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Insights into SARS-CoV-2 in Angola during the COVID-19 Peak: Molecular Epidemiology and Genome Surveillance
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  • NGIAMBUDULU M. FRANCISCO,
  • Stephanie Van Wyk,
  • Monika Moir,
  • James San,
  • Cruz Sebastiao,
  • Houriiyah Tegally,
  • Joicymara Xavier,
  • Akhil Maharaj,
  • Zoraima Neto,
  • Pedro Afonso,
  • Domingos Jandondo,
  • Joana Paixão,
  • Julio Miranda,
  • Kumbelembe David,
  • Luzia Inglês,
  • Amilton Pereira,
  • Agostinho Paulo,
  • Raisa Carralero,
  • Helga Freitas,
  • Franco Mufinda,
  • Silvia Lutucuta ,
  • Mahan Ghafari,
  • Marta Giovanetti,
  • Jennifer Giandhari,
  • Sureshnee Pillay,
  • Yeshnee Naidoo,
  • Lavanya Singh,
  • Derek Tshiabuila,
  • Darren Martin,
  • Lucious Chabuka,
  • Wonderful Choga,
  • Dorcas Wanjohi,
  • Sarah Mwangi,
  • Yusasha Pillay,
  • Yenew Kebede,
  • Edwin Shumba,
  • Pascale Ondoa,
  • Cheryl Baxter,
  • Eduan Wilkinson,
  • Sofonias Tessema,
  • Aris Katzourakis,
  • Richard Lessells,
  • Tulio de Oliveira,
  • Joana Morais
NGIAMBUDULU M. FRANCISCO
Instituto Nacional de Investigação em Saúde

Corresponding Author:franciscongiamb@gmail.com

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Stephanie Van Wyk
CERI, Stellenbosch University
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Monika Moir
CERI, Stellenbosch University
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James San
CERI, Stellenbosch University
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Cruz Sebastiao
INIS, Angola
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Houriiyah Tegally
University of KwaZulu-Natal Nelson R Mandela School of Medicine
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Joicymara Xavier
CERI, Stellenbosch University
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Akhil Maharaj
CERI, Stellenbosch University
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Zoraima Neto
MINSA, Angola
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Pedro Afonso
INIS, Angola
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Domingos Jandondo
INIS, Angola
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Joana Paixão
INIS, Luanda
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Julio Miranda
INIS, Angola
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Kumbelembe David
INIS, Angola
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Luzia Inglês
INIS, Angola
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Amilton Pereira
INIS, Angola
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Agostinho Paulo
INIS, ANGOLA
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Raisa Carralero
INIS, Angola
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Helga Freitas
DNSP, Angola
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Franco Mufinda
MINSA, Angola
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Silvia Lutucuta
MINSA
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Mahan Ghafari
KRISP, UKZN
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Marta Giovanetti
Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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Jennifer Giandhari
University of KwaZulu-Natal Nelson R Mandela School of Medicine
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Sureshnee Pillay
University of KwaZulu-Natal Nelson R Mandela School of Medicine
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Yeshnee Naidoo
CERI, Stellenbosch University
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Lavanya Singh
Stellenbosch University Faculty of Medicine and Health Sciences
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Derek Tshiabuila
Stellenbosch University Faculty of Medicine and Health Sciences
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Darren Martin
University of Cape Town Faculty of Health Sciences
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Lucious Chabuka
Stellenbosch University Faculty of Medicine and Health Sciences
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Wonderful Choga
Stellenbosch University Faculty of Medicine and Health Sciences
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Dorcas Wanjohi
Africa CDC
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Sarah Mwangi
Africa CDC
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Yusasha Pillay
Stellenbosch University Faculty of Medicine and Health Sciences
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Yenew Kebede
Africa CDC
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Edwin Shumba
ASLM
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Pascale Ondoa
ASLM
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Cheryl Baxter
Stellenbosch University Faculty of Medicine and Health Sciences
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Eduan Wilkinson
Stellenbosch University
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Sofonias Tessema
Africa CDC
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Aris Katzourakis
Oxford University
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Richard Lessells
KRISP, UKZN
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Tulio de Oliveira
KRISP, UKZN
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Joana Morais
INIS, Luanda
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Abstract

Background: In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1,900 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 1,210 whole-genome SARS-CoV-2 sequences, contributing West African data to the global context, that were phylogenetically compared against global strains. Viral movement events were inferred using ancestral state reconstruction. Results: The epidemic in Angola was marked by four distinct waves of infection, dominated by 12 viral lineages, including VOCs, VOIs, and the VUM C.16, which was unique to Southwestern Africa and circulated for an extended period within the region. Viral 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.
19 Jun 2023Submitted to Influenza and other respiratory viruses
21 Jun 2023Submission Checks Completed
21 Jun 2023Assigned to Editor
30 Jun 2023Reviewer(s) Assigned
22 Jul 2023Review(s) Completed, Editorial Evaluation Pending
26 Jul 2023Editorial Decision: Revise Minor
23 Aug 20231st Revision Received
26 Aug 2023Submission Checks Completed
26 Aug 2023Assigned to Editor
27 Aug 2023Editorial Decision: Accept