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 Epee; 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; Serge Alain Sadeuh Mba; Paul-Alain Tagnoukam Ngoupou; Moumbeket Yifomnjou Henri; Bertrand Eyoum; Grace Beloumou; Guy Pascal Ngaba; Christiane Medi; Lydie Nyatte; Melissa Sanders; Marie Amougou; Loko Bille; Kizito Atehambe Buyohnwenda; Claudine Ngomtcho; Abas Mouliom; Fai Karl Gwei Njuwa; Gisele Nke Ateba; Alex Nka; Laura Dimite; Adama N. Dir; Carole Eboumbou; Genomic Surveillance Study Grp

doi:10.1038/s41598-023-48773-3

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Genomic surveillance of SARS-CoV-2 reveals highest severity and mortality of delta over other variants: evidence from Cameroon

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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, …

Scientific reports, Vol.13(1), 21654

08/12/2023

DOI: https://doi.org/10.1038/s41598-023-48773-3

PMID: 38066020

Résumé

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

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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Titre: Genomic surveillance of SARS-CoV-2 reveals highest severity and mortality of delta over other variants: evidence from Cameroon
Créateurs - sans rôle: Joseph Fokam - Minist Publ Hlth, Natl Publ Hlth Emergencies Operat Coordinat Ctr NP, Yaounde, Cameroon
Rene Ghislain Essomba - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Richard Njouom - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Marie-Claire A. Okomo - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Sara Eyangoh - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Celestin Godwe - Ctr Rech Maladies Emergentes & Reemergentes CREMER, Yaounde, Cameroon
Bryan Tegomoh - Univ Calif Berkeley, Sch Publ Hlth, Berkeley, CA USA
John O. Otshudiema - World Hlth Org WHO, Cameroon Country Off, Yaounde, Cameroon
Julius Nwobegahay - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Lucy Ndip - Univ Buea, Fac Hlth Sci FHS, Buea, Cameroon
Blaise Akenji - Minist Publ Hlth, Natl Publ Hlth Lab NPHL, Yaounde, Cameroon
Desire Takou - Chantal BIYA Int Reference Ctr Res HIV AIDS Preven, Yaounde, Cameroon
Mohamed M. M. Moctar - USAIDs Infect Dis Detect & Surveillance, Yaounde, Cameroon
Cleophas Kahtita Mbah - USAIDs Infect Dis Detect & Surveillance, Yaounde, Cameroon
Valantine Ngum Ndze - Univ Buea, Fac Hlth Sci FHS, Buea, Cameroon
Martin Maidadi-Foudi - Ctr Rech Maladies Emergentes & Reemergentes CREMER, Yaounde, Cameroon
Charles Kouanfack - Ctr Rech Maladies Emergentes & Reemergentes CREMER, Yaounde, Cameroon
Sandrine Tonmeu - Minist Publ Hlth, Natl Publ Hlth Lab NPHL, Yaounde, Cameroon
Dorine Ngono - Univ Calif Berkeley, Sch Publ Hlth, Berkeley, CA USA
John Nkengasong - Africa Centres for Disease Control and Prevention
Nicaise Ndembi - Africa Ctr Dis Control & Prevent Africa CDC, Addis Ababa, Ethiopia
Anne-Cecile Z. K. Bissek - Univ Buea, Fac Hlth Sci FHS, Buea, Cameroon
Christian Mouangue - Minist Publ Hlth, Natl Publ Hlth Emergencies Operat Coordinat Ctr NP, Yaounde, Cameroon
Chanceline B. Ndongo - Minist Publ Hlth, Natl Publ Hlth Emergencies Operat Coordinat Ctr NP, Yaounde, Cameroon
Emilienne Epee - Minist Publ Hlth, Natl Publ Hlth Emergencies Operat Coordinat Ctr NP, Yaounde, Cameroon
