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.
【저자키워드】 COVID-19, whole-genome sequencing, SARS-CoV-2, Uganda, RT-PCR, Makerere University, PRESIDE, 【초록키워드】 coronavirus disease, whole-genome sequencing, public health, Uganda, Coronavirus disease 2019, coronavirus, protocol, Sequencing, Laboratory, Severe acute respiratory syndrome, polymerase chain reaction, RT-qPCR, Viral, outbreak, SARS-CoV-2 genome, Wuhan, Transmission dynamics, Lineage, High-throughput sequencing, reverse transcription, respiratory, WGS, adoption, disease outbreak, resource, disease, GISAID, Quantitative, optimization, Makerere University, ARTIC protocol, Phylogenetic, Chain Reaction, acute respiratory syndrome, SARS-CoV-2 genomes, individual, foundation, rapid expansion, quantitative polymerase chain reaction, genomic sequence, initiative, whole-genome, isolate, Wuhan, China, polymerase chain, selected, collected, sequenced, diagnosed, demonstrated, imperative, submitted, retrieved, 【제목키워드】 Sequencing, implementation,