When the U.S. Department of Agriculture announced late Sunday that it had made public new data from its investigation of an avian flu outbreak in cattle, scientists eagerly searched a well-known platform used globally to share the genetic sequences of viruses.
The desks were not there. As of Tuesday morning, they are still gone.
Researchers who want to track the development and spread of H5N1 say that the published information (raw data from the US server) is not very useful and is completely transparent. They also say the government has been painfully slow in releasing information about the outbreak, which was confirmed in cattle almost a month ago.
Following the announcement made by the USDA on Sunday, Dr. Rick BrightThe 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 Sharing of All Flu Data (GISAID) to make sure he wasn’t suspicious. Something is missing.
“’Look, tell me: Do you have data?’ I said. “They said ‘No,'” Bright said.
Brazilian data scientist Dr. Curator of GISAID. After checking even parts of the database where people can post rough drafts of series before their full release, Lucas Freitas confirmed that no new series had been released by the USDA since the announcement. .
“We won’t miss this,” said Peter Bogner, founder and president of GISAID. “H5 was the reason why GISAID was initially introduced. It raises the antennas.”
The highly pathogenic bird flu strain H5N1 has decimated bird populations worldwide and has crossed into an increasing number of mammal species in recent years, raising concerns that it is one step closer to becoming a virus that can spread effectively in humans.
When the USDA confirmed on March 25 that H5N1 had been detected in dairy cows in Texas and Kansas, the news alarmed infectious disease experts, and they were eager to learn more to see how the virus had evolved to target a new host. USDA’s Animal and Plant Health Inspection Service, or APHIS, It says H5N1 is now found in 32 herds in eight states.
But weeks passed and little data about the outbreak in the United States was shared with the global scientific community.
In its announcement published Sunday, APHIS said it 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 for public transparency and “to ensure that the scientific community has access to this information as quickly as possible…” it also “rapidly shares” the sequences in a US database maintained by the US. National Library of Medicine.
The announcement suggested to many scientists that the information would be available at GISAID, which is critical for tracking the evolution of the virus that causes Covid-19 as it travels around the world. Many countries, including the United States, use GISAID to quickly share genetic sequences, the exact sequence of four chemical building blocks that make up the blueprint of each virus.
Instead, USDA uploaded the raw sequencing data, called FASTQ files, to the publicly available National Library of Medicine database. But these FASTQ files lack critical information needed to help scientists track the evolution of the virus, such as the exact date the sample was collected and which state it came from.
Scientists use raw data when tracking the evolution of a virus, but they also use it in concert with the type of information typically sent to GISAID: consensus sequences that are refined and free of contamination and errors, known as FASTA files. Consensus sequences often provide more information about where and when the sample was collected, helping researchers better understand how a virus changes over time.
The researchers say it’s not clear how recently the samples on which the raw data was based were taken. The published dates only say “2024” and the locations are listed as “USA” only. There is no information on how the samples were obtained; Do these come from swabs taken from an animal’s respiratory tract, skin, or elsewhere?
In response to emailed questions from CNN, USDA public affairs specialist Shilo Weir said the agency sent the raw data to the US server for speed purposes and that the agency would work quickly to deliver selected sequences to GISAID.
“APHIS typically publishes selected sequence data on the GISAID platform. However, in order to make sequence data public as quickly as possible, APHIS uploaded these unanalyzed sequence data files to NCBI,” Weir wrote in an emailed response.
“These sequences will not be edited before publication, but this approach will provide us with the fastest way to publish sequence information. APHIS will continue to work as quickly as possible to publish GISAID-selected files that combine and analyze relevant epidemiological information along with sequence data,” Weir said.
It’s also unclear whether the final version represents all the genomes the agency has.
Professor of ecology and evolutionary biology at the University of Arizona, Dr. Michael Worobey said the USDA made a mistake by not sharing all the information it had as quickly as possible.
“There’s a community of people around the world, like myself and my colleagues, who have a lot of experience with this and can often see things or do analyzes that can point to things that others have missed,” Worobey said.
“You don’t actually want one group to be the only one looking at the data. You want everyone, every expert in the world, to be able to do this,” Worobey added.
D., who directs the Johns Hopkins Center for Health Security at the Bloomberg School of Public Health. Tom Inglesby said USDA’s public release of raw data is a step in the right direction, but it doesn’t go far enough.
“The additional information will be very useful for the public, scientists, public health agencies and research organizations to understand all the data collected so far, which farms have been tested, when they were tested, what the sampling strategy was. In general, what is happening across the country right now?” “Such tests are being carried out,” he said.
“Now that we know there are asymptomatic cows testing positive, what is the strategy to understand to what extent asymptomatic cows in other herds are infected? Because I think the most important goal here is to get the full picture of the outbreak.”
Flu viruses are changing rapidly and have caused some of the most devastating epidemics throughout history.
Dr. D., chief scientific officer of telehealth company eMed and an expert in the field of science. “What we are seeing now is chapter one of the book that keeps people like me and many infectious disease epidemiologists up at night,” said Michael Mina. Epidemiology, immunology and the spread of infectious diseases.
The Covid outbreak was bad, but Mina said an outbreak 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 allowing the virus to spread unchecked, “It’s a little hard to say we might be doing too much right now.”
Scientists have been tracking the spread of H5N1 among wild and domestic bird populations and, more recently, marine mammals such as sea lions for nearly two decades; however, human-to-human spread after contact with animals appears to be sporadic and not continuous; This shows that the virus is not permanent. has mutated to the point of becoming a fully human pathogen. There is no evidence that the current US outbreak is spreading from person to person, according to the US Centers for Disease Control and Prevention.
However, people become infected with the virus after coming into contact with animals; This reminds us that the virus is still in our target and needs to be followed closely.
“It’s critical that the U.S. government be as transparent as possible right now, hyper-transparent, and share all of these arrays and all of the data so the world can look at this, do their own risk assessments, and start doing their own risk assessments,” he said, CEO of Bright Global Health in Washington, DC. Su Bright said they should vaccinate in their own countries if they need it, rather than waiting for the United States to tell them what is good and what is bad.
“What would we say if this virus got out of control?” He said bright. “When we look back at the past two or three months, we say, ‘I wish we had done something else; I wish we were more transparent; ‘What if we shared all these scenes so the world could be prepared for this?’”
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