Initial detection of SARS-CoV-2 Omicron BA.4 and BA.5 sub variants associated with the onset of the fifth wave of COVID-19 in Cameroon between December 2021 and June 2022: phylogenetic and whole genome analysis

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Published Jan 24, 2025
DOI: https://doi.org/10.18103/mra.v13i1.6155

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John Otokoye Otshudiema
COVID-19 Genomic Surveillance, Incident Management System Team, World Health Organization (WHO), Yaounde, P.O. Box 155 Yaounde, Cameroon; Kinshasa School of Public Health and Faculty of Medicine, University of Kinshasa, Kinshasa I, P.O. Box 190 Kinshasa XI, Democratic Republic of the Congo
René Ghislain Essomba
Genomic Surveillance Department, National Public Health Laboratory (NPHL) of Cameroon, Ministry of Public Health, Yaounde I, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaounde 1, P.O. Box 337 Yaounde, Cameroon
Moussa Moise Diagne
WHO Reference Sequencing Laboratory, Virology and Genomic Surveillance, Institut Pasteur de Dakar, 12900 Dakar, Senegal
Valentina Josiane Ngo Bitoungui
Genomic Surveillance Department, National Public Health Laboratory (NPHL) of Cameroon, Ministry of Public Health, Yaounde I, Cameroon; Faculty of Medicine and Pharmaceutical Sciences, University of Dschang, P.O. Box 96 Dschang, Cameroon
Yvette Ebogo
Genomic Surveillance Department, National Public Health Laboratory (NPHL) of Cameroon, Ministry of Public Health, Yaounde I, Cameroon
Eric Minkala
Genomic Surveillance Department, National Public Health Laboratory (NPHL) of Cameroon, Ministry of Public Health, Yaounde I, Cameroon
Emmanuel Lofiko Lokilo
WHO Reference Sequencing Laboratory, Epidemiology and Global Health, Institut National de Recherche Biomédicale (INRB), Kinshasa, Kin I Gombe, Democratic Republic of Congo (DRC)
Karl Njuwa Fai
Epicentre Médecins Sans Frontières (MSF), Yaounde I, Cameroon
Sara Eyangoh
Virology Unit, Centre Pasteur du Cameroun (CPC), Yaounde, B.P. 1274 Yaounde, Cameroon
Selassie Kumordjie
Department of Parasitology, Noguchi Memorial Institute for Medical Research, Accra, GA-337-3045, Ghana
Dorine Ngono
COVID-19 Genomic Surveillance, Incident Management System Team, World Health Organization (WHO), Yaounde, P.O. Box 155 Yaounde, Cameroon
Moise Henri Moumbeket
Virology Unit, Centre Pasteur du Cameroun (CPC), Yaounde, B.P. 1274 Yaounde, Cameroon
Placide Mbala Kingebeni
Kinshasa School of Public Health and Faculty of Medicine, University of Kinshasa, Kinshasa I, P.O. Box 190 Kinshasa XI, Democratic Republic of the Congo; WHO Reference Sequencing Laboratory, Epidemiology and Global Health, Institut National de Recherche Biomédicale (INRB), Kinshasa, Kin I Gombe, Democratic Republic of Congo (DRC)
Steve Ahuka Mundeke2
Kinshasa School of Public Health and Faculty of Medicine, University of Kinshasa, Kinshasa I, P.O. Box 190 Kinshasa XI, Democratic Republic of the Congo; WHO Reference Sequencing Laboratory, Epidemiology and Global Health, Institut National de Recherche Biomédicale (INRB), Kinshasa, Kin I Gombe, Democratic Republic of Congo (DRC)
Nicksy Gumede
COVID-19 Incident Management Support Team, WHO Regional Office for Africa, World Health Organization, Brazzaville, P.O. Box 06 Brazzaville, Republic of Congo
Joseph Fokam
Virology Service, Centre International de Recherche Chantal Biya (CIRCB), Yaounde, P.O. Box. 3077 Yaounde, Cameroon; National COVID-19 Incident Management Team, Public Health Emergency Operations and Coordination Center, Ministry of Health, Yaounde I, Cameroon; Faculty of Health Sciences, University of Buea, P.O. Box 63 Buea, Cameroon
Linda Esso
Faculty of Medicine and Biomedical Sciences, University of Yaounde 1, P.O. Box 337 Yaounde, Cameroon; Virology Service, Centre International de Recherche Chantal Biya (CIRCB), Yaounde, P.O. Box. 3077 Yaounde, Cameroon; National COVID-19 Incident Management Team, Public Health Emergency Operations and Coordination Center, Ministry of Health, Yaounde I, Cameroon
Louis Richard Njock
Faculty of Medicine and Biomedical Sciences, University of Yaounde 1, P.O. Box 337 Yaounde, Cameroon; Virology Service, Centre International de Recherche Chantal Biya (CIRCB), Yaounde, P.O. Box. 3077 Yaounde, Cameroon; National COVID-19 Incident Management Team, Public Health Emergency Operations and Coordination Center, Ministry of Health, Yaounde I, Cameroon
Georges Alain Etoundi Mballa
 Virology Service, Centre International de Recherche Chantal Biya (CIRCB), Yaounde, P.O. Box. 3077 Yaounde, Cameroon; National COVID-19 Incident Management Team, Public Health Emergency Operations and Coordination Center, Ministry of Health, Yaounde I, Cameroon
Richard Njouom
Virology Unit, Centre Pasteur du Cameroun (CPC), Yaounde, B.P. 1274 Yaounde, Cameroon
Yap Boum II
Faculty of Medicine and Biomedical Sciences, University of Yaounde 1, P.O. Box 337 Yaounde, Cameroon; Virology Service, Centre International de Recherche Chantal Biya (CIRCB), Yaounde, P.O. Box. 3077 Yaounde, Cameroon; National COVID-19 Incident Management Team, Public Health Emergency Operations and Coordination Center, Ministry of Health, Yaounde I, Cameroon
Marie Claire Assoumou Okomo
Genomic Surveillance Department, National Public Health Laboratory (NPHL) of Cameroon, Ministry of Public Health, Yaounde I, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaounde 1, P.O. Box 337 Yaounde, Cameroon

