Heliyon (Apr 2024)
SARS-CoV-2 genomic surveillance and reliability of PCR single point mutation assay (SNPsig® SARS-CoV-2 EscapePLEX CE) for the rapid detection of variants of concern in Cameroon
- Joseph Fokam,
- Davy-Hyacinthe Gouissi Anguechia,
- Desire Takou,
- Ezechiel Ngoufack Jagni Semengue,
- Collins Chenwi,
- Grace Beloumou,
- Sandrine Djupsa,
- Alex Durand Nka,
- Willy Le Roi Togna Pabo,
- Aissatou Abba,
- Aude Christelle Ka'e,
- Aurelie Kengni,
- Naomi Karell Etame,
- Larissa Gaelle Moko,
- Evariste Molimbou,
- Rachel Audrey Nayang Mundo,
- Michel Tommo,
- Nadine Fainguem,
- Lionele Mba Fotsing,
- Luna Colagrossi,
- Claudia Alteri,
- Dorine Ngono,
- John Otokoye Otshudiema,
- Clement Ndongmo,
- Yap Boum,
- Georges Mballa Etoundi,
- Edie G.E. Halle,
- Emmanuel Eben-Moussi,
- Carla Montesano,
- Anne-Genevieve Marcelin,
- Vittorio Colizzi,
- Carlo-Federico Perno,
- Alexis Ndjolo,
- Nicaise Ndembi
Affiliations
- Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; Faculty of Health Sciences, University of Buea, Buea, Cameroon; National Public Health Emergency Operations Centre, Ministry of Public Health, Yaounde, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon; Central Technical Group, National AIDS Control Committee, Yaounde, Cameroon; Corresponding author. Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon.
- Davy-Hyacinthe Gouissi Anguechia
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
- Desire Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Ezechiel Ngoufack Jagni Semengue
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; University of Rome “Tor Vergata”, Rome, Italy; Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
- Collins Chenwi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; Mvangan District Hospital, Mvangan, Cameroon
- Grace Beloumou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Sandrine Djupsa
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Alex Durand Nka
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; University of Rome “Tor Vergata”, Rome, Italy; Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
- Willy Le Roi Togna Pabo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Aissatou Abba
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Aude Christelle Ka'e
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; University of Rome “Tor Vergata”, Rome, Italy
- Aurelie Kengni
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Naomi Karell Etame
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Larissa Gaelle Moko
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
- Evariste Molimbou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
- Rachel Audrey Nayang Mundo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Michel Tommo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Nadine Fainguem
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; University of Rome “Tor Vergata”, Rome, Italy; Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
- Lionele Mba Fotsing
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Luna Colagrossi
- Bambino Gesu Pediatric Hospital, Rome, Italy
- Claudia Alteri
- University of Milan, Milan, Italy
- Dorine Ngono
- World Health Organisation Afro, Country Office, Yaoundé, Cameroon
- John Otokoye Otshudiema
- World Health Organisation Afro, Country Office, Yaoundé, Cameroon
- Clement Ndongmo
- Centres for Disease Control and Prevention, Yaoundé, Cameroon
- Yap Boum
- National Public Health Emergency Operations Centre, Ministry of Public Health, Yaounde, Cameroon
- Georges Mballa Etoundi
- National Public Health Emergency Operations Centre, Ministry of Public Health, Yaounde, Cameroon
- Edie G.E. Halle
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
- Emmanuel Eben-Moussi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Carla Montesano
- University of Rome “Tor Vergata”, Rome, Italy
- Anne-Genevieve Marcelin
- Association de Recherche en Virologie et Dermatologie, Paris, France
- Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; University of Rome “Tor Vergata”, Rome, Italy
- Carlo-Federico Perno
- Bambino Gesu Pediatric Hospital, Rome, Italy
- Alexis Ndjolo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon; Faculty of Health Sciences, University of Buea, Buea, Cameroon
- Nicaise Ndembi
- Africa Centres for Disease Control and Prevention, Abbis Ababa, Ethiopia
- Journal volume & issue
-
Vol. 10,
no. 7
p. e29243
Abstract
Background: Surveillance of SARS-CoV-2 variants of concern (VOCs) and lineages is crucial for decision-making. Our objective was to study the SARS-CoV-2 clade dynamics across epidemiological waves and evaluate the reliability of SNPsig® SARS-CoV-2 EscapePLEX CE in detecting VOCs in Cameroon. Material and methods: A laboratory-based study was conducted on SARS-CoV-2 positive nasopharyngeal specimens cycle threshold (Ct)≤30 at the Chantal BIYA International Reference Centre in Yaoundé-Cameroon, between April-2020 to August-2022. Samples were analyzed in parallel with Sanger sequencing and (SNPsig® SARS-CoV-2 EscapePLEX CE), and performance characteristics were evaluated by Cohen's coefficient and McNemar test. Results: Of the 130 sequences generated, SARS-CoV-2 clades during wave-1 (April–November 2020) showed 97 % (30/31) wild-type lineages and 3 % (1/31) Gamma-variant; wave-2 (December-2020 to May-2021), 25 % (4/16) Alpha-variant, 25 % (4/16) Beta-variant, 44 % (7/16) wild-type and 6 % (1/16) mu; wave-3 (June–October 2021), 94 % (27/29) Delta-variant, 3 % (1/29) Alpha-variant, 3 % (1/29) wild-type; wave-4 (November-2021 to August-2022), 98 % (53/54) Omicron-variant and 2 % (1/54) Delta-variant. Omicron sub-variants were BA.1 (47 %), BA.5 (34 %), BA.2 (13 %) and BA.4 (6 %). Globally, the two genotyping methods accurately identified the SARS-CoV-2 VOCs (P = 0.17, McNemar test; Ka = 0.67). Conclusion: Genomic surveillance reveals a rapid dynamic in SARS-CoV-2 strains between epidemiological waves in Cameroon. For wide-spread variant surveillance in resource-limited settings, SNPsig® SARS-CoV-2 EscapePLEX CEkit represents a suitable tool, pending upgrading for distinguishing Omicron sub-lineages.
