Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing

dc.contributor.authorKia, Praiscillia
dc.contributor.authorKatagirya, Eric
dc.contributor.authorKakembo, Fredrick Elishama
dc.contributor.authorAdera, Doreen Ato
dc.contributor.authorNsubuga, Moses Luutu
dc.contributor.authorYiga, Fahim
dc.contributor.authorAloyo, Sharley Melissa
dc.contributor.authorAujat, Brendah Ronah
dc.contributor.authorAnguyo, Denis Foe
dc.contributor.authorKatabazi, Fred Ashaba
dc.contributor.authorKigozi, Edgar
dc.contributor.authorJoloba, Moses L.
dc.contributor.authorKateete, David Patrick
dc.date.accessioned2024-03-19T09:20:49Z
dc.date.available2024-03-19T09:20:49Z
dc.date.issued2023-11-22
dc.description.abstractSARS-CoV-2 undergoes frequent mutations, affecting COVID-19 diagnostics, transmission and vaccine efficacy. Here, we describe the genetic diversity of 49 SARS-CoV-2 samples from Uganda, collected during the COVID-19 waves of 2020/2021. Overall, the samples were similar to previously reported SARS-CoV-2 from Uganda and the Democratic Republic of Congo (DRC). The main lineages were AY.46 and A.23, which are considered to be Delta SARS-CoV-2 variants. Further, a total of 268 unique single nucleotide variants and 1456 mutations were found, with more than seventy percent mutations in the ORF1ab and S genes. The most common mutations were 2042C>G (83.4%), 14143C>T (79.5%), 245T>C (65%), and 1129G>T (51%), which occurred in the S, ORF1ab, ORF7a and N genes, respectively. As well, 28 structural variants—21 insertions and 7 deletions, occurred in 16 samples. Our findings point to the possibility that most SARS-CoV-2 infections in Uganda at the time arose from local spread and were not newly imported. Moreover, the relatedness of variants from Uganda and the DRC reflects high human mobility and interaction between the two countries, which is peculiar to this region of the world.en_US
dc.description.sponsorshipthe U.S. NIH-Fogarty International Center training Grant “Microbiology and Immunology Training for HIV and HIV-Related Research in Uganda (MITHU, D43TW010319)”; Intergrated Biorepository of H3Africa Uganda (IBRH3AU, U24HG007051)en_US
dc.identifier.citationKia, P., Katagirya, E., Kakembo, F. E., Adera, D. A., Nsubuga, M. L., Yiga, F., ... & Kateete, D. P. (2023). Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing. Scientific Reports, 13(1), 20507. https://doi.org/10.1038/s41598-023-47379-zen_US
dc.identifier.issn2045-2322
dc.identifier.urihttps://dir.muni.ac.ug/handle/20.500.12260/624
dc.language.isoenen_US
dc.publisherSpringer Natureen_US
dc.subjectGenomic characterizationen_US
dc.subjectSARS-CoV-2en_US
dc.subjectMinION nanopore sequencingen_US
dc.subjectUgandaen_US
dc.titleGenomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencingen_US
dc.typeArticleen_US

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