Abstract

Background: Two sub variants (BA.4 and BA.5) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant are concerning as they are spreading rapidly worldwide; however, no published data concerning these variants are available in Cameroon. We report the early detection of these new sub variants that are associated with the onset of the fifth wave of coronavirus 2019 (COVID-19) in Cameroon.


Methods: Positive samples were selected for next-generation sequencing (NGS). BA.4 and BA.5 complete genome sequences underwent sequence data analysis, epidemiology analysis of COVID-19’s resurgence and wave, recombination and pairwise matrix analysis, and phylogenetic analysis. We selected the first nine SARS-CoV-2 Omicron BA.4 and BA.5 sub variants detected in Cameroon using local whole genome sequencing for the NGS analysis.


Results: During the fifth wave of resurgence of COVID-19 cases in Cameroon, it was found that the Northwest and Littoral regions were the most affected areas, while the Center and Littoral regions recorded the highest number of new deaths. The study identified evidence of recombination between the BA.2 sub variant and BA.4 and BA.5 Cameroonian strains. This result highlights the dynamic nature of SARS-CoV-2 evolution. The BA.5 strain (entitled hCoV-19/Cameroon/23850/2022) showed the highest sequence similarity to the first reported genome of the Omicron strain with 497 mutations. Phylogenetic analysis revealed that these nine Omicron sub variants were grouped into a distinct and highly distant cluster separate from the first Omicron variant detected in Botswana and were intermixed with sequences from other countries (the United States, Denmark, Scotland, and England), thus implying multiple introductions of the BA.4 and BA.5 sub variants in Cameroon.


Conclusions: Omicron BA.4 and BA.5 sub-lineages are associated with the onset of the fifth wave of COVID-19 in Cameroon. In addition to providing early warning of COVID-19 resurgence, continuous local genome sequencing of emerging variants is essential for detecting variants of concern, thereby guiding the country's response. This study emphasizes the value of real-time surveillance.

Keywords: COVID-19, Omicron BA.4 and BA.5 sub-variants, fifth wave, whole genome analysis

Article Details

How to Cite
OTSHUDIEMA, John Otokoye et al. Initial detection of SARS-CoV-2 Omicron BA.4 and BA.5 sub variants associated with the onset of the fifth wave of COVID-19 in Cameroon between December 2021 and June 2022: phylogenetic and whole genome analysis. Medical Research Archives, [S.l.], v. 13, n. 1, jan. 2025. ISSN 2375-1924. Available at: <https://esmed.org/MRA/mra/article/view/6155>. Date accessed: 10 feb. 2025. doi: https://doi.org/10.18103/mra.v13i1.6155.
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Vol 13 No 1 (2025): Vol.13 issue 1 January 2025
Section
Research Articles

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