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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.
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Title
Genomic surveillance of SARS-CoV-2 reveals highest severity and mortality of delta over other variants: evidence from Cameroon
Author
Fokam, Joseph 1 ; Essomba, Rene Ghislain 2 ; Njouom, Richard 3 ; Okomo, Marie-Claire A. 2 ; Eyangoh, Sara 3 ; Godwe, Celestin 4 ; Tegomoh, Bryan 5 ; Otshudiema, John O. 6 ; Nwobegahay, Julius 7 ; Ndip, Lucy 8 ; Akenji, Blaise 9 ; Takou, Desire 10 ; Moctar, Mohamed M. M. 11 ; Mbah, Cleophas Kahtita 11 ; Ndze, Valantine Ngum 12 ; Maidadi-Foudi, Martin 13 ; Kouanfack, Charles 13 ; Tonmeu, Sandrine 9 ; Ngono, Dorine 5 ; Nkengasong, John 14 ; Ndembi, Nicaise 14 ; Bissek, Anne-Cecile Z. K. 15 ; Mouangue, Christian 16 ; Ndongo, Chanceline B. 17 ; Epée, Emilienne 18 ; Mandeng, Nadia 19 ; Kamso Belinga, Sandrine 16 ; Ayouba, Ahidjo 20 ; Fernandez, Nicolas 20 ; Tongo, Marcel 21 ; Colizzi, Vittorio 22 ; Halle-Ekane, Gregory-Edie 8 ; Perno, Carlo-Federico 23 ; Ndjolo, Alexis 24 ; Ndongmo, Clement B. 25 ; Shang, Judith 25 ; Esso, Linda 16 ; de-Tulio, Oliviera 26 ; Diagne, Moussa Moise 27 ; Boum, Yap 28 ; Mballa, Georges A. E. 18 ; Njock, Louis R. 29 ; Mba, Serge Alain Sadeuh 30 ; Ngoupou, Paul-Alain Tagnoukam 30 ; Henri, Moumbeket Yifomnjou 30 ; Eyoum, Bertrand 31 ; Beloumou, Grace 10 ; Ngaba, Guy Pascal 31 ; Medi, Christiane 31 ; Nyatte, Lydie 31 ; Sanders, Melissa 31 ; Amougou, Marie 31 ; Bille, Loko 32 ; Buyohnwenda, Kizito Atehambe 31 ; Ngomtcho, Claudine 9 ; Mouliom, Abas 31 ; Njuwa, Fai Karl Gwei 31 ; Ateba, Gisele Nke 31 ; Nka, Alex 33 ; Dimite, Laura 25 ; Dir, Adama N. 27 ; Eboumbou, Carole 34
1 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049); University of Buea, Faculty of Health Sciences (FHS), Buea, Cameroon (GRID:grid.29273.3d) (ISNI:0000 0001 2288 3199)
2 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Public Health, National Public Health Laboratory (NPHL), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Yaounde I, Faculty of Medicine and Biomedical Sciences (FMBS), Yaounde, Cameroon (GRID:grid.412661.6) (ISNI:0000 0001 2173 8504)
3 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Centre Pasteur du Cameroun (CPC), Yaoundé, Cameroon (GRID:grid.418179.2)
4 Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon (GRID:grid.418179.2)
5 University of California, Berkeley, School of Public Health, Berkeley, USA (GRID:grid.47840.3f) (ISNI:0000 0001 2181 7878)
6 World Health Organization (WHO), Yaounde, Cameroon (GRID:grid.47840.3f)
7 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Defence, Centre de Recherche Pour la Santé des Armées (CRESAR), Yaoundé, Cameroon (GRID:grid.415857.a)
8 University of Buea, Faculty of Health Sciences (FHS), Buea, Cameroon (GRID:grid.29273.3d) (ISNI:0000 0001 2288 3199)
9 Ministry of Public Health, National Public Health Laboratory (NPHL), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
10 Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049)
11 USAID’s Infectious Diseases Detection and Surveillance, Yaounde, Cameroon (GRID:grid.479171.d)
12 University of Buea, Faculty of Health Sciences (FHS), Buea, Cameroon (GRID:grid.29273.3d) (ISNI:0000 0001 2288 3199); African Society for Laboratory Medicine (ASLM), Yaounde, Cameroon (GRID:grid.29273.3d)
13 Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon (GRID:grid.29273.3d)
14 Africa Centres for Disease Control and Prevention (Africa CDC), Addis-Ababa, Ethiopia (GRID:grid.508167.d)
15 University of Buea, Faculty of Health Sciences (FHS), Buea, Cameroon (GRID:grid.29273.3d) (ISNI:0000 0001 2288 3199); Ministry of Public Health, Division for Operational Health Research (DROS), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
16 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Public Health, Department of Disease, Epidemic and Pandemic Control (DLMEP), Yaounde, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
17 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Public Health, Department of Disease, Epidemic and Pandemic Control (DLMEP), Yaounde, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Douala, Faculty of Medicine and Pharmaceutical Sciences (FMPS), Douala, Cameroon (GRID:grid.413096.9) (ISNI:0000 0001 2107 607X)
