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Background: Rotavirus remains a leading cause of severe gastroenteritis in children under five, particularly in low- and middle-income countries (LMICs). In Malawi, G9P[6] strains re-emerged in 2017, five years after the introduction of Rotarix rotavirus vaccine, necessitating an in-depth investigation of their genetic diversity, evolutionary origins, and public health implications.
Methods: Using whole-genome sequencing (WGS), we analysed and assigned complete genotype constellations and employed phylogeographic and phylogenetic network analyses to trace the evolutionary pathways of G9P[6] strains (n=11) between 2017 to 2022.
Findings: The re-emergent G9P[6] strains were characterized by a DS-1-like G9-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2 genotype constellation. Phylogeographic analysis of the VP7 gene revealed monophyletic clustering with contemporary G9P[6] strains from Mozambique. Phylogenetic network analysis demonstrated high genetic similarity of the inner capsid and non-structural genes of G9P[6] strains to previously circulating Malawian G2P[4], G2P[6], G3P[4], and G3P[6] strains. Bayesian inference dated the most recent common ancestor for the inner capsid and non-structural genes between 2009–2015. Host-pathogen co-evolution analysis suggested lineage spillover events associated with the VP6 segment, pointing to potential zoonotic transmission.
Conclusion: This study, for the first time in Malawi, elucidates the role of reassortment and zoonotic transmission in the re-emergence of G9P[6] strains. These findings highlight the evolutionary dynamics of rotaviruses and the need for continuous genomic surveillance. Considering the limited heterotypic protection provided by the Rotarix (G1P[8] strain) vaccine, tailored vaccination strategies and ongoing vaccine effectiveness studies are critical to addressing the emergence of novel rotavirus strains and improving vaccine performance in LMICs
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