in the lab. What’s more, the virus is just as lethal despite the mutations.

Fouchier is quoted as saying ”The virus is transmitted as efficiently as seasonal flu.” This is in direct contrast to what he reported at the ASMBiodefense meeting.

In describing the passage of H5N1 in ferrets, the writer concludes:

The tenth round of ferrets shed an H5N1 strain that spread to ferrets in separate cages – and killed them.

Again this is in direct contrast to what Fouchier reported this past week.

I do not understand the difference between what Fouchier said in Malta in 2011 and in Washington, DC in February 2012. However, there is one way to explain the apparent paradox, which derives from the following statment from the New Scientist article:

The process yielded viruses with many new mutations, but two were in all of them. Those plus the three added deliberately “suggest that as few as five are required to make the virus airborne”, says Fouchier. He will now test H5N1 made with only those five.

Perhaps the results that Fouchier reported in Washington, DC are from experiments using H5N1 virus with only those five mutations.

On episode #172 of the podcast This Week in Virology, Vincent and Kathy discuss how a virus may cause disease distant from its replication site, then review a day in the life of a senior microbiology professor.

You can find TWiV #172 at www.twiv.tv.

The fatality rate for human infections with avian influenza H5N1 is widely quoted at >50%, based on the number of deaths among the fewer than 600 cases confirmed by the World Health Organization. Wang, Parides, and Palese suggest that this number is an overestimate:

…the stringent criteria for confirmation of a human case of H5N1 by WHO does not account for a majority of infections, but rather, the select few hospitalized cases that are more likely to be severe and result  in poor clinical outcome.

To address this problem, the authors summarized the results of serological surveys in which human sera were examined for the presence of antibodies to influenza H5N1 virus. Because antibodies are part of our immune defenses, they are a good indicator of a previous infection.

The authors searched the scientific literature and identified 20 studies in which human sera were examined for the presence of H5N1 antibodies according to WHO guidelines (a 4-fold or greater increase in neutralizing antibody titer in paired acute and convalescent sera, with the convalescent serum having a titer of ≥1:80, or an antibody titer of ≥1:80 in a single serum collected at day 14 or later after onset of symptoms and a positive result using a different serological assay).

Studies that used the WHO criteria included 7,304 study participants. Rates of seropositivity were from 0 – 5.3%, with one study reporting 11.7% positivity. The meta-analysis yielded a seropositivity rate of 1.2% (95% confidence interval 0.6% – 2.1%). When only poultry workers were considered, the seropositivity rate was 1.4%.

Other studies were separately analyzed that did not utilize WHO guidelines; these included 6,774 participants and yielded a seropositivity rate of 1.9% (95% confidence interval 0.5 – 3.4%).

A total of 12,677 study participants from 20 studies were included in this meta-analysis, of which 1-2% had evidence for prior H5N1 infection. The authors conclude:

…avian H5N1 viruses can cause a rate of mild or subclinical infections in humans that is not currently accounted for and thus, the true fatality rate for H5N1 influenza viruses is likely to be less than the frequently reported rate of more than 50%.

It seems very clear that standardized, large scale studies are needed to determine the real number of human H5N1 infections. This information is critical for assessing the actual threat of H5N1 influenza for humans.

For the second time in a week I note the passing of an important virologist. Renato Dulbecco, together with David Baltimore and Howard Temin, received the 1975 Nobel Prize in Physiology or Medicine for discoveries about how tumor viruses interact with the genetic material of the cell. Dulbecco also devised my favorite virological method, the plaque assay, for determining the virus titer, the number of animal viruses in a sample.

Since the early 1920s bacteriologists had used the plaque assay to quantify the number of infectious bacteriophages (viruses that infect bacteria). Dulbecco noted in 1952 that “research on the growth characteristics and genetic properties of animal viruses has stood greatly in need of improved quantitative techniques, such as those used in the related field of bacteriophage studies.” One limiting factor was the development of suitable animal cell cultures that could be used to determine viral titer. By the 1950s the techniques for reliably producing and propagating human cell cultures were developed, and in 1951 the first immortal human cell line, HeLa, was isolated. Dulbecco took advantage of these advances and showed in 1952 that western equine encephalitis virus formed plaques on monolayers of chicken embryo fibroblasts (figure). Dulbecco also made the important observation that one virus particle is sufficient to produce one plaque. He drew this conclusion from his observation of a linear dependence of the number of plaques on virus concentration. This seminal advance made possible the application of genetic techniques to the study of animal viruses.

Dulbecco’s work on tumor viruses was focused on polyomaviruses – small DNA-containing viruses such as murine polyomavirus and SV40. He found that cells from the natural host of the virus – mice for polyomavirus and monkeys for SV40 – were killed as the viruses replicated and produced new viral progeny. However, these viruses did not replicate in or kill cells from other animals. For example, when hamster cells were infected with murine polyomavirus, no viral replication took place, the cells survived, and a few rare cell were transformed  - their growth properties in culture were altered and they induced tumors when injected into hamsters. Dulbecco later found that the polyomaviral DNA is a circular, double-stranded molecule; and that in non-permissive cells (in which the virus does not replicate) the viral DNA became integrated into the host cell chromosome. He also suspected that a viral protein called T (for tumor) antigen was a key to cell transformation.

Today we understand why polyomaviruses transform cells in which they do not replicate: infection does not kill these cells, and the rare transformed cells contain only viral DNA encoding T antigen. This protein is needed for viral replication in permissive cells because it drives cell proliferation, activating cellular DNA replication systems that are required for producing more viral DNA. In a non-permissive cell, T antigen drives the cell to divide endlessly, immortalizing it and allowing the accumulation of mutations in the cell genome that make the cells tumorigenic.

While the details of how DNA tumor viruses transform cells were being elucidated, other investigators were attempting to understand how another class of viruses – with RNA genomes – had similar effects on cells. In 1951 a young scientist named Howard Temin joined Dulbecco’s laboratory to study how Rous sarcoma virus (RSV) caused tumors. This virus had been discovered by Peyton Rous in 1911, but would only cause tumors in chickens, limiting progress. In Dulbecco’s laboratory, Temin found that RSV induced transformation of cultured chicken embryo fibroblasts – the same types of cells that were being used to develop the plaque assay for animal viruses. Temin took this transformation assay to his own laboratory, where he reasoned that a DNA copy of the RSV viral genome must be integrated into the chromosome of transformed cells. This led him to discover the enzyme reverse transcriptase in RSV particles, which produces a DNA copy of the viral RNA.

By embracing a new technology for the study of animal viruses – cell culture – Dulbecco set the study of both DNA and RNA tumor viruses on a path that would lead to understanding viral transformation, an achievement recognized by the 1975 Nobel Prize.

Dulbecco, R. (1952). Production of Plaques in Monolayer Tissue Cultures by Single Particles of an Animal Virus Proceedings of the National Academy of Sciences, 38 (8), 747-752 DOI: 10.1073/pnas.38.8.747

On episode #171 of the podcast This Week in Virology, Matt Frieman joins Vincent, Alan, and Dickson to review virus production in single cells and single virion genomics.

You can find TWiV #171 at www.twiv.tv.

Dr. Bruce Alberts, editor of Science magazine, said that the journal will publish the full version of the Fouchier H5N1 influenza virus paper if mechanisms are not developed to ensure circulation of the information to scientists. Alberts made his comments at the American Association for the Advancement of Science meeting in Vancouver:

Our position is that, in the absence of any mechanism to get the information to those scientists and health officials who need to know and need to protect their populations and to design new treatments and vaccines, our default position is that we have to publish in compete form.

Pallab Ghosh of BBC News, writes that Alberts ’says it is important to get the research out quickly to scientists and health officials monitoring the virus.’

Update: WHO has decided to delay the decision on whether to publish the H5N1 data:

The Geneva meeting of 22 scientists and journal representatives agreed that publishing only parts of the research would not be helpful, because they would not give the full context of a complete paper.

