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SARS-CoV-2 B.1.214.1, B.1.214.2 and B.1.620 are predominant lineages between December 2020 and July 2021 in the Republic of Congo

Published onJun 15, 2023
SARS-CoV-2 B.1.214.1, B.1.214.2 and B.1.620 are predominant lineages between December 2020 and July 2021 in the Republic of Congo

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus 2019 (COVID-19) disease, was first detected in China. Variants of SARS-CoV-2 have emerged and have been shown to increase transmissibility, pathogenicity, and decrease vaccine effectiveness. The objective of this study was to perform whole genome sequencing of SARS-CoV-2 from samples collected from Congolese individuals to determine the distribution, prevalence, and dynamics of SARS-CoV-2 variants circulating in the Republic of Congo. 

Between April 2020 and December 2021, a total of n=910 samples were tested positive with a Ct<30. All those samples were tested by conventional PCR from which n=589 were positive and were sequenced by Oxford Nanopore next generation sequencing (NGS) Technology, and all complete sequenced genomes (n=314) were submitted on GISAID for publication; variants were assigned using pangolin and Nextclade nomenclature and a phylogenetic tree was established. 

Three hundred and six (314) SARS-CoV-2 genomes were successfully sequenced and submitted on GISAID. A total of 21 variants circulated in the Republic of Congo during the study period corresponding to four waves of the virus epidemics. The B.1 variant (26%) was predominant in the first wave, while B.1.620 (12%) and B1.241.2 (18%) were predominant in the second wave; B.1.617.2 (Delta) (34%) and B.1.640.1 (4%) in the third wave, and the Omicron variant (B.1.1.529) (90%) predominant in the fourth wave. The variants of concern alpha (B.1.1.7), delta (B.1.617.2) and Omicron (B.1.1.519) were identified circulating in the country. In addition, the B.1.640.1 reported for the first time in the Republic of Congo through this study, was observed to be spreading locally and regionally. The phylogenetic analysis suggest that the Omicron (B.1.1.529) variant might share the same ancestor with C.16 variant which have circulated from December 2020 to January 2021, mostly in South and East African area. The distribution of SARS-CoV-2 variants was heterogeneous in Brazzaville, with the densely populated arrondissements of Poto-Poto and Moungali likely to have been the epicentre of the virus spread. 

This study provides valuable information on SARS-CoV-2 transmission in the Republic of Congo, contributing to SARS-CoV-2 surveillance on a temporal and spatial scale.

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