H5N1

US: New developments in Midwestern canine influenza outbreak

Via the University of Wisconsin-Madison: New developments in Midwestern canine influenza outbreak. Excerpt:

New laboratory tests show that a strain of canine influenza virus (CIV) associated with more than 1,000 sick dogs throughout the Midwest, including one dog in Madison, is virtually identical to an Asian strain of the virus and is not a mutated form. 

A week ago, initial tests at the Wisconsin Veterinary Diagnostic Laboratory (WVDL) and Cornell University identified the strain as H3N2, which has previously only been seen in Asia and is different than the H3N8 strain circulating in North America. Genetic sequencing conducted at the National Veterinary Service Laboratory in Ames, Iowa, now confirms that the H3N2 strain found in the Midwest is almost identical to its Asian counterpart and was likely brought to the United States by an infected animal. 

"This means there is no evidence of genetic reassortment," says Kathy Toohey-Kurth, virology section head at WVDL. "This is good news because mutations are unpredictable, and we would not necessarily know what the safety implications are for humans or other animals." 

There is no evidence at this time that the H3N2 CIV strain can infect humans; it is distinctly different from human seasonal influenza H3N2 strains. However, the Asian H3N2 CIV strain has been reported to infect domestic cats. 

"No cats have reported positive in the United States at this time," says Keith Poulsen, WVDL diagnostic and case outreach coordinator and clinical assistant professor at the UW-Madison School of Veterinary Medicine (SVM). "Two cats and a dog, housemates of the infected dog in the Madison area, tested negative today despite showing clinical signs of the virus. It's possible the tests were done too late to catch the viral shedding phase. Either way, it's good news for those animals." 

Both CIV strains can cause persistent cough, runny nose, and fever. A small percentage of dogs will develop more severe clinical signs, and some will not show any symptoms at all. The infection has been associated with some deaths. 

Neither CIV strain is related to the highly pathogenic H5N2 avian flu, which has been reported in Wisconsin this week; they are completely different strains that affect separate species. 

The commercially available vaccines for CIV are made to protect against the H3N8 strain, and their effectiveness against the H3N2 strain is unknown at this time, but it is likely to be less effective. 

"We're still recommending that owners vaccinate their dogs because H3N8 is still around," says Sandi Sawchuk, primary care veterinarian at UW Veterinary Care (UWVC) and SVM clinical instructor.

Coston: It’s not just Ebola

Via his blog Avian Flu Diary, Mike Coston reminds us It’s Not Just Ebola. This is a summary of other disease threats we face, documented with many links. Excerpt:

And of course, to this rogues gallery of pandemic threats you can also add any number of influenza subtypes in the wild (including old pandemic viruses like H2N2 and H3N8), the growing ranks of antibiotic resistant bacteria which could prove every bit as deadly as a pandemic, and Virus X . . .  the one that isn’t on our radar, yet.   

The point here is that once Ebola is contained (I remain cautiously optimistic that it will be, but fully expect it to exact a horrendous cost) the threat posed to global public health by these emerging diseases doesn’t go away. If anything, with our growing population and increasing mobility, the threat grows greater with each passing year.   

If fact, we will be lucky if another shoe doesn’t drop this winter while our international efforts are focused primarily on West Africa.

Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus

Via PNAS, an article including Andrew Rambaut as one of the three authors: Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus.

Significance 

The origin of the 1918 pandemic influenza A virus (IAV) and the reasons for its unusual severity are two of the foremost biomedical mysteries of the past century. We infer that the virus arose via reassortment between a preexisting human H1 IAV lineage and an avian virus. 

Phylogenetic, seroarcheological, and epidemiological evidence indicates those born earlier or later than ∼1880–1900 would have had some protection against the 1918 H1N1 virus, whereas many young adults born from ∼1880–1900 may have lacked such protection because of childhood exposure to an antigenically distinct H3N8 virus. Our findings suggest that better understanding of how initial exposure shapes lifetime immunity may enhance the prediction and control of future IAV pandemics and seasonal epidemics. 

Abstract 

The source, timing, and geographical origin of the 1918–1920 pandemic influenza A virus have remained tenaciously obscure for nearly a century, as have the reasons for its unusual severity among young adults. 

Here, we reconstruct the origins of the pandemic virus and the classic swine influenza and (postpandemic) seasonal H1N1 lineages using a host-specific molecular clock approach that is demonstrably more accurate than previous methods. 

