Identification of Recombinant Human Rhinovirus A and C in Circulating Strains from Upper and Lower Respiratory Infections

Hak Kim,Ki Hwan Kim,Dae-Won Kim,Dong Soo Kim,Kisoon Kim,You-Jin Kim,Hee-Dong Jung,Hyang Min Cheong,Thomas F Schulz

doi:10.1371/journal.pone.0068081

Abstract

Human rhinoviruses (HRVs), in the Enterovirus genus within the family Picornaviridae, are a highly prevalent cause of acute respiratory infection (ARI). Enteroviruses are genetically highly variable, and recombination between serotypes is known to be a major contribution to their diversity. Recently it was reported that recombination events in HRVs cause the diversity of HRV-C. This study analyzed parts of the viral genes spanning the 5′ non- coding region (NCR) through to the viral protein (VP) encoding sequences of 105 HRV field isolates from 51 outpatient cases of Acute Respiratory Infectious Network (ARINET) and 54 inpatient cases of severe lower respiratory infection (SLRI) surveillance, in order to identify recombination in field samples. When analyzing parts of the 5′NCR and VP4/VP2 encoding sequences, we found intra- and interspecies recombinants in field strains of HRV-A and -C. Nineteen cases of recombination events (18.1%) were found among 105 field strains. For HRV-A, there were five cases (4.8%) of intraspecies recombination events and three cases (2.8%) of interspecies recombination events. For HRV-C, there were four cases (3.8%) of intraspecies recombination events and seven cases (6.7%) of interspecies recombination events. Recombination events were significantly more frequently observed in the ARINET samples (18 cases) than in the SLRI samples (1 case; P< 0.0001). The recombination breakpoints were located in nucleotides (nt) 472–554, which comprise stem-loop 5 in the internal ribosomal entry site (IRES), based on the HRV-B 35 sequence (accession no. FJ445187). Our findings regarding genomic recombination in circulating HRV-A and -C strains suggest that recombination might play a role in HRV fitness and could be a possible determinant of disease severity caused by various HRV infections in patients with ARI.

Highlights

Human rhinoviruses (HRVs), first discovered in 1953, are nonenveloped, positive single-strand RNA viruses of the genus Enterovirus in the family Picornaviridae [1,2]
This study aimed to understand and characterize the various recombination events between 5’ non-coding region (NCR) and VP4/VP2 region of field strains of HRV including species A, B and C, using 105 HRVs identified from two distinctive laboratory surveillance systems, the Acute Respiratory Infectious Network (ARINET) and Severe Lower Respiratory Tract Infections (SLRI) surveillances undertaken from October 2008 to March 2009
Among HRV-positive samples, 51 ARINET samples and 54 severe lower respiratory infection (SLRI) samples collected during the 2008-2009 winter season were selected for further analysis

Summary

Introduction

Human rhinoviruses (HRVs), first discovered in 1953, are nonenveloped, positive single-strand RNA viruses of the genus Enterovirus in the family Picornaviridae [1,2]. HRVs are the major cause of upper and lower respiratory tract infections in humans [3]. It is recognized that 50–85% of most asthma exacerbations are caused by HRV infections [5,6,7,8]. HRVs have a genome of approximately 7,200 base pairs (bp) containing a single reading frame that encodes four viral capsid proteins (VP1, VP2, VP3 and VP4) and seven nonstructural proteins (2Apro, 2B, 2C, 3A, 3B, 3Cpro and 3Dpol) [8,10]. The IRES of HRVs contains five secondary RNA structures called stem-loops (SLs) 2–6 and a polypyrimidine tract (PPT) located between SL5 and SL6 [11]

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