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

• Published in: Scientific reports Vol. 13; no. 1; p. 20507
• Main Authors: Kia, Praiscillia, Katagirya, Eric, Kakembo, Fredrick Elishama, Adera, Doreen Ato, Nsubuga, Moses Luutu, Yiga, Fahim, Aloyo, Sharley Melissa, Aujat, Brendah Ronah, Anguyo, Denis Foe, Katabazi, Fred Ashaba, Kigozi, Edgar, Joloba, Moses L., Kateete, David Patrick
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22-11-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/326; 631/326/596; 631/326/596/4130; 692/699/255; 692/699/255/2514; COVID-19; COVID-19 - diagnosis; COVID-19 - epidemiology; Disease transmission; Genetic diversity; Genomics; Humanities and Social Sciences; Humans; multidisciplinary; Mutation; Nanopore Sequencing; SARS-CoV-2 - genetics; Science; Science (multidisciplinary); Severe acute respiratory syndrome coronavirus 2; Uganda - epidemiology; Vaccine efficacy; Uganda
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-47379-z

SARS-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.