Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance.
Angola
COVID‐19
SARS‐CoV‐2
genomic surveillance
variants of concern
Journal
Influenza and other respiratory viruses
ISSN: 1750-2659
Titre abrégé: Influenza Other Respir Viruses
Pays: England
ID NLM: 101304007
Informations de publication
Date de publication:
09 2023
09 2023
Historique:
received:
20
06
2023
revised:
25
08
2023
accepted:
27
08
2023
medline:
26
9
2023
pubmed:
25
9
2023
entrez:
25
9
2023
Statut:
epublish
Résumé
In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression during the peak of the COVID-19 pandemic in Angola. We generated 1210 whole-genome SARS-CoV-2 sequences, contributing West African data to the global context, that were phylogenetically compared against global strains. Virus movement events were inferred using ancestral state reconstruction. The epidemic in Angola was marked by four distinct waves of infection, dominated by 12 virus lineages, including VOCs, VOIs, and the VUM C.16, which was unique to South-Western Africa and circulated for an extended period within the region. Virus exchanges occurred between Angola and its neighboring countries, and strong links with Brazil and Portugal reflected the historical and cultural ties shared between these countries. The first case likely originated from southern Africa. A lack of a robust genome surveillance network and strong dependence on out-of-country sequencing limit real-time data generation to achieve timely disease outbreak responses, which remains of the utmost importance to mitigate future disease outbreaks in Angola.
Sections du résumé
Background
In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression during the peak of the COVID-19 pandemic in Angola.
Methods
We generated 1210 whole-genome SARS-CoV-2 sequences, contributing West African data to the global context, that were phylogenetically compared against global strains. Virus movement events were inferred using ancestral state reconstruction.
Results
The epidemic in Angola was marked by four distinct waves of infection, dominated by 12 virus lineages, including VOCs, VOIs, and the VUM C.16, which was unique to South-Western Africa and circulated for an extended period within the region. Virus exchanges occurred between Angola and its neighboring countries, and strong links with Brazil and Portugal reflected the historical and cultural ties shared between these countries. The first case likely originated from southern Africa.
Conclusion
A lack of a robust genome surveillance network and strong dependence on out-of-country sequencing limit real-time data generation to achieve timely disease outbreak responses, which remains of the utmost importance to mitigate future disease outbreaks in Angola.
Identifiants
pubmed: 37744993
doi: 10.1111/irv.13198
pii: IRV13198
pmc: PMC10515134
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e13198Subventions
Organisme : NIAID NIH HHS
ID : U01 AI151698
Pays : United States
Organisme : FIC NIH HHS
ID : U54 TW012041
Pays : United States
Informations de copyright
© 2023 The Authors. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.
Déclaration de conflit d'intérêts
The authors declare no conflicts of interest.
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