TWiV 213: Not bad for a hobby

On the final episode of the year of the science show This Week in Virology, the TWiV team reviews twelve cool virology stories from 2012.

You can find TWiV #213 at

TWiV 198: Pox has got a squeeze-box, seals are gonna sneeze all night

On episode #198 of the science show This Week in Virology, Vincent, Alan, Rich, and Kathy review fatal avian influenza virus in harbor seals, and poxvirus deployment of genomic accordions to counter antiviral defenses.

There once was a virus named pox
Whose genome contained a squeeze-box
When placed under pressure
It expanded its measure
Overcoming the new cellular blocks

You can find TWiV #198 at

TWiV 182: One flu over the ferrets’ nest

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

Moratorium on influenza H5N1 transmission research

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.


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

Should we fear avian H5N1 influenza?

influenza virus

The only thing we have to fear is fear itself – Franklin D. Roosevelt

Why is there such widespread fear of avian H5N1 influenza virus?

Why did Paul Keim, chair of the National Science Advisory Board for Biosecurity (NSABB) say “I can’t think of another pathogenic organism that is as scary as this one”.  What lead Donald McNeil, writing about H5N1 in the New York Times, to conclude that “In its natural form, it is known to have infected only about 600 people since its discovery in 1997, but it killed more than half of them.”

McNeil’s statement is incorrect. Yet it summarizes why Paul Keim, the NSABB, and many others fear the virus.

The problem is that we cannot say with any certainty that the virus has infected only about 600 people. What we do know is that among the 600 seriously ill individuals infected with influenza H5N1 who are admitted to hospital, over half of them die.

To know the fatality rate of avian H5N1 influenza virus in humans, we need to divide the number of fatalities by the number of infections. We do not know that last number – but there are hints that it could be quite large. In a recent study of rural Thai villagers, sera from 800 individuals were collected and analyzed for antibodies against several avian influenza viruses, including H5N1, by hemagglutination-inhibition and neutralization assays. The results indicate that 73 participants (9.1%) had antibody titers against one of two different H5N1 strains. The authors conclude that ‘people in rural central Thailand may have experienced subclinical avian influenza virus infections’. A subclinical infection is one without apparent signs of illness.

If 9% of the rural Asian population has been subclinically infected with avian H5N1 influenza virus strains, it would dramatically change our view of the pathogenicity of the virus. Extensive serological studies must be done to determine the extent of human infection with avian H5N1 influenza viruses.

Until we know how many individuals are infected with avian influenza H5N1, we must refrain from making dire conclusions about the pathogenicity of the virus. Doing so has only lead us down a dangerous path of fearing that H5N1 influenza virus might be used as a weapon of bioterrorism, and restricting the publication of scientific papers on the virus.

Update. A meta-analysis reveals that about 1.3% of over 8,500 study participants had serological evidence of infection with influenza H5N1 (Palese, personal communication).

Khuntirat, B., Yoon, I., Blair, P., Krueger, W., Chittaganpitch, M., Putnam, S., Supawat, K., Gibbons, R., Pattamadilok, S., Sawanpanyalert, P., Heil, G., Friary, J., Capuano, A., & Gray, G. (2011). Evidence for Subclinical Avian Influenza Virus Infections Among Rural Thai Villagers Clinical Infectious Diseases, 53 (8) DOI: 10.1093/cid/cir525

Influenza neuraminidase and H5N1 pathogenicity

influenza_virion_250There are two glycoproteins embedded in the influenza viral membrane: the hemagglutinin (HA) and neuraminidase (NA). The NA, shown in yellow in the illustration, is an enzyme that removes sialic acids from the surface of the cell, so that newly formed virions can be released. The NA protein is composed of a box-like head attached to the viral membrane via a stalk. The length of the stalk may be an important determinant of the virulence of avian influenza H5N1 viruses.

Examination of the sequence of all known influenza N1 NAs reveals that the proteins can be grouped into six classes depending on the length of the stalk region. The stalk regions of some NAs are intact, while others lack from 15 to 22 amino acids. In 2000, influenza H5N1 isolates from humans were identified with a deletion of stalk amino acids 49-68. The percent of human H5N1 isolates with this deletion has steadily increased from 15.8% in 2000 to 100% in 2007. This observation led to the question: does stalk length influence H5N1 pathogenesis in animals?

The authors produced a series of H5N1 reassortant viruses with NA stalks of different lengths. Six of the 8 viral RNAs were derived from the 1933 H1N1 isolate WSN. The pathogenicity of the reassortant viruses was determined in chickens and in mice. Three of the viruses were highly pathogenic in chickens: one with the NA from a 2004 H5N1 isolate containing the deletion of amino acids 49-68, a second with the NA from WSN virus, and a third with the N1 from a 1997 H5N1 isolate. The NA stalks from the latter two viruses have deletions, but they are different from the one in the 2004 H5N1 NA. The other viruses tested were found to be of low pathogenicity in chickens. These included a virus with an N1 from an 1996 H5N1 virus with an intact stalk, as well as viruses with NAs harboring different deletions of various lengths. The findings in mice paralleled those obtained in chickens.

These results show that the NA stalk plays a critical role in virulence of H5N1 avian influenza virus in chickens and in mice. The 20 amino acid deletion from amino acids 49-68 is associated with high virulence, although similar pathogenicity was observed for viruses with different stalk deletions. These results do not answer the important question: why viruses with this particular NA deletion have become prevalent among human H5N1 influenza virus isolates. H5N1 viruses with the same stalk deletion have been isolated from aquatic birds and terrestrial poultry since 2002. It has been suggested that the stalk deletion is associated with adaptation of influenza viruses to land-based poultry, but the advantages conferred by this particular NA are unknown.

