First evidence of UK coronavirus variant in California — Scripps Research

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A research partnership between scientists at Scripps Research Institute and University of California San Diego has found the first evidence that the B.1.1.7 coronavirus variant first uncovered in the UK is now present in California.

On the afternoon of Tuesday, 29 December, personnel at the EXCITE COVID-19 clinical testing laboratory at UC San Diego School of Medicine identified a positive sample that showed a specific pattern that can indicate the B.1.1.7 lineage, which is believed to spread more easily than the earlier forms of the virus.

They immediately transported the sample to the Scripps Research laboratory of Dr Kristian Anderson to perform full genome sequencing of the virus. In early morning hours of Wednesday, 30 December, the Scripps Research team confirmed the tell-tale mutations characteristic of the B.1.1.7 variant. The sample came from a local man in his 30s who had not recently travelled, indicating the variant was already spreading in the community, Andersen said.

"Coronaviruses mutate all the time, but the UK lineage has a number of additional mutations that are outside what we’ve seen before,” said Dr Mark Zeller, a post-doctoral associate in the Andersen laboratory and part of the team that did the sequencing. “These mutations are somewhat unusual and appear to make the virus more transmissible.”

The scientists immediately shared the sequencing data on their website and with public resources, including the National Centre for Biotechnology Information, so it can be accessed by other researchers.

On 28 December, just one day before the sample was collected at UC San Diego as part of its Return to Learn programme, the US Centres for Disease Control and Prevention (CDC) asked clinical laboratories to start watching for an unusual pattern known as the “S dropout” in COVID-19 tests. This abnormality might indicate the new variant.

“As I was reviewing results for Tuesday afternoon’s tests, I noted that a strong positive sample had no signal for the S gene and immediately notified my supervisor that it had the pattern the CDC asked us to watch for,” said Dr Phoebe Seaver, a member of the testing team in UC San Diego’s EXCITE laboratory.

Andersen’s lab finalised the sequence and made it public on Wednesday afternoon, then shared the findings more widely during a county press conference at 2:30 p.m.

UC San Diego’s Dr Louise Laurent credits the speed of discovery to the seamless cooperation between UC San Diego, Scripps Research, San Diego County Public Health Services and the CDC.

Since the team’s discovery, several additional cases of the UK variant have been identified across California. Andersen said efforts to contain the virus must continue – especially through social distancing and mask wearing. “We need to double down on everything we’ve been doing, and we need to do it better and more consistently,” Andersen said.

Andersen and Laurent have been working closely with the UC San Diego School of Medicine laboratories of Dr Rob Knight and Dr Gene Yeo, to help track the local spread of COVID-19 through rapid viral genome sequencing as part of the SEARCH alliance they established in February 2020.

By analysing genomic data, scientists are able to reconstruct how the virus makes its way through a community or region, providing valuable information to public health officials. The team recently received a $2.5m contract from the CDC to support this work.

 

Study details
Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

Nicole L Washington, Karthik Gangavarapu, Mark Zeller, Alexandre Bolze, Elizabeth T Cirulli, Kelly M Schiabor Barrett, Brendan B Larsen, Catelyn Anderson, Simon White, Tyler Cassens, Sharoni Jacobs, Geraint Levan, Jason Nguyen, Jimmy M Ramirez III, Charlotte Rivera-Garcia, Efren Sandoval, Xueqing Wang, David Wong, Emily Spencer, Refugio RoblesSikisaka, Ezra Kurzban, Laura D Hughes, Xianding Deng, Candace Wang, Venice Servellita, Holly Valentine, Peter De Hoff, Phoebe Seaver, Shashank Sathe, Kimberly Gietzen, Brad Sickler, Jay Antico, Kelly Hoon, Jingtao Liu, Aaron Harding, Omid Bakhtar, Tracy Basler, Brett Austin, Magnus Isaksson, Phillip G Febbo, David Becker, Marc Laurent, Eric McDonald, Gene W Yeo, Rob Knight, Louise C Laurent, Eileen de Feo, Michael Worobey, Charles Chiu, Marc A Suchard, James T Lu, William Lee, Kristian G Andersen

Published in medRxiv on 7 February 2021

Abstract
As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

 

Scripps Translational Research Institute material

 

medRxiv study (Open access)

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