Scientists anxiously searched a well-known platform used worldwide to discuss virus genetic sequences when the US Department of Agriculture stated late Sunday that it had publicly disclosed new data from its study into an epidemic of bird flu in cattle.
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| Researchers claim that USDA is releasing H5N1 flu data too slowly and with insufficient data. |
There were no sequences. Tuesday morning finds them still not.
The raw data that was uploaded to a US computer by researchers attempting to monitor the emergence and spread of H5N1 is said to be of little utility and to be anything but transparent. Additionally, they claim that the government has been releasing information on the outbreak, which was confirmed in cattle nearly a month ago, at an excruciatingly slow pace.
Dr. Rick Bright, an immunologist and vaccine researcher who oversaw the Biomedical Advanced Research and Development Authority from 2016 to 2020, said he immediately contacted the Global Initiative on Sharing All Influenza Data, or GISAID, to make sure he wasn't missing anything following the USDA's announcement on Sunday.
"Look, just tell me: Do you have data?" I replied. and they said, "No," Bright remarked.
Dr. Lucas Freitas, the principal data scientist for GISAID and a Brazilian, checked the database, even areas where users can publish draft sequences before they are released to the public, and he verified that the USDA has not posted any new sequences since the announcement.
GISAID's president and founder, Peter Bogner, declared, "We wouldn't miss it." H5 is the primary driver behind the creation of GISAID. Antelopes are raised by it.
The deadly H5N1 avian flu virus, which has decimated bird populations worldwide, has been making the jump to mammals in recent years, raising concerns that the virus may not be able to spreading positively to the nearest person. When the USDA confirmed on March 25 that the H5N1 virus had been detected in dairy cattle in Texas and Kansas, the news alerted infectious disease experts to be alert and wanted more information. to know the virus. According to the US Animal and Plant Health Inspection Service (APHIS) the H5N1 virus has now been detected on 32 livestock farms in eight states. But in the past few weeks, the international scientific community has shared little information about the epidemic in the US. In an announcement issued Sunday, APHIS said it has isolated 239 gene sequences from H5N1 outbreaks in cattle, cats, chickens, skunks, raccoons, wrens, blackbirds and geese. The agency said GISAID is "regularly published" but "promptly" shares its sequences with the US National Library of Medicine, which is managed by the National Library of Medicine for public information and "to ensuring that the scientific community has access to these information for speed." It was announced to many scientists that this information can be found in GISAID and is important to track the spread of the virus that causes Covid-19 around the world. Many countries, including the United States, use GISAID to quickly share genetic sequences - the exact sequence of the four chemicals that make up the blueprint of each virus. Instead, the USDA sends raw sequence data, called the FASTQ archive, to the National Library of Medicine, where it is available. However, these FASTQ files lack important information that would help scientists track the evolution of the virus, such as the exact date the samples were collected and the country of origin. Scientists use the raw data when tracking virus evolution, but it is often used in conjunction with other types of information submitted to GISAID: the approval sequences, also known as FASTA files , refined and cleansed of impurities and defects. The sequences often provide more information about where and when the samples were collected, helping researchers better understand how viruses have changed over time. The researchers said it was unclear how long the samples were for when the original data was collected. The release date is "2024" and the target location is "United States". Shilo Weir, a public affairs specialist at the USDA, said in an emailed response to questions from CNN that the agency has moved the raw data to a US server to speed up processing. work and say that the office will immediately begin to work and provide a series collection. to GISAID.
– APHIS generally publishes the selected sequence data on the GISAID platform. "However, in an effort to quickly produce sequence data, APHIS sent these unanalyzed sequence data files to NCBI," Weir wrote in an emailed response.– These series are not compiled before publishing, but this way we can quickly publish the series information. "APHIS will continue to submit collected documents to GISAID as soon as possible that capture and analyze epidemiologic information and sequence data," Weir said.
It is not clear whether the newly released data represents all the genes involved in the industry. 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 earlier.
"There's a global community of people like me and my colleagues who have a lot of experience with this and can see something or do analysis that points to something that others have missed," Worobey said.
– You don't want just one group of people watching your story. You want everyone, every expert, around the world to be able to do this," Worobey said.
Tom Ingelsby, director of the Johns Hopkins Center for Public Health at the Bloomberg School of Public Health, said the USDA's release of raw data to the public is a step in the right direction, but not enough. – Additional information will be useful for the general public, scientists and public health agencies, research organizations to understand all the data collected so far, the farms tested and the time tested i.e., what models were adopted, and the general strategy being implemented throughout. the country. it's a kind of experiment," he said.
