TWiV 303: Borna this way

On episode #303 of the science show This Week in Virology, the TWiV team discusses transmission of Ebola virus, and inhibition of Borna disease virus replication by viral DNA in the ground squirrel genome.

You can find TWiV #303 at www.microbe.tv/twiv.

The value of influenza aerosol transmission experiments

ferretA Harvard epidemiologist has been on a crusade to curtail aerosol transmission experiments on avian influenza H5N1 virus because he believes that they are too dangerous and of little value. Recently he has taken his arguments to the Op-Ed pages of the New York Times. While Dr. Lipsitch is certainly entitled to his opinion, his arguments do not support his conclusions.

In early 2013 Lipsitch was the subject of a piece in Harvard Magazine about avian influenza H5N1 virus entitled The Deadliest Virus.  I have previously criticized this article  in which Lipsitch calls for more stringent H5N1 policies. More recently Lipsitch published an opinion in PLoS Medicine in which he called for alternatives to experiments with potential pandemic pathogens. We discussed this piece thoroughly on This Week in Virology #287.  The arguments he uses in both cases are similar to those in the OpEd.

The Times OpEd is entitled Anthrax? That’s not the real worry. The title is a reference to the possible exposure to anthrax bacteria of workers at the Centers for Disease Control. Even worse than anthrax, argues Lipsitch, would be accidental exposure to a pathogen that could transmit readily among humans. He then argues that such a pathogen is being created in laboratories that study avian influenza H5N1 transmission.

Lipsitch tells us ‘These experiments use flu strains like H5N1, which kills up to 60 percent of humans who catch it from birds.’ As an epidemiologist Lipsitch knows that this statement is wrong. The case fatality ratio for avian H5N1 influenza virus in humans is 60% – the number of deaths divided by the cases of human infections that are diagnosed according to WHO criteria. The mortality rate is quite different: it is the number of fatalities divided by the total number of H5N1 infections of humans. For a number of reasons the H5N1 mortality ratio in humans has been a difficult number to determine.

Next Lipsitch incorrectly states that the goal of experiments in which avian influenza H5N1 viruses are given the ability to transmit by aerosol among ferrets is ‘to see what gives a flu virus the potential to create a pandemic.’ The goal of these experiments is to identify mechanistically what is needed to make an avian influenza virus transmit among mammals. Transmission of a virus is required for a pandemic, but by no means does it assure one. I do hope that Lipsitch knows better, and is simply trying to scare the readers.

He then turns to the experiments of Kawaoka and colleagues who recently reconstructed a 1918-like avian influenza virus and provided it with the ability to transmit by aerosol among ferrets. These experiments are inaccurately described. Lipsitch writes that the reconstructed virus was ‘both contagious and comparably deadly to the 1918 flu that killed tens of millions of people worldwide’. In fact the reconstructed virus is less virulent in ferrets than the 1918 H1N1 virus that infected humans. In the same sentence Lipsitch mixes virulence in ferrets with virulence in humans – something even my virology students know is wrong. Then he writes that ‘Unlike experiments with anthrax, creating such flu strains in the lab presents a danger that affects us all, because once it is out, such a strain would be extremely hard to control.’ This is not true for the 1918-like avian influenza virus assembled by the Kawaoka lab: it was shown that antibodies to the 2009 pandemic H1N1 influenza virus can block its replication. The current influenza virus vaccine contains a 2009 H1N1 component that would protect against the 1918-like avian influenza virus.

The crux of the problem seems to be that Lipsitch does not understand the purpose of influenza virus transmission experiments. He writes that ‘The virologists conducting these experiments say that by learning about how flu transmits in ferrets, we will be able to develop better vaccines and spot dangerous strains in birds before they become pandemic threats.’ This justification for the work is wrong.

Both Kawaoka and Fouchier have suggested that identifying mutations that improve aerosol transmission of avian influenza viruses in ferrets might help to detect strains with transmission potential, and help vaccine manufacture. I think it was an error to focus on these potential benefits because it detracted from the real value of the work, to provide mechanistic information on what allows aerosol transmission of influenza viruses among mammals.

