Speaker
Description
Background: G1P[8] rotaviruses consistently circulated in Malawi from 1997 to 2019. They represent genogroup I and normally possess a Wa-like genetic backbone. However, the majority of G1P[8] strains that circulated between 2013 and 2014 in Blantyre, Malawi soon after the introduction of Rotarix® rotavirus vaccine, exhibited a DS-1-like genetic backbone more common of genogroup II rotaviruses. Here we conducted a whole genome sequencing (WGS) study to determine the phylodynamics of G1P[8] post 2014 as well as elucidate reasons behind their disappearance in 2019.
Methods: We recruited under-five children presenting with acute gastroenteritis at Queen Elizabeth Central Hospital. We systematically sampled and generated WGS for G1P[8] strains (n=84) that circulated from 2015 to 2019 in Blantyre. We used time-resolved phylogenetic analysis and Maximum likelihood trees to define clades and explore phylogeographical distribution respectively. Haplotype inference was used to estimate the population genetic diversity.
Results: WGS revealed that the G1P[8] (n=82) strains had the G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 while two strains had the G1-P[8]-I1-R1-C1-M1-A1-N2-T1-E1-H1 genotype constellations. Genome segment time-resolved phylogenetic analysis revealed new clusters L4 and L5, genetically distinct from L1, L2 and L3 previously described to circulate in Malawi from 1997 – 2014. Phylogeographic analysis revealed a monophyletic cluster between L4 strains to contemporary G1P[8] strains characterised in Mozambique and India. Phylogenetic networks suggest both inter- and intragenogroup reassortment events contributed to the genetic diversity of G1P[8] strains post 2014. Haplotype inference of the VP7 and VP4 genome segments of G1P[8] strains revealed a wider genetic diversity within these segments before vaccine introduction compared to post-vaccine strains.
Conclusion: Malawian G1P[8] strains reverted from a DS-1-like to a Wa-like genotype constellation after 2014. Our work uncovered addition clusters L4 and L5 from 2015 to 2019. Our findings suggest cross-border introduction and reassortments events as major drivers of diversity. Our data suggest reassortment events and reduced genetic diversity led to the disappearance of G1P[8] in 2019.