Update 2: The New York Times reports that the H5N1 papers will be published in a few months, “to give researchers and officials an opportunity to provide better information to the public about the research and its importance, and would also give safety experts a chance to assess the conditions in which the work is being done.”

Apparently the decision was not unanimous, and it was opposed by the US.

The other important news is that the issue of the H5N1 fatality rate has finally made it to the front page:

The experiments involve a type of bird flu virus known as H5N1. Of about 600 known cases, more than half have been fatal. The exact death rate is not known, however, because some deaths may go uncounted and mild cases may go undiagnosed.

Norton Zinder made two important discoveries in the field of virology. While a Ph.D. student with Joshua Lederberg at the University of Wisconsin-Madison he found that viruses of bacteria (bacteriophages) could move genes from one host to another, a process called transduction. Later in his own laboratory at The Rockefeller University he isolated the first bacteriophages that contain RNA as genetic material. These were seminal findings in the growing field of molecular biology.

By the 1950s it was well known that different strains of the bacterium Escherichia coli could exchange genes in a process called recombination. Zinder wanted to know if other bacteria could also exchange genes in a similar manner, and therefore began to study Salmonella typhimurium. The strains that Zinder used for his experiments were lysogens: their chromosomal DNA contained integrated copies of the DNA genomes of bacteriophages. Zinder readily detected genetic exchange in Salmonella, but suspected that the latent phages might play a role. To test this idea, he grew Salmonella in tubes that were connected by a fine filter that allowed passage of viruses but not bacteria between the two cultures. The results showed that a filterable agent, or virus, could mediate the exchange of genetic material between bacterial strains; direct contact between bacteria was not necessary. The authors coined transduction to describe this process. We now understand that transduction occurs because bacteriophages may incorporate bacterial DNA into the viral particle. Transduction remains a common tool to stably introduce a foreign gene into a host cell.

Zinder describes the discovery of RNA-containing bacteriophages, which took place after he had moved to The Rockefeller University, in the Preface to RNA Phages:

In the late fifties, Tim Loeb, a new graduate student at The Rockefeller University, came into my laboratory and asked whether I thought it was possible that there were male-specific bacteriophages for E. coli. I….quickly responded in the affirmative and off he went to a raw sewage plant in New York City. …f2, the second isolate, was chosen for further study. Little did we think at the time that a whole new area of study was in the offing….

The first two bacteriophages that Loeb had isolated from New York City sewage were called f1 and f2. During purification of the phages it was clear that the genome of f1 was DNA. Chemical analyses subsequently demonstrated that the genome of f2 was RNA (later found to be positive-strand RNA). Similar phages were since isolated all over the world, and their study provided much basic information on viral replication, protein biosynthesis, and genome replication. The first genome sequence determined was in 1976 for the related RNA bacteriophage MS2.

Update: Moving eulogy by Jeffrey Ravetch in Eulogy for a brilliant mentor and teacher.

Loeb, T. (1961). A Bacteriophage Containing RNA Proceedings of the National Academy of Sciences, 47 (3), 282-289 DOI: 10.1073/pnas.47.3.282

On This Week in Virology #170, hosts Alan, Rich, and Dickson discuss Edward Jenner’s paper on cowpox vaccine, then move 200 years later to modern vaccines against norovirus, influenza H5N1, and more.

You can find TWiV #170 at www.twiv.tv

Several panelists from the recent influenza H5N1 dual-use forum at the New York Academy of Sciences spoke with Brendan Maher of Nature News to discuss their position. Participants in this video include Laurie Garrett, Michael Osterholm, Ian Lipkin, Vincent Racaniello, and Veronique Kiermer.

Update: The New York Academy of Sciences has posted video of the full two hour panel discussion.

On This Week in Virology #169, Michael Walsh and the TWiV team review epidemiology basics, including fatality ratios.

You can find TWiV #169 at www.twiv.tv.

Howard Markel, Professor of the history of medicine at the University of Michigan, in the New York Times:

The censorship of influenza research will do little to prevent its misuse by evildoers — and it may well hinder our ability to stop influenza outbreaks, whether natural or otherwise, when they do occur. In this case, censorship is too little, too late. The data generated by one of the research teams was already presented at a conference in Malta in September, where copies of the paper were distributed. But even if the data weren’t already available, the key details could likely be inferred from other information that is already available.

Dr. Markel also agrees that influenza H5N1 virus would not be a good terrorist weapon:

Even if terrorists got their hands on the new data, it’s not certain they could weaponize the virus: no one knows for certain that the virus’s transmissibility and virulence in ferrets means transmissibility and virulence in humans. In any event, the influenza virus, highly variable in its power and spread, is not an optimal terrorist weapon, not least because no one would know for sure if it was unleashed by a terrorist or natural forces.

The implications of the H5N1 story go far beyond ferrets:

In the years since the 9/11 attacks, we’ve witnessed a disturbing trend in the oversight of sensitive science. [...] Several prominent scientists, including Donald Kennedy, the former editor of Science, have publicly worried that the federal government is thwarting scientific advancement.

The action by the NSABB has propelled us full-tilt into this controversy. Their incorrect decision to censor the influenza H5N1 data not only will inhibit work on this important virus, but will have far-reaching consequences for scientific research. To this day I cannot understand why the NSABB did not more thoughtfully consider not only the data, but the future of science in coming to their decision.

Thanks to Dr. Markel for writing the Op-Ed I’ve been meaning to put together for a long time.

Related:

The NSABB speaks on influenza H5N1

H5N1 facts, not fear

Moratorium on influenza H5N1 transmission research

Palese: Don’t censor live-saving science

N.Y. Times: H5N1 ferret research should not have been done

Should we fear avian H5N1 influenza?

Ferreting out influenza H5N1

The National Science Advisory Board for Biosecurity (NSABB) has published “Adaptations of Avian Flu Virus Are a Cause for Concern”, an explanation of their recommendations with respect to influenza H5N1 research (versions at Science and Nature). It starts with the statement that advances in technology now allow manipulation of microbial genomes in ways that could be misused, leading to global harm. They define dual-use research as “research that could be used for good or bad purposes”.

The authors begin their discussion of influenza H5N1 with the usual incorrect statement about the lethality of the virus:

Highly pathogenic avian influenza A/H5N1 infection of humans has been a serious public health concern since its identification in 1997 in Asia. This virus rarely infects humans, but when it does, it causes severe disease with case fatality rates of 59%.

The reference for this information is a WHO summary of confirmed human cases of H5N1. Both WHO and NSABB ignore the serological evidence for many mild or inapparent H5N1 infections. Omitting these data leads to an overestimation of the virulence of the virus, which has apparently played a large role in the NSABB’s decision.

Next, they engage in extensive speculation:

If influenza A/H5N1 virus acquired the capacity for human-to-human spread and retained its current virulence, we could face an epidemic of substantial proportions.

The virus has been circulating since the 1990s and has not acquired the capacity for human to human spread. This doesn’t mean it never will, but the possibility seems remote. The statement ‘retaining its current virulence’ of course refers to the erroneous 59% case fatality rate. What if the fatality rate is 0.1%, like seasonal influenza?

In discussing influenza H5N1 transmission in ferrets, the NSABB notes the value of the research:

The research teams that performed this work did so in a well-intended effort to discover evolutionary routes by which avian influenza A/H5N1 viruses might adapt to humans. Such knowledge may be valuable for improving the public health response to a looming natural threat.

Many have written that the research should never have been done, and that there are no benefits for human health (New York Times, Tom Inglesby, DA Henderson). Clearly the NSABB believes otherwise.

Next the NSABB describes their consideration of risk assessment of the H5N1 ferret studies. Their conclusion:

We found the potential risk of public harm to be of unusually high magnitude. Because the NSABB found that there was significant potential for harm in fully publishing these results and that the harm exceeded the benefits of publication, we therefore recommended that the work not be fully communicated in an open forum.