18 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Yaounde I, Faculty of Medicine and Biomedical Sciences (FMBS), Yaounde, Cameroon (GRID:grid.412661.6) (ISNI:0000 0001 2173 8504); Ministry of Public Health, Department of Disease, Epidemic and Pandemic Control (DLMEP), Yaounde, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
19 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Public Health, Department of Disease, Epidemic and Pandemic Control (DLMEP), Yaounde, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Bamenda, Faculty of Health Sciences (FHS), Bamenda, Cameroon (GRID:grid.449799.e) (ISNI:0000 0004 4684 0857)
20 Institut de Recherche Pour le Developpement (IRD), Montpellier, France (GRID:grid.4399.7) (ISNI:0000 0001 2287 9528)
21 Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon (GRID:grid.4399.7)
22 Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049); University of Rome Tor Vergata, Chair of UNESCO Biotechnology, Rome, Italy (GRID:grid.6530.0) (ISNI:0000 0001 2300 0941)
23 Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049); Bambino Gesu Pediatric Hospital, Rome, Italy (GRID:grid.414125.7) (ISNI:0000 0001 0727 6809)
24 Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049); University of Yaounde I, Faculty of Medicine and Biomedical Sciences (FMBS), Yaounde, Cameroon (GRID:grid.412661.6) (ISNI:0000 0001 2173 8504)
25 US Centres for Disease Control and Prevention (CDC), Yaounde, Cameroon (GRID:grid.416738.f) (ISNI:0000 0001 2163 0069)
26 University of KwaZulu-Natal and Stellenbosch University, Stellenbosch, South Africa (GRID:grid.11956.3a) (ISNI:0000 0001 2214 904X)
27 Institut Pasteur de Dakar, Dakar, Senegal (GRID:grid.418508.0) (ISNI:0000 0001 1956 9596)
28 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Yaounde I, Faculty of Medicine and Biomedical Sciences (FMBS), Yaounde, Cameroon (GRID:grid.412661.6) (ISNI:0000 0001 2173 8504); Medecins Sans Frontières (MSF), Epicentre, Yaounde, Cameroon (GRID:grid.412661.6)
29 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Yaounde I, Faculty of Medicine and Biomedical Sciences (FMBS), Yaounde, Cameroon (GRID:grid.412661.6) (ISNI:0000 0001 2173 8504); University of Douala, Faculty of Medicine and Pharmaceutical Sciences (FMPS), Douala, Cameroon (GRID:grid.413096.9) (ISNI:0000 0001 2107 607X); Ministry of Public Health, General Secretariat, Yaounde, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
30 Centre Pasteur du Cameroun (CPC), Yaoundé, Cameroon (GRID:grid.418179.2)
31 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
32 Ministry of Defence, Centre de Recherche Pour la Santé des Armées (CRESAR), Yaoundé, Cameroon (GRID:grid.415857.a)
33 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049)
34 University of Douala, Faculty of Medicine and Pharmaceutical Sciences (FMPS), Douala, Cameroon (GRID:grid.413096.9) (ISNI:0000 0001 2107 607X)
1 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049); University of Buea, Faculty of Health Sciences (FHS), Buea, Cameroon (GRID:grid.29273.3d) (ISNI:0000 0001 2288 3199)
2 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Public Health, National Public Health Laboratory (NPHL), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Yaounde I, Faculty of Medicine and Biomedical Sciences (FMBS), Yaounde, Cameroon (GRID:grid.412661.6) (ISNI:0000 0001 2173 8504)
3 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Centre Pasteur du Cameroun (CPC), Yaoundé, Cameroon (GRID:grid.418179.2)
4 Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon (GRID:grid.418179.2)
5 University of California, Berkeley, School of Public Health, Berkeley, USA (GRID:grid.47840.3f) (ISNI:0000 0001 2181 7878)
6 World Health Organization (WHO), Yaounde, Cameroon (GRID:grid.47840.3f)
7 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Defence, Centre de Recherche Pour la Santé des Armées (CRESAR), Yaoundé, Cameroon (GRID:grid.415857.a)
8 University of Buea, Faculty of Health Sciences (FHS), Buea, Cameroon (GRID:grid.29273.3d) (ISNI:0000 0001 2288 3199)
9 Ministry of Public Health, National Public Health Laboratory (NPHL), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
10 Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049)
11 USAID’s Infectious Diseases Detection and Surveillance, Yaounde, Cameroon (GRID:grid.479171.d)
12 University of Buea, Faculty of Health Sciences (FHS), Buea, Cameroon (GRID:grid.29273.3d) (ISNI:0000 0001 2288 3199); African Society for Laboratory Medicine (ASLM), Yaounde, Cameroon (GRID:grid.29273.3d)
