Deep sequence characterisation of a divergent HPIV-4a from an adult with prolonged influenza-like illness

Human parainfluenza virus 4 (HPIV-4) subtypes 4a and 4b are seldom sought during molecular diagnostic screening of respiratory samples from patients with influenza like illnesses (ILIs). Nonetheless, HPIV-4a and HPIV-4b are to be found in such cases, occasionally in the absence of another pathogen. Little is known about the spectrum of genetic variation among HPIV-4 genotypes; thus the impact of genetic change on transmission, pathogenicity, and shedding cannot yet be quantified. We deduced the near-complete genome of a divergent genotype of HPIV-4a (QPID08-0015) identified in a respiratory tract sample from an adult with prolonged ILI in Victoria, Australia, in 2008. Two other variants had been previously reported from Denmark during 2002–2003 (HPIV-4a|DK(459)) and Japan in 2010 (HPIV-4a| 321-Yamagata-2010).A novel concentration, enrichment, purification and amplification (CEPA) deep sequencing process yielded > 90% coverage of the 17,140 bp HPIV-4a-QPID08-0015 genome, including all coding and intergenic regions using material from a single stored clinical sample. Genomic variation was highest between coding regions (Alquezar-Planas et al., 2013).Deep sequencing allowed identification and genomic characterisation of a possible pathogen from an ILI as well as being an important tool to aid future understanding of the linkages between viral genetic variation, transmission and disease prognosis.