ABSTRACT
Background: : SARS-CoV-2 variants have been emerging and are shown to increase transmissibility, pathogenicity, and decreased vaccine efficacies. The objective of this study was to determine the distribution, prevalence, and dynamics of SARS-CoV-2 variants circulating in Brazzaville, the Republic of Congo (ROC). Methods: : Between December 2020 and July 2021, a total of n=600 oropharyngeal specimens collected in the community were tested for COVID-19. Of the samples tested, 317 (53%) were SARS-CoV-2 positive. All samples that had a threshold of Ct <30 (n=182) were sequenced by next-generation sequencing (NGS), and all complete sequenced genomes were submitted to GISAID; lineages were assigned using pangolin nomenclature and a phylogenetic tree was reconstructed. In addition, the global prevalence of the predominant lineages was analysed using data from GISAID and Outbreak databases. Results: : A total of 15 lineages circulated with B.1.214.2 (26%), B.1.214.1 (19%) and B.1.620 (18%) being predominant. The variants of concern (VOC) alpha (B.1.1.7) (6%) and for the first time in June delta (B.1.617.2) (4%) were observed. In addition, the B.1.214.1 lineage first reported from ROC was observed to be spreading locally and regionally. Phylogenetic analysis suggests that the B.1.620 variant (VUM) under observation may have originated from either Cameroon or the Central African Republic. SARS-CoV-2 lineages were heterogeneous, with the densely populated districts of Poto-Poto and Moungali likely the epicenter of spread. Conclusion: : Longitudinal monitoring and molecular surveillance across time and space are critical to understanding viral phylodynamics, which could have important implications for transmissibility and impact infection prevention and control measures.
ABSTRACT
OBJECTIVE: The aim of this study was to carry out whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using samples collected from Congolese individuals between April and July 2020. METHODS: Ninety-six samples were screened for SARS-CoV-2 using RT-PCR, and 19 samples with Ct values <30 were sequenced using Illumina Next-Generation Sequencing (NGS). The genomes were annotated and screened for mutations using the web tool 'coronapp'. Subsequently, different SARS-CoV-2 lineages were assigned using PANGOLIN and Nextclade. RESULTS: Eleven SARS-CoV-2 genomes were successfully sequenced and submitted to the GSAID database. All genomes carried the spike mutation D614G and were classified as part of the GH clade. The Congolese SARS-CoV-2 sequences were shown to belong to lineage B1 and Nextclade 20A and 20C, which split them into distinct clusters, indicating two separate introductions of the virus into the Republic of Congo. CONCLUSION: This first study provides valuable information on SARS CoV-2 transmission in the central African region, contributing to SARS CoV-2 surveillance on a temporal and spatial scale.