But there is no description of how they reached this conclusion. What data did they consider when making this decision? What were the benefits and the potential harms, and how did they weigh them? Apparently we must take the word of the panel that they reached the right decision, even though we cannot know what information they used. To convey their decision in this manner is unacceptable and sends the message that the committee did not consider specific data during their deliberations.

They conclude:

The life sciences have reached a crossroads. The direction we choose and the process by which we arrive at this decision must be undertaken as a community and not relegated to small segments of government, the scientific community, or society.

This is precisely why the decision to redact publication should not have been made by the NSABB or any small group of individuals. I agree that this is an ‘Asilomar moment’, a time when scientists must meet to decide what types of microbial research should be regulated. This should be a discussion among a large group of scientists, not bioterrorism policy analysts.

I understand the need to regulate certain types of experiments on microbes. But when I balance the benefits and risks of the H5N1 ferret transmission experiments, it does not make sense to stamp them as dual use and restrict publication of the results. Let publication proceed and then decide how to decide on how to move forward.

Hosts: Vincent Racaniello, Dickson Despommier, Rich Condit, Alan Dove, and Welkin Johnson

Welkin joins the TWiV team for a discussion of HIV prophlaxis using vectored antibodies, and the influenza H5N1 virus studies in ferrets that were not redacted.

Click the arrow above to play, or right-click to download TWiV 168 (59 MB .mp3, 98 minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, by email, or listen on your mobile device with the Microbeworld app.

Links for this episode:

• Vectored HIV immunoprophylaxis (Nature)
• Vectored immunoprophylaxis – the Movie (YouTube)
• Adeno-associated virus (Wikipedia)
• In vitro evolution of H5N1 towards human receptor specificity (Virology)
• Endogenous viral genes non-essential in chicken (Nature)
• Rates of HIV transmission per coital act (J Inf Dis)
• TWiV on Facebook
• Letters read on TWiV 168

Weekly Science Picks

Welkin – Virtual PI (Nature)
Dickson – Drain the Ocean
Rich – Nova: To the Moon
Alan - Robert Falcon Scott on Twitter and the Terra Nova expedition
Vincent – Hello, Mr. Chips (I, Cringely)

Listener Pick of the Week

Charlotte – And the Band Played On

Send your virology questions and comments (email or mp3 file) to twiv@twiv.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

Peter Palese and Taia Wang have written a compelling article that uses scientific facts to address the controversy over publication of research involving transmission of avian influenza H5N1 in ferrets. In response to calls in the media to destroy the viruses, curtail the research, and protect the public from frightening research, they write that “fear needs to be put to rest with solid science and not speculation”.

The authors begin with the facts: they indicate that the object of ferret-to-ferret passage of avian H5N1 influenza virus was to determine whether sustainable aerosol transmission could be achieved in this animal model. The finding that transmission in ferrets is conferred by a small number of mutations emphasizes the need for continued surveillance of H5 viruses and development of vaccines and antivirals.

Are these studies relevant to humans?

Ferrets are quite susceptible to infection with influenza viruses. However, it is not clear that all virus strains that replicate in and transmit between ferrets necessarily do so in humans. Ferrets are also more likely than humans to have disseminated, multiorgan influenza disease including neurological sequelae….one cannot directly extrapolate from the data to make predictions about humans.

Under the heading ‘fear’, they address the heart of this controversy, the notion that the fatality rate for human H5 infections is greater than 50%:

…in order for a case to be confirmed by WHO, a person must have an acute, febrile respiratory illness with known H5 exposure in the 7 days preceding and have molecular confirmation of H5 infection by a WHO approved laboratory. This definition does not allow for asymptomatic infections and essentially requires that a person actively seek medical help at a hospital that is equipped to draw samples and ship them to an approved laboratory….it seems unlikely that even a small fraction of the total number of infected cases has been accounted for under the WHO surveillance system.

They also review seroevidence in humans for H5 infections:

Of the 10 largest studies of which we are aware…eight report rates ranging from 0.2% to 5.6%….even if only a low percentage of the rural population is asymptomatically/subclinically infected, the case fatality rate that is offered by the WHO – and that is driving this controversy – is likely orders of magnitude too high.

The authors believe that selection of these papers for redaction by the National Science Advisory Board for Biosecurity appears arbitrary, considering what has been published on influenza in the past:

In 2005, the complete sequences for the 1918 pandemic influenza virus were published…in 2006, both Science and Nature published reports of specific mutations that enable the H5 viral hemagglutinin to bind human, rather than avian tissues. In 2012, a report from the CDC that bears striking resemblance, in principle, to the works by Fouchier and Kawaoka was already published in Virology: it describes mutations in an H5N1 virus that confer airborne transmissibility between ferrets.

Finally the address the question: Could the data from these two papers realistically be used to generate an H5N1 biologic weapon?

The answer is simply no.

Everyone should read this article, including anyone who is concerned about the safety of the H5N1 experiments; biosecurity analysts who do not seem to understand the underlying science; and science writers who propagate misinformation about the virus.

Hosts: Vincent Racaniello, Dickson Despommier, Rich Condit, and Alan Dove

The complete TWiVome deconstructs the movie Contagion.

Click the arrow above to play, or right-click to download TWiV 167 (53 MB .mp3, 88  minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, by email, or listen on your mobile device with the Microbeworld app.

Links for this episode:

• R0 explained (pdf)
• Hendra and Nipah encephalitis (CDC)
• Contagion (IMdB)
• TWiV on Facebook
• Letters read on TWiV 167

Weekly Science Picks

Dickson – Guinea Pig Doctors by Jon Franklin
Rich – Learn to appreciate technology and Everythings amazing and nobodys happy (YouTube)
Alan – JD Hooker slide collection
Vincent – iTunes U app and iBooks Author

Listener Pick of the Week

Judi – Makers of Many Things by Eva March Tappan

Send your virology questions and comments (email or mp3 file) to twiv@twiv.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

In letters to Science and Nature, the authors of the controversial avian H5N1 influenza virus transmission experiments in ferrets, together with other influenza virologists, have agreed to a 60 day moratorium on transmission research:

…we have agreed on a voluntary pause of 60 days on any research involving highly pathogenic avian influenza H5N1 viruses leading to the generation of viruses that are more transmissible in mammals. In addition, no experiments with live H5N1 or H5 HA reassortant viruses already shown to be transmissible in ferrets will be conducted during this time.

They write that research will continue on assessing the “transmissibility of H5N1 influenza viruses that emerge in nature and pose a continuing threat to human health”.

This research is being halted because of the concerns that ferret-transmissible H5N1 viruses may escape from laboratories. They argue that the finding in two laboratories that viruses with a hemagglutinin (HA) protein from highly pathogenic avian H5N1 influenza viruses can become transmissible in ferrets advances our understanding of influenza transmission. Nevertheless,

We recognize that we and the rest of the scientific community need to clearly explain the benefits of this important research and the measures taken to minimize its possible risks. We propose to do so in an international forum in which the scientific community comes together to discuss and debate these issues.

I agree in principle with this decision, because the argument over this research has become increasingly polarized in recent weeks, with a distressing demarcation between those who believe the work should proceed, and those who feel it should not be done. A dialogue to identify the crucial issues and develop plans to address them, while continuing this important line of research, is certainly welcome.

I am curious to see who will participate in the proposed dialogue. I do hope it will be a balanced forum: a fair mix of microbiologists, especially those working on influenza virus, and those interested in biosecurity. As I have said before, scientists will listen to the policy analysts, but the latter must also understand the science.

Update: Alan Dove has written an honest analysis of the moratorium announcement.

Related:

Palese: Don’t censor live-saving science
N.Y. Times: H5N1 ferret research should not have been done
Should we fear avian H5N1 influenza?
A bad day for science
Ferreting out influenza H5N1

Inside History Magazine is a periodical “for people passionate about Australian and New Zealand genealogy, history and heritage.”  The current May-June 2012 issue has an article entitled “Entering the Blogsphere” in which author Jill Ball (of Geniaus) writes about the prevalence of genealogy bloggers.  As part of the article, she compiled a list of 50 blogs that “every genealogist needs to follow.”

