B.1.1.7 Variant of COVID-19 spreading rapidly in the United States: study

The faster-spreading B.1.1.7 variant of SARS-CoV-2 first detected in the UK, the coronavirus responsible for COVID-19, is set to become the dominant variant of the virus in the United States, according to a study by scientists at Scripps Research and COVID-19 test maker Helix.

The results, which appear today in Cell, suggest that future COVID-19 case numbers and death rates in the United States will be higher than they otherwise would have been. The analysis suggests that the variant, which has been detectable in an increasing proportion of SARS-CoV-2 samples, is 40 to 50 percent more transmissible than the previously dominant SARS-CoV-2 lines. Other studies have shown that the B.1.1.7 variant could be about 50% more likely to cause fatal COVID-19.

“B.1.1.7 quickly became the dominant variant of SARS-CoV-2 in the UK and other countries following its emergence late last year, and the US is now on a trajectory similar, ”says study co-author Kristian Andersen, Ph .D., Professor in the Department of Immunology and Microbiology at Scripps Research and Director of Infectious Disease Genomics at the Scripps Research Translational Research Institute. “We need immediate and decisive action to minimize the morbidity and mortality associated with COVID-19.”

Besides Andersen, the other lead author was William Lee, Ph.D., vice president of science at Helix, which provides PCR-based COVID-19 testing to organizations across the United States. The study was also authored by Nicole Washington, Ph.D., associate director of research at Helix, and Karthik Gangavarapu of the Andersen lab.

“B.1.1.7 has a doubling rate of just over a week and an increased transmission rate of 40 to 50 percent, which means it could have a significant impact on public health”, Lee said. “It is essential that we continue to monitor the spread of this disease and other emerging variants, but our current level of surveillance is inadequate and lags behind that of other countries.” We need a more comprehensive national SARS-CoV-2 genomic surveillance program to address this. “

The B.1.1.7 variant appeared in the south of England last year and has since become the dominant variant in the UK In December, Andersen’s team at Scripps Research with colleagues from the University of California at San Diego has confirmed the first evidence for the variant in California.

A model of domination

The B.1.1.7 variant contains several mutations, including several in the gene that codes for the viral spike protein. These mutations increase the ability of the peak to bind to the ACE2 receptor on human cells. While there is no evidence yet that the B.1.1.7 variant can escape COVID-19 vaccines, public health officials fear its relatively high rate of spread will significantly worsen the pandemic before the vaccines cannot end it.

Standard swab tests for the coronavirus verify distinctive genetic sequences at three sites in the viral genome; the B.1.1.7 variant, due to its mutations, appears to be positive for two of these sites, but negative for the third site, which is found in the peak gene of the virus.

New analysis of around 500,000 Helix test results since July 2020 found that this two-in-three pattern, known as S gene target failure, or SGTF, became consistently evident at a low frequency (0 , 2%) in mid-October. By the third week of February, it had risen to 10.6% and was detected in patients from 25 different states and territories in the United States.

The SGTF pattern may occur with other variants of SARS-CoV-2 that have advanced genetic mutations, but the researchers found that by sequencing every SGTF sample they had from December to February, 662 of the 986 samples (67%) contained B.1.1. 7 variant. This suggests that the SGTF model on swab testing may provide a quick but approximate indication of prevalence B.1.1.7.

Variant has entered the country several times

The analysis also indicated that B.1.1.7 since December has represented a rapidly increasing proportion of SGTF results – for example, reaching around 95 percent in California in mid-January. In addition to the 659 B.1.1.7 cases they detected via the SGTF method, researchers found three other cases of variant B.1.1.7 among samples collected as part of unbiased genomic surveillance efforts for SARS. -CoV-2 in California.

The 662 instances of B.1.1.7 sequenced in the study were from samples collected in 10 US states, although the researchers note that other testing labs covering a total of 33 US states and territories have now reported to the CDC. at least one B .1.1.7 case.

The researchers’ family tree-type analysis of the detected B.1.1.7 sequences shows that the variant has been introduced into the United States on several occasions since at least the end of November 2020, particularly in California and Florida, and at periods coinciding with an increase in travel including Thanksgiving Week.

Scientists also found that the variant, overall, appears to spread 40-50% faster than the previously dominant SARS-CoV-2 variants. They estimated that in the first week of February 2021, B.1.1.7 accounted for about 4.3% of COVID-19 cases in the United States, with 4.2% of cases in California and about 11.5% cases in Florida.