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

Abstract

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.

Figure 1

Position on SARS-CoV-2 genome where insertions were detected spanning from ORF1ab to start of the S gene.

Figure 2

All sequenced SARS-CoV-2 samples belonged to the ‘Delta’ lineage.

Figure 3

Maximum likelihood phylogenetic tree depicting genetic relatedness between the sequenced SARS-CoV-2 samples in this study (i.e., ‘Sequenced’) and the rest of East Africa. Nodes are colored per country. The 49 samples from Uganda clustered and shared a root with other Ugandan sequences from GISAID.