Our results suggest that the 1918 pandemic virus originated shortly before 1918 when a human H1 virus, which we infer emerged before ∼1907, acquired avian N1 neuraminidase and internal protein genes. We find that the resulting pandemic virus jumped directly to swine but was likely displaced in humans by ∼1922 by a reassortant with an antigenically distinct H1 HA. Hence, although the swine lineage was a direct descendent of the pandemic virus, the post-1918 seasonal H1N1 lineage evidently was not, at least for HA. These findings help resolve several seemingly disparate observations from 20th century influenza epidemiology, seroarcheology, and immunology. 

The phylogenetic results, combined with these other lines of evidence, suggest that the high mortality in 1918 among adults aged ∼20 to ∼40 y may have been due primarily to their childhood exposure to a doubly heterosubtypic putative H3N8 virus, which we estimate circulated from ∼1889–1900. All other age groups (except immunologically naive infants) were likely partially protected by childhood exposure to N1 and/or H1-related antigens. Similar processes may underlie age-specific mortality differences between seasonal H1N1 vs. H3N2 and human H5N1 vs. H7N9 infections.

South Korea: No new H5N8 cases reported in past three days

Via Yonhap News: No new bird flu cases reported in past three days.

No new cases of bird flu have been reported in the past three days but it's still possible that the highly contagious poultry disease may spread further in South Korea, the agriculture ministry said Friday. 

"Given the past experience, there could be more cases of bird flu," said a ministry official, adding the development of the animal diseases should be kept under close observation.

US: Marine biologist calls for protocols to deal with dead seals

Via Seacoastonline.com in New Hampshire: Marine biologist calls for protocols to deal with dead seals. Excerpt:

A marine biologist and member of Hampton's Conservation Commission said the same environmental conditions that occurred last year when 162 dead seals washed ashore on Seacoast beaches exist today and it will likely happen again. 

A recent study revealed the seals perished as a result of a new strain of avian flu capable of being transmitted from birds to mammals, possibly humans. 

Ellen Goethel will go before the Hampton Board of Selectmen on Monday, Aug. 13, because she wants to see protocols put in place to protect the public in case there is a reoccurrence. "

It may never happen again, but my gut feeling is that it's going to," Goethel said. 

The report, titled "Emergence of Fatal Avian Influenza in New England Harbor Seals," was released last week by a team of experts tasked with determining why the seals turned up dead from southern Maine to northern Massachusetts last fall. In the report, researchers identify the cause of death as an influenza A virus subtype, "H3N8," a new strain of avian flu that can jump from birds to marine mammals. 

While there have been no known human cases to date, researchers urged caution, given the history of bird flu and its ability to evolve into forms that can infect people. 

Goethel said the findings are a big concern. 

"It's dangerous," she said. "We are a coastal community and we need to be on top of it. As a marine biologist, common sense tells you there is possibility of human infection whenever there is infection in a mammal. It's a human health risk and we have to decide how we are going to deal with it." 

A big part of that, she said, is coming up with a protocol on the local level for removing the carcasses. 

"In the past, they just left the carcass on the beach to float away," Goethel said. "But if they're possibly carrying something that can contaminate another animal, we have to dispose of them and figure out how we are going to do it." 

Under the federal Marine Mammal Protection Act, it's illegal and punishable to pick up, handle or interact with free-swimming, dead or beached marine protected species. 

Last year, due to the number of seal deaths, Goethel helped the town of Hampton receive permission from the National Oceanic and Atmospheric Administration to remove the dead seals. Goethel said she wants to make sure that permission is in place again because she said dead seals should not be left on a beach for days at a time. 

"We also need to protect our town workers, if they're the ones that will be disposing of the carcasses," Goethel said. 

She said the town can do other things on the local level to protect the public, including banning dogs on beaches when there are dead seals on shore. 

Goethel said she wants the town to be proactive rather than wait for recommendations from the federal government or the Centers for Disease Control and Prevention, which may take some time to get out.

How did H3N8 kill 162 baby seals?

The bird-to-seal flu finding has attracted a lot of attention. Via The Atlantic.com, Brian Fung has a good article: How Did Bird Flu Kill 162 Baby Seals? Excerpt:.

It's pretty much the saddest thing one can possibly read: baby harbor seals are dying, one by one. They began washing up on the beaches of New England last fall, apparently the victims of a viral disease researchers identified this week as bird flu. To be precise, a genetic mutation of avian flu known as H3N8.  

Although the chances are small, some epidemiologists worry that the flu virus' leap from waterfowl to harbor seals could someday repeat itself, endangering humans in the process. 

