Genomic surveillance of SARS-CoV-2 reveals highest severity and mortality of delta over other variants: evidence from Cameroon
Joseph Fokam, René Ghislain Essomba, Richard Njouom, Marie-Claire Okomo, Sara Eyangoh, Célestin Godwe, Bryan Tegomoh, John Otokoye Otshudiema, Julius Nwobegahay, Lucy Ndip, Blaise Akenji, Désiré Takou, Mohamed M. M. Moctar, Cleophas Kahtita Mbah, Valantine Ngum Ndze, Martin Maïdadi‐Foudi, Charles Kouanfack, Sandrine Chimène Douyong Tonmeu, Dorine Ngono, John N. Nkengasong, Nicaise Ndembi, Anne‐Cecile Zoung‐Kanyi Bissek, Christian Mouangue, Chanceline Bilounga Ndongo, Emilienne Epée, Nadia Mandeng, Sandrine Belinga, Ahidjo Ayouba, Nicolas Fernandez, Marcel Tongo, Vittorio Colizzi, Gregory Halle‐Ekane, Carlo Federico Perno, Alexis Ndjolo, Clement B. Ndongmo, Judith Shang, Linda Esso, Oliviera de-Tulio, Moussa Moïse Diagne, Yap Boum, Georges Alain Etoundi Mballa, Louis Richard Njock, Genomic Surveillance Study Group, Serge Alain Sadeuh‐Mba, Paul-Alain Tagnoukam Ngoupou, Moumbeket Yifomnjou Henri, Bertrand Bille Eyoum, Grâce Beloumou, Guy Pascal Ngaba, Christiane Ingrid Medi, Lydie Nyatte, Melissa Sanders, Marie Amougou, Loko Bille, Kizito Atehambe Buyohnwenda, Claudine Sen Henriette Ngomtcho, Abas Mouliom, Fai Karl Gwei Njuwa, Gisele Nke Ateba, Alex Durand Nka, Laura Eno Dimite, Adama N. Dir, Carole Eboumbou
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.