Genome-wide replacement by DS-1-like equine-like G3P[8] rotaviruses in Taiwan and implications for vaccine effectiveness

Abstract Rotavirus vaccines reduce severe gastroenteritis, but reassortment and the emergence of animal-like strains raise concerns about vaccine mismatch. We analyzed hospital-based surveillance in Taiwan during 2005–2017, integrating VP7/VP4 genotyping, whole-genome sequencing (WGS), and a test-negative vaccine-effectiveness study during 2014–2017. Rotavirus positivity among hospitalized children with acute gastroenteritis declined from 25.6% in 2005–2007 to 18.4% in 2008–2011 and 10.3% in 2014–2017, while the detection of G3P[8] strains increased in the late-vaccine period. By 2014, equine-like VP7 G3P[8] viruses had largely replaced previously circulating typical human Wa-like G3P[8] strains; 271/276 G3P[8] detections were equine-like. Whole-genome sequencing of a subset yielded 132 near-complete genomes overall, including 61 G3P[8] genomes; all G3P[8] genomes sequenced from 2005 to 2011 were Wa-like, whereas 37 of 40 sequenced post-2014 G3P[8] genomes had DS-1-like backbones. In the 2014–2017 test-negative vaccine-effectiveness analysis, unconditional logistic regression controlling for age in months, hospital site, calendar year, and calendar month showed high protection against rotavirus-associated hospitalization for Rotarix (82.0%, 95% CI 75.9–86.6) and RotaTeq (90.1%, 95% CI 83.5–94.0). Vaccine effectiveness estimates restricted to WGS-confirmed G3P[8] DS-1-like cases were imprecise and exploratory. These data provide indirect epidemiologic evidence that protection against severe rotavirus hospitalization was maintained during the emergence of the dominant equine-like DS-1-like G3P[8] lineage.