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

Abstract

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus with a single-stranded, positive-sense RNA genome of approx. 29.9 kilobase pairs. The genome undergoes genetic mutations resulting in single nucleotide and structural variants which has affected SARS-CoV-2 detection, transmission and vaccine development. Since the first case of SARS-CoV-2 was reported, sequencing technologies and bioinformatic analyses have revealed unique variants of SARS-CoV-2 globally. Here, we aimed to determine the genomic variation of SARS-CoV-2 that circulated in Uganda between April 2020 and July 2021. We also report on the genetic relatedness between SARS-CoV-2 detected in Uganda, Kenya, Rwanda, Burundi, the Democratic Republic of Congo and South Sudan within the same period. Me¬thods: Whole genome sequencing was performed using the MinION Oxford Nanopore sequencer on RNA extracted from a total of 49 respiratory samples from COVID-19 confirmed cases in Kampala, Uganda in the period between April 2020 and July 2021. Additionally, SARS-CoV-2 sequences from East African countries were downloaded from the GISIAD EpiCoV™, and included in the analysis. Bioinformatics analysis was performed using Medaka, Sniffles and SnpEff tools. A maximum likelihood phylogenetic tree was constructed in MEGA, reported in R and manipulated using the ggtree package. Results: A total of 268 unique single nucleotide variants and 1,456 mutations were found with > 70% mutations in the ORF1ab and S genes. Twenty-eight structural variants were detected; 21 insertions and 7 deletions in 16 samples. The most common mutations were 2042C>G (83.4%), 14143C>T (79.5%), 245T>C (65%), and 1129G>T (51%), detected in the S, ORF1ab, ORF7a and N genes, respectively. The sequenced SARS-CoV-2 samples clustered together, and were more closely related to the previously reported Ugandan and Democratic Republic of Congo (DRC) variants than those from other neighboring countries. We also, found the most prevalent lineages to be AY.46 and A.23, both which are considered Delta variants. Conclusion: MinION Oxford Nanopore sequencing identified both single nucleotides and structural variants in the SARS-CoV-2 genomes. Bioinformatics analysis of the SARS-CoV-2 variants detected in Uganda between April 2020 and July 2021 points to the possibility that infections arose from local spread and were not newly imported. Moreover, the genetic relatedness of the variants from Uganda and DR Congo could be as a result of globalization, settlement, and population characteristics related to high unique human mobility and interaction between the two countries, which is peculiar to this region of the world. Lineages AY.46 and A.23 being more prevalent could indicate that these mutations originated locally in East Africa and were being transmitted locally.