Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda

Bugembe, D. L. et al. (2021) Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda. Nature Microbiology, 6(8), pp. 1094-1101. (doi: 10.1038/s41564-021-00933-9) (PMID:34163035) (PMCID:PMC8318884)

Abstract

Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the reported cases. Phylogenetic analyses of these sequences revealed the emergence of lineage A.23.1 from lineage A.23. Lineage A.23.1 represented 88% of the genomes observed in December 2020, then 100% of the genomes observed in January 2021. The A.23.1 lineage was also reported in 26 other countries. Although the precise changes in A.23.1 differ from those reported in the first three SARS-CoV-2 variants of concern (VOCs), the A.23.1 spike-protein-coding region has changes similar to VOCs including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1 lineage has changes in non-spike proteins including nsp6, ORF8 and ORF9 that are also altered in other VOCs. The clinical impact of the A.23.1 variant is not yet clear and it has not been designated as a VOC. However, our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable.

• Item Type: Articles
• Additional Information: The SARS-CoV-2 diagnostic and sequencing award is jointly funded by the UK Medical Research Council (MRC/UK Research and Innovation) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement (grant agreement no. NC_PC_19060) and is also part of the European & Developing Countries Clinical Trials Partnership (EDCTP2) programme supported by the European Union. The UMIC HPC was supported by the MRC (grant no. MC_EX_MR/L016273/1) to P.K. A.R. acknowledges the support of the Wellcome Trust (Collaborators Award no. 206298/Z/17/Z ARTIC network) and the European Research Council (grant agreement no. 725422—ReservoirDOCS). The study is additionally funded by the Wellcome Trust, DFID—Wellcome Epidemic Preparedness—Coronavirus (grant agreement no. 220977/Z/20/Z) awarded to M.C.
• Keywords: SARS-CoV-2, viral infection.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Cotten, Professor Matthew
• Authors: Bugembe, D. L., Phan, M. V. T., Ssewanyana, I., Semanda, P., Nansumba, H., Dhaala, B., Nabadda, S., O'Toole, Á. N., Rambaut, A., Kaleebu, P., and Cotten, M.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Nature Microbiology
• Publisher: Nature Research
• ISSN: 2058-5276
• ISSN (Online): 2058-5276
• Published Online: 23 June 2021
• Copyright Holders: Copyright © 2021 The Authors
• First Published: First published in Nature Microbiology 6(8): 1094-1101
• Publisher Policy: Reproduced under a Creative Commons License