Scientists say USDA shares too little data and too slowly on H5N1 flu


When the U.S. Department of Agriculture announced Sunday evening that it had released new data from its investigation into an outbreak of avian flu in cattle, scientists eagerly sought a well-known and globally used platform to share the genetic sequences of viruses.

The footage wasn’t there. Tuesday morning, they still are not.

Researchers seeking to track the evolution and spread of H5N1 say the information released — raw data on a U.S. server — is not very useful and is anything but transparent. They also say the government’s release of information about the outbreak, which was confirmed in cattle almost a month ago, has been extremely slow.

After the announcement on Sunday by the USDA Dr. Rick Bright, an immunologist and vaccine researcher who led the Biomedical Advanced Research and Development Authority from 2016 to 2020, said he immediately called his contacts at the database, called the Global Initiative on Sharing All Influenza Data, or GISAID, to make sure nothing was missing.

“I said, ‘Look, just tell me: Do you have any data?’ and they said, ‘No,'” Bright said.

After checking even the parts of the database where people can post drafts of footage before their full public release, Dr. Lucas Freitas, a Brazilian conservation scientist at GISAID, confirmed that there was no no new footage released by the USDA since its announcement. .

“We wouldn’t miss it,” said Peter Bogner, founder and president of GISAID. “H5 is why GISAID was created. This raises the antennae.

The highly pathogenic H5N1 strain of avian influenza has decimated bird populations around the world and, in recent years, has spread to an increasing variety of mammals, raising fears it is on the verge of become a virus capable of spreading effectively in humans.

When the USDA confirmed that H5N1 had been detected in dairy cows in Texas and Kansas on March 25, the news put infectious disease experts on alert, and they were eager to get more information to see how the virus had changed to target a new host. The USDA Animal and Plant Health Inspection Service, or APHIS, reports that the H5N1 virus has now been detected in 32 herds across eight states.

But weeks have passed and little data on the U.S. outbreak has been shared with the global scientific community.

In its advisory released Sunday, APHIS said it had shared 239 genetic sequences from the H5N1 outbreak “from cattle, cats, chickens, skunks, raccoons, grackles, blackbirds and geese.” .

The agency said it “publishes regularly” on GISAID, but in the interest of public transparency and “to ensure that the scientific community has access to this information as quickly as possible…” it was also “promptly sharing” sequences with an American database maintained by the agency. National Library of Medicine.

The announcement suggested to many scientists that the information would be found in GISAID, which was It is essential to monitor the evolution of the virus that causes Covid-19 as it moves around the world. Many countries, including the United States, use GISAID to quickly share genetic sequences – the exact order of four chemical elements that make up the blueprints of each virus.

Instead, the USDA uploaded raw sequencing data, called FASTQ files, to the National Library of Medicine database, which is publicly available. These FASTQ files, however, do not contain critical information needed to help scientists track the evolution of the virus, such as the exact date the sample was collected and its original state.

Scientists use raw data to track the evolution of a virus, but they also typically use it in concert with the type of information typically published on GISAID: consensus sequences, known as FASTA files, which have been refined and cleared of all contamination and errors. Consensus sequences generally give more information about where the sample was collected and when, helping researchers better understand how a virus evolves over time.

The researchers say it is unclear how long the samples that form the basis of the raw data were taken. The only dates shown say “2024” and locations are only listed as “United States”. There is no information on how the samples were obtained – whether they came from swabs from an animal’s respiratory tract. skin, or elsewhere.

In response to emailed questions from CNN, Shilo Weir, public affairs specialist for the USDA, said the agency released the raw data to the U.S. server in the interest of speed and said the agency would work quickly to transmit the selected sequences to GISAID.

“APHIS typically publishes curated sequence data on the GISAID platform. However, in order to make the sequence data public as soon as possible, APHIS has uploaded these unanalyzed sequence data files to NCBI,” Weir wrote in the emailed response.

“This footage will not be curated before release, but this approach will allow us to access footage information as quickly as possible. APHIS will continue to work as quickly as possible to publish selected files to GISAID that integrate and analyze relevant epidemiological information as well as sequence data,” Weir said.

It is also unclear whether the latest version represents all the genomes the agency has.

Dr. Michael Worobey, a professor of ecology and evolutionary biology at the University of Arizona, said the USDA is making a mistake by not sharing all the information it has as quickly as possible.

“There is a whole community around the world of people like me and my colleagues, who have a lot of experience in this area and can often see things or do analysis that might show something that others have missed,” he said. Worobey said.

“You don’t want one group to be the only one looking at the data. You want everyone, all the experts around the world, to be able to do it,” Worobey added.

Dr. Tom Inglesby, who directs the Johns Hopkins Center for Health Security at the Bloomberg School of Public Health, said the USDA’s public release of the raw data is a step in the right direction, but it doesn’t didn’t go far enough.

“The additional information would be very helpful to the public and to scientists, public health agencies and research organizations in understanding all the data that has been collected so far, which farms were tested, when they were tested, what is the sampling strategy. Overall, what kind of testing is going on right now across the country,” he said.

“Now that we know there are asymptomatic cows that have tested positive, what is the strategy to understand to what extent cows that are not showing symptoms in other herds are infected? Because I think the most important goal here is to have a complete picture of the epidemic.

Influenza viruses evolve rapidly and have caused some of the most devastating pandemics in history.

“What we are seeing right now is the first chapter of the book that keeps people like me and many infectious disease epidemiologists up at night,” said Dr. Michael Mina, chief scientific officer of telehealth company eMed and an expert in epidemiology, immunology and the spread of infectious diseases.

The Covid pandemic was serious, but Mina said a pandemic caused by this virus could be worse.

“The genie isn’t out of the bottle yet, and that’s a good thing,” Mina said, but given the potential consequences of letting the virus spread unchecked, “it’s a little difficult to suggest that we could be doing too much right now.”

Scientists have tracked the H5N1 virus for about two decades as it ravaged populations of wild and domestic birds and, more recently, marine mammals like sea lions, but human-to-human spread after contact with animals has been sporadic and not sustained, suggesting that the virus has not increased. mutated enough to become a fully human pathogen. There has been no evidence of person-to-person spread in the current outbreak in the United States, according to the U.S. Centers for Disease Control and Prevention.

However, humans have been infected after contact with animals – a frightening reminder that the virus still has us in its sights and requires close monitoring.

“It’s so critical that the U.S. government be as transparent as possible right now, too transparent, and share all of this footage and all of this data so that the world can look at it, do their own risk assessment and start to make their own vaccine if they need it in their own country instead of waiting for the United States to say what’s good and what’s bad,” said Bright, CEO of Bright Global Health in Washington, DC.

“What would we say if this particular virus got out of control? » said Bright. “Could we look back on the last two or three months and say, ‘I wish we were doing something else; I wish we were more transparent; I wish we’d shared all this footage so the world could prepare for this?’

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