Nature: Genome analysis reveals Alpha and Delta variants swept England

With the evolution of the new crown pneumonia epidemic, new variants continue to emerge, requiring timely epidemiological monitoring
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Researchers in the United Kingdom recently conducted genome analysis of multiple isolates and found that COVID-19 in the United Kingdom is characterized by different SARS-CoV-2 virus strains that produce a variety of epidemics and sub-epidemics

Jeffrey Barrett, head of the COVID-19 genomics project at the Wellcome Sanger Institute, said: "These genomic monitoring data provide us with a new way to observe the outbreak, allowing us to understand how a new infectious pathogen spreads and evolves
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"I hope that similar genome monitoring programs can be developed on a global scale," Barrett said
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"This way we can be fully prepared to deal with future outbreaks of infectious diseases, whether it is a familiar pathogen or a new pathogen

This paper entitled "Genomic reconstruction of the SARS-CoV-2 epidemic in England" was published in the journal Nature last week
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Researchers from the European Institute for Bioinformatics (EMBL-EBI), the Sanger Institute and other institutions used systematic geographic analysis and other methods to analyze the genome sequences of nearly 281,200 SARS-CoV-2 isolates.
These isolates were released in September 2020.
It was collected from 315 health departments in England from January to June 2021
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The researchers explained that the sequenced viruses accounted for more than 7% of the PCR-positive samples identified during this time period and spanned about 71 virus lineages.
Over time, the prevalent lineages continue to change
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By analyzing the SARS-CoV-2 genomes in different geographical locations, they were able to trace the introduction, spread and interaction of new strains in different regions

This work is based on the SARS-CoV-2 genome produced by the British COVID-19 Genomics Consortium (COG-UK)
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During the outbreak, the COG-UK team has sequenced nearly 600,000 SARS-CoV-2 isolates

Researchers found through analysis that multiple lineages existed in the early autumn of 2020, and then Alpha variant strains (B.
1.
1.
7) began to increase.
This variant strain seems to be more disseminated than the previously widely circulated lineages
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Although the Alpha mutant strain continued to spread despite the implementation of the second national lockdown at the end of 2020, the virus strain seems to be contained by the third stricter lockdown at the beginning of 2021

After that, virus strains that replaced Alpha mutant strains and other lineages began to appear
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The virus strain at that time was gradually replaced by the Delta mutant strain (B.

"These data reveal multiple lineages in the fall of 2020, followed by a sweep of Alpha and Delta variants," the authors report, noting that "mutants with higher transmission have the strongest positive selection, and are selected in 10 Swept England in a month's time
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The researchers pointed out that more monitoring and analysis are needed to pay close attention to other versions of the virus, which tend to adapt to the increasing immunity of the human host
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Meera Chand, head of the COVID-19 incident at the UK Health and Security Agency, said: “Thanks to the genomic monitoring in the UK and internationally, it is clear that the virus we are facing has changed a lot since March 2020.

We will continue to monitor SARS.

-CoV-2 virus to ensure that we can use effective vaccines, treatments and public health measures to deal with current and future variants

Original Search

Vöhringer, HS, Sanderson, T.
, Sinnott, M.
et al.
Genomic reconstruction of the SARS-CoV-2 epidemic in England.
Nature (2021).
https://doi.
org/10.
1038/s41586-021-04069- y