Scientific Reports (Dec 2023)
Genomic surveillance of SARS-CoV-2 reveals highest severity and mortality of delta over other variants: evidence from Cameroon
- Joseph Fokam,
- Rene Ghislain Essomba,
- Richard Njouom,
- Marie-Claire A. Okomo,
- Sara Eyangoh,
- Celestin Godwe,
- Bryan Tegomoh,
- John O. Otshudiema,
- Julius Nwobegahay,
- Lucy Ndip,
- Blaise Akenji,
- Desire Takou,
- Mohamed M. M. Moctar,
- Cleophas Kahtita Mbah,
- Valantine Ngum Ndze,
- Martin Maidadi-Foudi,
- Charles Kouanfack,
- Sandrine Tonmeu,
- Dorine Ngono,
- John Nkengasong,
- Nicaise Ndembi,
- Anne-Cecile Z. K. Bissek,
- Christian Mouangue,
- Chanceline B. Ndongo,
- Emilienne Epée,
- Nadia Mandeng,
- Sandrine Kamso Belinga,
- Ahidjo Ayouba,
- Nicolas Fernandez,
- Marcel Tongo,
- Vittorio Colizzi,
- Gregory-Edie Halle-Ekane,
- Carlo-Federico Perno,
- Alexis Ndjolo,
- Clement B. Ndongmo,
- Judith Shang,
- Linda Esso,
- Oliviera de-Tulio,
- Moussa Moise Diagne,
- Yap Boum,
- Georges A. E. Mballa,
- Louis R. Njock,
- Genomic Surveillance Study Group
Affiliations
- Joseph Fokam
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health
- Rene Ghislain Essomba
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health
- Richard Njouom
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health
- Marie-Claire A. Okomo
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health
- Sara Eyangoh
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health
- Celestin Godwe
- Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER)
- Bryan Tegomoh
- School of Public Health, University of California, Berkeley
- John O. Otshudiema
- World Health Organization (WHO)
- Julius Nwobegahay
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health
- Lucy Ndip
- Faculty of Health Sciences (FHS), University of Buea
- Blaise Akenji
- National Public Health Laboratory (NPHL), Ministry of Public Health
- Desire Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB)
- Mohamed M. M. Moctar
- USAID’s Infectious Diseases Detection and Surveillance
- Cleophas Kahtita Mbah
- USAID’s Infectious Diseases Detection and Surveillance
- Valantine Ngum Ndze
- Faculty of Health Sciences (FHS), University of Buea
- Martin Maidadi-Foudi
- Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER)
- Charles Kouanfack
- Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER)
- Sandrine Tonmeu
- National Public Health Laboratory (NPHL), Ministry of Public Health
- Dorine Ngono
- School of Public Health, University of California, Berkeley
- John Nkengasong
- Africa Centres for Disease Control and Prevention (Africa CDC)
- Nicaise Ndembi
- Africa Centres for Disease Control and Prevention (Africa CDC)
- Anne-Cecile Z. K. Bissek
- Faculty of Health Sciences (FHS), University of Buea
- Christian Mouangue
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health
- Chanceline B. Ndongo
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health
- Emilienne Epée
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health
- Nadia Mandeng
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health
- Sandrine Kamso Belinga
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health
- Ahidjo Ayouba
- Institut de Recherche Pour le Developpement (IRD)
- Nicolas Fernandez
- Institut de Recherche Pour le Developpement (IRD)
- Marcel Tongo
- Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER)
- Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB)
- Gregory-Edie Halle-Ekane
- Faculty of Health Sciences (FHS), University of Buea
- Carlo-Federico Perno
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB)
- Alexis Ndjolo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB)
- Clement B. Ndongmo
- US Centres for Disease Control and Prevention (CDC)
- Judith Shang
- US Centres for Disease Control and Prevention (CDC)
- Linda Esso
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health
- Oliviera de-Tulio
- University of KwaZulu-Natal and Stellenbosch University
- Moussa Moise Diagne
- Institut Pasteur de Dakar
- Yap Boum
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health
- Georges A. E. Mballa
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health
- Louis R. Njock
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health
- Genomic Surveillance Study Group
- DOI
- https://doi.org/10.1038/s41598-023-48773-3
- Journal volume & issue
-
Vol. 13,
no. 1
pp. 1 – 10
Abstract
Abstract 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.