I’m honored that The Genetic Genealogist was included in this list, especially considering the others blogs, many of which I’ve been reading for years!

Be sure to check out Inside History Magazine and the many terrific blogs listed in the article.  Also, Jill just included a nice follow-up list of “the blogs that got away.”

Today, Ancestry.com announced the official release of AncestryDNA (see press release below).  It is initially available only to Ancestry.com subscribers, at a cost of $99.

The launch page is here.

Press Release:

Ancestry.com Launches new AncestryDNA Service: The Next Generation of DNA Science Poised to Enrich Family History Research

Affordable DNA Test Combines Depth of Ancestry.com Family History Database with An Extensive Collection of DNA Samples to Open New Doors to Family Discovery

Many scientists and health care experts believe that genetics will be a vital component to several facets of our lives in the future, especially in the field of medicine.  Indeed, some consider the study of genetics to be one of the most promising solutions to many of the health dilemmas facing society today, including advancing our understanding of interactions between genetics and the environment.  Accordingly, today’s students should have at least a basic grasp of genetics, and science educators must find innovative ways to share those concepts with their students.

A Need for Genetics Education

Unfortunately, some studies suggest that many of today’s students lack comprehension of some of the most basic concepts in genetics.  See, e.g., Wood-Robinson, C., Lewis, J. and Leach, J. 2000, Young people’s understanding of the nature of genetic information in the cells of an organism, J Bio Educ 35(1):29-36; and Quinn, F., Pegg, J., and Panizzon, D. 2009, First-Year Biology Students’ Understandings of Meiosis: An Investigation Using a Structural Theoretical Framework, Int’l J. Sci Educ 31(10):1279-1305.

While students certainly can learn about genetics through lectures and textbooks, there is little doubt that hands-on experiences help reinforce concepts and may even reach some students that are less likely to learn from passive methods.

Over the next few weeks, we’ll examine several instances of genetic genealogy and/or personal genomics being used in the classroom to examine and reinforce concepts of genetics, race, and ethics, including the following:

• The Genographic Project  in High Schools (Chicago Public Schools, Soldan International High School, Edward Bleeker Middle School, and Olympic High School) (2007-)
• The Cornell Genetic Ancestry Project (2011)
• 23andMe Testing for Freshman at Berkeley (2010)
• Medical School Testing (SUNY Upstate Medical University and Stanford) (2010-)
• Anthropology and Genetics at Penn State University (2012)
• Personal Genetics Education Project (www.pged.com)

Without further ado, let’s begin with the use of genetic genealogy in schools.

The Genographic Project in Middle and High Schools

Each of the school projects below were conducted in conjunction with the The Genographic Project, which has done a tremendous job of working with public schools to educate students about their genetic ancestry.

A.  Chicago Public High Schools in 2007

The earliest reference I can find of commercial genetic genealogy being used in the classroom is from 2007, when The Genographic Project (National Geographic, IBM, and Family Tree DNA) donated 150 testing kits to each of five Chicago Public Schools and 50 kits to each of their international partner schools in England, Jordan, France, South Africa, and China (a total of 1000 kits, priced at approximately $100 each).

According to several reports, the teachers at these schools expected the testing to provide the students with valuable information and experiences:

Parents ‘hear DNA, all they think about is “CSI.” It’s not like that at all,’ said Brian McKay, who teaches European history at the Charles A. Prosser Career Academy and scraped his own cheeks for cells on Tuesday. ‘Our kids are going to get a lot out of this. (Students) are very positive, they’re very excited.’  Source.

Prosser Principal Ken Hunter stated that:

“We are more than excited to help our students learn about our world’s common threads. At Prosser we tell our students to “extend the world”—this project presents them with a wonderful opportunity to make those words come alive in real world application. My teachers are thrilled to be taking part in such a thoughtful learning activity that brings the idea of common ancestry and shared humanity to our students in such a powerful and compelling way. This ‘learning tool’ has really helped make the education experience here at Prosser ‘the stuff that dreams are made of.” Source.

Interestingly, the schools involved were chosen based in part on the diversity of the student population:  “‘Chicago is a melting pot, a multicultural melting pot, it’s a great place to illustrate how interrelated we are,’ [Spencer] Wells said.”

The launch of the project was covered by The Genographic Project itself, and by the media:

• “Who Are You and Where did You Come From? Tracing Your Ancient Ancestors in the Classroom,” The Genographic Project (January 23, 2007);
• “The Silk Road Project Meets the Genographic Project,” The Genogrpahic Project (date unknown);
• “Chicago 10th-graders trace ancestry through DNA,” AP report (January 22, 2007); and
• “Tracing a Common Ancestry,” Chicago Tribune (January 24, 2007)

Unfortunately I was unable to find any reports of the outcome of the testing, so it’s unclear what lessons the students derived from the experience.

B. Soldan International High School in Chicago in 2007

In 2007, forty advanced placement science students at Soldan International High School in St. Louis, Missouri submitted their DNA for testing with the Genographic Project.  (see “High school students uncover their past through their DNA“) (several articles also appeared in the St. Louis Dispatch, but are now found only in the newspaper’s archives).

At Discovering Biology in a Digital World, blogger Sandra Porter wrote the following about the Soldan project:

Most science instructors steer clear of these sorts of activities because there is a real possibility that children might learn some things in class that their parents would prefer remain secret. Any science instructor who’s had to find a really creative way to explain why a student has the “wrong blood type” based on their parentage, will appreciate that analyzing Y chromosomes has potential for trouble.  I wonder how the teachers at Soldan will answer those questions.

I actually wrote about this project here on TGG back in 2007, the early days of the blog, partially to address the concerns that were raised (see “Genetic Genealogy in the Classroom”).  As Sandra’s blog post suggested, some were concerned that testing in the classroom had the potential to reveal non-parental events.  To address this issue, I posited the following:

“although there is surely a chance of there BEING a non-parental event in a large group of students, the chance of CONCLUDING that there was a non-parental event is quite small. Most genetic genealogy companies return a list of allele numbers (12 alleles for the Genographic Project) for Y-DNA or a list of mutations for mtDNA along with a probable haplogroup designation. Armed with that knowledge, how is a student going to determine that there was a non-parental event?”

There are certainly some ethical concerns with genetic genealogy testing in the classroom, but non-paternal events are unlikely to be of serious concern.

C.  Other Schools

Following the apparent success of the Chicago school experiment, the Genographic Project worked with several other schools in the following years:

• Newark High School in western New York state (2007) – approximately 10 students contributed DNA to the Genographic Project for testing (see “Connecting Some Dots With Our DNA”);

• Edward Bleeker Middle School in Flushing, New York (2011) – several sixth graders participated in testing, as roughly 400 students at four different New York City public schools would trace their ancestry with the Genographic Project (see “Am I Related to Justin Bieber?”);

• Olympic High School (2012) – teacher Anthony Fuller used his results to educate the students about the Genographic Project and genetics (see “L.A. High Schoolers Dig in to the Genographic Project”); and

• Harlem Children’s Zone in Harlem, NY (2011) – In last Sunday’s episode of “Finding Your Roots with Henry Louis Gates, Jr.,” Gates tested a group of six or so African American students at Harlem Children’s Zone.  The testing appears to have analyzed only their ethnicity, which varied considerably.  What was most interesting, however, was that Gates discussed with them the implications of their testing, and asked for their thoughts after receiving their test results.

A Useful Exercise: Estimating Admixture Before Testing

On Finding Your Roots, Gates also had the students estimate their admixture before they received their results, which is a great way to introduce the scientific and historical concepts associated with admixture testing.  This is a tool that Gates has already used at least once in the series, and I’m sure we’ll see it again.

Another useful component of this exercise might be to have the kids do some preliminary research on their own family tree before estimating their admixture, including research as simple as asking parents and grandparents.  With this information, they could make a more educated estimate of their admixture.

Conclusions

Although using genetic genealogy in the classroom is not new, it hasn’t been used as extensively as it could be.  What suggestions do you have for the successful use of testing in the classroom?