In the Kawaoka and Fouchier studies, it was found that adaptation of H5N1 influenza virus from avian to mammalian receptors lead to a decrease in the stability of the viral HA glycoprotein. This property had to be reversed in order for these viruses to transmit by aerosol among ferrets. Similar stabilization of the HA protein was observed when the reconstructed 1918-like avian influenza virus was adapted to aerosol transmission among ferrets. It is not simply coincidence when three independent studies come up with the same outcome: clearly HA stability is important for aerosol transmission among mammals. This is one property to look for in circulating H5N1 strains, not simply amino acid changes.

Lipsitch mentions nothing about the mechanism of transmission; he focuses on identifying mutations for surveillance and vaccine development. He ignores the fundamental importance of this work. In this context, the work has tremendous value.

The remainder of the Times OpEd reminds us how often accidents occur in high security biological labortories. There are problems with these arguments. Lipsitch cites the emergence of an H1N1 influenza virus in 1977 as ‘escaped from a lab in China or the Soviet Union’. While is seems clear that the 1977 H1N1 virus probably came from a laboratory, there is zero evidence that it was a laboratory accident. It is equally likely that the virus was part of a clinical trial in which it was deliberately administered to humans.

Lipsitch also cites the numerous incidents that occur in American laboratories involving select agents. I suggest the reader listen to Ron Fouchier explain on TWiV #291 how a computer crash must be recorded as an incident in high biosecurity laboratories, but does not lead to the release of infectious agents.

Lipsitch clearly feels that the benefits of aerosol transmission research do not justify the risks involved. I agree that the experiments do have some risk, but it is not as clear cut as Lipsitch would suggest. Although ferrets are a good model for influenza virus pathogenesis, like any animal model, they are not predictive of what occurs in humans. An influenza virus that transmits by aerosol among ferrets cannot be assumed to transmit in the same way among humans. This is the assumption made by Lipsitch, and it is wrong.

I agree that transmission work on avian H5N1 influenza virus must be done under the proper containment. Before these experiments can be done they are subject to extensive review of the proposed containment and mitigation procedures. There is no justification for the additional regulation proposed by Lipsitch.

In my opinion aerosol transmission experiments on avian influenza viruses are well worth the risk. We know nothing about what controls aerosol transmission of viruses. The way to obtain this information is to take a virus that does not transmit by aerosol, derive a transmissible version, and determine why the virus has this new property. To conclude that such experiments are not worth the risk not only ignores the importance of understanding transmission, but also fails to acknowledge the unpredictable nature of science. Often the best experimental results are those which were never anticipated.

Lipsitch ends by saying that ‘There are dozens of safe research strategies to understand, prevent and treat pandemic flu. Only one strategy — creating virulent, contagious strains — risks inciting such a pandemic.’ Creating a virulent strain is not part of the strategy. Lipsitch conveniently ignores the fact that Fouchier’s H5N1 strain that transmits by aerosol among ferrets is not virulent when transmitted by that route. And of course we do not know if these strains would be transmissible in humans.

I am very disappointed that the Times chose to publish this OpEd without checking Lipsitch’s statements. He is certainly entitled to his own opinion, but he is not entitled to his own facts.

An epidemic of porcine diarrhea in North America

pig farmPorcine epidemic diarrhea arrived in the United States in the spring of 2013. The disease, caused by a coronavirus, was first identified in the United Kingdom in 1971, and has subsequently spread throughout Europe and Asia. The disease is a concern for the swine industry because it is associated with high case fatality ratios in suckling pigs.

Porcine epidemic diarrhea virus is a member of the coronavirus family, which also includes the SARS and MERS coronaviruses (CoV). Before 2013 the virus had not been isolated in North America. It was detected on a farm in Iowa in May and subsequently spread to 22 states. It is estimated that between 1-4 million pigs have died of the disease in the US.  Recently the virus was found on a Canadian pig farm in Middlesex County, where it most likely arrived from the US.

PEDV can infect pigs of all ages, but is most serious in nursing pigs in which the clinical symptoms are the most severe. The disease is characterized by acute vomiting and watery diarrhea which in nursing pigs leads to dehydration and frequently death. There is no treatment for the disease other than rehydration; no antiviral drugs are available, but a vaccine was developed in 2013. The virus does not infect humans.

