Preliminary Data on COVID-19 Variants in Different Waves in Cameroon

The presentation outlines the preliminary data from Sanger sequencing of 140 COVID-19 samples in Cameroon from four waves since March 2020. It details the demographics, symptoms, and circulating variants in each wave, showing the predominance of Omicron in the recent wave. The study provides insights into the prevalence and characteristics of COVID-19 variants over time in Cameroon.

• COVID-19
• Cameroon
• Variants
• Sanger sequencing
• Preliminary data

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1. CIRCB CENTRE INTERNATIONAL DE R F RENCE CHANTAL BIYA Pour la RECHERCHE SUR LA PR VENTION ET LA PRISE EN CHARGE DU VIH/SIDA EDCTP PERFECT-Study (RIA2020EF-3000): Project Meeting Updates on preliminary activities carried at the Virology laboratory, CIRCB, Cameroon (Tuesday, 08th February 2022)

2. PRESENTATION OUTLINE Preliminary data from Sanger sequencing; Comparison of RT-PCR Abbott versus Da An gene; Launching of Ag-RDT performance evaluation; Ordering of other reagents and materials; Planning for activities scheduled at partner institutions; General issues, etc.

3. 1- PRELIMINARY DATA FROM SANGER SEQUENCING Since disease outbreak in March 2020 in Cameroon, 58,000 PCR tests performed. Selection of 140 COVID-19 samples from the 4 waves in Cameroon (Sitrep 2021) All Camerooonians 62.14 %( 87/140) males; Median age: 36 [29 48] years; About 22.86% (32/140) symptomatic with cough (59.37%; 19/32) being the most prevailing symptom We successfully amplified and sequenced 81.43%( 114/140) with CT values 15.65 4.

4. A- Data from the 1st wave Data collection: 22/04/2020 to 17/11/2020 N=32 samples sequenced 17/32 (53.12%) were symptomatic (cough 13/17; Tiredness 5/17) Circulating COVID-19 variants: Wild type (31/32); Gamma (1/32)*

5. B- Data from the 2nd wave Data collection: 23/01/2021 to 17/04/2021 N=32 samples sequenced 06/32 (18.75%) were symptomatic (cough 4/6; Tiredness 3/6; Dyspnea 3/6) Circulating COVID-19 variants: Wild type (19/32); Alpha (10/32); Beta (3/32)

6. C- Data from the 3rd wave Data collection: 02/07/2021 to 01/11/2021 N=35 samples sequenced 02/35 (5.71%) were symptomatic (cough 1/2; Tiredness 1/2; Sore throat 1/2) Circulating COVID-19 variants: Delta(34/35); Alpha(1/35)*

7. D- Data from the 4th wave Data collection: 12/2021 to date N=15 samples sequenced 3/15(20%) were symptomatic (Fever 3/3; Headache 3/3; cough 2/3; Tiredness 2/3) Circulating COVID-19 variants: Omicron (13/15); Delta (2/15)

8. 2- Comparison of RT-PCR Abbott vs. Da An gene Aim: To ensure field interoperability in COVID-19 assays, we evaluated the diagnostic concordance of SARS-CoV-2 between an automated (Abbott) and a manual (DaAn Gene) real-time PCR (rRT-PCR), two commonly used assays in sub-SaharanAfrica. N= 287 samples (273 nasopharyngeal clinical swabs and 14 quality control [CQ] panels) Selection period: 02/2021 through 05/2021 (probably WT, Alpha and Beta variants circulating) 57.88% (158/273) males; Median age: 36 [26 46] years; 4% (10/273) symptomatic cases.

9. A- Overall concordance Kappa Abbott (k, 95% CI) Positive Negative Total Positive 72 36 (36/108) 108 (72/108) 0.82 DaAn gene Negative 14 (0.78 0.86) 165 (179) 179 (14/179) Total 86 201 287 (86/287) (201/287)

10. B- Concordance according to positivity thresholds Concordance (CT<35) Positive concordance (67/93; 72.04%) Kappa k:0.84 (95%CI: 0.795-0.883) Negative concordance (175/194; 90.20%) Concordance (CT<37) Positive concordance (72/108; 66.66%) Negative concordance (165/179; 92.18.%) Concordance CT<40 Positive concordance (73/122; 59.83%) Negative concordance (152/165; 92.12%) Concordance (QC) Positive concordance (9/9) Negative concordance (5/5) k : 0.82 (95%CI: 0.777-0.863) k : 0.78 (95%CI: 0.735-0.820) 100% 100%

11. C- Correlation between Abbott CN and the DaAn gene CT values according to gene of interest