Molecular characterization of a Canadian human Parechovirus (HPeV)-3 isolate and its relationship to other HPeVs

A new member of the Parechovirus genus (HPeV-3) has been recently isolated from a stool specimen of a young Japanese child with transient paralysis (isolate A308/99). Three additional HPeV-3 Canadian cases associated with severe neonatal infections were subsequently described by our group. At this time, limited information is available on the molecular characterization of the HPeV-3 genome. In this study, we report the complete genome sequence of a Canadian HPeV-3 isolate (Can82853-01) recovered in 2001 from the nasopharyngeal aspirate of a neonate with a sepsis-like syndrome. The Can82853-01 genome was 7,322 nucleotides (nt) in length and had 96.4%, 77.7%, and 77.5% nt identity with the A308/99 (HPeV-3), HPeV-1, and HPeV-2 reference strains, respectively. Furthermore, the Can82853-01 polyprotein had 98.2%, 86.9%, and 84.7% amino acids identity compared to the same viruses. Most differences between the polyproteins of HPeV-3 isolates and those of HPeV-1 and -2 were located in the VP0-VP3-VP1 capsid region whereas the non-structural proteins were relatively conserved. The primary and predicted secondary structures of 5'UTR and 3'UTR of the HPeV-3 isolates were also different than those of HPeV-1 and -2 reference strains. Phylogenetic analysis confirmed the relatedness between Can82853-01 and A308/99 and their divergence from other picornaviruses.