Abstract
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.
Highlights
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) which has spread throughout the entire world, causing more than 175 million infections and over 3.7 million deaths globally.[1]
We further show phylogenetic relatedness of these isolates alongside other 328 Uganda SARS-CoV-2 genomes available in GISAID by April 22, 2021 and submitted by the Uganda Virus Research Institute
This article is included in the Coronavirus collection
Summary
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) which has spread throughout the entire world, causing more than 175 million infections and over 3.7 million deaths globally.[1]. Of the 131 Uganda full SARS-CoV-2 genomes analysed in December 2020, 50 (38%) belonged to lineage A and the rest belonged to a variety of B lineages with the majority lineages being B.1 (N = 30; 23%) and B.1.5 (N = 17; 13%) which were found predominantly in cross border truck drivers seeking to enter the country.[4] As of April 26, 2021, a total of 328 SARSCoV-2 samples had been sequenced and deposited in the GISAID5 by the Uganda Virus Research Institute (UVRI).[6] This represented 0.8% of the total COVID-19 cases that had been detected in the country at that time This situation is very similar to almost all other African countries, yet this ongoing global pandemic has already demonstrated the importance of widespread access to rapid novel pathogen discovery and subsequent surveillance, as well as comprehensive pathogen information sharing. Whole-genome sequencing (WGS) is imperative in investigating disease outbreak transmission dynamics and guiding decision-making in public health
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