SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control

Abstract

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.

Fig 1. Symptomatology of COVID-19 cases.

(A) COVID-19 cases are plotted on the Y-axis, while symptoms of suspected and confirmed cases are plotted on the x-axis. Bars represent percentages of students (grey) and non-students (white). Figure shows χ² tests between student and non-student groups of suspected COVID-19 cases (n = 705): flu-like (χ² = 85.566, df = 1, p = 0.0000), gastrointestinal (χ² = 7.487, df = 1, p = 0.006), non-specific (χ² = 84.532, df = 1, p = 0.000), chemosensory symptoms (χ² = 8.438, df = 1, p = 0.004) and asymptomatic (χ² = 12.489, df = 1, p = 0.000) (ns = not significant, ***p<0.001, ****p<0.0001). Figure also shows χ² test between student and non-student groups of confirmed COVID-19 cases (n = 372): flu-like symptoms (χ² = 12.906, df = 1, p = 0.0000), gastrointestinal disorders (χ² = 1.368, df = 1, p = 0.242), non-specific (χ² = 12.344, df = 1, p = 0.0000), chemosensory symptoms (χ² = 2.647, df = 1, p = 0.104), and asymptomatic (χ² = 4.399, df = 1, p = 0.036) (ns = non-significant, *p<0.05, ****p<0.0001). (B) The RT-PCR Ct values of the SARS-CoV-2 RNA are shown in reverse order on the y-axis; while the number of days, post-onset of symptoms was plotted on the x-axis against the. Scatter plot shows data points represented as grey circles; the average Ct values are shown as thick short bars; error bars represent standard deviation; dashed line represents negative Ct cut-off. Pearson’s correlation (r) of confirmed COVID-19 cases against the duration of symptoms was non-linear (r = 0.05, p = 0.471, N = 249).

Fig 2

(A) Weekly positive COVID-19 samples showing distribution of variants in circulation during outbreaks. Figure shows the non-VOC/VOI (dark grey), Eta (pink), Delta (magenta) and Omicron (red) and other VOC/VOI (green). Non-sequenced samples termed not applicable (N/A) are also shown (light grey). (B) Percentage VOC/VOI Epi-weekly. non-VOC/VOI (dark grey), Eta (pink), Delta (magenta) and Omicron (red), and other VOC/VOI (green). (C) The maximum likelihood phylogenetic tree inferred from SARS-CoV-2 genomic isolates from the University community. Tips are labelled with specimen’s identification numbers corresponding with GISAID assigned accession numbers in S1 Table. The heatmap from first to third columns (left to right) indicates the accommodation type, variants of concern (VOC), and severity of infection respectively. Variant column was coloured with the major variant assigned by GISAID. The scale bar indicates distance substitution per site.