Genomic surveillance of SARS-CoV-2 in the Republic of Congo

Abstract

\n Objective\n We performed whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from Congolese individuals sampled between April and July 2020.\n \n Methods\n We screened 96 samples 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.\n \n Results\n Eleven SARS-CoV-2 genomes were successfully sequenced and submitted to the GSAID database. All genomes carried the spike mutation D614\u2009G and were classified as part of the GH clade. The Congolese SARS-CoV-2 sequences belong to lineage B1 and nextclade 20A and 20C, which split into distinct clusters, indicating two separate introductions of the virus into the Republic of Congo.\n \n Conclusion\n 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.\n