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

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...

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Published in:	Frontiers in medicine Vol. 9; p. 1034682
Main Authors:	Mziray, Shabani Ramadhani, van Zwetselaar, Marco, Kayuki, Charles C, Mbelele, Peter M, Makubi, Abel N, Magesa, Alex S, Kisonga, Riziki M, Sonda, Tolbert B, Kibiki, Gibson S, Githinji, George, Heysell, Scott K, Chilongola, Jaffu O, Mpagama, Stellah G
Format:	Journal Article
Language:	English
Published:	Switzerland Frontiers Media S.A 04-01-2023
Subjects:	COVID-19 Medicine MinION SARS-CoV-2 variant of interest variants of concern whole-genome sequencing COVID-19 SARS-CoV-2 Oxford Nanopore Technologies (ONT) variants of concern whole-genome sequencing MinION variant of interest
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Summary:	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. 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. genomic data analysis was done on ARTIC pipeline version 1.2.1 using ARTIC nCoV-2019 bioinformatics protocol version 1.1.0. 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 ( = 22); and Delta ( = 4)]. Other variants included Eta ( = 2) and B.1.530 ( = 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. 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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Reviewed by: Edwin Kamau, Tripler Army Medical Center, United States; Anissa Chouikha, Pasteur Institute of Tunis, Tunisia Edited by: Pragya Dhruv Yadav, ICMR-National Institute of Virology, India This article was submitted to Infectious Diseases: Pathogenesis and Therapy, a section of the journal Frontiers in Medicine
ISSN:	2296-858X 2296-858X
DOI:	10.3389/fmed.2022.1034682