Genotypic diversity and dynamic nomenclature of Parechovirus A

Human parechoviruses (PeV-A) can cause severe sepsis and neurological syndromes in neonates and children and are currently classified into 19 genotypes based on genetic divergence in the VP1 gene. However, the genotyping system has notable limitations including an arbitrary distance threshold and reliance on insufficiently robust phylogenetic reconstruction approaches leading to inconsistent genotype definitions. In order to improve the genotyping system, we investigated the molecular epidemiology of human parechoviruses, including the evolutionary history of the different PeV-A lineages as far as is possible. We found that PeV-A lineages suffer from severe substitution saturation in the VP1 gene which limit the inference of deep evolutionary timescales among the extant PeV-A and suggest that the degree of evolutionary divergence among current PeV-A lineages has been substantially underestimated, further confounding the current genotyping system. We propose an alternative nomenclature system based on robust, amino-acid level phylogenetic reconstruction and clustering with the PhyCLIP algorithm which delineates highly divergent currently designated genotypes more informatively. We also describe a dynamic nomenclature framework that combines PhyCLIP’s progressive clustering with phylogenetic placement for genotype assignment.