Nadia Mandeng - Minist Publ Hlth, Natl Publ Hlth Emergencies Operat Coordinat Ctr NP, Yaounde, Cameroon
Sandrine Kamso Belinga - Minist Publ Hlth, Natl Publ Hlth Emergencies Operat Coordinat Ctr NP, Yaounde, Cameroon
Ahidjo Ayouba - Inst Rech Dev IRD, Montpellier, France
Nicolas Fernandez - Inst Rech Dev IRD, Montpellier, France
Marcel Tongo - Ctr Rech Maladies Emergentes & Reemergentes CREMER, Yaounde, Cameroon
Vittorio Colizzi - Chantal BIYA Int Reference Ctr Res HIV AIDS Preven, Yaounde, Cameroon
Gregory-Edie Halle-Ekane - Univ Buea, Fac Hlth Sci FHS, Buea, Cameroon
Carlo-Federico Perno - Chantal BIYA Int Reference Ctr Res HIV AIDS Preven, Yaounde, Cameroon
Alexis Ndjolo - Chantal BIYA Int Reference Ctr Res HIV AIDS Preven, Yaounde, Cameroon
Clement B. Ndongmo - US Ctr Dis Control & Prevent CDC, Cameroon Country Off, Yaounde, Cameroon
Judith Shang - US Ctr Dis Control & Prevent CDC, Cameroon Country Off, Yaounde, Cameroon
Linda Esso - Minist Publ Hlth, Natl Publ Hlth Emergencies Operat Coordinat Ctr NP, Yaounde, Cameroon
Oliviera de-Tulio - Univ Kwazulu Natal, Stellenbosch, South Africa
Moussa Moise Diagne - Inst Pasteur, Dakar, Senegal
Yap Boum - Minist Publ Hlth, Natl Publ Hlth Emergencies Operat Coordinat Ctr NP, Yaounde, Cameroon
Georges A. E. Mballa - Minist Publ Hlth, Natl Publ Hlth Emergencies Operat Coordinat Ctr NP, Yaounde, Cameroon
Louis R. Njock - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Serge Alain Sadeuh Mba - Ctr Pasteur Cameroun CPC, Yaounde, Cameroon
Paul-Alain Tagnoukam Ngoupou - Ctr Pasteur Cameroun CPC, Yaounde, Cameroon
Moumbeket Yifomnjou Henri - Ctr Pasteur Cameroun CPC, Yaounde, Cameroon
Bertrand Eyoum - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Grace Beloumou - Chantal BIYA Int Reference Ctr Res HIV AIDS Preven, Yaounde, Cameroon
Guy Pascal Ngaba - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Christiane Medi - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Lydie Nyatte - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Melissa Sanders - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Marie Amougou - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Loko Bille - Ctr Rech Sante Armees CRESAR, Minist Def, Yaounde, Cameroon
Kizito Atehambe Buyohnwenda - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Claudine Ngomtcho - Minist Publ Hlth, Natl Publ Hlth Lab NPHL, Yaounde, Cameroon
Abas Mouliom - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Fai Karl Gwei Njuwa - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Gisele Nke Ateba - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Alex Nka - Minist Publ Hlth, Genom Surveillance Platform PSG COVID 19, Yaounde, Cameroon
Laura Dimite - US Ctr Dis Control & Prevent CDC, Cameroon Country Off, Yaounde, Cameroon
Adama N. Dir - Inst Pasteur, Dakar, Senegal
Carole Eboumbou - University of Douala
Genomic Surveillance Study Grp
Détails de publication: Scientific reports, Vol.13(1), 21654
Éditeur: NATURE PORTFOLIO
Nombre de pages: 10
Note de subvention: European and Developing Countries Clinical Trials Partnership; European & Developing Countries Clinical Trials Partnership (EDCTP)
Identifiants: 99148920609311
Unité académique: Recherches translationnelles sur le VIH et les Maladies Infect. Endém. émerg. - TransVIHMI
Langue: English
Type de ressource: Journal article