Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, in the period spanning the COVID-19 pandemic, 2019-2022

BackgroundThe non-pharmaceutical interventions (NPIs) implemented to curb the spread of SARS-CoV-2 early in the COVID-19 pandemic years, disrupted the activity of other respiratory viruses. There is limited data from low-and-middle income countries (LMICs) to determine whether COVID-19 NPIs also impacted the epidemiology of enteric viruses. We investigated the changes in infection patterns of common enteric viruses among hospitalised children who presented with diarrhoea to a referral hospital in coastal Kenya, in the period spanning the COVID-19 pandemic. MethodsA total of 870 stool samples from children under 13 years of age admitted to Kilifi County Hospital between January 2019, and December 2022 were screened for rotavirus group A (RVA), norovirus genogroup II (GII), astrovirus, sapovirus, and adenovirus type F40/41 using real-time reverse-transcription polymerase chain reaction. The proportions positive across the four years were compared using the chi-squared test statistic. ResultsOne or more of the five virus targets were detected in 282 (32.4%) cases. A reduction in the positivity rate of RVA cases was observed from 2019 (12.1%, 95% confidence interval (CI) 8.7% - 16.2%) to 2020 (1.7%, 95% CI 0.2% - 6.0%; p < 0.001). However, in the 2022, RVA positivity rate rebounded to 23.5% (95% CI 18.2% - 29.4%). For norovirus GII, the positivity rate fluctuated over the four years with its highest positivity rate observed in 2020 (16.2%; 95% C.I, 10.0% - 24.1%). No astrovirus cases were detected in 2020 and 2021, but the positivity rate in 2022 was similar to that in 2019 (3.1% (95% CI 1.5% - 5.7%) vs 3.3% (95% CI 1.4% - 6.5%)). A higher case fatality rate was observed in 2021 (9.0%) compared to the 2019 (3.2%), 2020 (6.8%) and 2022 (2.1%) (p <0.001). ConclusionOur study finds that in 2020 the transmission of common enteric viruses, especially RVA and astrovirus, in Kilifi Kenya may have been disrupted due to the COVID-19 NPIs. After 2020, local enteric virus transmission patterns appeared to return to pre-pandemic levels coinciding with the removal of most of the government COVID-19 NPIs.