Identification of variants of concern
The recent identification of a number of SARS-CoV-2 variants of concern (VOC) has demonstrated the importance of ongoing genomic surveillance to monitor changes in the viral genome sequence and their impact on virus biology. In the UK, the world-leading genomic surveillance infrastructure established by the COG-UK consortium, funded by the UK government and the Wellcome Trust, had sequenced over 200,000 SARS-CoV-2 genomes by late January 2021, around half of the global total at that point 1,2.
This infrastructure enabled COG-UK to monitor different mutations emerging in the viral genome as the virus circulated in the population, including a new lineage of SARS-CoV-2 called B.1.1.7 (VOC202012/01), often referred to as the ‘UK variant’ 3. B.1.1.7 has a number of changes, particularly in the Spike protein, and increased in frequency in late 2020, even with lockdown measures in place, compared to other variants. These data showed that the genetic changes in B.1.1.7 had made the virus more transmissible4. Changes to the Spike protein are of particular interest and concern because it is this protein that enables the virus to enter human cells; it is also the target for many current vaccines and diagnostics5.
The identification of B.1.1.7 alerted the global community to the emergence of a more transmissible variant. Subsequent international sequencing efforts identified other lineages — B1.351 and P1, first identified in South Africa6 and Brazil/Japan7 respectively – also associated with increased transmissibility. Further variants are also being identified in the United States8.
The identification of these variants led to widespread global public health action, including renewed national lockdowns and a decrease in or total ban on travel between specific areas or countries. It also precipitated intensive study of these variants in the laboratory, to better understand any potential impact on the effectiveness of vaccines and diagnostics developed from genome sequences produced early in the pandemic.
1. Peacock, S. J. Reflections on the achievements of COGUK. COG Consortium. 2021. Available at: https://www. cogconsortium.uk/news_item/reflections-on-theachievements-of-cog-uk [Accessed: 01 February 2021]
2. SARS-CoV-2 genomes. GISAID. 2021. Available at: https:// www.gisaid.org [Accessed: 26 January 2021]
3. COG Consortium. COG Consortium COG-UK report on SARS-CoV-2 Spike mutations of interest in the UK. 2021. Available at: https://www.cogconsortium.uk/wp-content/ uploads/2021/01/Report-2_COG-UK_SARS-CoV-2- Mutations.pdf [Accessed: 01 February 2021]
4. Rambaut, A., Loman, N., Pybus, O. G., et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological. 2020; Available at: https://virological.org/t/ preliminary-genomic-characterisation-of-an-emergent-sarscov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spikemutations/563 [Accessed: 01 February 2021] 5.
5. Peacock, S. J. Reflections on the achievements of COGUK. COG Consortium. 2021; Available at: https://www. cogconsortium.uk/news_item/reflections-on-theachievements-of-cog-uk
6. Tegally, H., Wilkinson, E., Giovanetti, M. , et al. Emergence and rapid spread of a new severe acute respiratory syndromerelated coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv. 20248640 (2020).
7. Faria, N. R., Morales Claro, I., Candido, D., et al. Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings. Virological. 2021; Available at: https://virological.org/t/genomic-characterisation-of-anemergent-sars-cov-2-lineage-in-manaus-preliminaryfindings/586 [Accessed: 01 February 2021]
8.Pater, A. A., Bosmeny, M. S., Barkau, C. L., et al. Emergence and evolution of a prevalent new SARS-CoV-2 variant in the United States. bioRxiv. 426287 (2021).