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SARS-CoV-2 Genomes Reveal Dynamics of England's Alpha, Delta Variant Surges

SARS-CoV-2 particles

NEW YORK – The UK's COVID-19 experience has been marked by multiple epidemics and sub-epidemics spawned by distinct SARS-CoV-2 strains, according to new research that relied on an ever-growing set of SARS-CoV-2 genomes generated by the Covid-19 Genomics UK (COG-UK) consortium.

"These genomic surveillance data have given us a totally new way of watching an outbreak unfold, which has taught us a lot about how a new infectious agent spreads and evolves," co-senior and co-corresponding author Jeffrey Barrett, director of the Wellcome Sanger Institute's COVID-19 Genomics Initiative, said in a statement.

"My hope is that similar genomic surveillance programs will be developed across the world," Barrett said, "so that we are as well-prepared as we can be to respond to future infectious disease outbreaks — whether they be familiar pathogens or new ones."

As they reported in Nature on Thursday, researchers from the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), the Wellcome Sanger Institute, and elsewhere used phylogeographic analyses and other approaches to interrogate genome sequences for almost 281,200 SARS-CoV-2 isolates collected across 315 local health authorities in England from early September 2020 until late June 2021.

The sequenced viral set represented more than 7 percent of the PCR-positive samples identified during that time frame, the team explained, and spanned some 71 viral lineages with shifting prevalence over time. By analyzing the SARS-CoV-2 genomes in relation to geography, the investigators were able to retrace the introduction, spread, and interactions between new strains in different parts of the country.

"Being able to see lineages side by side, mapped to specific locations, has been incredibly informative in terms of understanding how this series of epidemics has unfolded," co-senior and co-corresponding author Moritz Gerstung, a researcher affiliated with the EMBL-EBI and the German Cancer Research Center, said in a statement.

Over the broader COVID-19 pandemic, the authors noted, the COG-UK team has sequenced almost 600,000 SARS-CoV-2 isolates.

"Our dense genomic surveillance analysis identifies lineages which consistently grew faster than others in each local health authority — and thus at the same time, under the same restrictions, and in a comparable population," they explained.

As the fall of 2020 edged into winter, for example, the researchers saw a rise in representation from the so-called "Alpha" variant of SARS-CoV-2, which appeared to be more transmissible than the widely circulating lineages that preceded it. While the Alpha strain continued to spread despite restrictions introduced in late 2020, viruses from that strain seemed to be tamped down in early 2021 during another, stricter national "lockdown" in England.

In the place of the Alpha variant and other leading lineages found in the lead-up to that lockdown, other versions of the virus — often those with mutations altering the SARS-CoV-2 spike protein — began nudging ahead. Those, too, were largely replaced by a "Delta" SARS-CoV-2 variant that got a toehold and started to dominate as restrictions eased, making up roughly 98 percent of the SARS-CoV-2 isolates being identified in the region by late June.

"These data reveal a diversity of lineages in the fall of 2020 followed by sweeps of the Alpha and Delta variants," the authors reported, noting that "variants with considerably higher transmissibility have had strongest positive selection, and swept through England during the 10 months of this investigation."

The team noted that additional surveillance and analyses will be needed to keep tabs on still other versions of the virus that adapt to increasing rates of immunity in human host populations.

"Thanks to genomic surveillance in the UK and internationally, it is clear that we are dealing with a virus that has changed considerably since the one that we faced in March 2020," co-author Meera Chand, the UK Health Security Agency's COVID-19 incident director, said in a statement. "We will continue to monitor the SARS-CoV-2 virus to ensure that we can use the most effective vaccines, treatments, and public health measures against current and future variants."