When the U.S. Department of Agriculture announced late Sunday that it had publicly posted new data from its investigation into an outbreak of bird flu in cattle, scientists eagerly sought out a well-known platform used worldwide to share the genetic sequences of viruses.
The sequences weren’t there. As of Tuesday morning, they still aren’t.
Researchers looking to track the evolution and spread of H5N1 say the information posted – raw data on a US 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 nearly a month ago, has been painfully slow.
Following Sunday’s announcement by the USDA, Dr. Rik Helderan immunologist and vaccine researcher who headed the Biomedical Advanced Research and Development Authority from 2016 to 2020, said he immediately called his contacts at the database, the Global Initiative on Sharing All Influenza Data (GISAID), to make sure that he didn’t. to miss something.
“I said, ‘Look, just tell me: do you have any data?’ and they said, ‘No,'” Bright said.
After even checking parts of the database where people can post rough drafts of sequences before their full public release, Dr. Lucas Freitas, a Brazilian data scientist who leads GISAID management, said no new sequences have been posted by the USDA since the announcement. .
“We wouldn’t want to miss it,” said Peter Bogner, founder and president of GISAID. “H5 is the reason GISAID came into being in the first place. It raises antennas.”
The highly pathogenic bird flu strain H5N1 has decimated bird populations around the world and has spread to a growing variety of mammals in recent years, raising concerns that it is one step closer to becoming a virus that can spread efficiently among humans.
When the USDA confirmed on March 25 that H5N1 had been found in dairy cows in Texas and Kansas, the news put infectious disease experts on edge. They were eager to get more information to see how the virus had changed to target a new host. The USDA’s Animal and Plant Health Inspection Service (APHIS)., says H5N1 has now been found in 32 herds in eight states.
But weeks have passed and little data about the US outbreak has been shared with the global scientific community.
In its notice published Sunday, APHIS said it had shared 239 genetic sequences from the H5N1 outbreak “from cattle, cats, chickens, skunks, raccoon, grackle, blackbird and goose.”
The agency said it “routinely publishes” to 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 “also quickly” shared sequences with a U.S. database maintained by the National Library of Medicine.
The announcement suggested to many scientists that the information would be found in GISAID, which has been crucial for tracking the evolution of the virus that causes Covid-19 as it spreads around the world. Many countries, including the United States, are using GISAID to quickly share genetic sequences – the exact sequence of four chemical building blocks that make up the blueprints of each virus.
Instead, the USDA uploaded raw sequence data, called FASTQ files, to the National Library of Medicine database, which is available to the public. However, these FASTQ files lack crucial information needed to help scientists track the evolution of the virus, such as the exact date the sample was collected and what state it came from.
Scientists use raw data when tracking the evolution of a virus, but they also typically use it in combination with the kind of information typically posted on GISAID: consensus sequences, known as FASTA files, that have been refined and cleared of contamination and errors . Consensus sequences typically provide more information about where the sample was collected and when, allowing researchers to better understand how a virus changes over time.
Researchers say it is not clear how recently the samples that form the basis for the raw data were taken. The only dates posted read ‘2024’ and the locations are only listed as ‘USA’. There is no information on how the samples were obtained – whether they came from swabs of an animal’s respiratory tract, its skin, or elsewhere.
In response to emailed questions from CNN, Shilo Weir, a public affairs specialist for USDA, said the agency placed the raw data on the U.S. server in the interest of speed and said the agency would work quickly to compile compiled sequences to GISAID.
“APHIS typically posts curated sequence data to the GISAID platform. However, in order to make the sequence data publicly available as quickly as possible, APHIS has uploaded these unanalyzed sequence data files to NCBI,” Weir wrote in the email response.
“These sequences will not be assembled before posting, but this approach will provide us with the fastest path to posting sequence information. APHIS will continue to work as quickly as possible to publish to GISAID curated files that contain and analyze relevant epidemiological information together with the sequence data,” Weir said.
It’s also not clear whether the latest release 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 made a mistake by not sharing all the information it has as quickly as possible.
“There’s a whole community around the world of people like me and my colleagues, who have a lot of experience with this and can often see things or do analysis that can show something that others have missed,” Worobey said.
“You don’t want essentially 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 that,” Worobey added.
Dr. Tom Inglesby, director of the Johns Hopkins Center for Health Security at the Bloomberg School of Public Health, said the USDA’s public release of the raw data was a step in the right direction but did not go far enough.
“The additional information would be very useful for the public and for scientists, public health agencies and research organizations to understand all the data collected so far, which farms have been tested, when they have been tested, what the sampling strategy is. Overall, what kind of testing is happening across the country now,” he said.
“Now that we know that there are asymptomatic cows that have tested positive, what is the strategy to understand the extent to which cows that do not show symptoms in other herds are infected? Because I think the main goal here is to get a complete picture of the outbreak.”
Influenza viruses change rapidly and have caused some of the most devastating pandemics throughout history.
“What we’re seeing now is chapter one of the book that keeps people like me and many infectious disease epidemiologists up at night,” said Dr. Michael Mina, chief scientific officer of the telehealth company eMed and an expert in the field healthcare. epidemiology, immunology and spread of infectious diseases.
The Covid pandemic was bad, but Mina said a pandemic caused by this virus could be worse.
“The genie is not 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 bit difficult to suggest that we’re doing too much at this point.” doing. ”
Scientists have been tracking H5N1 for about two decades as it ripped through populations of wild and domestic birds and more recently through marine mammals such as sea lions, but human-to-human spread after contact with animals has proven sporadic and unsustainable, suggesting that the virus has not survived. mutated enough to become a fully human pathogen. According to the US Centers for Disease Control and Prevention, there is no evidence of person-to-person spread in the current outbreak in the US.
However, people have become infected after contact with animals – a chilling reminder that the virus is still in our sights and must be closely monitored.
“It’s so critical that the US government be as transparent as possible at this point, overly transparent, and share all these series and all this data so that the world can look at it and make their own risk assessments and make their own risk assessments . vaccinate as needed in their own countries, rather than waiting for the United States to say what is good and what is 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. “Would we look back on the last two or three months and say, ‘I wish we had done something different; I wish we had been more transparent; I wish we had shared all these sequences so the world can prepare for this?’”
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