Alternate primers for whole-genome SARS-CoV-2 sequencing

Cotten, M. , Bugembe, D. L., Kaleebu, P. and Phan, M. V.T. (2021) Alternate primers for whole-genome SARS-CoV-2 sequencing. Virus Evolution, 7(1), veab006. (doi: 10.1093/ve/veab006) (PMID:33841912) (PMCID:PMC7928614)

Abstract

As the world is struggling to control the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is an urgency to develop effective control measures. Essential information is encoded in the virus genome sequence with accurate and complete SARS-CoV-2 sequences essential for tracking the movement and evolution of the virus and for guiding efforts to develop vaccines and antiviral drugs. While there is unprecedented SARS-CoV-2 sequencing efforts globally, approximately 19 to 43 per cent of the genomes generated monthly are gapped, reducing their information content. The current study documents the genome gap frequencies and their positions in the currently available data and provides an alternative primer set and a sequencing scheme to help improve the quality and coverage of the genomes.

• Item Type: Articles
• Additional Information: We acknowledge the support of the Uganda Ministry of Health and its COVID-19 Scientific Advisory Committee, the National COVID-19 Task Force, and the staff of the Emerging and Remerging Infections Department of the Uganda Virus Research Institute, and the US Centers for Disease Control and Prevention. The SARS-CoV-2 diagnostic and sequencing award is jointly funded by the UK MRC and the UK DFID under the MRC–DFID Concordat agreement (NC_PC_19060) and is also part of the European and Developing Countries Clinical Trials Partnership 2 program supported by the European Union. The diagnostics were also supported by the UK Research and Innovation/MRC, the Global Fund, the Government of Uganda, the Islamic Development Bank, the World Health Organization, GAVI, the US Centers for Disease Control and Prevention, and the Jack Ma Foundation, among others. M.V.T.P. was supported by a Marie Sklodowska-Curie Individual Fellowship, funded by European Union’s Horizon 2020 research and innovation programme (799417). The Uganda Medical Informatics Centre high performance computer was supported by the UK MRC (MC_EX_MR/L016273/1) to P.K. The study is supported by a Wellcome Epidemic Preparedness–Coronavirus grant, jointly funded by the Wellcome Trust and UK DFID (220977/Z/20/Z) awarded to M.C.
• Keywords: SARS-CoV-2, COVID-19, primers, next generation sequencing.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Cotten, Professor Matthew
• Authors: Cotten, M., Bugembe, D. L., Kaleebu, P., and Phan, M. V.T.
• 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: Virus Evolution
• Publisher: Oxford University Press
• ISSN: 2057-1577
• ISSN (Online): 2057-1577
• Published Online: 04 February 2021
• Copyright Holders: Copyright © 2021 The Authors
• First Published: First published in Virus Evolution 7(1): veab006
• Publisher Policy: Reproduced under a Creative Commons License