Partial spike gene sequencing for the identification of SARS-CoV-2 variants circulating in Cameroon in 2021

Chavely Gwladys Monamele; Serge Alain Sadeuh-Mba; Pauliana Vanessa Ilouga; Moïse Henri Y Moumbeket; Loique Landry E Messanga; Aristide Mounchili Njifon; Estelle L Madaha; Ripa M Njankouo; Paul Alain Tagnouokam-Ngoupo; Jules Brice M Tchatchueng; Mathurin Cyrille Tejiokem; Ronald Perraut; Sara Eyangoh; Richard Njouom

doi:10.3855/jidc.18155

Partial spike gene sequencing for the identification of SARS-CoV-2 variants circulating in Cameroon in 2021

Authors

Chavely Gwladys Monamele Virology Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon https://orcid.org/0000-0002-2637-2078
Serge Alain Sadeuh-Mba Virology Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon https://orcid.org/0000-0003-3377-8225
Pauliana Vanessa Ilouga Virology Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon https://orcid.org/0000-0002-9290-8328
Moïse Henri Y Moumbeket Virology Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon
Loique Landry E Messanga Virology Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon https://orcid.org/0000-0003-3702-3110
Aristide Mounchili Njifon Virology Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon https://orcid.org/0009-0004-2173-3817
Estelle L Madaha Virology Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon
Ripa M Njankouo Virology Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon
Paul Alain Tagnouokam-Ngoupo Virology Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon
Jules Brice M Tchatchueng Epidemiology and Public Health Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon
Mathurin Cyrille Tejiokem Epidemiology and Public Health Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon
Ronald Perraut Garoua Annex, Centre Pasteur of Cameroon; PO Box Garoua, Cameroon
Sara Eyangoh Scientific Department, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon
Richard Njouom Virology Service, Centre Pasteur of Cameroon; PO Box 1274, Yaounde, Cameroon https://orcid.org/0000-0003-3112-6370

DOI:

https://doi.org/10.3855/jidc.18155

Keywords:

SARS-CoV-2, genome, Sanger, sequencing, variants

Abstract

Introduction: Global monitoring of severe acute respiratory syndrome related coronavirus 2 (SARS-CoV-2) genetic sequences and associated metadata is essential for coronavirus disease 2019 (COVID-19) response. Therefore, Sanger's partial genome sequencing technique was used to monitor the circulating variants of SARS-CoV-2 in Cameroon.

Methodology: Nasopharyngeal specimen was collected from persons suspected of SARS-CoV-2 following the national guidelines between January and December 2021. All specimens with cycle threshold (Ct) below 30 after amplification were eligible for sequencing of the partial spike (S) gene of SARS-CoV-2 using the Sanger sequencing method.

Results: During the year 2021, 1481 real time reverse transcriptase polymerase chain reaction (RT-PCR) SARS-CoV-2 positive samples were selected for partial sequencing of the S gene of SARS-CoV-2. Amongst these, 878 yielded good sequencing products. A total of 231 probable variants (26.3%) were identified. The variants were mainly represented by Delta (70.6%), Alpha (15.6%), Omicron (7.4%), Beta (3.5%), Mu (1.7%) and Gamma (0.4%). Phylogenetic analysis of the probable variants from Cameroon with reference strains confirmed that all prior and current variants of concern (VOC) clustered with their respective reference sequences.

Conclusions: The surveillance strategy implemented in Cameroon, based on partial sequencing of the S gene enabled identification of the major circulating variants and provided information on the distribution of these variants, which contributed to implementing public health measures to control disease spread in the country.

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Published

2024-05-30

How to Cite

Monamele CG, Sadeuh-Mba SA, Ilouga PV, Moumbeket MHY, Messanga LLE, Mounchili Njifon A, Madaha EL, Njankouo RM, Tagnouokam-Ngoupo PA, Tchatchueng JBM, Tejiokem MC, Perraut R, Eyangoh S, Njouom R (2024) Partial spike gene sequencing for the identification of SARS-CoV-2 variants circulating in Cameroon in 2021. J Infect Dev Ctries 18:701–709. doi: 10.3855/jidc.18155

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Issue

Vol. 18 No. 05: May 2024

Section

Coronavirus Pandemic

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Copyright (c) 2024 Chavely Gwladys Monamele, Serge Alain Sadeuh-Mba, Pauliana Vanessa Ilouga, Moïse Henri Yifomnjou Moumbeket , Loique Landry Essengue Messanga , Aristide Mounchili Njifon, Estelle Longla Madaha, Ripa Mohamadou Njankouo, Paul Alain Tagnouokam-Ngoupo, Jules Brice Mbougua Tchatchueng, Mathurin Cyrille Tejiokem, Ronald Perraut, Sara Eyangoh, Richard Njouom

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