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

Kiyota, Naoko; Kushibuchi, Izumi; Kobayashi, Miho; Tsukagoshi, Hiroyuki; Ryo, Akihide; Nishimura, Koichi; Hirata-Saito, Asumi; Harada, Seiya; Arakawa, Mika; Kozawa, Kunihisa; Noda, Masahiro; Kimura, Hirokazu

doi:10.1099/jmm.0.049072-0

Cited by 9 publications

(13 citation statements)

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“…The numerous negatively selected sites found in the Kenyan HRV strains may indicate that portion of the genome has attained genetic stability and therefore resist deleterious mutations. These findings echo those of previous reports …”

Section: Discussionmentioning

confidence: 99%

Serotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008

Milanoi

Ongus

Gachara

et al. 2016

Influenza Resp Viruses

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BackgroundHuman rhinoviruses (HRVs) are a well‐established cause of the common cold and recent studies indicated that they may be associated with severe acute respiratory illnesses (SARIs) like pneumonia, asthma, and bronchiolitis. Despite global studies on the genetic diversity of the virus, the serotype diversity of these viruses across diverse geographic regions in Kenya has not been characterized.ObjectivesThis study sought to characterize the serotype diversity of HRV strains that circulated in Kenya in 2008.MethodsA total of 517 archived nasopharyngeal samples collected in a previous respiratory virus surveillance program across Kenya in 2008 were selected. Participants enrolled were outpatients who presented with influenza‐like (ILI) symptoms. Real‐time RT‐PCR was employed for preliminary HRV detection. HRV‐positive samples were amplified using RT‐PCR and thereafter the nucleotide sequences of the amplicons were determined followed by phylogenetic analysis.ResultsTwenty‐five percent of the samples tested positive for HRV. Phylogenetic analysis revealed that the Kenyan HRVs clustered into three main species comprising HRV‐A (54%), HRV‐B (12%), and HRV‐C (35%). Overall, 20 different serotypes were identified. Intrastrain sequence homology among the Kenyan strains ranged from 58% to 100% at the nucleotide level and 55% to 100% at the amino acid level.ConclusionThese results show that a wide range of HRV serotypes with different levels of nucleotide variation were present in Kenya. Furthermore, our data show that HRVs contributed substantially to influenza‐like illness in Kenya in 2008.

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Section: Discussionmentioning

confidence: 99%

Serotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008

Milanoi

Ongus

Gachara

et al. 2016

Influenza Resp Viruses

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“…HRV-A and -C appear to be mainly associated with ARIs and virus-induced asthma, while HRV-B has been detected in a relatively small number of patients with ARIs (Linsuwanon et al, 2009;Wisdom et al, 2009;Smuts et al, 2011). Our previous findings obtained from samples from children with ARIs in Japan indicated that HRV-A and -C can be classified into many clusters in the phylogenetic tree, with 30% nucleotide divergence of the VP4/VP2 coding region (Mizuta et al, 2010a;Arakawa et al, 2012;Kiyota et al, 2013). In addition, Kiyota et al (2013) estimated that the rate of molecular evolution of the VP4/VP2 coding region was rapid (3.07 × 10 −3 substitutions/site/year) in HRV-C.…”

Section: Molecular Epidemiology Of Hrvmentioning

confidence: 94%

“…Our previous findings obtained from samples from children with ARIs in Japan indicated that HRV-A and -C can be classified into many clusters in the phylogenetic tree, with 30% nucleotide divergence of the VP4/VP2 coding region (Mizuta et al, 2010a;Arakawa et al, 2012;Kiyota et al, 2013). In addition, Kiyota et al (2013) estimated that the rate of molecular evolution of the VP4/VP2 coding region was rapid (3.07 × 10 −3 substitutions/site/year) in HRV-C. These results suggest that HRV-A and -C detected in ARI cases are the predominant strains and have varied genetic properties (Wisdom et al, 2009;Mizuta et al, 2010a;Arakawa et al, 2012).…”

Section: Molecular Epidemiology Of Hrvmentioning

confidence: 99%

Molecular epidemiology of respiratory viruses in virus-induced asthma

Tsukagoshi¹,

Ishioka²,

Noda³

et al. 2013

Front. Microbiol.

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Acute respiratory illness (ARI) due to various viruses is not only the most common cause of upper respiratory infection in humans but is also a major cause of morbidity and mortality, leading to diseases such as bronchiolitis and pneumonia. Previous studies have shown that respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (HPIV), and human enterovirus infections may be associated with virus-induced asthma. For example, it has been suggested that HRV infection is detected in the acute exacerbation of asthma and infection is prolonged. Thus it is believed that the main etiological cause of asthma is ARI viruses. Furthermore, the number of asthma patients in most industrial countries has greatly increased, resulting in a morbidity rate of around 10-15% of the population. However, the relationships between viral infections, host immune response, and host factors in the pathophysiology of asthma remain unclear. To gain a better understanding of the epidemiology of virus-induced asthma, it is important to assess both the characteristics of the viruses and the host defense mechanisms. Molecular epidemiology enables us to understand the pathogenesis of microorganisms by identifying specific pathways, molecules, and genes that influence the risk of developing a disease. However, the epidemiology of various respiratory viruses associated with virus-induced asthma is not fully understood. Therefore, in this article, we review molecular epidemiological studies of RSV, HRV, HPIV, and HMPV infection associated with virus-induced asthma.

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“…Few studies have been reported on pathogen profiles, including respiratory viruses, in adult Japanese CAP patients [31]. In addition, the molecular epidemiology of CAPassociated viruses is poorly understood; although, some CAP-associated respiratory viruses such as HMPV and HRV-C have recently been confirmed [32][33][34]. Our results show that HMPV, RSV, HRV, and HPIV are associated with CAP in adult inpatients.…”

Section: Discussionmentioning

confidence: 62%

Pathogen profiles and molecular epidemiology of respiratory viruses in Japanese inpatients with community-acquired pneumonia

Kurai

Sasaki

Saraya

et al. 2016

Respiratory Investigation

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

Cited by 9 publications

References 50 publications

Serotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008

Serotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008

Molecular epidemiology of respiratory viruses in virus-induced asthma

Pathogen profiles and molecular epidemiology of respiratory viruses in Japanese inpatients with community-acquired pneumonia

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