Bird flu virus has been spreading among US cows for months, RNA reveals
Genomic analysis suggests that the outbreak probably began in December or January, but a shortage of data is hampering efforts to pin down the source. By Smriti Mallapaty
A strain of highly pathogenic avian influenza has silently been spreading among US cattle for months, according to preliminary analysis of genomic data. The outbreak likely began when the virus jumped from an infected bird to a cow, probably around late last December or early January. This implies a protracted, undetected spread of the virus — suggesting that more cattle than currently reported, across the United States and even in neighbouring regions, could have been infected with avian influenza.
These conclusions are based on swift analyses following a dump of genomic data by the US Department of Agriculture (USDA), headquartered in Washington DC, into a public repository on 21 April. But to scientists’ dismay, the data do not include crucial information that would shed light on the outbreak’s origins and evolution. Researchers also express concern that the genomic data wasn’t released until almost four weeks after the outbreak was announced, on 25 March.
Speed in sharing data is especially important for fast-spreading respiratory pathogens that have the potential to spark pandemics, says Tulio de Oliveira, a bioinformatician at Stellenbosch University in South Africa. The cattle outbreak shouldn’t give the virus the ability to spread between people, but researchers say that it is important to be vigilant.
"In an outbreak response, the faster you get data, the sooner you can act,” says Martha Nelson, a genomic epidemiologist at the US National Center for Biotechnology Information (NCBI) in Bethesda, Maryland. Nelson adds that, with every week that goes by, the window for controlling the outbreak narrows. “Whether we’re not too late, to me, that’s kind of the million-dollar question."
Single spillover
US federal officials announced on 25 March that a highly pathogenic bird-flu strain had been detected in dairy cows. The USDA has since confirmed infections with the strain, named H5N1, in 34 dairy herds in nine states as of 30 April. In late March and early April, the USDA posted a handful of viral sequences from cows sampled in Texas and a sequence from a human case, on the widely used repository GISAID.
On 21 April, the USDA posted more sequencing data on the Sequence Read Archive (SRA), a repository maintained by the NCBI. The latest upload includes some 10 gigabytes of sequencing information from 239 animals, including cows, chickens and cats, says Karthik Gangavarapu, a computational biologist at Scripps Research in La Jolla, California.
“This virus is clearly transmitting among cows in some way" says Louise Moncla, an evolutionary virologist at the University of Pennsylvania in Philadelphia.
Nelson says that she was most surprised by the extent of the genetic diversity in the virus that infected the cattle, which indicates that the virus had months to evolve. Among the mutations are changes to a viral-protein section that scientists have linked to possible adaptation to spread in mammals, she says.
The data also show occasional jumps back from infected cows to birds and cats. “This is a multi-host outbreak” says Nelson.
A single jump, many months ago, is “the most reliable conclusion you can make”, on the basis of available data, says Eric Bortz, a virologist at the University of Alaska Anchorage. But an important caveat is that it isn’t clear what percentage of infected cows the samples represent, he says.
Fill in the blank
That’s only one of many data gaps. Scientists lack information about each sample’s precise collection date and the state where it was collected. Such gaps are “very abnormal”, Nelson says.
The missing metadata make it harder to answer many questions, such as how the virus is transmitted between individual cows and between herds, and exactly when the virus jumped to cows. These insights could help to control further viral spread, and protect workers on cattle farms “who can least afford to be exposed”, says Worobey.
Worobey, Gangavarapu and their colleagues are now racing to analyse some metadata uncovered through online sleuthing by Florence Débarre, an evolutionary biologist at the French national research agency CNRS in Paris. Gangavarapu says that dates and geographic information for 152 of the 239 samples have been extracted from a USDA presentation posted on YouTube on 26 April
Another less likely scenario, which can’t be ruled out, says Nelson, is that the person was infected directly from a wild bird. “It raises just a whole slew of questions about what black box of samples we are missing.”
Shilo Weir, a public-affairs specialist at the USDA, says that the agency decided to post the unanalysed sequence data on the SRA to make it public as soon as possible. Weir says that the agency will “work as quickly as possible” to publish curated files on GISAID with relevant epidemiological information, and will continue to make raw data available on the SRA on a rolling basis.
News date: 2024-04-27
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