Molecular Epidemiology of SARS-CoV-2 within Accra Metropolis Postlockdown

Abstract

Introduction. Currently, sequencing has been the only tool for the identification of circulating severe acute respiratory syndrome coronavirus-2 (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 postlockdown in Accra, this study presents an alternative method that leverages polymerase chain reaction (PCR) to identify circulating SARS-CoV-2 variants in the Accra Metropolis postlockdown. Methods. This prospective cross-sectional study was conducted between July and December 2022. Nasopharyngeal samples were collected from 268 consenting participants. Samples were subjected to nucleic acid extraction and followed by real-time polymerase chain reaction for the detection and quantification of SARS-CoV-2 RNA. SARS-CoV-2 positive samples were subsequently subjected to variant identification using rapid PCR. Findings. The prevalence of SARS-CoV-2 within the Accra Metropolis was 30.2%. The majority 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 years recorded 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 dyspnoea in order of decreasing association with SARS-CoV-2 infection. There was a strong association between symptom status, gender, age, and SARS-CoV-2 infection. Conclusion. There was a high prevalence of SARS-CoV-2 within the Accra Metropolis postlockdown 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.