Set-C Covid genome analysis

17 September 2020

A review of genomic evidence has shown that SARS-CoV-2, the virus that causes COVID-19, has so far shown a relatively low level of mutation compared to most other RNA viruses, which means it is unlikely to escape the immune response produced by prior infection or from vaccination.

The authors of The SARS-CoV-2 genome: variation, implication and application (PDF), highlight that to date there are no genetic changes to the virus proven to alter its virulence. However, some mutations are occurring and these are useful to follow the spread of virus, identify likely routes of transmission and implement control measures to disrupt these. The authors urge continued vigilance as mutations might allow the virus to develop resistance to drug treatment or allow it to go undetected by diagnostic tests.

Professor Geoffrey L. Smith, Department of Pathology at the University of Cambridge and lead author said; “It is good news that  SARS-CoV-2 has so far proven pretty stable, because it is easier to detect and treat a virus that is fairly stationary.  Whole genome sequencing allows us to understand not just that some-one is infected, but to define precisely the strain of virus and so work out where the infection probably came from.  It also allows us to track strains of virus that become dominant and that might replicate or transmit more efficiently.”

The findings are reported in a rapid review of published and pre-print evidence on the SARS-CoV-2 genome, carried out by the Royal Society’s SET-C (Science in Emergencies Tasking: COVID-19) group.

The analysis also debunks myths about the possible origin of the virus that causes COVID-19. It concludes that the genome is sufficiently different to all known coronaviruses to refute the assertion that the COVID-19 pandemic arose by deliberate or accidental release of a known virus and make it highly improbable that the virus arose by artificial construction in a laboratory. The review concludes that the origin of the virus was likely to be directly from bats or via an unknown intermediate mammalian host.

Professor Smith added; “There is nothing like solid evidence to bust the myths that are spread by conspiracy theorists.  It is understandable that when a new virus emerges there will be speculation about its origins, but the pace at which the global science community has developed our understanding of the genetics of SARS-CoV-2 has been spectacular. That has allowed us to trace its spread and develop diagnostic tests and candidate vaccines.  It also allows us to debunk some of the more colourful conspiracy theories.”

Analysis of the SARS-CoV-2 genome has also shown that from mid-February to mid-March the great majority of the strains of the virus in the UK originated in three European nations - Spain (34%), France (29%) and Italy (14%) - via incoming international travel. In contrast, less than 1% derived from China. 

The report was submitted to Government in late August.