For the scientists who P.A.SThey spent all meticulously studying hundreds of thousands of coronovirus genomes by 2020, the United States has been an enigma.. Despite having a world-leading genome sequencing infrastructure and experiencing high rates of COVID-19 infections, it has lagged far behind in coronovirus genome sequencing and until recently to detect worrisome variants.
But, in recent studies, American researchers identified several new variants in states such as California, New York and Louisiana. And SARS-CoV-2 sequencing efforts continue to increase. This brings with it another challenge: making sense of discovered variants. They carry potentially worrisome mutations and may be more common, but how the data are spread means there is a danger that they are not clear..
Jeremy Kamil, a virologist at the Louisiana State University Health Sciences Center in Shreveport, led a team that explored the fast-growing version in the states of Louisiana and New Mexico, among other places. In the absence of clear data on the behavior of a variant, the expert commented: “It is as if there is an informal policy that each version is a new concern until proven otherwise.”
Part of the challenge is the decentralized form of American coronavirus surveillance and sequencing efforts. “Right now, it is individual laboratories or states or cities that are doing their part,” he explained. David Ho, a virologist at Columbia University in New York City, whose team Identified There is a type in the city with a mutation that can compromise immune responses. As a result of this fragmented effort, states such as New York, California, and Washington have each contributed thousands of sequences, while others such as Iowa, Tennessee, and New Hampshire have received sequences from far fewer COVID-19 cases.
in the United Kingdom, Instead, National indexing effort, Which works with public health, medical and research institutes. Has generated more than 300,000 coronavirus viruses. Thanks to the nuanced nuances of its figures, the UK effort showed by the end of 2020 that a version called B.1.1.7 apparently spread faster than circulating strains that it would later displace. Further research suggests that B.1.1.7 may be more fatal, but does not compromise vaccines.
The US National Institutes of Health and the Centers for Disease Control and Prevention (CDC), federal agencies responsible for biomedical research and public health “should move the country in a more concrete way,” he said. The CDC, which launched in November, had a target of sequencing approximately 7,000 samples per week, a goal first reached in late February., And since then they have established a new parameter of 25,000 per week.
In the absence of clear epidemiological or medical data, Scientists have assessed some potential dangers of such mutations. Researchers have come up with a growing list of mutations that can drive transmission or help the virus avoid immune responsesIs based on epidemiological and laboratory studies.
The team identified in New York as variants B. Ho, also known as B.1.526, carries a major mutation called E484K, which has been found in variants identified in South Africa and Brazil. Studies by various laboratories have shown that changes in E484K, which are found in a portion of coronovirus spike proteins that recognize host cells, weaken the potency of antibodies that can normally inactivate the virus. . It may help to see that similar variants in South Africa and Brazil lag behind in terms of reintegration and reduced the efficacy of the vaccine in field trials.
Building on those concerns, a team led by Microbiologist Anne-Katerin Uhleman of Columbia University and Ho was founded A monitoring network Identifying E484K-carrying viruses in New York City. The first cases of variant B.1.526 appeared in November, increasing to 5% of the city’s total cases in mid-January and up to 12% in February.. In the public indexing database, researchers found B.1.526 up and down the north-east coast of the US, and as far away as Singapore. E484K’s notoriety also inspired a team Structural biologist at the California Institute of Technology in Pasadena, led by Pamela Bjarkman and Anthony West To locate public indexing data, where they tracked down the emerging lineage in New York.
For Ho, B.1.526 requires more study. It has not yet been shown to impair the immune response and the frequency of its apparent increase may not be related to any biological properties. It took months for the UK variant B.1.1.7 to prove to be more variable and more viral. I think we should do the same.
Strong sequencing efforts in the US are generating variants with new or rarely seen mutations, which are more difficult to understand. Kamil partnered with researchers in New Mexico, as he saw an increase in the number of cases that he called Pelican, With a mutation they had not seen before. They identified several other variants in the US sequencing data that made a similar change.
The mutation, called Q677P, is near a region of the spike protein that needs to be split into two to allow the viral particle to enter the host cell. Mutations in this region occur in fast-spreading variants such as B.1.1.7, but Kamil stated that The Pelican variant, for now, is not one to watch and worry about.
“It is too early to say with scientific belief that this is a particularly worrisome mutation,” he explains. Researchers in California raised a red flag on variants found there Spike protein called L452R . A team from the University of California San francisco (UCSF) found that A variant with the mutation was growing rapidly in the city’s neighborhoods: it was present in 16% of the samples sequenced in November, more than half in mid-January.. Another team at UCSF found in laboratory tests that a variant with the L452R mutation was more infectious and less susceptible to antibodies.
But many researchers have expressed doubts about the importance of the L452R variant. The mutation has not occurred in laboratory studies that have indicated many other worrisome changes, such as the E484K, and the same L452R mutation has changed in other parts of the United States and has not increased rapidly, said Jeffrey Barat, a statistical Welcome Sanger Institute Genetic in Off Hintaxon, UK. “Probably not hurt.” It is a matter of waiting and watching, ”he said.
How the variant will premonate is unknown, but as vaccination increases, susceptible variants such as B.1.1.7 may decline, while those who may develop partial immunity may give rise to regional outbreaks. “I don’t think we’re going to have years of New York or California variants,” Barrett predicted. Finding out what is going on will not only depend on the sequencing of more samples, but will also develop the ability to understand them.