Genomique surveillance of severe acute respiratry  syndrome coronavirus-2 (SARS-CoV-2) in Brazzaville, 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 [1]. Variants of SARS-CoV-2 have emerged, increasing the transmissibility, pathogenicity of the disease [2] and decreasing the anti-Covid-19 vaccine effectiveness [3]. SARS-CoV-2 is a relatively rapidly mutating RNA virus [4], and the accumulation of its mutations during infection can serve as a molecular signal for monitoring epidemiological events. The objective of this study was to determine the prevalence and dynamics of SARS-CoV-2 variants circulating in the Republic of Congo during the epidemic period Between April 2020 and August 2022, samples collected from individuals with  symptomatic and asymptomatic SARS-CoV-2 infection (positive RT-PCR test with a Ct<28)  were used for the  viral whole genome amplification by the conventional PCR.  The  positive PCR samples were qualified for sequencing using MinION (Oxford Nanopore next generation sequencing (NGS) Technology). The complete genomes of SARS-CoV-2 were analyzed using the ARTIC network pipelines. The sequenced genomes were submitted on GISAID for publication. The variants were assigned using pangolin and Nextclade nomenclature, and a complete distribution map of variants circulating in Brazzaville in 2021 was established. Out of the 589 samples qualified for sequencing, Three hundred and eighty one (381) SARS-CoV-2 genomes were successfully sequenced and submitted on GISAID. A total of 21 variants circulated, with the presence of variants of concern including alpha (B.1.1.7), delta (B.1.617.2) and Omicron (B.1.1.519) in the Republic of Congo. Four waves of the virus epidemics were observed in this study period. The B.1 variant (26%) was predominant in the first wave, 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 B.1.640.1 reported for the first time in the Republic of Congo in 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.