• Genetic Testing With 23andMe
• Genetic Testing With 23andMe – Ancestry Testing
• A Review of Family Tree DNA’s Family Finder – Part I
• A Review of Family Tree DNA’s Family Finder – Part II

Today, I’m reviewing the new autosomal DNA test from Ancestry.com called “AncestryDNA.” I’ve already written at length about AncestryDNA, so I won’t cover too many of the basics here.  I have an in-depth introduction to the product located at “Ancestry.com’s AncestryDNA Product,” which you might want to check out before or after reading this review in order to gather more information.

AncestryDNA: An Introduction

The introduction page, which appears after clicking on “View Results” on the front page, consists of my Genetic Ethnicity Summary and the Member DNA Matches (which is further broken into close cousins and distant cousins, as discussed in detail below).  Please note that for purposes of this review I’ve removed the identifying information for my genetic matches.

Genetic Ethnicity Summary:

My genetic ethnicity results, which suggest 90% European and 10% Uncertain, are very interesting.  In a recent webinar with the AncestryDNA team, they reported that the genetic ethnicity analysis is still very early in the beta phase, and will continue to be updated and refined as new reference populations are added.  Indeed, I’m predicting that over time as new information is added and the algorithm is refined, some or all of my10% Uncertain will be categorized (perhaps to reflect my maternal Asian and African contributions, which I’ve written about before), and that some of of my 90% European may very well change.

Under a heading “About Your Ethnicity” is a pop-up file with more information about Ancestry.com’s ethnicity estimation algorithm.  In that file, under “Is It Accurate,” for example, Ancestry.com provides the following:

When determining your genetic ethnicity, we hold our process and results to an extremely high standard of accuracy.  Our lab’s analysis uses some of the most advanced equipment and techniques to measure approximately 700,000 points in your genome (with at least a 98% rate of accuracy).  We compare that to one of the most comprehensive and unique collections of genetic signatures from around the world.  And as this collection improves over time, it can only get better.

I’m not sure whether the AncestryDNA tests these 700,000 SNPs, or whether it tests more SNPs but is currently using a subset of 700,000 for its analysis.  I’ll try to find this information.

I thought it might be interesting to compare my genetic ethnicity results from the three companies (Ancestry.com, 23andMe, and FTDNA):

Ancestry.com’s AncestryDNA:

• 78% Scandinavian
• 12% Central European
• 10% Uncertain

23andMe’s Ancestry Painting:

• 98% European
• 2% Asian
• <1% African

Family Tree DNA’s Population Finder:

• 68% European (Northeast European) – Finnish
• 32% Middle East (Jewish) – Jewish

After reviewing the results one thing is certain: all three companies estimate a strong European contribution to my genome, particularly Scandinavian (ranging from 68% to 78%).  It’s ironic, however, that I have yet to identify a single Northern European ancestor!  I certainly won’t be surprised when one pops up someday.

Clicking on “See Full Results” takes me to a more detailed analysis of my ethnicity results, but not before I click through the following pop-up:

Please keep in mind…Our prediction of your genetic ethnicity is not yet finalized. As we gather more DNA samples and continue our research we expect your ethnicity results to become more accurate and perhaps more detailed.

As I stated above, the ethnicity results are likely to change over time, so be forewarned.

The Full Results page – reproduced below – includes historical and anthropological information about each of the identified regions from your ethnicity profile (Scandinavian and Central European, for me).  It also shows a list of genetic matches who share the relevant region (it’s a long list along the right lower side of the page, but it’s not shown below for privacy reasons).  You can also zoom into the map where ancestors from a tree you’ve linked to your account are displayed.  For example, I have 8 listed in Ireland and 2 in Central Europe.

In summary, Ancestry.com’s AncestryDNA test provides a genetic ethnicity/region calculation based on about 700,000 SNPs and a large collection of both public and proprietary reference databases.  The product can currently categorize DNA into at least 22 different ethnicities/regions, with more to come.  So be prepared for changes to your estimation as their algorithm and databases grow.

Member DNA Matches

Also on the introductory page is a listing of genetic matches.  These are individuals that, based on shared segments of DNA, you are predicted to share a common ancestor with.  An interesting aspect of the DNA matches list, however, is a sliding scale for the relationship confidence level, which ranges from 99% to 10%:

• 99% Confidence – Immediate Family
• 99% Confidence – 1st Cousins
• 99% Confidence – 2nd Cousins
• 98% Confidence – 3rd Cousins
• 96% Confidence – 4th Cousins
• 50% Confidence – Distance Cousins
• 20% Confidence – Distance Cousins
• 10% Confidence – Distance Cousins

Accordingly, the introductory page can be customized to only display cousins of a certain confidence level.  If I reduce the confidence level to 96%, for example, I only have two matches (my two predicted fourth cousins shown in the picture above).

Clicking on the “What Does This Mean” link next to the  possible relationship range on the “Review Matches” page for each genetic cousin (see the figure below) causes the following information to be displayed, along with some nice inheritance charts:

Predicted Relationship Info: FOURTH COUSIN

…

It’s interesting to note that (at this degree of separation) we are accurately able to predict only about 85% of the possible relatives that are out there—in other words there is a 15% chance that our DNA analysis does NOT recognize an actual relative of yours. One way to be more certain that the DNA testing captures as many relatives as possible is to have multiple members of your immediate family tested.

It is also interesting to note that at this degree of separation we are sometimes wrong in our prediction of a real relationship. We’ve found that for this relationship about 15% of the time we predict a relationship that cannot be found in any family tree.

This provides some interesting insight into AncestryDNA’s matching algorithm and, accordingly, the algorithm’s results.  For example, it’s important to always keep in mind that there is a roughly 15% chance of incorrectly labeling an individual either as a match or as not being a match.

As the user slides the scale from 99% down to 10%, more results typically appear.  For example, I currently have two 4th cousins listed as matches, 9 matches with 50% confidence, 14 matches with 20% confidence, and 38 matches with 10% confidence.  I expect these numbers to increase considerably once more test results become available.  I don’t know how big the AncestryDNA database currently is, but I’m guessing that only a few 100 to a few 1000 people, at the very most, have undergone testing so far.

Comparing Family Trees

The true power of the AncestryDNA test lies in the ability to automatically compare your uploaded family tree with the uploaded family tree(s) of genetic matches.  For example, one of my predicted fourth cousin matches has a public tree with 408 people.  Clicking on “Review Match” takes me to the next page with more information (see the next screenshot) including each of the following:

• A predicted relationship and predicted relationship range;
• Our ethnicity comparison (a very cool and potentially very useful feature);
• My genetic cousins’ entire tree out to 7 generations (and a link to see more);
• A possible shared ancestor (a “shaky leaf” hint) if one is identified;
• Surnames that we share in common; and
• My genetic cousins’ surnames through 10 generations.

I especially like the Genetic Ethnicity Bar (I just made that up, but I guess it fits) comparison, which shows your ethnicity prediction next to your matches ethnicity prediction.  For example, my fourth cousin displayed in the image below is 93% British Isles and 7% Uncertain.  Since I have no reported British Isles genetic contribution, my Genetic Ethnicity Bar is gray:

 On the other hand, if there is some matching ethnicity contribution, the Genetic Ethnicity Bar comparison will look like this:

This genetic match and I, predicted to be distant cousins, both have contributions from Central Europe and Scandinavia.  My match also has British Isles and Middle Eastern, which I am estimated not to have.

Also on the the “Review Match” page is a link to send a message to the match (very important for genealogists).  I also like the “Last signed in” information, which lets people know just how active a genetic match might be (and why they aren’t answering your email!).

Common Ancestor and Shared Surnames

As can be seen from the last two screenshots, the list of shared surnames (if there are any) is prominently displayed near the top of the page.  If there was an individual in common between our trees, he or she would also be displayed there.  Unfortunately, when I review the match with each of my possible genetic cousins, I typically have one or more shared surnames, but none have a single identified common ancestor.  I was hoping for such a match, but I’ll have to be a bit more patient.   While I currently have about 55 matches, only some of those have public trees, and even fewer have substantial family trees (larger trees increase the likelihood of identifying a possible shared ancestor, of course).

