Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance.

Autor: Francisco NM; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola., van Wyk S; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa., Moir M; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa., San JE; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa.; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine University of KwaZulu-Natal Durban South Africa., Sebastião CS; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola.; Centro de Investigação em Saúde de Angola (CISA) Caxito Angola., Tegally H; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa.; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine University of KwaZulu-Natal Durban South Africa., Xavier J; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa., Maharaj A; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa., Neto Z; Ministério da Saúde Luanda Angola., Afonso P; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola., Jandondo D; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola., Paixão J; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola., Miranda J; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola., David K; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola., Inglês L; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola., Pereira A; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola., Paulo A; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola., Carralero RR; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola., Freitas HR; Direcção Nacional de Saúde Pública Ministério da Saúde Luanda Angola., Mufinda F; Ministério da Saúde Luanda Angola., Lutucuta S; Ministério da Saúde Luanda Angola., Ghafari M; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine University of KwaZulu-Natal Durban South Africa., Giovanetti M; Reference Laboratory of Flavivirus Oswaldo Cruz Foundation Rio de Janeiro Brazil., Giandhari J; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine University of KwaZulu-Natal Durban South Africa., Pillay S; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine University of KwaZulu-Natal Durban South Africa., Naidoo Y; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa., Singh L; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine University of KwaZulu-Natal Durban South Africa., Tshiabuila D; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa., Martin DP; Division of Computational Biology, Department of Integrative Biomedical Sciences University of Cape Town Cape Town South Africa.; Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town Cape Town South Africa., Chabuka L; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa., Choga W; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa., Wanjohi D; Africa CDC Institute of Pathogen Genomics Africa Centre for Disease Control and Prevention Addis Ababa Ethiopia., Mwangi S; Africa CDC Institute of Pathogen Genomics Africa Centre for Disease Control and Prevention Addis Ababa Ethiopia., Pillay Y; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa., Kebede Y; Africa CDC Institute of Pathogen Genomics Africa Centre for Disease Control and Prevention Addis Ababa Ethiopia., Shumba E; African Society for Laboratory Medicine Addis Ababa Ethiopia., Ondoa P; African Society for Laboratory Medicine Addis Ababa Ethiopia., Baxter C; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa.; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine University of KwaZulu-Natal Durban South Africa., Wilkinson E; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa.; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine University of KwaZulu-Natal Durban South Africa., Tessema SK; Africa CDC Institute of Pathogen Genomics Africa Centre for Disease Control and Prevention Addis Ababa Ethiopia., Katzourakis A; Department of Biology Oxford University Oxford UK.; Big Data Institute, Nuffield Department of Medicine University of Oxford Oxford UK., Lessells R; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine University of KwaZulu-Natal Durban South Africa., de Oliveira T; Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa.; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine University of KwaZulu-Natal Durban South Africa., Morais J; Grupo de Investigação Microbiana e Imunológica Instituto Nacional de Investigação em Saúde Luanda Angola.
Jazyk: angličtina
Zdroj: Influenza and other respiratory viruses [Influenza Other Respir Viruses] 2023 Sep 22; Vol. 17 (9), pp. e13198. Date of Electronic Publication: 2023 Sep 22 (Print Publication: 2023).
DOI: 10.1111/irv.13198
Abstrakt: 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.
Competing Interests: The authors declare no conflicts of interest.
(© 2023 The Authors. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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