That raises the question: how exactly does a virus make the jump from one species to the next? We've seen it happen with HIV, SARS, and West Nile virus. Pretty much all forms of influenza that can make humans sick came from birds. What's the mechanism behind cross-species infection, and how do scientists know what to look for? 

The first step is to narrow down the range of possibilities. Dr. Simon Anthony, a postdoctoral researcher at Columbia University's Center for Infection and Immunity and the lead author of the headline-making seal flu study published in mBio, said that in a different time, scientists might have deliberately exposed test animals to various strains of a virus in an attempt to pinpoint the right one. But with the advance of research technology, scientists can now use molecular analysis to find out what they're dealing with. 

Here's how it works: after a pathologist has performed an autopsy on a diseased animal -- in this case, a baby seal -- epidemiologists come up with a list of likely suspects that may have contributed to the creature's death. Then comes a battery of genetic tests designed to eliminate the wrong culprits. With a bit of synthetic DNA called a fluorescent probe, scientists can screen a sample of infected tissue for genes that serve as identifiers of specific viruses or bacteria. 

These probes work a bit like litmus tests: they change color when they come into contact with the right illness gene. But the probes are programmed beforehand only to respond to a particular gene. This allows researchers to rule out diseases as they go. 

Once the researchers have struck some options from the list, things get easier. "When we identify influenza," Anthony told me, "the next thing to do is sequence the entire genome [of the virus] and identify where the virus likely originated. And what we do is, we compare the sequence of the virus we found with a large database of influenza viruses, and we look to see what is the closest related to it." 

As it happens, the virus Anthony and his team discovered in the baby seals shares a 96 percent genetic match with H3N8, an avian flu that affects North American ducks. Because seals and ducks have been known to interact with one another on shorelines, the researchers think that's how the germ was passed from one species to the other -- although they still aren't sure when the spillover happened, or how severe it was.

Zimmer on H3N8 bird flu in seals

Via The New York Times, a report by Carl Zimmer: Flu That Leapt From Birds to Seals Is Studied for Human Threat. Excerpt:

Evolution recently carried out an influenza experiment of its own on the coast of New England. Last fall, 162 dead harbor seal pups washed up on the beaches of New Hampshire and Massachusetts. 

In a paper published Tuesday in the journal mBio, a team of scientists reports that the pups were killed by a new strain of influenza. Their research indicates that the virus evolved from bird flu, gaining the ability to spread from seal to seal — a real-life example of the transformation that scientists have been exploring in their labs. 

“It’s a beautiful study,” said Eddie Holmes, an expert on flu evolution at Penn State who was not involved in the research. He praised the scientists’ speed in identifying the new virus and convincingly tying it to the seal die-off. 

Dr. Holmes believes the new virus needs to be carefully monitored to see what sort of threat, if any, it poses. “The question mark is what it means for seals, and what it means for us,” he said.

US: New bird flu virus killing baby seals

Via nzherald.co.nz, a report datelined July 31: New bird flu virus killing baby seals - study. You'll see I've put in a link to mBio, but the report is presumably embargoed until whenever July 31 arrives in your time zone. Excerpt:

A new kind of bird flu has been causing deadly pneumonia in baby seals off the northeastern US coast and could pose a risk to humans, according to US research released Tuesday. 

The new strain has been named avian H3N8, and is blamed for the deaths of 162 seals along the US coastlines last year, said the study in mBio, a journal of the American Society for Microbiology. 

Most of the dead seals were younger than six months of age. 

While there have been no known human cases to date, scientists at Columbia University in New York urged caution, given the history of bird flu and its ability to evolve into forms that can infect people, like H5N1. 

"Our findings reinforce the importance of wildlife surveillance in predicting and preventing pandemics," said W. Ian Lipkin, professor of epidemiology at the Columbia University Mailman School of Public Health. 

"HIV/AIDS, SARS, West Nile, Nipah and influenza are all examples of emerging infectious diseases that originated in animals," Lipkin added. 

"Any outbreak of disease in domestic animals or wildlife, while an immediate threat to wildlife conservation, must also be considered potentially hazardous to humans." 

Scientists sequenced the full genome of the new strain and found it originated from a bird flu virus that had been circulating in North American waterfowl since 2002. 

Over time, the virus gained the ability to infect mammals by latching on to receptors in their respiratory tracts. 

Wildlife experts first grew alarmed in September 2011 when an increasing number of seals from the coasts of Maine to Massachusetts began developing pneumonia and skin lesions. 

A total of 162 dead or dying seals were recovered over the next three months, the researchers said.