Sequence analysis of genomes from three US isolates of PEDV indicate that they are most closely related to a virus isolated in 2012 in Anhui, China. These data suggest, but do not prove, that the US PEDV originated from China. How the virus might have arrived from that country is a matter of speculation. The virus is believed to move from farm to farm on trucks that are used to carry pigs, as well as on contaminated boots and clothing. Many farms observe strict biosecurity procedures in which trucks are properly washed, disinfected, and heated to inactivate the virus. However these procedures cost money and take time, and may be bypassed in some cases. If older pigs are asymptomatically infected, they might be transported to other farms and spread the virus. Once in a farm, stopping spread of the virus is difficult: it is spread by fecal-oral contamination.

The coronavirus family is divided into four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. Several human coronaviruses that cause common cold-like illness, as well as PEDV, are alphacoronaviruses. SARS-CoV and MERS-CoV are betacoronaviruses. Viruses in the alphacoronavirus and betacoronavirus genera are believed to have originated from bats, while birds might have been the origin of viruses in the other two genera. Analysis of the PEDV genome sequence indicate that the 5’-untranslated region is similar to that of a bat coronavirus. Based on this information it has been suggested that PEDV originated from a cross-species transfer of a bat alphacoronavirus into pigs.

National Hog Farmer is not usually on my reading list, but it has a good summary of porcine epidemic diarrhea.

TWiV 268: Transmission is inevitable

On episode #268 of the science show This Week in Virology, Vincent, Alan, Kathy, and Ashlee discuss fomites in physicians offices, plant virus factories involved in aphid transmission, and clues from the bat genome about flight and immunity.

You can find TWiV #268 at www.microbe.tv/twiv.

Fouchier vs the Dutch government on influenza H5N1 research

ferretFrom Martin Enserink at ScienceInsider:

Virologist Ron Fouchier has suffered a loss in a legal battle with the Dutch government over the publication of his controversial H5N1 influenza research. On Friday, a Dutch district court ruled that the government was right to ask Fouchier to obtain an export license before sending two hotly debated papers out for publication.

Readers of this blog will remember the furor sparked by Fouchier’s experiments in 2011 in which he developed an avian influenza H5N1 isolate that could transmit among ferrets by aerosol. When Fouchier was ready to publish the results, the Dutch government required that Fouchier apply for an export license. In so doing they were applying EU regulations that are designed to prevent the spread of biological weapons.

Fouchier applied for and was granted an export license on 27 April 2012. Fouchier’s employer, Erasmus Medical Center, appealed the decision to require an export license for this type of work. It is this appeal that was recently denied by a Dutch district court.

Fouchier rightfully claims that such EU regulations put him at a disadvantage compared with other groups. For example, Kawaoka’s findings on aerosol-transmitted avian influenza H5N1 virus in ferrets were not subject to EU export rules and were published ahead of Fouchier’s paper. I can understand Fouchier’s position; science is very competitive and being the first to publish is a coveted position. I am not sure that this is an issue worth bringing to the courts: even though Fouchier published after Kawaoka, most virologists credit the observations to both laboratories. The Dutch government should recognize that its scientists must be internationally competitive and expedite such future requests.

In my view, there is a larger issue at stake here: what constitutes research that requires an export license? I would argue that the avian influenza H5N1 virus that Fouchier produced is not a biological weapon. Remember that while this virus could transmit among caged ferrets by aerosol, it was markedly attenuated. In other words, gaining the ability to transmit by aerosol came at a fitness cost that reduced the virulence of the virus in ferrets. Such a virus is not a biological weapon, and should not have been subject to EU export requirements.

I do not know who in the Dutch government reviews such export license requests, but hopefully the next time Fouchier or any other virologist applies, there will be knowledgeable virologists involved in making the correct decision.

TWiV 230: Gene goes to Washington, flu chickens out

On episode #230 of the science show This Week in Virology, Vincent, Rich, Alan and Kathy review H7N9 infections in China, the debate over patenting genes, and receptor-binding by ferret-transmissible avian H5 influenza virus.

You can find TWiV #230 at www.microbe.tv/twiv.

