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

doi:10.1016/j.heliyon.2024.e29243

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

Heliyon. 2024 Apr 6;10(7):e29243. doi: 10.1016/j.heliyon.2024.e29243. eCollection 2024 Apr 15.

Authors

Joseph Fokam^{1

2

3

4

5}, Davy-Hyacinthe Gouissi Anguechia^{1

4}, Desire Takou¹, Ezechiel Ngoufack Jagni Semengue^{1

6

7}, Collins Chenwi^{1

8}, Grace Beloumou¹, Sandrine Djupsa¹, Alex Durand Nka^{1

6

7}, Willy Le Roi Togna Pabo¹, Aissatou Abba¹, Aude Christelle Ka'e^{1

6}, Aurelie Kengni¹, Naomi Karell Etame¹, Larissa Gaelle Moko^{1

4}, Evariste Molimbou^{1

7}, Rachel Audrey Nayang Mundo¹, Michel Tommo¹, Nadine Fainguem^{1

6

7}, Lionele Mba Fotsing¹, Luna Colagrossi⁹, Claudia Alteri¹⁰, Dorine Ngono¹¹, John Otokoye Otshudiema¹¹, Clement Ndongmo¹², Yap Boum³, Georges Mballa Etoundi³, Edie G E Halle², Emmanuel Eben-Moussi¹, Carla Montesano⁶, Anne-Genevieve Marcelin¹³, Vittorio Colizzi^{1

6}, Carlo-Federico Perno⁹, Alexis Ndjolo^{1

2}, Nicaise Ndembi¹⁴

Affiliations

¹ Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon.
² Faculty of Health Sciences, University of Buea, Buea, Cameroon.
³ National Public Health Emergency Operations Centre, Ministry of Public Health, Yaounde, Cameroon.
⁴ Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon.
⁵ Central Technical Group, National AIDS Control Committee, Yaounde, Cameroon.
⁶ University of Rome "Tor Vergata", Rome, Italy.
⁷ Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon.
⁸ Mvangan District Hospital, Mvangan, Cameroon.
⁹ Bambino Gesu Pediatric Hospital, Rome, Italy.
¹⁰ University of Milan, Milan, Italy.
¹¹ World Health Organisation Afro, Country Office, Yaoundé, Cameroon.
¹² Centres for Disease Control and Prevention, Yaoundé, Cameroon.
¹³ Association de Recherche en Virologie et Dermatologie, Paris, France.
¹⁴ Africa Centres for Disease Control and Prevention, Abbis Ababa, Ethiopia.

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.

Keywords: Cameroon; SARS-CoV-2; SNPsig®EscapePLEX CE; Variants of concern.