The genomic diversity of Sars-CoV-2 omicron lineages collected during routine sentinel surveillance in Tanzania between November 2022 and July 2023

Abstract

Background: The genetic diversity and epidemiological characteristics of SARS-CoV-2 lineages in Tanzania have not yet been fully explored, despite their critical impact on public health. Methods: We conducted a comprehensive genomic analysis of 80 sequences derived from 90 samples collected between November 2022 and July 2023 from multiple regions in Tanzania. Results: Our findings reveal a complex landscape of 7 Omicron clades, with clades 22 F (XBB*) and 22E (BQ.1) emerging as the predominant variants, comprising 56.3% and 21.35% of all samples, respectively. Notably, there were regional variations in the distribution of lineages. We observed that four lineages were introduced in November 2022, which later led to local transmissions through virus imports and exports, with the majority of exports originating from Dar es Salaam to other regions. Phylogenetic analysis revealed distinct clades comprising only Tanzanian sequences, demonstrating localised transmission within the country. Conclusions: This study provides key insights into the genetic diversity and transmission dynamics of SARS-CoV-2 in Tanzania. It highlights regional discrepancies in lineage distribution, identifying sixteen Omicron lineages and the dominance of clades 22 F (XBB*) and 22E (BQ.1) in the country. The presence of Tanzania-specific clades suggests sustained local transmission of the virus. These findings underscore the importance of enhanced integrated genomic surveillance systems and ongoing monitoring of SARS-CoV-2 evolution.