Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa.
Genotype
SARS-CoV-2
SNPs
Tunisia
Whole genome sequencing
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
14 Jul 2021
14 Jul 2021
Historique:
received:
24
06
2020
accepted:
05
07
2021
entrez:
15
7
2021
pubmed:
16
7
2021
medline:
17
7
2021
Statut:
epublish
Résumé
In Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020. Since then, an increase of cases number was observed from either imported or local cases. The aim of this preliminary study was to better understand the molecular epidemiology and genetic variability of SARS-CoV-2 viruses circulating in Tunisia and worldwide. Whole genome sequencing was performed using NGS approach on six SARS. CoV-2 highly positive samples detected during the early phase of the outbreak. Full genomes sequences of six Tunisian SARS-CoV-2 strains were obtained from imported and locally transmission cases during the COVID-19 outbreak. Reported sequences were non-identical with 0.1% nucleotide divergence rate and clustered into 6 different clades with worldwide sequences. SNPs results favor the distribution of the reported Tunisian sequences into 3 major genotypes. These SNP mutations are critical for diagnosis and vaccine development. These results indicate multiple introductions of the virus in Tunisia and add new genomic data on SARS-CoV-2 at the international level.
Sections du résumé
BACKGROUND
BACKGROUND
In Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020. Since then, an increase of cases number was observed from either imported or local cases. The aim of this preliminary study was to better understand the molecular epidemiology and genetic variability of SARS-CoV-2 viruses circulating in Tunisia and worldwide.
METHODS
METHODS
Whole genome sequencing was performed using NGS approach on six SARS. CoV-2 highly positive samples detected during the early phase of the outbreak.
RESULTS
RESULTS
Full genomes sequences of six Tunisian SARS-CoV-2 strains were obtained from imported and locally transmission cases during the COVID-19 outbreak. Reported sequences were non-identical with 0.1% nucleotide divergence rate and clustered into 6 different clades with worldwide sequences. SNPs results favor the distribution of the reported Tunisian sequences into 3 major genotypes. These SNP mutations are critical for diagnosis and vaccine development.
CONCLUSIONS
CONCLUSIONS
These results indicate multiple introductions of the virus in Tunisia and add new genomic data on SARS-CoV-2 at the international level.
Identifiants
pubmed: 34261445
doi: 10.1186/s12864-021-07870-1
pii: 10.1186/s12864-021-07870-1
pmc: PMC8278182
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
540Subventions
Organisme : European Commission
ID : DEVCO: IFS/2018/402-247)
Informations de copyright
© 2021. The Author(s).
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