13 Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon (GRID:grid.29273.3d)
14 Africa Centres for Disease Control and Prevention (Africa CDC), Addis-Ababa, Ethiopia (GRID:grid.508167.d)
15 University of Buea, Faculty of Health Sciences (FHS), Buea, Cameroon (GRID:grid.29273.3d) (ISNI:0000 0001 2288 3199); Ministry of Public Health, Division for Operational Health Research (DROS), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
16 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Public Health, Department of Disease, Epidemic and Pandemic Control (DLMEP), Yaounde, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
17 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Public Health, Department of Disease, Epidemic and Pandemic Control (DLMEP), Yaounde, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Douala, Faculty of Medicine and Pharmaceutical Sciences (FMPS), Douala, Cameroon (GRID:grid.413096.9) (ISNI:0000 0001 2107 607X)
18 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Yaounde I, Faculty of Medicine and Biomedical Sciences (FMBS), Yaounde, Cameroon (GRID:grid.412661.6) (ISNI:0000 0001 2173 8504); Ministry of Public Health, Department of Disease, Epidemic and Pandemic Control (DLMEP), Yaounde, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
19 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Ministry of Public Health, Department of Disease, Epidemic and Pandemic Control (DLMEP), Yaounde, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Bamenda, Faculty of Health Sciences (FHS), Bamenda, Cameroon (GRID:grid.449799.e) (ISNI:0000 0004 4684 0857)
20 Institut de Recherche Pour le Developpement (IRD), Montpellier, France (GRID:grid.4399.7) (ISNI:0000 0001 2287 9528)
21 Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon (GRID:grid.4399.7)
22 Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049); University of Rome Tor Vergata, Chair of UNESCO Biotechnology, Rome, Italy (GRID:grid.6530.0) (ISNI:0000 0001 2300 0941)
23 Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049); Bambino Gesu Pediatric Hospital, Rome, Italy (GRID:grid.414125.7) (ISNI:0000 0001 0727 6809)
24 Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049); University of Yaounde I, Faculty of Medicine and Biomedical Sciences (FMBS), Yaounde, Cameroon (GRID:grid.412661.6) (ISNI:0000 0001 2173 8504)
25 US Centres for Disease Control and Prevention (CDC), Yaounde, Cameroon (GRID:grid.416738.f) (ISNI:0000 0001 2163 0069)
26 University of KwaZulu-Natal and Stellenbosch University, Stellenbosch, South Africa (GRID:grid.11956.3a) (ISNI:0000 0001 2214 904X)
27 Institut Pasteur de Dakar, Dakar, Senegal (GRID:grid.418508.0) (ISNI:0000 0001 1956 9596)
28 Ministry of Public Health, National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Yaounde I, Faculty of Medicine and Biomedical Sciences (FMBS), Yaounde, Cameroon (GRID:grid.412661.6) (ISNI:0000 0001 2173 8504); Medecins Sans Frontières (MSF), Epicentre, Yaounde, Cameroon (GRID:grid.412661.6)
29 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); University of Yaounde I, Faculty of Medicine and Biomedical Sciences (FMBS), Yaounde, Cameroon (GRID:grid.412661.6) (ISNI:0000 0001 2173 8504); University of Douala, Faculty of Medicine and Pharmaceutical Sciences (FMPS), Douala, Cameroon (GRID:grid.413096.9) (ISNI:0000 0001 2107 607X); Ministry of Public Health, General Secretariat, Yaounde, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
30 Centre Pasteur du Cameroun (CPC), Yaoundé, Cameroon (GRID:grid.418179.2)
31 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654)
32 Ministry of Defence, Centre de Recherche Pour la Santé des Armées (CRESAR), Yaoundé, Cameroon (GRID:grid.415857.a)
33 Ministry of Public Health, COVID-19 Genomic Surveillance Platform (PSG), Yaoundé, Cameroon (GRID:grid.415857.a) (ISNI:0000 0001 0668 6654); Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon (GRID:grid.479171.d) (ISNI:0000 0004 0369 2049)
34 University of Douala, Faculty of Medicine and Pharmaceutical Sciences (FMPS), Douala, Cameroon (GRID:grid.413096.9) (ISNI:0000 0001 2107 607X)
Pages
21654
Publication year
2023
Publication date
2023
e-ISSN
20452322
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2899561962
Copyright
© The Author(s) 2023. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.