I joined Buddhini Samarasinghe and Scott Lewis on a Science Sunday Hangout on Air to talk about my career in virology: how I came to be interested in viruses, and what goes on in my laboratory. You can find hangouts and more at the ScienceSunday community.

 

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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.twiv.tv.

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.

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Hilary Koprowski, 96

26 April 2013

Racaniello, Koprowski, KessinVirologist Hilary Koprowski died on 11 April 2013 at the age of 96. His main accomplishments are nicely summarized in the New York Times, but for a more comprehensive overview of his life, I highly recommend his biography Listen to the Music by Roger Vaughan. I did not have many opportunities to interact with Dr. Koprowski, but I did follow his work on poliovirus vaccines and I have a few reminiscences.

In the 1930s Max Theiler had found that propagating yellow fever virus in an unnatural host – the chick embryo – dramatically reduced its capacity to cause disease in humans. Theiler’s work (which garnered him a Nobel Prize) lead to the production of the infectious, attenuated yellow fever vaccine which helped to vastly reduce the global incidence of yellow fever. Koprowski was inspired by Theiler’s work and decided to take a similar approach to developing a poliovirus vaccine – his first efforts involved passage of a type 2 strain of poliovirus in mice and then in cotton rats. After passage in  rodents, the virus did not cause paralysis in monkeys. Koprowski tested the candidate vaccine strain in humans, and ultimately produced two other attenuated poliovirus strains. By the 1960s these attenuated poliovirus vaccine candidates had been tested in millions of humans. However, they were never licensed for use in the US. While Koprowski was carrying out his work, Albert Sabin was also developed attenuated vaccine strains of poliovirus. Both Sabin’s and Koprowski’s strains were tested side by side in a monkey neurovirulence test carried out by Joseph Melnick at Baylor University. Sabin’s virus strains were slightly more attenuated, and in 1961-62 those were selected for licensing in the US. Sabin’s oral poliovirus vaccines (OPV) have been the mainstay of the World Health Organization in its polio eradication campaign.

Koprowski’s polio vaccines were tested by human clinical trials, notably in the former Belgian Congo in 1957-58. It was subsequently suggested that this clinical trial initiated the AIDS pandemic. The idea, first proposed by Tom Curtis (19 March 1992 “The Origin of AIDS: A startling new theory attempts to answer the question, ‘Was it an act of God or an act of man?” Rolling Stone pp. 54–9, 61, 106, 108) and subsequently by Edward Hooper in ‘The River‘, was that Koprowski had propagated the vaccine strains in kidney cell cultures produced from locally captured chimpanzees. If these animals were infected with the precursor of HIV-1, simian immunodeficiency virus (SIV), then the virus might have entered the human population during the polio vaccine trials. This hypothesis was subsequently shown to be incorrect as phylogenetic analysis showed that the main group of HIV-1 viruses, the M group, clearly crossed from chimpanzees to humans in the early 1900s.

A committee was established to investigate the virological aspects of the HIV-polio vaccine controversy, and towards the end of its work I was asked to join. When it was discovered that samples of Koprowski’s polio vaccines were frozen at the Wistar Institute in Philadelphia, it was decided to determine whether these vaccines had been propagated in rhesus monkey or chimpanzee cells.

I was given the job of dividing and coding the samples. I met a representative of the Wistar Institute in the parking lot of a restaurant just off the New Jersey Turnpike, halfway between New York and Philadelphia. He handed me a white styrofoam box, packed with ice, that contained  vials of the Koprowski vaccine. To the uninformed observer, it might have looked like a drug exchange.

CHAT vialsI took the vials back to the lab (see photo), thawed them, separated them into aliquots, and gave each a code. I then returned them to the Wistar in the same way, after a second trip on the New Jersey Turnpike. The samples were sent to three different laboratories where experiments were done to determine the mitochondrial DNA type of the cells in which the viruses had been propagated (although the samples were free of cells, some mitochondrial DNA would still be present from virus induced cell lysis). The results, which have been published (reference one, two), clearly showed that the vaccines had not been grown in chimpanzee cells. I was pleased to have played a small role in this story.