Human infections with avian influenza H7N9 virus from wet market poultry

Results of a study of four patients in Zhejiang, China, who developed influenza H7N9 virus infection suggests sporadic poultry-to-human transmission:

We diagnosed avian influenza A H7N9 in all four patients (who were epidemiologically unlinked), two of whom died and two of whom were recovering at the time of writing. All patients had histories of occupational or wet market exposure to poultry. The genes of the H7N9 virus in patient 3’s isolate were phylogenetically clustered with those of the epidemiologically linked wet market chicken H7N9 isolate. These findings suggest sporadic poultry-to-person transmission.

The four patients had occupational contact with poultry: one was a chef, one slaughtered and cooked live market poultry, and two bought live market poultry. Each had contact with poultry 3-8 days before onset of disease, and all were positive for influenza H7N9 virus by polymerase chain reaction of sputum or throat swab samples (virus was cultured from three of the four patients). Two of five pigeons and four of 20 chickens from two different wet markets were also positive for influenza H7N9 virus. Sequence analysis of virus recovered from patient 3 revealed that the HA and NA genes are nearly identical with those of two viruses isolated from epidemiologically linked chickens (1673 of 1683 bases for HA, 1394 of 1398 bases for NA).

While these H7N9 infections might have been acquired from poultry, the origin of other infections in different areas of China (>100) is unclear. According to the Ministry of Agriculture, as of 26 April 2013, only 46 of the 68,060 samples collected from poultry markets, habitats, farms and slaughterhouses across the country have tested positive for H7N9 virus, and none of these positive samples have been from poultry farms.

End of moratorium on influenza H5N1 research

In early 2012 influenza virus researchers around the world decided to stop working on highly pathogenic avian influenza H5N1 virus. This decision came after work from the Fouchier and Kawaoka laboratories revealed the isolation of influenza H5N1 strains that can be passed among ferrets by aerosol. The moratorium on influenza H5N1 virus research has now been lifted, as described in a letter from influenza virologists to Science and Nature.

Lifting the embargo on H5N1 research is an important step forward for understanding what regulates influenza transmission. In my view it was an ill-conceived move, done to quell the growing concern over the adaptation of influenza H5N1 virus to aerosol transmission in ferrets. We now know that these viruses are not lethal for ferrets, and much of the outrage expressed about this work was misguided. In my view the moratorium has accomplished little other than delaying the conduct of important virology research.

According to the influenza virus researchers who signed on to the moratorium, its purpose was to:

…provide time to explain the public-health benefits of this work, to describe the measures in place to minimize pos- sible risks, and to enable organizations and governments around the world to review their policies (for example on biosafety, biosecurity, oversight, and communication) regarding these experiments.

An important consideration is the level of containment that will be required for studying influenza H5N1 transmission. WHO has released recommendations on risk control measures for H5N1 research, and individual countries will decided how to proceed. The US has not yet made a decision on the level of containment needed for H5N1 virus transmission research. Influenza virologists who participated in the moratorium have their own view:

We consider biosafety level 3 conditions with the considerable enhancements (BSL-3+) outlined in the referenced publications (11–13) as appropriate for this type of work, but recognize that some countries may require BSL-4 conditions in ac- cordance with applicable standards (such as Canada).

Their last statement forms the crux of the issue on H5N1 transmission research:

We fully acknowledge that this research—as with any work on infectious agents—is not without risks. However, because the risk exists in nature that an H5N1 virus capable of transmission in mammals may emerge, the benefits of this work outweigh the risks.

Slow motion sneezing

A bit unsettling, but this is what happens when a sneeze is not contained:

If you have a respiratory viral infection, each drop expelled can contain tens of thousands of infectious virions.

Made by South Australian Health.

TWiV 199: Of mice, ticks, and pigs

On episode #199 of the science show This Week in Virology, Vincent, Alan, Rich, and Kathy discuss recent outbreaks of hantavirus pulmonary syndrome in Yosemite National Park and novel swine-origin influenza in the US midwest, and isolation of the Heartland virus from two patients in Missouri with severe febrile illness.

You can find TWiV #199 at www.microbe.tv/twiv.