Conclusion

This post included just a few initial thoughts about my testing experience and results.  I may add more information, or create a new post, as I continue to review my results.  If you have any questions about the testing process or ancestry results that I didn’t address, please feel free to leave a comment.  I’m sure many other people have the same question, so don’t hesitate to ask.  I’ll also try to get the AncestryDNA team to answer any questions I can’t answer.

While there is currently no information about when AncestryDNA will be available, or pricing, I’m sure that this will be available soon.

I’m looking forward to your comments, ideas, and questions.

(Disclosure:  I received my AncestryDNA test without charge from Ancestry.com for review purposes and beta testing.  Regardless, I have attempted to review this product as honestly and as objectively as possible in order to provide valuable information about AncestryDNA to my readers.)

• Ancestry.com’s Autosomal DNA Product – An Update
• The Legal Genealogist Discusses Ancestry.com’s New Autosomal Testing 
• WDYTYA Reveals More Information About Ancestry.com’s New Autosomal DNA Testing

Webinar with Ancestry.com

Last week, I participated in a webinar with Ancestry.com regarding the AncestryDNA test (although, unfortunately, I had to leave a bit early due to a previous engagement).  It was a great list of about 10 well-known genealogy bloggers, each one of whom is someone I’ve been reading or following for years.  It was an honor to be included among them.

One of the participants was CeCe Moore of Your Genetic Genealogist.  CeCe has a nice summary of the webinar and the important points about the autosomal test and the user interface at “New Information on Ancestry.com’s AncestryDNA Product.”  If you’re interested in autosomal DNA testing, or in Ancestry.com, I highly recommend reading her post.

The Power of DNA

The highlight of the webinar – and of the AncestryDNA product – was the combination of DNA and family trees.  I’ve said before that the ability to combine DNA and the paper trail is the future of genetic genealogy, and the true power of DNA.

The AncestryDNA test automatically compares your family tree (if you have one hosted at Ancestry.com) to the family tree of your genetic matches (if they have one hosted at Ancestry.com, and if it’s public).  The user interface then suggests overlapping individuals that might be the source of the shared DNA!  The user interface presents this information as a “Potential Common Ancestor,” and provides it as a “shaky leaf” hint.  Thus, as with all shaky leaf hints, it should be subjected to further research and not blindly accepted.

You can also see the first 7 generations of each genetic match in your user interface (again, if their tree is public), another great benefit.

While there are of course MANY caveats to this matching algorithm, it eliminates a time-consuming step in sharing information with genetic matches, as many of us know from [many hours of] experience.  (I didn’t get a chance to ask if the matching algorithm takes into account the predicted relationship range of the genetic cousins being matched, but I’ll try to get that information for you.)

If you think about it for a moment, the power of this approach is mind-boggling.  Over time it will create a mesh of DNA and genealogies, with individual data points that can be confirmed or rejected based on the results of numerous test-takers.  In other words, there will be an enormous DNA family tree.  Not only that, but that enormous DNA family tree can then be used to test genealogical hypotheses (was John Smith’s mother a White?  was John Smith Jr. adopted? etc…).  While a long way down the road, the possibilities are endless.

Concerns About Combining DNA and Family Trees

I know there is a lot of criticism and concern about the quality of third-party genealogies on Ancestry.com.  It’s impossible to know just how subjective or objective the data in any given tree is.  It’s true that there will always be concerns about third-party genealogies, and that there will be many, many errors as genealogists begin to tie DNA to specific ancestors.

But these concerns are equally true for paper records.  Any time you tie a paper record to a certain individual in your family tree, there’s a serious possibility of error, and this error can be propagated throughout numerous genealogies.  Every genealogist has seen this before, probably many times. But the fact that we’ve recognized the error likely means that the error has been corrected through careful research.

There is nothing different or exceptional about tying DNA to ancestors.  Any time you tie a piece of DNA to a certain individual in your family tree, there’s a serious possibility of error.  Over time, however, careful and methodical research – likely contributed by many different test-takers – will allow genealogists to make the most reasoned and knowledgeable judgment.

There’s enormous power in numbers.

A Roundup of AncestryDNA Posts

Here’s a complete roundup of posts around the genealogy blogosphere about Ancestry.com’s new Autosomal DNA product (AncestryDNA):

• “Science and the “10th” cousin”at The Legal Genealogist;
•  “Ancestry.com Venturing into Autosomal DNA Testing?” at Your Genetic Genealogist
• “More Details on Ancestry.com’s New Autosomal DNA Test Offering” at Your Genetic Genealogist
• “Update on the New Autosomal DNA Test from Ancestry.com” at Your Genetic Genealogist
• “My (free) Ancestry.com DNA results – a comparison to FamilyTreeDNA” at genejourneys
• “Ancestry.com autosomal DNA test – Part II” at genejourneys

Did I miss any?  Feel free to mention them below.

Disclosure: I received a free beta test from Ancestry.com, although I have not yet received my results (I will receive them this week, I believe).  However, I have tried to review this product objectively.

Last week I participated in a conference call with members of the show, including Senior Story Editor and Producer Leslie Asako Gladsjo and Chief Genealogist Johni Cerny.  Also on the call, although only able to participate for a few minutes, was Henry Louis Gates Jr.

Here are some interesting tidbits about Finding Your Roots – and genealogy in general – that I learned from the conversation:

• Gates believes that genetic genealogy is deconstructing the notion of race; never has FTDNA or 23andMe returned an African American’s testing results and reported 100% African, for example.  In other words, science is demonstrating that things are much more complicated than we would have guessed without the benefit of DNA.

• All guests on Finding Your Roots used both 23andMe and FTDNA for DNA testing – all African Americans participating in the series also used African Ancestry.  While the guests receive all their results, we may not always see them.

• Many are still wary of genetic genealogy; many potential guests even turned down the series largely because of the DNA testing involved.

• Gladsjo and Cerny noted that DNA is just another tool for the genealogist; sometimes the guests’ DNA results were very interesting, and sometimes they were “pretty boring.”

I hope you’ll be tuning in tomorrow to see Finding Your Roots.  I have a feeling that this is going to be a fascinating series.

By the way, did you catch last night’s episode of “Who Do You Think You Are” with Helen Hunt? It was another fantastic episode.  Too bad they didn’t bring in DNA testing.  With Hunt’s Jewish ancestry, it would have been a terrific opportunity to education viewers about the many unique facets of genetic genealogy testing in this population.

I spoke with Carol a few months about this piece, and she included a few quotes from the interview in the article.  Also included is a 2-minute soundbite of our conversation:

Also featured in the main article are the always-fantastic Daniel MacArthur and Joe Pickrell (you can find both of them at Genomes Unzipped).

Both Daniel and I also contributed short companion pieces:

• “Genetic Genealogy: A Powerful Tool for the Family Historian” by me; and
• “Ready to Test Your DNA: How To Choose A Genetic Testing Company” by Daniel.

As I noted in a recent blog post (see “WDYTYA Reveals More Information About Ancestry.com’s New Autosomal DNA Testing“), autosomal DNA testing was featured in the recent episode of Who Do You Think You Are with actor Blair Underwood.  After revealing Mr. Underwood’s biogeographical estimates (74% African American and 26% European), they revealed a genetic cousin found in the Ancestry.com’s database:

The service identified a distant cousin (somewhere around the 10^th cousin range) who lived in Cameroon (an Eric Sonjowoh). Mr. Sonjowoh was already in the Ancestry.com database, which is why they were able to compare him to Mr. Underwood. According to Eric, someone approached him in 2005 and asked him for his DNA because African Americans were trying to trace their family back to Cameroon. I’m not sure what database the DNA was in, but it shows that Ancestry.com has pre-populated its database with at least some samples from other public and/or proprietary data sources.

