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

Ntoumi, Francine; Mapanguy, Claujens Chastel Mfoutou; Tomazatos, Alexandru; Pallerla, Srinivas Reddy; Linh, Le Thi Kieu; Casadei, Nicolas; Angelov, Angel; Sonnabend, Michael; Peter, Silke; Kremsner, Peter G; Velavan, Thirumalaisamy P.

OBJECTIVE: 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. METHODS: 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. RESULTS: Eleven SARS-CoV-2 genomes were successfully sequenced and submitted to the GSAID database. All genomes carried the spike mutation D614 G 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. 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.