– Now that we know that some asymptomatic cows are testing positive, what are the strategies to know how many asymptomatic cows of other groups are infected? Because I think the main goal here is to really understand this epidemic situation.
Influenza viruses change rapidly and have caused the worst epidemics in history.
"What we're seeing now is the first chapter of the book that's keeping people like me and many other infectious disease athletes awake at night," said Dr. Michael Mina, chief scientist at infectious disease telemedicine company eMed.
The coronavirus epidemic is very dangerous, but Mina said that the epidemic caused by this virus will be worse. "The virus is still not out of the woods, and that's a good thing," Mina said, but considering the consequences of letting the virus spread unchecked, "it seems like a long shot." " to say that we are doing too much. right now.
Scientists have tracked the H5N1 virus for two decades as it spreads among wild and domestic birds and, more recently, marine mammals such as sea lions. However, human-to-human transmission after contact with animals occurs at regular and irregular intervals, indicating the presence of the virus. it will not happen. According to the Centers for Disease Control and Prevention, there is no evidence of human-to-human transmission in the current outbreak in the United States.
However, humans become infected after contact with animals - a reminder that this virus is still affecting us and needs to be monitored closely.
— It is important for the US government at this time to be transparent, transparent, and share all the series and all the data so that the world can see and make its own risk assessment, according to Bright , CEO of Bright Global Health in Washington. If necessary, they can start producing their own vaccines in their countries, instead of waiting for the United States to decide which ones are good and which ones are bad.
"What will we say if this virus disappears?" Bright said. "When we look back on the past two or three months, will we say, 'If only we had done something else; I wish we could be more clear; I wish we could share all these series to make the world equal?– APHIS generally publishes the selected sequence data on the GISAID platform. "However, in an effort to quickly produce sequence data, APHIS sent these unanalyzed sequence data files to NCBI," Weir wrote in an emailed response.
– These series are not compiled before publishing, but this way we can quickly publish the series information. "APHIS will continue to submit collected documents to GISAID as soon as possible that capture and analyze epidemiologic information and sequence data," Weir said.
It is not clear whether the newly released data represents all the genes involved in the industry. 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 earlier.
"There's a global community of people like me and my colleagues who have a lot of experience with this and can see something or do analysis that points to something that others have missed," Worobey said.
– You don't want just one group of people watching your story. You want everyone, every expert, around the world to be able to do this," Worobey said.
Tom Ingelsby, director of the Johns Hopkins Center for Public Health at the Bloomberg School of Public Health, said the USDA's release of raw data to the public is a step in the right direction, but not enough. – Additional information will be useful for the general public, scientists and public health agencies, research organizations to understand all the data collected so far, the farms tested and the time tested i.e., what models were adopted, and the general strategy being implemented throughout. the country. it's a kind of experiment," he said.
– Now that we know that some asymptomatic cows are testing positive, what are the strategies to know how many asymptomatic cows of other groups are infected? Because I think the main goal here is to really understand this epidemic situation.
Influenza viruses change rapidly and have caused the worst epidemics in history.
"What we're seeing now is the first chapter of the book that's keeping people like me and many other infectious disease athletes awake at night," said Dr. Michael Mina, chief scientist at infectious disease telemedicine company eMed.
The coronavirus epidemic is very dangerous, but Mina said that the epidemic caused by this virus will be worse. "The virus is still not out of the woods, and that's a good thing," Mina said, but considering the consequences of letting the virus spread unchecked, "it seems like a long shot." " to say that we are doing too much. right now.
Scientists have tracked the H5N1 virus for two decades as it spreads among wild and domestic birds and, more recently, marine mammals such as sea lions. However, human-to-human transmission after contact with animals occurs at regular and irregular intervals, indicating the presence of the virus. it will not happen. According to the Centers for Disease Control and Prevention, there is no evidence of human-to-human transmission in the current outbreak in the United States.
However, humans become infected after contact with animals - a reminder that this virus is still affecting us and needs to be monitored closely.
— It is important for the US government at this time to be transparent, transparent, and share all the series and all the data so that the world can see and make its own risk assessment, according to Bright , CEO of Bright Global Health in Washington. If necessary, they can start producing their own vaccines in their countries, instead of waiting for the United States to decide which ones are good and which ones are bad.
"What will we say if this virus disappears?" Bright said. "When we look back on the past two or three months, will we say, 'If only we had done something else; I wish we could be more clear; I wish we could share all these series to make the world equal?
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