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Phylogenetic analysis of human rhinoviruses collected over four successive years in Sydney, Australia.
Influenza Other Respir Viruses. 2016 11; 10(6):493-503.IO

Abstract

BACKGROUND

Human rhinoviruses (HRV) cause a wide spectrum of disease, ranging from a mild influenza-like illness (ILI) to severe respiratory infection. Molecular epidemiological data are limited for HRV circulating in the Southern Hemisphere.

OBJECTIVES

To identify the species and genotypes of HRV from clinical samples collected in Sydney, Australia, from 2006 to 2009.

METHODS

Combined nose and throat swabs or nasopharyngeal aspirates collected from individuals with ILI were tested for HRV using real-time reverse-transcriptase polymerase chain reaction (RT-PCR). Sequencing data of 5'UTR and VP4/VP2 coding regions on RT-PCR-positive specimens were analysed.

RESULTS

Human rhinoviruses were detected by real-time PCR in 20.9% (116/555) of samples tested. Phylogenetic analysis of 5'UTR and VP4/VP2 on HRV-positive samples was concordant in the grouping of HRV A and B species but not HRV C species. Eighty per cent (16/20) of sequences that grouped as HRV C in the VP4/VP2 tree clustered as HRV A, alongside some previously described C strains as subspecies C/A. Discordant branching was seen within HRV A group: two sequences clustering as A in the VP4/VP2 tree branched within the C/A subspecies in the 5'UTR tree, and one sequence showed identity to different HRV A strains in the two genes. The prevalence of HRV C and C/A species was greater in paediatric compared to adult patients (47.9% vs 25.5%, P = .032).

CONCLUSION

Human rhinoviruses are a common cause of respiratory infections, and HRV C is present in the Southern Hemisphere. Sequencing of multiple HRV regions may be necessary to determine exact phylogenetic relationships.

Authors+Show Affiliations

Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia.Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia.Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia.School of Public Health and Community Medicine, University of New South Wales, Kensington, NSW, Australia.Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia. jen.kok@health.nsw.gov.au. Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Hospital, University of Sydney, Westmead, NSW, Australia. jen.kok@health.nsw.gov.au. Centre for Research Excellence in Critical Infections, Westmead Hospital, University of Sydney, Westmead, NSW, Australia. jen.kok@health.nsw.gov.au.Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia. Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Hospital, University of Sydney, Westmead, NSW, Australia. Centre for Research Excellence in Critical Infections, Westmead Hospital, University of Sydney, Westmead, NSW, Australia.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

27383422

Citation

Ratnamohan, Vigneswary M., et al. "Phylogenetic Analysis of Human Rhinoviruses Collected Over Four Successive Years in Sydney, Australia." Influenza and Other Respiratory Viruses, vol. 10, no. 6, 2016, pp. 493-503.
Ratnamohan VM, Zeng F, Donovan L, et al. Phylogenetic analysis of human rhinoviruses collected over four successive years in Sydney, Australia. Influenza Other Respir Viruses. 2016;10(6):493-503.
Ratnamohan, V. M., Zeng, F., Donovan, L., MacIntyre, C. R., Kok, J., & Dwyer, D. E. (2016). Phylogenetic analysis of human rhinoviruses collected over four successive years in Sydney, Australia. Influenza and Other Respiratory Viruses, 10(6), 493-503. https://doi.org/10.1111/irv.12404
Ratnamohan VM, et al. Phylogenetic Analysis of Human Rhinoviruses Collected Over Four Successive Years in Sydney, Australia. Influenza Other Respir Viruses. 2016;10(6):493-503. PubMed PMID: 27383422.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Phylogenetic analysis of human rhinoviruses collected over four successive years in Sydney, Australia. AU - Ratnamohan,Vigneswary M, AU - Zeng,Frank, AU - Donovan,Linda, AU - MacIntyre,Chandini R, AU - Kok,Jen, AU - Dwyer,Dominic E, Y1 - 2016/08/09/ PY - 2016/06/29/accepted PY - 2016/7/8/pubmed PY - 2017/9/26/medline PY - 2016/7/8/entrez KW - human rhinovirus KW - influenza-like illness KW - molecular typing KW - phylogeny SP - 493 EP - 503 JF - Influenza and other respiratory viruses JO - Influenza Other Respir Viruses VL - 10 IS - 6 N2 - BACKGROUND: Human rhinoviruses (HRV) cause a wide spectrum of disease, ranging from a mild influenza-like illness (ILI) to severe respiratory infection. Molecular epidemiological data are limited for HRV circulating in the Southern Hemisphere. OBJECTIVES: To identify the species and genotypes of HRV from clinical samples collected in Sydney, Australia, from 2006 to 2009. METHODS: Combined nose and throat swabs or nasopharyngeal aspirates collected from individuals with ILI were tested for HRV using real-time reverse-transcriptase polymerase chain reaction (RT-PCR). Sequencing data of 5'UTR and VP4/VP2 coding regions on RT-PCR-positive specimens were analysed. RESULTS: Human rhinoviruses were detected by real-time PCR in 20.9% (116/555) of samples tested. Phylogenetic analysis of 5'UTR and VP4/VP2 on HRV-positive samples was concordant in the grouping of HRV A and B species but not HRV C species. Eighty per cent (16/20) of sequences that grouped as HRV C in the VP4/VP2 tree clustered as HRV A, alongside some previously described C strains as subspecies C/A. Discordant branching was seen within HRV A group: two sequences clustering as A in the VP4/VP2 tree branched within the C/A subspecies in the 5'UTR tree, and one sequence showed identity to different HRV A strains in the two genes. The prevalence of HRV C and C/A species was greater in paediatric compared to adult patients (47.9% vs 25.5%, P = .032). CONCLUSION: Human rhinoviruses are a common cause of respiratory infections, and HRV C is present in the Southern Hemisphere. Sequencing of multiple HRV regions may be necessary to determine exact phylogenetic relationships. SN - 1750-2659 UR - https://www.unboundmedicine.com/medline/citation/27383422/Phylogenetic_analysis_of_human_rhinoviruses_collected_over_four_successive_years_in_Sydney_Australia_ DB - PRIME DP - Unbound Medicine ER -