key: cord-309193-v8lphej4
authors: Lemriss, Sanaâ; Souiri, Amal; Amar, Narjis; Lemzaoui, Nabil; Mestoui, Omar; Labioui, Mohamed; Ouaariba, Nabil; Jibjibe, Ayoub; Yartaoui, Mahmoud; Chahmi, Mohamed; El Rhouila, Marouane; Sellak, Samiha; Kandoussi, Nadia; El Kabbaj, Saâd
title: Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco
date: 2020-07-02
journal: Microbiol Resour Announc
DOI: 10.1128/mra.00633-20
sha: 
doc_id: 309193
cord_uid: v8lphej4

Here, we report a complete genome sequence obtained for a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from a nasopharyngeal swab specimen of a Moroccan patient with coronavirus disease 2019 (COVID-19).

Phylogenetic tree of the complete nucleotide sequence of hCoV-19_Morocco_OUA677_19_2020 and 54 other global strains obtained from the GISAID database, associated with a table representing single-nucleotide polymorphisms (SNPs). The phylogenetic tree was constructed with the neighbor-joining method using MEGAX, and the reliability of each tree branch was estimated by performing 1,000 bootstrap replicates. Compared with the reference strain (GenBank accession number MN908947.3), the hCoV-19_Morocco_OUA677_19_2020 genome has a total of 10 nucleotide variations. We detected mutations in noncoding positions of G to A (position 198), another one of C to T (position 241), two mutations of A to T (position 29881 to 29882), and other mutations in coding regions that generated amino acid changes, such as F924F, P4715L, S5039I, and L6082F in the polyprotein encoded by the ORF1ab gene, D614G in the spike glycoprotein (S), and A155A in the nucleocapsid protein (N) (Fig. 1) .

The single-nucleotide polymorphisms (SNPs) of the Moroccan sequence were further defined from 54 sequences of SARS-CoV-2 representing 50 countries all over the world (Fig. 1) . Important substitutions were observed among the different ORFs (ORF1ab, 82; S segment, 33; N segment, 18; ORF3a, 10; noncoding region 5= UTR, 35).

Phylogenetic analysis of this virus genome compared with 54 selected sequences showed that it was grouped in SARS-CoV-2 clade G, which includes strains from Asia, Europe, North America, Australia, and Africa (Fig. 1) .

We are currently sequencing and analyzing more complete genomes from different regions of Morocco to understand the virus dispersion and to associate this information with epidemiological data.

Data availability. The consensus data for the hCoV-19_Morocco_OUA677_19_2020 genome have been deposited in the GISAID database (accession number EPI_ ISL_451400) and GenBank (accession number MT513758). The accession numbers for the Illumina MiSeq sequence raw reads in the NCBI Sequence Read Archive (SRA) are PRJNA637892 (BioProject), SRR11945456 (SRA), and SAMN15160097 (BioSample).

This study was supported by the Fraternal Gendarmerie Royale, Morocco.

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