Koprowski autograph

Although I had spoken with Dr. Koprowski several times on the telephone, I did not meet him until 2005 when he presented a talk on the history of rabies in the History of Science series at Columbia University Medical Center. I was his host for that visit, during which I was photographed with Dr. Koprowski and Dr. Rich Kessin, another Columbia professor. We invited Dr. Koprowski to dinner after the seminar but he declined, but he did want to have a drink together. After being warned by his driver not to keep him too late, we walked to a local bar and Dr. Koprowski ordered a Boodles gin martini. The bartender noted that he didn’t receive many calls for that brand. Dr. Koprowski said it was his favorite gin. We talked for a while and then returned Dr. Koprowski to his car for the trip back to Philadelphia. During his visit I had Dr. Koprowski autograph my copy of Listen to the Music (photo). He wrote: “To my friend Vince, with warmest regards, Hilary, 4/14/05.” It was the first and last time I saw him.

I would like to relate one last story which has nothing to do with me, but is irresistible. It takes place in the opening pages of Listen to the Music. Koprowski and his technician Thomas Norton are about to drink an early version of his attenuated polio vaccine. The virus has been passaged in rats and appears to be attenuated in monkeys. On a January day in 1948 Koprowski and Norton are in a laboratory at Lederle Laboratories in Pearl River, NY., where they are blending the brains and spinal cords of rats that had been infected with the vaccine strain virus. They both drink a milliliter of the cold, greasy, mix which flows thickly over their tongues and is difficult to swallow.

Here is the best part:

When he can speak, Norton asks, “Have another?”

“Better not,” Koprowski says. “I’m driving.”

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The World Health Organization has been publishing weekly reports on the avian influenza A(H7N9) outbreak which include the geographical location of each case, the cumulative number of cases, and the epidemiological curve. Go to this page at the WHO website for an archive of the weekly reports (there you will also find other useful information on the H7N9 outbreak). Images for report #3 of 24 April 2013 are reproduced below. Click each image for a larger view.

03_ReportWebH7N9Number_1
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From the Centers for Disease Control in Taiwan:

In the late afternoon of April 24, 2013, the Central Epidemic Command Center (CECC) confirmed the first imported case of H7N9 avian influenza in a 53-year-old male Taiwanese citizen who worked in Suzhou, Jiangsu Province, China prior to illness onset. He developed his illness three days after returning to Taiwan. Infection with avian influenza A (H7N9) was confirmed on April 24, 2013. The patient is currently in a severe condition and being treated in a negative-pressure isolation room.

It’s not clear how the patient acquired the infection in China; he had no contact with birds or poultry and did not eat undercooked poultry or eggs.

The patient has had contact with 139 others, and all but 3 have used the appropriate personal protective equipment to prevent infection.

There is still no evidence for human-to-human transmission of avian influenza H7N9 virus in China. If this trend continues in Taiwan there should be no spread of the virus to others.

As long as people are allowed to travel from China, this probably won’t be the only imported case.

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During my visit to Berkeley, CA to record TWiV #228, I met Deb Sklut, an artist who is inspired by the power of science. I recorded a brief conversation with Deb which you can view below. Her work can be found at SqueakySqueegeeArt.etsy.com.

 

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On episode #229 of the science show This Week in Virology, Vincent, Rich, Dickson, and Alan review the current status of human infections with avian influenza H7N9 virus.

You can find TWiV #229 at www.twiv.tv.

