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

Arden, Katherine E., Beatson, Scott A., Lambert, Stephen B., Wang, Claire W. T., McVernon, Jodie, Nissen, Michael D., Nolan, Terry, Sloots, Theo P. and Mackay, Ian M. (2015) Deep sequence characterisation of a divergent HPIV-4a from an adult with prolonged influenza-like illness. Virology Reports, 5 19-28. doi:10.1016/j.virep.2015.02.001


Author Arden, Katherine E.
Beatson, Scott A.
Lambert, Stephen B.
Wang, Claire W. T.
McVernon, Jodie
Nissen, Michael D.
Nolan, Terry
Sloots, Theo P.
Mackay, Ian M.
Title Deep sequence characterisation of a divergent HPIV-4a from an adult with prolonged influenza-like illness
Journal name Virology Reports   Check publisher's open access policy
ISSN 2214-6695
Publication date 2015-03
Year available 2015
Sub-type Article (original research)
DOI 10.1016/j.virep.2015.02.001
Open Access Status DOI
Volume 5
Start page 19
End page 28
Total pages 10
Place of publication Amsterdam, Netherlands
Publisher Elsevier
Collection year 2016
Language eng
Formatted abstract
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.
Keyword Deep sequencing
Illumina
Respiratory virus
Human parainfluenza virus 4
Virus discovery
Virus characterisation
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Available online 18 February 2015

 
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Created: Fri, 06 Mar 2015, 11:49:24 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences