Screening Respiratory Samples for Detection of Human Rhinoviruses (HRVs) and Enteroviruses: Comprehensive VP4-VP2 Typing Reveals High Incidence and Genetic Diversity of HRV Species C

Abstract

Rhinovirus infections are the most common cause of viral illness in humans, and there is increasing evidence of their etiological role in severe acute respiratory tract infections (ARTIs). Human rhinoviruses (HRVs) are classified into two species, species A and B, which contain over 100 serotypes, and a recently discovered genetically heterogeneous third species (HRV species C). To investigate their diversity and population turnover, screening for the detection and the genetic characterization of HRV variants in diagnostic respiratory samples was performed by using nested primers for the efficient amplification of the VP4-VP2 region of HRV (and enterovirus) species and serotype identification. HRV species A, B, and C variants were detected in 14%, 1.8%, and 6.8%, respectively, of 456 diagnostic respiratory samples from 345 subjects (6 samples also contained enteroviruses), predominantly among children under age 10 years. HRV species A and B variants were remarkably heterogeneous, with 22 and 6 different serotypes, respectively, detected among 73 positive samples. Similarly, by using a pairwise distance threshold of 0.1, species C variants occurring worldwide were provisionally assigned to 47 different types, of which 15 were present among samples from Edinburgh, United Kingdom. There was a rapid turnover of variants, with only 5 of 43 serotypes detected during both sampling periods. By using divergence thresholds and phylogenetic analysis, several species A and C variants could provisionally be assigned to new types. An initial investigation of the clinical differences between rhinovirus species found HRV species C to be nearly twice as frequently associated with ARTIs than other rhinovirus species, which matches the frequencies of detection of respiratory syncytial virus. The study demonstrates the extraordinary genetic diversity of HRVs, their rapid population turnover, and their extensive involvement in childhood respiratory disease.

Spread of different rhinovirus B genotypes in hospitalized children in Spain

“…According to the analysis of Wisdom et al. 6 and Simmonds et al. , 4 novel HRVs may be classified following these criteria.…”

“…A remarkable finding is the high HRV‐B diversity found in our study, with 13 of 25 serotypes detected, compared with other surveys. Studies performed in Edinburgh 6 and Switzerland 13 detected six different serotypes each, while four different types were found in China, 14 South Africa, 15 and the USA, 16 respectively. This lower diversity may be due to the number of years spanned in these studies –usually one or two – compared with our study of a 6·5‐year period.…”

Atypical hand, foot, and mouth disease associated with coxsackievirus A6 infection, Edinburgh, United Kingdom, January to February 2014

“…Molecular typing [2] identified coxsackievirus A6 (CV-A6) in all 11 of the typed 16 cases, including the first four.…”

“…EV RNA was detected in vesicle fluid specimens by real-time RT-PCR targeting the 5'untranslated region [1]. For genotyping, the VP4 gene was amplified and sequenced as previously described [2]. The VP1 region was amplified using a newly designed nested primers specific for CV-A6 (outer sense: GARGCTAACATYATAGCTCTTGGAGC; inner sense: GACACYGAYGARATY CAACAAACAGC; inner antisense: CGRTCRGTTGCAGTGTTWGTTATTGT; outer antisense: CCYTCATARTCHGTGGTGG TTATGCT).…”

Genetic analysis of the VP4/VP2 coding region in human rhinovirus species C in patients with acute respiratory infection in Japan

“…HRV-C may be associated with various ARIs, such as upper respiratory infection (URI), bronchiolitis and pneumonia (Arakawa et al, 2012;Smuts et al, 2011;Watanabe et al, 2010), as well as with other diseases such as virus-induced asthma in many countries (Fujitsuka et al, 2011;Linsuwanon et al, 2009;Smuts et al, 2011). HRV-C has been shown to have a wide genetic divergence (Arakawa et al, 2012;Wisdom et al, 2009). Indeed, our previous report suggested that the genomes of HRV-C detected in Japanese subjects with various ARIs showed .30 % divergence based on sequences in the VP4/VP2 coding region, and these strains could be classified into many genotypes by phylogenetic analysis (Arakawa et al, 2012).…”