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As the U.S. Department of Agriculture announced late Sunday that it had released new data from its investigation into a bird flu outbreak in cattle, scientists eagerly sought the world-renowned forum for sharing the genetic sequences of viruses.
The sequences weren't there. As of Tuesday morning, they still aren't there.
Researchers looking to track the evolution and spread of H5N1 say the data posted — raw data — on US servers is less useful and less transparent. They also say that the information released by the government was very slow following the outbreak that was confirmed in cattle about a month ago.
After Sunday announcement at 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 in a database called the Global Initiative on Influenza Information, or GISAID. Make sure nothing is missing.
“Look, just tell me. Do you have data?” I told him. And they said, 'No.'” Brit said.
After checking even the parts of the database where people post sequence drafts prior to full disclosure, Brazilian data scientist Dr. Lucas Freitas, lead researcher at GIAID, confirmed that no new sequences were posted by the USDA after the announcement. .
“We weren't going to miss it,” said Peter Bogner, founder and president of GSAID. “H5 is the reason why GISAID came to start. It raises the antennae.
The highly pathogenic avian influenza H5N1 has decimated bird populations around the world and, in recent years, has spread to various mammals, raising concerns that it is on the verge of becoming a virus that can easily spread to humans.
When the USDA confirmed H5N1 in dairy cows in Texas and Kansas on March 25, the news put infectious disease experts on alert, eager to learn more about how the virus has evolved to target a new host. USDA's Animal and Plant Health Inspection Service, or APHIS, He said H5N1 was found in 32 herds in eight states.
But weeks passed, and little information on the American epidemic was shared with the international scientific community.
in the advertisement Posted Sunday, APHIS said it shared 239 genetic sequences from “cattle, cats, chickens, skunks, raccoons, grackles, blackbirds and geese” from the H5N1 outbreak.
The agency said it would “regularly publish” it on GISAID, but said it was “promptly sharing” the sequences to a US database maintained for public transparency and “to make the scientific community have access to this information as quickly as possible…” National Library of Medicine.
The announcement indicated to many scientists that the information is available in GISAID As Covid-19 moves around the world, tracking the virus's progress is critical. Many countries, including the United States, use GISAID to quickly share genetic sequences — the sequence of four chemical building blocks that make up the blueprint of each virus.
Instead, USDA uploads raw sequence data, FASTQ files, to the National Library of Medicine database, which is available to the public. These FASTQ files, however, lack critical information for scientists to track the evolution of the virus, such as the exact date the sample was collected and where it came from.
Scientists use raw data when tracking the evolution of the virus, but they usually use it in conjunction with the type of data posted on GIAID: communication sequences, known as FASTA files, clean and free of contamination and errors. Consensus sequences typically provide additional information about where and when the sample was collected, which helps researchers better understand how the virus changes over time.
It is unclear how often the samples that form the basis of the raw data were taken, researchers said. The only dates posted say “2024”, and the locations are only listed as “USA”. There is no information on how the samples were obtained – they were obtained from the respiratory tract of animals. skin, or elsewhere.
Shiloh Weir, a public affairs specialist at the USDA, said in an emailed response to 's questions that the agency has posted the raw data on a US server for immediate use, and that the agency will work quickly to get the collected sequences to GISAID.
“APHIS typically posts series data collected on the GISAID platform. However, in order to release sequence data as quickly as possible, APHIS has uploaded these unanalyzed sequence data files to NCBI,” Weir wrote in an emailed response.
“These sequences are not screened before they are posted, but this approach allows us the fastest way to post sequence data. APHIS will continue to work as quickly as possible to publish files collected by GISAID, including relevant epidemiologic data that are included and analyzed with the sequence data,” Weir said.
It's also unclear whether the latest release represents the agency's entire genome.
Dr. Michael Wrobey, a professor of ecological and evolutionary biology at the University of Arizona, said the USDA is making a mistake by not sharing all the information it has as soon as possible.
“There's a whole community of people like me and my colleagues around the world who have a lot of experience with this and can often see things or do analytics that show things that others have missed,” Worobey said.
You don't want only one group to see the information. You need everybody, all the experts around the world to be able to do that,” added Worobey.
Dr. Tom Inglesby, who directs the Johns Hopkins Center for Health Security at the Bloomberg School of Public Health, said the USDA's release of the raw data is a step in the right direction, but it doesn't go far.
“The additional information will be very useful for the public and scientists and public health agencies, research organizations to understand all the data that has been collected so far, which farms have been tested, when they have been tested, what the sampling strategy is. In general, what kind of testing is being done across the country now,” he said.
“Now that we know there are asymptomatic cows that have tested positive, what method is there to understand the prevalence of asymptomatic cows in other herds? Because I think the most important objective here is to get the full picture of the epidemic.
Influenza viruses mutate rapidly and have caused some of the worst pandemics in history.
“What we are seeing now is phase one. A book that keeps people like me and many infectious disease epidemiologists awake at night,” said Dr. Michael Mina, chief scientific officer of the telehealth company eMed and an expert in epidemiology, immunology and infectious disease transmission.
The Covid outbreak was bad, but Meena said an outbreak caused by this virus could be worse.
“The genie's not out of the bottle yet, and that's a good thing,” Mina says, but given the consequences of letting the virus spread unchecked, “it's a little hard to suggest we're doing too much right now.” ”
Scientists have watched H5N1 wreak havoc on wild and domestic bird populations for nearly two decades. Recent marine mammals Like sea lions, but human-to-human transmission after contact with animals is sporadic and not persistent, suggesting that the virus has not become a fully human pathogen. have been There is no evidence According to the US Centers for Disease Control and Prevention, the current US outbreak has spread from person to person.
Humans have contracted the virus after contact with animals, but it is worrying that the virus is still in our sights and requires close monitoring.
“It's critical that the U.S. government is as transparent, as transparent as it can be, and sharing all of these procedures and all of this information so that the world can look at it and do their own risk assessment and start doing their own,” said Bright, CEO of Bright Global Health in Washington, D.C., USA. Instead of waiting for you to say what's good and what's bad, they should give vaccinations if they want to in their countries.
“What do we say if this particular virus is out of control?” Bright said. “If we look back on these last two or three months, we'll say, 'What if we had done something else?' I wish we had more clarity; I wish we could share all these steps so the world can prepare for this?'