SARS-CoV-2 Variant Identification within Accra Metropolis Post-Lockdown: Prevalence, Associations and Implications

Currently, sequencing is the only tool for identifying circulating SARS-CoV-2 variants. However, it is known to be an expensive and laborious approach involving high technical expertise. Considering the reduced adherence to preventive measures post-lockdown in Accra, this study presents an alternative method that leverages PCR for identifying circulating SARS-CoV-2 variants in the Accra Metropolis post-lockdown. This was a prospective cross-sectional study conducted between July and November 2022. Nasopharyngeal samples were collected from 268 consenting participants. Samples were subjected to nucleic acid extraction followed by a real-time polymerase chain reaction to detect and quantify SARS-CoV-2 RNA. SARS-CoV-2-positive samples were subsequently subjected to variant identification using rapid PCR. The prevalence of SARS-CoV-2 within the Accra Metropolis was 30.2%. Most of the SARS-CoV-2 infection was diagnosed in females, participants aged 41–50 years, and symptomatic participants. Participants aged ≤10 years and females recorded the highest viral load, while participants aged 41–50 had the highest number of infections. The SARS-CoV-2 variants detected were Alpha (64.2%), Delta (22.2%), and Omicron (13.6%). Predictors of SARS-CoV-2 infection identified were chills, cough, headache, body weakness, sore throat, and dyspnea, in order of decreasing association with SARS-CoV-2 infection. There was a strong association between symptom status, gender, and age and SARS-CoV-2 infection. There is a high prevalence of SARS-CoV-2 within the Accra Metropolis post-lockdown within the sampling period. The Alpha variant of SARS-CoV-2 is the predominant circulating variant, and persons presenting with symptoms are most likely to be diagnosed with COVID-19. Children aged ≤10 years serve as a reservoir for infection transmission.