Zhou, H., Yu, Z., Hu, Y., Tu, J., Zou, W., Peng, Y., Zhu, J., Li, Y., Zhang, A., Yu, Z., Ye, Z., Chen, H., & Jin, M. (2009). The Special Neuraminidase Stalk-Motif Responsible for Increased Virulence and Pathogenesis of H5N1 Influenza A Virus PLoS ONE, 4 (7) DOI: 10.1371/journal.pone.0006277

New swine influenza viruses in humans

swineA new strain of swine influenza virus has been recently isolated from seven persons in the US. Is it time to break out the swine flu vaccine of 1976?

Last week the CDC reported that swine influenza virus had been isolated from two children with respiratory illness in California. The cases were not linked and the children recovered from the illness. The virus was identified as a swine influenza H1N1 strain, similar to viruses that have circulated in American pigs for the past ten years. However some of the viral genes are derived from Eurasian swine influenza viruses. The isolates are new because this particular combination of swine influenza virus RNAs has not been observed before among swine or human viruses.

A similar virus was subsequently identified in five additional individuals in Texas. It’s curious that one of the California children had traveled to Texas before becoming ill, but whether or not the cases are related has not been revealed.

What is the origin of these new swine viruses? None of the people who were infected had known contact with pigs. Others must have acquired the virus from pigs, who then passed it on – demonstrating that the virus can be transmitted among humans.

At the moment these infections don’t seem to be cause for alarm. Because influenza virus surveillance is more intense than ever before, it is likely that new viruses will always be detected. Furthermore, respiratory disease caused by these new viruses has not been very severe. Another mitigating factor is that the influenza season is nearly over – viral transmission wanes when the weather becomes warmer and more humid.

It is believed that swine influenza originated in 1918-19, when pigs became infected with the pandemic influenza virus strain. Since that time, the H1N1 swine virus has been transmitted back to humans. The hypothesis for the origin of swine influenza is supported by the finding that pigs can be experimentally infected with the human 1918 pandemic influenza virus strain. Furthermore, other human influenza virus strains are known to infect pigs. For example, in the early 1970s, a human H3N2 subtype entered the European swine population.

Pigs can be infected with both human and avian influenza virus strains because the cells of their respiratory tract bear receptors for both kinds of viruses. Based on this observation, it has been suggested that influenza viruses pass from birds through pigs on their way to infecting people. For example, if a pig is infected with avian and human influenza A viruses, reassortment of the viral RNAs occurs, leading to new virus strains to which humans are not immune. The 1957 and 1968 human pandemic viruses were reassortants of human and bird strains, although there is no evidence that these viruses arose in pigs. The role of pigs as a ‘mixing vessel’ for influenza virus has been questioned in view of the recent transmission of avian influenza viruses directly to humans.

Swine influenza viruses probably routinely pass among humans and swine; in this case they were detected as a consequence of heightened surveillance. Gerald Ford won’t be rolling over in his grave over this incident.

Weingartl, H., Albrecht, R., Lager, K., Babiuk, S., Marszal, P., Neufeld, J., Embury-Hyatt, C., Lekcharoensuk, P., Tumpey, T., Garcia-Sastre, A., & Richt, J. (2009). Experimental Infection of Pigs with the Human 1918 Pandemic Influenza Virus Journal of Virology, 83 (9), 4287-4296 DOI: 10.1128/JVI.02399-08

de Jong, J., Smith, D., Lapedes, A., Donatelli, I., Campitelli, L., Barigazzi, G., Van Reeth, K., Jones, T., Rimmelzwaan, G., Osterhaus, A., & Fouchier, R. (2007). Antigenic and Genetic Evolution of Swine Influenza A (H3N2) Viruses in Europe Journal of Virology, 81 (8), 4315-4322 DOI: 10.1128/JVI.02458-06

Van Reeth, K. (2007). Avian and swine influenza viruses: our current understanding of the zoonotic risk Veterinary Research, 38 (2), 243-260 DOI: 10.1051/vetres:2006062

H5N1 expert says ‘The virus is definitely mutating’

Guan Yi, an expert on H5N1 influenza virus, is quoted in China Daily as saying that “The virus is definitely mutating”.

Yi’s comments were in reference to the continuing pandemic of H5N1 influenza in poultry farms. He indicates that some farms are using a vaccine against an American H5N2 strain, which is not likely to be fully protective against the currently circulating H5N1 strains. In the past 10 years, at least 10 strains of the H5N1 virus have been identified, providing the fodder for Dr. Yi’s overly obvious statement.

I find it hard to believe that a virus ‘expert’ would ever make such a statement as ‘the virus is definitely mutating’. Virus genomes continuously undergo mutation, as a consequence of error-prone nucleic acid polymerases. The error rate for RNA virus genomes is phenomenal, because the viral polymerases cannot correct its mistakes. The error rates for viral RNA-dependent RNA polymerases have been estimated to be between 1 in 10,000 to 100,000 nucleotides polymerized. For a virus with a 10 kb genome, a frequency of 1 in 10,000 means that each RNA produced contains at least one mutation. Dr. Yi states the obvious when he says that the H5N1 virus is mutating. The genomes of these viruses are constantly undergoing change, not just in this specific outbreak.

What should Dr. Yi have said? I would have indicated that the rapid change in the antigenic composition of circulating H5N1 strains is likely rendering the vaccine ineffective. Maybe he said that, but was misquoted by the press. These things do happen, right?