2 Jun 2021

EMBL-EBI: Genomic surveillance of SARS-CoV-2 in England


Summary of evidence from the UK

Original announcement available here on EMBL-EBI’s website. 

This is a summary of work that has yet to be peer reviewed and is currently published as an online preprint.

This document has been prepared by the European Molecular Biology Laboratory to provide a summary of epidemiological information for public health officials and governments. The lead authors of the preprint are Dr Moritz Gerstung of EMBL’s European Bioinformatics Institute (EMBL-EBI) and Dr Jeffrey Barrett, Director of the COVID-19 Genomics Initiative at the Wellcome Sanger Institute.

Gerstung and colleagues have performed the largest in-depth analysis of genomic surveillance data generated by the Wellcome Sanger Institute’s SARS-CoV-2 genomic surveillance programme as part of the COVID-19 Genomics UK Consortium (COG-UK), mapping out the dynamics of 62 lineages – or variants – of the SARS-CoV-2 virus. This analysis covers data from England between September 2020 and May 2021, and tracks the fate of these lineages in 315 Lower Tier Local Authorities (LTLAs, meaning administrative regions with approximately 100,000–200,000 inhabitants) in England.

The scientists calculated the relative growth rates of each of the 62 lineages, including the variants of concern (VOC) B.1.1.7, B.1.351, P.1, and B.1.617.2, as well as other variants under investigation (VUI) by Public Health England.

These data provide important context for the current epidemic situation:

  • At the end of 2020, B.1.1.7 spread despite a series of restrictions, including a national lockdown in November and regionally tiered restrictions in December, which slowed the spread of other variants but were insufficient to control B.1.1.7, due to its intrinsic growth advantage.
  • Between January and March 2021, a third national lockdown controlled B.1.1.7 and, as a side-effect, eliminated most variants that had been dominant in September and October 2020.
  • E484K-containing variants persisted despite this trend, in part due to repeated introductions of these variants, but were largely confined to short-lived local outbreaks.
    B.1.617.2 was first observed in the week ending on 3 April 2021, has spread to more than 200 local authorities, and was found in more than 40% of viral genomes during the week ending on 15 May 2021.
  • The analysis of B.1.617.2 indicates that its current growth rate is 35% (20–50%) higher than that of B.1.1.7, with the highest rates of spread seen in North West England. Such a growth advantage has not been observed for any other VOC or VUI.

The mechanisms for this increased spread are unknown, but are likely to be a combination of viral biology (transmission or the ability to evade the immune system), repeated introductions, and epidemiological factors in the communities where it was introduced.

The growth of B.1.617.2 is also much greater than that of its sister lineage B.1.617.1, which is likely to have experienced similar rates of introductions and similar demographic factors.

Read the full preprint HERE.


Source article

VOHRINGER. H.S., et al. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021. MedRxiv. Published online 26 05; DOI:10.1101/2021.05.22.21257633

COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.