Whole-genome sequencing of SARS-CoV-2 isolates from symptomatic and asymptomatic individuals in Tanzania

Whole-genome sequencing of SARS-CoV-2 isolates from symptomatic and asymptomatic individuals in Tanzania

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BackgroundCoronavirus Disease-2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) accounts for considerable morbidity and mortality globally.Paucity of SARS-CoV-2 genetic data from Tanzania challenges in-country tracking of the pandemic.We sequenced Chaste Tree Berry SARS-CoV-2 isolated in the country to determine circulating strains, mutations and phylogenies and finally enrich international genetic databases especially with sequences from Africa.MethodsThis cross-sectional study utilized nasopharyngeal swabs of symptomatic and asymptomatic adults with positive polymerase chain reaction tests for COVID-19 from January to May 2021.Viral genomic libraries were prepared using ARTIC nCoV-2019 sequencing protocol version three.

Whole-genome sequencing (WGS) was performed using Oxford Nanopore Technologies MinION device.In silico genomic data analysis was done on ARTIC pipeline version 1.2.1 using ARTIC nCoV-2019 bioinformatics protocol version 1.1.

0.ResultsTwenty-nine (42%) out of 69 samples qualified for sequencing based on gel electrophoretic band intensity of multiplex PCR amplicons.Out of 29 isolates, 26 were variants of concern [Beta (n = 22); and Delta (n = 4)].Other variants included Eta (n = 2) and B.1.

530 (n = 1).We found combination of mutations (S: D80A, S: D215G, S: K417N, ORF3a: Q57H, E: P71L) in all Beta variants and absent in other lineages.The B.1.530 lineage carried mutations with very low 5 Piece Sectional cumulative global prevalence, these were nsp13:M233I, nsp14:S434G, ORF3a:A99S, S: T22I and S: N164H.

The B.1.530 lineage clustered phylogenetically with isolates first reported in south-east Kenya, suggesting regional evolution of SARS-CoV-2.ConclusionWe provide evidence of existence of Beta, Delta, Eta variants and a locally evolving lineage (B.1.

530) from samples collected in early 2021 in Tanzania.This work provides a model for ongoing WGS surveillance that will be required to inform on emerging and circulating SARS-CoV-2 diversity in Tanzania and East Africa.