SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control
by Oluwapelumi Olufemi Adeyemi, Nnaemeka Darlington Ndodo, Mariam Kehinde Sulaiman, Oyeronke Temidayo Ayansola, Oluwabunmi Idera Nimat Buhari, Olusola Anuoluwapo Akanbi, Oladimeji Akeem Bolarinwa, Chimaobi Chukwu, Ireoluwa Yinka Joel, Adesuyi Ayodeji Omoare, Kolawole Wasiu Wahab, Celestina Obiekea, Mikhail Olayinka Buhari, Anthony Ahumibe, Caroline Folasade Kolawole, Catherine Okoi, Olumuyiwa Babagbemi Omotesho, Nwando Mba, Oluwafemi Adeniyi, Olajumoke Babatunde, Nathaniel Akintunde, Ganiu Ayinla, Oluwatosin Wuraola Akande, Rasheed Adekeye Odunola, Mohammed Jimoh Saka, Omotosho Ibrahim Musa, Idayat Adenike Durotoye, Chikwe Ihekweazu, Ifedayo Morayo Adetifa, Abayomi Fadeyi
The COVID-19 global pandemic is being driven by evolving SARS-CoV-2 variants with consequential implications on virus transmissibility, host immunity, and disease severity. Continuous molecular and genomic surveillance of the SARS-CoV-2 variants is therefore necessary for public health interventions toward the management of the pandemic. This study is a retrospective analysis of COVID-19 cases reported in a Nigerian tertiary institution from July to December 2021. In total, 705 suspected COVID-19 cases that comprised 547 students and 158 non-students were investigated by real time PCR (RT-PCR); of which 372 (~52.8%) tested positive for COVID-19. Using a set of selection criteria, 74 (~19.9%) COVID-19 positive samples were selected for next generation sequencing. Data showed that there were two outbreaks of COVID-19 within the university community over the study period, during which more females (56.8%) tested positive than males (47.8%) (p<0.05). Clinical data together with phylogenetic analysis suggested community transmission of SARS-CoV-2 through mostly asymptomatic and/or pre-symptomatic individuals. Confirmed COVID-19 cases were mostly mild, however, SARS-CoV-2 delta (77%) and omicron (4.1%) variants were implicated as major drivers of respective waves of infections during the study period. This study highlights the importance of integrated surveillance of communicable disease during outbreaks.