Distribution of Rotavirus alphagastroenteritidis Strains in Blantyre, Malawi, During and After the COVID-19 Pandemic

<i>Rotavirus alphagastroenteritidis</i> remains the leading cause of severe gastroenteritis in children under five years, despite widespread vaccine use. The COVID-19 pandemic disrupted healthcare and vaccination delivery, while non-pharmacological interventions may have influenced <i>R. alphagastroenteritidis</i> transmission. We conducted hospital-based surveillance of <i>R. alphagastroenteritidis</i> gastroenteritis at Queen Elizabeth Central Hospital (QECH) in Blantyre, Malawi, from October 2019 to October 2024. Children under five presenting with acute gastroenteritis were enrolled; 99.1% of vaccine-eligible participants had received at least one <i>R. alphagastroenteritidis</i> vaccine dose. Stool samples were tested for <i>R. alphagastroenteritidis</i> by enzyme immunoassay (EIA) and genotyped using RT-PCR. Among 1135 enrolled children, 29.1% (330/1135) were <i>R. alphagastroenteritidis</i>-positive. Cases occurred year-round except for December 2020-January 2021, when no <i>R. alphagastroenteritidis</i> infections were detected, and February-March 2023, when no samples were collected. The prevalence varied significantly by age group between children greater than 23 months of age to the rest of the age groups (<6 months, 6-11 months, and 12-22 months) (<i>p</i> = 0.0046). The most common <i>R. alphagastroenteritidis</i> G-genotypes were G3 (38.7%), G2 (25.4%), and G12 (17.2%), with G2 emerging as the predominant strain from June 2023. G3P[8] was the most frequent G-P combination (25%). Its overall prevalence did not change during the pandemic; however, genotype distribution shifted compared to pre-COVID-19 patterns. Sustained surveillance and genomic analyses are essential to monitor evolving strain dynamics and inform vaccine policy.