Influenza H7 diversityAn outbreak of high-pathogenicity avian influenza H7N7 virus that took place on 255 poultry farms in the Netherlands during 2003 has been used to provide clues about the current avian influenza H7N9 viruses in China. During the Dutch outbreak 453 humans showed symptoms of illness and 89 were confirmed to have infection with the virus. Some interesting observations from that outbreak:

  • Conjunctivitis (inflammation of the membranes surrounding the eyelids) was observed in many of the human cases, as well as in later human infections with H7 influenza viruses. Apparently these viruses replicate well in the eye, which bears alpha-2,3 sialic acid receptors. From there the viruses could reach the nasal cavity via the nasolacrimal duct. 
  • There was one fatal infection during the Dutch outbreak, and virus isolated from this individual contained the amino acid change E627K in viral protein PB2, which is associated with higher replication of avian influenza viruses in mammals. This change likely arose during replication of virus in the patient as it was not observed in other isolates. The recent H7N9 isolates from China all have the PB2 E627K mutation.
  • In the Dutch outbreak there was no evidence for human to human transmission of H7N7 viruses. This conclusion is in part supported by phylogenetic analysis of viral sequences, which showed that during the outbreak the viruses diversified into multiple lineages with human strains at the ends of the trees (Figure; click to enlarge. Credit: Eurosurveillance).

So far the H7N9 virus does not appear to be spreading from human to human. This observation suggests that the virus is widespread in poultry in China, and that there have been multiple introductions into humans. It seems likely that these novel viruses arose relatively recently in China and some time thereafter had to opportunity to infect humans.

The question on everyone’s mind is whether the avian influenza H7N9 viruses will acquire the ability to transmit among humans. On this subject the authors have the following comment:

Although human infections with H7 influenza viruses have occurred repeatedly over the last decades without evidence of sustained human-to-human transmission, the absence of sustained human-to-human transmission of A(H7N9) viruses does not come with any guarantee.

It is possible that during replication in birds or humans, the H7N9 viruses might randomly acquire a mutation that allows for transmission. In the right place at the right time, such a virus could spread through the human population. Alternatively, such a transmission-facilitating mutation might interfere with the overall fitness of the virus, thereby preventing it from spreading. I favor the latter hypothesis because the H7N9 viruses have been transmitting since at least February 2013; they have undergone many replication cycles without such a mutation arising. If the virus has not entered wild birds, culling poultry could eradicate it from China – assuming that it has not gone elsewhere.

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from Brian Foley:

18th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
University of Florida, Emerging Pathogens Institute
Gainesville, Florida, USA
August 25th – August 30th, 2013
Bioinformatics Methods Applied to Virology and Epidemiology

Announcing the organization of the international workshop on Virus Evolution and Molecular Epidemiology (VEME) in 2013, hosted by the Emerging Pathogens Institute in the warm city of Gainesville and sponsored by several local partners.

We plan to organize a ‘Phylogenetic Inference’ module that offers the theoretical background and hands-on experience in phylogenetic analysis for those who have little or no prior expertise in sequence analysis. An ‘Evolutionary Hypothesis Testing’ is targeted to participants who are well familiar with alignments and phylogenetic trees, and would like to extend their expertise to likelihood and Bayesian inference in phylogenetics, coalescent and phylogeographic analyses (‘phylodynamics’) and molecular adaptation. A ‘Large Dataset Analysis’ module will cover the more complex analysis of full genomes, huge datasets of pathogens including Next Generation Sequencing data, and combined analyses of pathogen and host. Practical sessions in these modules will involve software like, PHYLIP, PAUP*, PHYML, MEGA, PAML or HYPHY, TREE-PUZZLE, SplitsTree, BEAST, MrBayes Simplot and RDP3.

We recommend participants to buy The Phylogenetic Handbook as a guide during the workshop, and to bring their own data set.

For further information and applications check this website.

Abstract and application deadline is April 30th.

Selections will be made by end of May 2013.

The registration fee of 1000 USD covers attendance, lunches and coffee breaks.

Participation is limited to 25 scientists in each module and is dependent on a selection procedure based on the submitted abstract and statement of motivation. A limited number of grants are available for scientists who experience difficulties to attend because of financial reasons.

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