Characterization of human parainfluenza virus type 2 circulating in southern France between 2017 and 2022 using whole-genome sequencing

Abstract

Genomic surveillance of respiratory viruses is an expanding field. As of 2024, only 110 (near-) complete genomes of human parainfluenza virus type 2 (HPIV2) were available in GenBank, none being from France. Here we aimed to obtain and analyze HPIV2 genomes from residues of HPIV2 RNA-positive respiratory samples from patients diagnosed in university hospitals of Marseille, Southern France, between 2017 and 2022. Prior to next-generation sequencing (NGS), an in-house PCR-based enrichment strategy was implemented with primers chosen with PrimalScheme. NGS used Illumina technology on a NovaSeq 6000 instrument. HPIV2 genomes were generated from NGS reads by mapping and de novo assembly using CLC Genomics. Mutations were identified by NextClade, and phylogeny was performed by MEGA and NextClade. Seventy-seven near-complete (≥ 90% coverage) genomes and 239 genomes with ≥ 70% coverage were recovered from 318 HPIV2 RNA-positive samples. Two major genotypes, G1a (n = 129 genomes) and G3 (110), were identified, and five subgenotypes, namely G1a.5 (n = 23 genomes), G1a.8 (68), G3.4 (4), G3.5 (7), and G3.7 (23), were newly proposed. Genotype-specific mutations were in the L gene (encoding RNA polymerase) for G1a (T14612A/T11981A/T12374C) and the hemagglutinin-neuraminidase-encoding gene for G3 (G8171A/A14057G/10367G). Subgenotype G3 was only detected in 2019. Subgenotype G1a was absent during the 2021-2022 winter, before becoming majority again during autumn 2022. Although preliminary, this work increased by 70% the number of HPIV2 genomes available worldwide and produced the first genomes from France. It shows an evolution of genotypes, with significant genetic diversity, and of their distribution. It justifies the genomic surveillance of this virus.

Keywords: Evolution; Genome; Genotype; Human parainfluenza virus 2; Mutation; Next-generation sequencing.