Ms. Russell expresses concerns over the identification of the relationship between Mr. Underwood and Mr. Sonjowoh as “1oth Cousins:”

I have a bit of an issue with telling person A (Blair Underwood) that person B (Eric Sonjowoh) is a 10th cousin when there isn’t a prayer of a paper trail to support that statement — and the science isn’t good enough to say it either.

She notes – very correctly – that autosomal testing alone cannot identify a relationship as being 10th cousins rather than anything ranging from 5th, 12th, or 15th cousins, or even beyond.

As you can see from my summary above, I had assumed that the label “10th Cousins” was not intended to be an exact identification of the relationship (I wrote: “somewhere around the 10th cousin range”), but an approximation similar to those used by both 23andMe (for example, “3rd to Distant Cousin”) and Family Tree DNA (for example, “5th Cousin – Remote Cousin”).  Unfortunately, it’s difficult to determine from the portion of the user interface we saw in the program whether or not the “10th cousins” applies to a range or is intended to be a more definitive determination.

In any event, I agree with Ms. Russell’s conclusion.  It is vital that users of any autosomal DNA testing service understand both the capabilities and limitations of the science, and that testing providers work to educate their customers.  It will be interesting to see more of the Ancestry.com user interface when the product officially launches.

Here’s a few links to some other discussion of DNA testing and Ancestry.com’s service following Mr. Underwood’s episode of WDYTYA:

• “Blair Underwood, Who Do You Think You Are?” at tracingthetree;
• “Blair Underwood talks tracing his African roots and ‘Streetcar’ role” at the grio; and
• “Blair Underwood’s African Roots on WDYTYA?” at Ancestor Search Blog.

By the way, a congratulations to Ms. Russell on her recent certification as a Certified Genealogist!

[Update (2/24/12): Some genealogy forums are reporting that callers to Ancestry.com are being told that the autosomal DNA test will publicly launch in approximately 1 month (late March or early April).]

Tonight’s episode of Who Do You Think You Are? featured African-American actor Blair Underwood. For those not familiar with Who Do You Think You Are, the 1-hour program examines the genealogy of a celebrity, typically focusing on one or two of their most interesting families.

DNA Testing

This episode was of particular interest to me because it featured Ancestry.com’s new autosomal DNA testing service, which I’ve written about before (see “Ancestry.com’s Autosomal DNA Product – An Update”). While there wasn’t too much new information about the DNA product in this episode, it was an interesting sneak peek at the service.

In the beginning of the episode, as Mr. Underwood visits with his family to get a start with his genealogy, he shows a DNA collection kit with two long swabs and a mail return envelope. Ancestry.com is using cheek swabs rather than a saliva sample to collect DNA.

Admixture Results

Later in the episode, Mr. Underwood reviews his DNA test results with Dr. Ken Chahine (LinkedIn profile), who is described as the “General Manager Ancestry DNA” in the episode. Dr. Chahine has a Ph.D. in biochemistry and a J.D. (very similar to my own background). According to Dr. Chahine, the test Mr. Underwood used examined approximately 700,000 “links” (or SNPs) in the DNA chain.

Mr. Underwood’s results suggested that the DNA examined was approximately 26% European and 74% African, which is a fairly common admixture for African Americans. Under the “European” tab of the user interface, he was described as 20% French/Swiss and 6% German. Under the “African” tab, the results showed 27% Bamoun, 22% Brong, 13% Yoruba, and 12% Igbo (a total of 74%).

Genetic Cousins

Next, Dr. Chahine asked, “Where would we find your closest DNA matches?” In other words, the Ancestry.com autosomal testing service will also include the ability to identify genetic cousins in the database.

The service identified a distant cousin (somewhere around the 10^th cousin range) who lived in Cameroon (an Eric Sonjowoh). Mr. Sonjowoh was already in the Ancestry.com database, which is why they were able to compare him to Mr. Underwood. According to Eric, someone approached him in 2005 and asked him for his DNA because African Americans were trying to trace their family back to Cameroon. I’m not sure what database the DNA was in, but it shows that Ancestry.com has pre-populated its database with at least some samples from other public and/or proprietary data sources.

Interestingly, Dr. Chahine indicated that Mr. Underwood and Mr. Sonjowoh are related through Mr. Underwood’s paternal line. I’m guessing that they determined this by also testing one of Mr. Underwood’s parents (either directly testing his father, or by process of elimination by testing his mother).

At the end of the episode, Mr. Underwood and his father traveled to Cameroon to meet Mr. Sonjowoh and his family, which was a touching reunion. Although their relationship is extremely distant (perhaps as much as 300 to 400 years), it provided Mr. Underwood with a connection to his roots in Africa.

• RT @GeneSherpas: “@GeneticsUpdate: Can You Be Fired for Your Genes? sns.mx/REiMy1” Hopefully our future doesn’t come down to this! Feb 20, 10:44pm via HootSuite 

• RT @openSNPorg: You can now apply for a free genotyping. Find more details and the planned schedule here: opensnp.wordpress.com/2012/02/20/app… Feb 20, 5:45pm via HootSuite 

• RT @Sagebio: RT @gnshealthcare: It’s not the $1,000 genome that’s important, it’s the analysis that’s valuable. onforb.es/xzzht0 Feb 16, 1:06pm via HootSuite

• Wow! MT @genomicslawyer: New GeneWatch entitled “Genetics in 20 years”: bit.ly/zF3kVO Commentaries from Evans, Greely, Church, others  Feb 16, 11:52am via HootSuite

• New at TGG: “@23andMe is Hiring a Marketing Team” – ow.ly/96I1e (via @businessinsider)  Feb 16, 9:00am via HootSuite

• New at TGG: @MyHeritage & Family Tree DNA partner to offer genetic genealogy tests to MyHeritage’s 62 million members – ow.ly/96Flp  Feb 16, 8:23am via HootSuite

• Congratulations @johnhawks! RT @paleoanth: My appointment as HHMI Fellow dlvr.it/1CRWmp #johnhawksweblog  Feb 16, 7:26am via HootSuite

• RT @dgmacarthur: RT @EricTopol Interesting perspective from a Bloomberg journalist who has his genome sequenced bloom.bg/w6QXnW  Feb 15, 10:38am via HootSuite

• An interesting Kickstarter project involving Sitting Bull’s DNA and his great-grandson Ernie LaPointe – ow.ly/94lpA  Feb 14, 2:15pm via HootSuite

• “Genetics and privacy” at john hawks weblog (@johnhawks) – “‘Privacy advocates’ seem like they’re living in the 1980′s”  Feb 14, 12:19pm via HootSuite

• Technically his mom’s bedroom! MT @drbachinsky: “Doing Biotech in My Bedroom” at ow.ly/93TZM (via @techreview) Feb 14, 10:05am via HootSuite

• 2 containing “ancestry” – MT @DNAlawyer: This morning Rothenberg touted NHGRI searchable DB of all ELSI projects: ow.ly/92V4x  Feb 13, 3:41pm via HootSuite

• “Oh, mama…a use for mtDNA” by Judy G. Russell at The Legal Genealogist – ow.ly/926G1  Feb 13, 7:46am via HootSuite

• Interesting SNPedia analysis of the new Denisova genome – ow.ly/926lh (by @CarisO) – straight hair or curly? Feb 13, 7:43am via HootSuite

• MT @genomicslawyer: New study raises concerns about use of familial matching in forensic DNA: bit.ly/xF1MCm  Feb 11, 11:32am via HootSuite

• New post at Higher Education IP Law Report – “Does an Instructor Have Rights in a Student’s Class Notes?” ow.ly/8YgQ9  Feb 09, 10:26am via HootSuite

• Fascinating post about consumer genomics by Madeleine Price Ball at the Personal Genome Project’s new blog – ow.ly/8Ybol  Feb 09, 9:37am via HootSuite

• The hitherto mysterious “The Genealogy Event” (@GenealogyEvent) in NYC in Oct. 2012 is now requesting speakers – ow.ly/8V5hY  Feb 07, 7:49am via HootSuite

• Ancestry.com‘s exciting new autosomal DNA test discussed at #Rootstech keynote today – ow.ly/1Fz9tf  Feb 04, 7:34pm via HootSuite

• I plan to be there!! RT @RootsTechConf Mark your calendars: #RootsTech 2013 is March 21-23, 2013  Feb 04, 7:30pm via HootSuite

• Listening to Kenneth Chahine (Sr. Vice President & General Manager at Ancestry.com) talk about DNA at #Rootstech 2012 Feb 04, 10:53am via TweetDeck

Ewan Birney reported on results from the ENCODE project, a truly massive consortium project to look at the role of non-coding functional DNA. My take-home message was that a chunk of the genome significantly larger than the entire exome can be confidently said to be bound by a protein in at least one cell line. This includes bound transcription factor motifs and DNase1 footprints: these aren’t wooly definitions, and certainly miss out lots of important non-coding annotations. Ewan also presented evidence implying that we have only captured half of what we eventually could if we sequenced all human cell types. Overall, we can guess that for every base pair that codes for part of an exon, there will be another four base pairs responsible for binding proteins. A few other ENCODE talks dug deeper into the data, including one from Mark Gerstein about using transcription factor binding to construct gene networks. Interestingly, he showed that networks connected via distal regulation (i.e. regulation via proteins bound outside the promoter) are very different to those formed by proximal regulation.

As well as cataloging this variation, researchers are also getting better and better at figuring out the mechanisms of genome regulation, and there were quite a few talks that really dug down into the specific dynamics of the genome and its assorted bound products.

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As usual, there were a few talks in the first session describing large consortium analyses of human complex disease. For instance, I presented work (on behalf of the International IBD Genetics Consortium) on the Inflammatory Bowel Disease immunochip project. We have genotyped tens of thousands of cases from 15 different countries, and discovered a host of new common loci for IBD. I’ll be writing about this project on Genomes Unzipped soon. On the other end of the allele frequency spectrum, Mark McCarthy reported on some of the next-generation sequencing projects that are going on in Type 2 Diabetes; these have less samples (something like 7K cases in total), but generated high quality calls for a large number of rare variants. Mark reported on a few interesting hints of rare T2D associations, but his overall conclusion was that we will need tens of thousands of samples to be well powered to find rare variants that underlie common disease. We will need to go beyond just sequencing a few thousand samples, and start designing well-powered replication studies to follow up what we find.

But I wanted to talk about some more non-standard, and slightly cleverer studies of non-human phenotypes that I found interesting. Three speakers described pretty nifty studies that used the particular properties of non-human sequence data to do some well-powered sequencing experiments that wouldn’t be possible with humans.

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To cut straight to the chase, the first session (High Throughput Genomics and Genetics) included a total of four different talks on sequencing the genomes of single cells. A clear theme if ever there was one.

Two of these talks discussed creating personal genetic maps of recombination by directly sequencing single sperm cells. Adam Auton went first – his dataset was an example of a particularly tricky setup, including massive amplification biases and a whopping 75% of his samples showing evidence of contamination. Despite this, he showed that with the right QC and statistical model you can still get a good map that is very similar to existing maps, even given these problems. Stephen Quake presented a somewhat less difficult sperm sequencing study, which used a special microfluidic chip (previously used for chromosome separation) to separate out the sperm cells. Low coverage sequencing could produce a map that closely recapitulated existing maps, and higher coverage could be used to estimate rates of aneuploidy and de novo mutation.

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I am lucky enough to be staying on site again this year, rather than having to endure the daily death-defying suspensionless bus ride from one of the satellite hotels. However, the cabin that I have been put in this year breaks my current record for the longest climb from lecture theater to front door:

At its heart, this paper is a challenge to a common assumption used in statistic genetics: the assumption of additive genetic risk. This states that genetic risk factors act independently of each other, with each variant increasing genetic risk by the same amount regardless of what other risk factors are present*. Of course, this is clearly a spherical cow situation, we know that the cell is full of complex interactions of various sorts, and a mutation cannot help but be effected in some way by the rest of the genome. But mathematically the assumption simplifies much of the complexity of statistical genetics, and allows you to do a number of things that would be very hard otherwise. We generally think additivity is a good approximation; it doesn’t matter if it is slightly wrong, and we’d have picked up if it were very wrong.

Zuk et al’s claim is that it is possible that additivity is wrong, that did not pick it up, and that it really does matter. This blog post will discuss the specific arguments that Zuk et al make against additivity. Some of the broader implications of the research is discussed over at Genomes Unzipped, and in particular looking at what this does and doesn’t say about total (not additive) heritability.

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A new group blog, res gerendae, came online at the end of last year, and is interesting for a few reasons. Firstly, it is written by Classics students (those who study Roman, Greek and other societies of the Classical antiquity), who aren’t really known for their blogging. Secondly, the blog is open to all the Classics grads of Cambridge University, potentially acting as a voice for all students of the Faculty of Classics.

So far you can read about graffiti then and now, the real location of Troy and a surprisingly technical reading of a postcard.

Lets hope other student bodies take inspiration from this, and do their bit to get students involve in writing about their field.

For me, the hightlight of yesterday was (somewhat obviously) the Individual Resequencing for Complex Trait Genetics session. This was organised by Mark Daly and Ben Neale of Mass. Gens. Analytic and Translational Genetics Unit, and gathered together a number of the Big Men (all men, unfortunately) of disease association together to talk about the many and varied Next-Generation sequencing studies they have been working on. I’ve summarised some of what was said below.

As always, you can find more coverage of ICHG on twitter (@lukejostins for me, #ICHG2011 for aggregated coverage).

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The debate was pretty lively, and in parts both enlivening and depressing. Below are a few points that I found interesting.

As always, you can find more coverage of ICHG on twitter (@lukejostins for me, #ICHG2011 for aggregated coverage).

Different perspectives

Joris Veltman described his exome sequencing of 500 individuals with intractable disease, and noted that there has been much success, and very little evidence of harm. Ségolène Aymé mentioned NIH targts that hope to see almost all genetic diseases diagnosed by 2020, and new treatments for rare diseases to be developed simultaneously. There seemed to be a solid consensus across the panel that sequencing should be rolled out as a standard tool in the diagnosis of genetic diseases, provided that the approach is a targeted one, restricted to finding the pathogenic mutation(s) causing the disease.

More controversial was the role of sequencing of healthy individuals, and the general return of data to patients or doctors for any reason other than directly diagnosing a genetic disease. Rade Drmanac, chief scientific officer of Complete Genomics, was obviously strongly in favour of everyone having their genome sequenced, and made it clear that Complete Genomics intends to start offering sequencing to doctors in the future. In his vision, genomes are sequenced at birth, and an initial analysis of immediately actionable results (e.g. potential genetic diseases) is passed to the doctor and patient, with further analyses being carried out if and when they are required.

Michael Hayden immediately dismissed this as hype. He pointed out how unable the US is to handle medical sequencing, with no good systems of reimbursement, a massive shortage of genetic councilors, and a general lack of training in the medical profession.While more positive in general, Louanne Hudgins also expressed worries about the lack of knowledge of genetics among doctors, with some truly scary examples of MDs failing to understanding even the most basic genetics.

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As always, I aim to report on this blog at least one thing that I found interesting for every day of the conference. Also as always, I will be tweeting the odd thing of interest from my twitter feed @lukejostins, and you can get more in-depth coverage on the hashtag #ICHG2011.

This year I am also giving a talk. In fact I am giving one of the closing talks of the conference! (to put an overly positive spin on the graveyard slot). I’ll be talking at 3.15pm on Saturday in the Statistical Genetics IV session (room 517BC), so if anyone is interested in seeing a little something on disease risk prediction in families, come along!

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The quality of all the talks remains very high, but today I am only going to write about two. What I liked about both of these talks was the link between recent human evolution, geography and phenotype-associated traits, despite being two very different methodologies.

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