Published December 8, 2023
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Genomic surveillance of SARS-CoV-2 reveals highest severity and mortality of delta over other variants: evidence from Cameroon.

Creators

  • 1. National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon. josephfokam@gmail.com.
  • 2. COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health, Yaoundé, Cameroon. josephfokam@gmail.com.
  • 3. Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon. josephfokam@gmail.com.
  • 4. Faculty of Health Sciences (FHS), University of Buea, Buea, Cameroon. josephfokam@gmail.com.
  • 5. COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health, Yaoundé, Cameroon.
  • 6. National Public Health Laboratory (NPHL), Ministry of Public Health, Yaoundé, Cameroon.
  • 7. Faculty of Medicine and Biomedical Sciences (FMBS), University of Yaounde I, Yaounde, Cameroon.
  • 8. Centre Pasteur du Cameroun (CPC), Yaoundé, Cameroon.
  • 9. Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon.
  • 10. School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
  • 11. University of California, Berkeley
  • 12. World Health Organization (WHO), Cameroon Country Office, Yaounde, Cameroon.
  • 13. Centre de Recherche Pour la Santé des Armées (CRESAR), Ministry of Defence, Yaoundé, Cameroon.
  • 14. Faculty of Health Sciences (FHS), University of Buea, Buea, Cameroon.
  • 15. Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.
  • 16. USAID's Infectious Diseases Detection and Surveillance, Yaounde, Cameroon.
  • 17. African Society for Laboratory Medicine (ASLM), Yaounde, Cameroon.
  • 18. Africa Centres for Disease Control and Prevention (Africa CDC), Addis-Ababa, Ethiopia.
  • 19. Division for Operational Health Research (DROS), Ministry of Public Health, Yaoundé, Cameroon.
  • 20. National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon.
  • 21. Department of Disease, Epidemic and Pandemic Control (DLMEP), Ministry of Public Health, Yaounde, Cameroon.
  • 22. Faculty of Medicine and Pharmaceutical Sciences (FMPS), University of Douala, Douala, Cameroon.
  • 23. Faculty of Health Sciences (FHS), University of Bamenda, Bamenda, Cameroon.
  • 24. Institut de Recherche Pour le Developpement (IRD), Montpellier, France.
  • 25. Institut de recherche pour le développement
  • 26. Chair of UNESCO Biotechnology, University of Rome Tor Vergata, Rome, Italy.
  • 27. University of Rome Tor Vergata
  • 28. Bambino Gesu Pediatric Hospital, Rome, Italy.
  • 29. US Centres for Disease Control and Prevention (CDC), Cameroon Country Office, Yaounde, Cameroon.
  • 30. US Centres for Disease Control and Prevention (CDC), Cameroon Country Office, Yaounde, Cameroon. ioz6@cdc.gov.
  • 31. University of KwaZulu-Natal and Stellenbosch University, Stellenbosch, South Africa.
  • 32. Institut Pasteur de Dakar, Dakar, Senegal.
  • 33. Epicentre, Medecins Sans Frontières (MSF), Yaounde, Cameroon.
  • 34. General Secretariat, Ministry of Public Health, Yaounde, Cameroon.

Description

While the SARS-CoV-2 dynamic has been described globally, there is a lack of data from Sub-Saharan Africa. We herein report the dynamics of SARS-CoV-2 lineages from March 2020 to March 2022 in Cameroon. Of the 760 whole-genome sequences successfully generated by the national genomic surveillance network, 74% were viral sub-lineages of origin and non-variants of concern, 15% Delta, 6% Omicron, 3% Alpha and 2% Beta variants. The pandemic was driven by SARS-CoV-2 lineages of origin in wave 1 (16 weeks, 2.3% CFR), the Alpha and Beta variants in wave 2 (21 weeks, 1.6% CFR), Delta variants in wave 3 (11 weeks, 2.0% CFR), and omicron variants in wave 4 (8 weeks, 0.73% CFR), with a declining trend over time (p = 0.01208). Even though SARS-CoV-2 heterogeneity did not seemingly contribute to the breadth of transmission, the viral lineages of origin and especially the Delta variants appeared as drivers of COVID-19 severity in Cameroon.
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