Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria.
Molecular Diagnostic and Research Laboratory, College of Health Sciences, University of Ilorin, Ilorin, Nigeria.
PLoS One. 2023 Jan 25;18(1):e0280756. doi: 10.1371/journal.pone.0280756. eCollection 2023.
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.
COVID-19 全球大流行是由不断进化的 SARS-CoV-2 变体驱动的，这对病毒的传染性、宿主免疫力和疾病严重程度都有影响。因此，对 SARS-CoV-2 变体进行持续的分子和基因组监测对于公共卫生干预措施管理大流行是必要的。本研究回顾性分析了 2021 年 7 月至 12 月尼日利亚一所高校报告的 COVID-19 病例。共有 705 例疑似 COVID-19 病例接受了实时 PCR（RT-PCR）检测，其中包括 547 名学生和 158 名非学生；其中 372 例（~52.8%）COVID-19 检测呈阳性。使用一套选择标准，从 74 例（19.9%）COVID-19 阳性样本中选择了进行下一代测序。数据显示，在研究期间，大学校园内发生了两起 COVID-19 暴发，在此期间，女性（56.8%）的阳性检测结果多于男性（47.8%）（p<0.05）。临床数据和系统发育分析表明，SARS-CoV-2 通过大多数无症状和/或症状前个体进行社区传播。确诊的 COVID-19 病例大多为轻症，但在研究期间，SARS-CoV-2 delta（77%）和 omicron（4.1%）变体被认为是各自感染浪潮的主要驱动因素。本研究强调了在暴发期间对传染病进行综合监测的重要性。
