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Peer Review Report For: Whole-genome sequencing of SARS-CoV-2 in Uganda: implementation of the low-cost ARTIC protocol in resource-limited settings [version 1; peer review: 2 approved]

Article scientifique 2021 Autre

Résumé

Background: In January 2020, a previously unknown coronavirus strain was identified as the cause of a severe acute respiratory syndrome (SARS-CoV-2). The first viral whole-genome was sequenced using high-throughput sequencing from a sample collected in Wuhan, China. Whole-genome sequencing (WGS) is imperative in investigating disease outbreak transmission dynamics and guiding decision-making in public health. Methods: We retrieved archived SARS-CoV-2 samples at the Integrated Biorepository of H3Africa Uganda, Makerere University (IBRH3AU). These samples were collected previously from individuals diagnosed with coronavirus disease 2019 (COVID-19) using real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR). 30 samples with cycle thresholds (Cts) values <25 were selected for WGS using SARS-CoV-2 ARTIC protocol at Makerere University Molecular Diagnostics Laboratory. Results: 28 out of 30 (93.3%) samples generated analyzable genomic sequence reads. We detected SARS-CoV-2 and lineages A (22/28) and B (6/28) from the samples. We further show phylogenetic relatedness of these isolates alongside other 328 Uganda (lineage A = 222, lineage B = 106) SARS-CoV-2 genomes available in GISAID by April 22, 2021 and submitted by the Uganda Virus Research Institute. Conclusions: Our study demonstrated adoption and optimization of the low-cost ARTIC SARS-CoV-2 WGS protocol in a resource limited laboratory setting. This work has set a foundation to enable rapid expansion of SARS-CoV-2 WGS in Uganda as part of the Presidential Scientific Initiative on Epidemics (PRESIDE) CoV-bank project and IBRH3AU.

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Mboowa, G., Mwesigwa, S., Kateete, D., Wayengera, M., Nasinghe, E., Katagirya, E., Katabazi, A., Kigozi, E., Kirimunda, S., Kamulegeya, R., Kabahita, J., Luutu, M., Nabisubi, P., Kanyerezi, S., Bagaya, B., Joloba, M. (2021). Peer Review Report For: Whole-genome sequencing of SARS-CoV-2 in Uganda: implementation of the low-cost ARTIC protocol in resource-limited settings [version 1; peer review: 2 approved]. https://doi.org/10.5256/f1000research.56967.r89860

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Auteur(s)

Gerald Mboowa Savannah Mwesigwa David Kateete Misaki Wayengera Emmanuel Nasinghe Eric Katagirya Ashaba Fred Katabazi Edgar Kigozi Samuel Kirimunda Rogers Kamulegeya Jupiter Marina Kabahita Moses Nsubuga Luutu Patricia Nabisubi Stephen Kanyerezi Bernard S. Bagaya Moses L Joloba

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