Human Parainfluenza viruses (HPIV) type 1 and 3 are important causes of respiratory tract
infections in young children globally. HPIV infections do not confer complete protective
immunity so reinfections occur throughout life. Since no effective vaccine is available for the
two virus subtypes, comprehensive understanding of HPIV-1 and HPIV-3 genetic and epidemic
features is important for diagnosis, prevention, and treatment of HPIV-1 and HPIV-3
infections. Relatively few whole genome sequences are available for both HPIV-1 and
HPIV-3 viruses, so our study sought to provide whole genome sequences from multiple
countries to further the understanding of the global diversity of HPIV at a whole-genome
level. We collected HPIV-1 and HPIV-3 samples and isolates from Argentina, Australia,
France, Mexico, South Africa, Switzerland, and USA from the years 2003–2011 and
sequenced the genomes of 40 HPIV-1 and 75 HPIV-3 viruses with Sanger and next-generation
sequencing with the Ion Torrent, Illumina, and 454 platforms. Phylogenetic analysis
showed that the HPIV-1 genome is evolving at an estimated rate of 4.97 × 10−4 mutations/
site/year (95% highest posterior density 4.55 × 10−4 to 5.38 × 10−4) and the HPIV-3 genome
is evolving at a similar rate (3.59 × 10−4 mutations/site/year, 95% highest posterior density 3.26 × 10−4 to 3.94 × 10−4). There were multiple genetically distinct lineages of both HPIV-1
and 3 circulating on a global scale. Further surveillance and whole-genome sequencing are
greatly needed to better understand the spatial dynamics of these important respiratory
viruses in humans.S1 Text. HPIV-1 Sanger sequencing primers.S2 Text. HPIV-3 Sanger sequencing primers.S1 Table. The sequence information of the 40 HPIV-1 genomes.S2 Table. The sequence information of the 75 HPIV-3 genomes.S3 Table. MEME episodic selection results for HPIV-1 and HPIV-3.The National Institute
of Allergy and Infectious Diseases, National
Institutes of Health, Department of Health and
Human Services under contract number
HHSN272200900007C and grant numbers
U19AI110819, with the sub-project directed by HAL, and grants U01AI070428 and U01AI077988
awarded to KJH.http://www.plosone.orgam2019Medical Virolog
