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

View ORCID ProfileMatthew Cotten, View ORCID ProfileDan Lule Bugembe, View ORCID ProfilePontiano Kaleebu, View ORCID ProfileMy V.T. Phan
doi: https://doi.org/10.1101/2020.10.12.335513
Matthew Cotten
1UK Medical Research Council–Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
4UK Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
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  • For correspondence: matthew.cotten@lshtm.ac.uk
Dan Lule Bugembe
1UK Medical Research Council–Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
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Pontiano Kaleebu
1UK Medical Research Council–Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
2Uganda Virus Research Institute, Entebbe
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My V.T. Phan
3Erasmus Medical Center, Rotterdam, the Netherlands
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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% 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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Manuscript revised to address peer reviewers's comments. Revisions included improved resolution of graphics in Figure 1 and 2, additional Figure 5 with testing of primers on a larger set of clinical samples, correction of typos and grammatical errors.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted November 09, 2020.
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Alternate primers for whole-genome SARS-CoV-2 sequencing
Matthew Cotten, Dan Lule Bugembe, Pontiano Kaleebu, My V.T. Phan
bioRxiv 2020.10.12.335513; doi: https://doi.org/10.1101/2020.10.12.335513
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Alternate primers for whole-genome SARS-CoV-2 sequencing
Matthew Cotten, Dan Lule Bugembe, Pontiano Kaleebu, My V.T. Phan
bioRxiv 2020.10.12.335513; doi: https://doi.org/10.1101/2020.10.12.335513

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