Phylogenetic analysis of human rhinoviruses collected over four successive years in Sydney, Australia
Autor: | Frank Zeng, Dominic E. Dwyer, Vigneswary Mala Ratnamohan, Chandini Raina MacIntyre, Jen Kok, Linda Donovan |
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Rok vydání: | 2016 |
Předmět: |
Male
0301 basic medicine Time Factors Rhinovirus Epidemiology viruses Subspecies phylogeny law.invention law Nasopharynx Genotype Prevalence Child Respiratory Tract Infections Polymerase chain reaction influenza‐like illness Phylogenetic tree virus diseases Respiratory infection Infectious Diseases medicine.anatomical_structure RNA Viral Female Original Article circulatory and respiratory physiology Adult Pulmonary and Respiratory Medicine 030106 microbiology Nose Biology Real-Time Polymerase Chain Reaction 03 medical and health sciences stomatognathic system Phylogenetics Throat otorhinolaryngologic diseases medicine Humans human rhinovirus Influenza-like illness Picornaviridae Infections molecular typing Australia Public Health Environmental and Occupational Health Genetic Variation Sequence Analysis DNA Original Articles Virology 030104 developmental biology Pharynx |
Zdroj: | Influenza and Other Respiratory Viruses |
ISSN: | 1750-2659 1750-2640 |
Popis: | 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. |
Databáze: | OpenAIRE |
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