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. 2021 Apr:105:735-738.
doi: 10.1016/j.ijid.2021.03.036. Epub 2021 Mar 15.

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

Francine Ntoumi  1 , Claujens Chastel Mfoutou Mapanguy  2 , Alexandru Tomazatos  3 , Srinivas Reddy Pallerla  3 , Le Thi Kieu Linh  4 , Nicolas Casadei  5 , Angel Angelov  6 , Michael Sonnabend  6 , Silke Peter  6 , Peter G Kremsner  7 , Thirumalaisamy P Velavan  8
Affiliations

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

Francine Ntoumi et al. Int J Infect Dis. 2021 Apr.

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.

Keywords: D614G; Lineage B1; Republic of Congo; SARS-CoV-2; SARS-CoV-2 variants; Whole genome sequencing.

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Conflict of interest statement

Declaration of Competing Interest The authors report no declarations of interest.

Figures

Figure 1
Figure 1
Maximum likelihood phylogenetic tree of currently available SARS-CoV-2 genomes from the Republic of Congo (bold text). The genomes were classified into lineages using PANGOLIN and into clades using Nextclade. The tree was rooted between lineages A and B. Branch lengths are drawn according to the number of nucleotide substitutions per site. DRC stands for Democratic Republic of Congo.
See this image and copyright information in PMC

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