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. 2023 Jan 4:9:1034682.
doi: 10.3389/fmed.2022.1034682. eCollection 2022.

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

Shabani Ramadhani Mziray  1   2 , Marco van Zwetselaar  3 , Charles C Kayuki  4 , Peter M Mbelele  2 , Abel N Makubi  5 , Alex S Magesa  5 , Riziki M Kisonga  2 , Tolbert B Sonda  3 , Gibson S Kibiki  6 , George Githinji  7   8 , Scott K Heysell  9 , Jaffu O Chilongola  1   3 , Stellah G Mpagama  2
Affiliations

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

Shabani Ramadhani Mziray et al. Front Med (Lausanne). .

Abstract

Background: Coronavirus 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 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.

Methods: This 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.

Results: Twenty-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 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.

Conclusion: We 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.

Keywords: COVID-19; MinION; Oxford Nanopore Technologies (ONT); SARS-CoV-2; variant of interest; variants of concern; whole-genome sequencing.

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Conflict of interest statement

CCK was employed by Oxford Nanopore Technologies. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Sample collection sites. A Google Earth map showing the locations in Tanzania where 69 nasopharyngeal swabs were collected from individuals confirmed with coronavirus disease-2019 (COVID-19) for this study. Labels with star show the locations where the 29 samples that were sequenced originated; these match the place names in Table 2.
FIGURE 2
FIGURE 2
A maximum likelihood phylogenetic tree of B.1.530 lineage placed against 150 global genomes belonging to B.1.530 lineage. Isolate Tanzania/KIDH-01B06/2021 is colored red.
See this image and copyright information in PMC

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