Molecular epidemiology and genetic evolutionary patterns of parechovirus A1 circulating in Chiang Mai, Thailand: A decade-long analysis

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BACKGROUND: As part of gastroenteritis surveillance among pediatric patients in Chiang Mai, Thailand, parechovirus A (PeV‑A) was examined in fecal specimens due to its established role as a causative agent of gastroenteritis in children under five years of age. METHODS: Stool samples were collected from pediatric patients with acute gastroenteritis who admitted to the hospitals in Chiang Mai, Thailand during January 2017 to December 2022. The viral RNA genome was extracted and reverse-transcribed into cDNA, followed by amplification of PeV-A genome by using primers specific for the 5' untranslated region (5'UTR). All positive specimens were further characterized by amplification of VP1 gene, sequencing and comprehensive bioinformatic analysis. The VP1 sequences of PeV-A1 detected in this study (2017-2022) were analyzed alongside those of 2011-2016 reported previously from the same geographical area. RESULTS: Of 2415 samples, 2.86% (69/2415) were positive for PeV-A. Genotyping showed that PeV-A1 was the predominant genotype, followed by PeV-A4, PeV-A14, PeV-A3, PeV-A6, PeV-A5, PeV-A8, and PeV-A2. The prevalence of PeV-A infection before the COVID-19 pandemic (2017-2019) was significantly higher than during the pandemic (2020-2022) (OR, 2.96; 95% CI: 1.54-5.69). Phylogenetic analysis revealed the presence of clades PeV-A1a and PeV-A1b. Several amino acid substitutions were identified relative to the prototype Harris strain, but these changes were conserved within clades. Selection pressure analysis detected one positively selected site at amino acid position 627 and 162 negatively selected sites (p < 0.05). The overall evolutionary rate of PeV-A1 was estimated at 1.49 × 10⁻⁴ substitutions/site/year with PeV-A1b evolving faster than PeV-A1a. CONCLUSION: Despite genetic diversity, PeV-A1 strains remained locally established in Chiang Mai, Thailand for more than a decade. The conserved characteristics and evolutionary patterns of PeV-A1 may contribute to its sustainable predominance.

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