key: cord-0731317-lgp6aquz
authors: Njouom, Richard; Sadeuh-Mba, Serge Alain; Tchatchueng, Jules; Diagne, Moussa Moïse; Dia, Ndongo; Tagnouokam, Paul Alain Ngoupo; Boum, Yap; Hamadou, Achta; Esso, Linda; Faye, Ousmane; Tejiokem, Mathurin Cyrille; Okomo, Marie Claire; Etoundi, Alain; Carniel, Elisabeth; Eyangoh, Sara
title: Coding-Complete Genome Sequence and Phylogenetic Relatedness of a SARS-CoV-2 Strain Detected in March 2020 in Cameroon
date: 2021-03-11
journal: Microbiol Resour Announc
DOI: 10.1128/mra.00093-21
sha: 8b1af2df71444ffecbe1f9cb834c263be355ccde
doc_id: 731317
cord_uid: lgp6aquz

We describe the coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain obtained in Cameroon from a 58-year-old French patient who arrived from France on 24 February 2020. Phylogenetic analysis showed that this virus, named hCoV-19/Cameroon/1958-CMR-YAO/2020, belongs to lineage B.1.5 and is closely related to an isolate from France.

trimmed for quality and length and assembled by mapping to the reference genome from Wuhan (GenBank accession number NC_045512.2) using the already published USAMRIID-WRAIR pipeline (8) . All tools were run with default parameters unless otherwise specified. Multiple sequence alignment and pairwise sequence comparisons with the hCoV-19/Cameroon/1958-CMR-YAO/2020 sequence obtained were carried out with CLC Main Workbench v5.7.2 software. Estimation of the best-fitting substitution model (GTR1I1C4) was conducted with Smart Model Selection (9) based on the Bayesian information criterion. Inference of the phylogenetic tree was conducted with the maximum likelihood approach using PhyML v3.0 (10) with subtree pruning and regrafting (SPR) branch swapping. The reliability of the tree topology was estimated with 1,000 bootstrap replicates.

The consensus sequence length was 29,686 bp, corresponding to 99.25% of the genome, with a GC content of 33.02%. The amino acid substitutions found in the hCoV-19/Cameroon/1958-CMR-YAO/2020 virus, compared with the reference, were M protein L206V, M protein N207D, nonstructural protein 6 (NSP6) L227F, and NSP12 P323L. The maximum likelihood phylogenetic tree (Fig. 1) shows that hCoV-19/Cameroon/ 1958-CMR-YAO/2020 clusters with B.1.1.5 SARS-CoV-2 lineage sequences isolated in France in March 2020.

The report of a SARS-CoV-2 coding-complete genome from Cameroon will allow investigators to follow the spread of this strain in the country and to evaluate its potential accumulation of mutations over time, improving our understanding of the molecular epidemiology of SARS-CoV-2 in Cameroon.

Data availability. The viral sequence from the patient was deposited in the GISAID EpiCoV SARS-CoV-2 database with the following identifiers: virus name, hCoV-19/ Cameroon/1958-CMR-YAO/2020; GISAID accession number, EPI_ISL_512873; NCBI GenBank accession number, MW566800. The raw reads were submitted to the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA701254 and SRA accession number SRR13677539.

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We are thankful to the members of the SARS-CoV-2 surveillance system network in Cameroon for their fruitful contributions in field activities. This study was funded by the French Ministry for Europe and Foreign Affairs via the project "REPAIR Covid-19-Africa," coordinated by the Pasteur International Network association.