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Mizuta K, Tanaka W, Komabayashi K, Tanaka S, Seto J, Aoki Y, Ikeda T. Longitudinal Epidemiology of Viral Infectious Diseases Combining Virus Isolation, Antigenic Analysis, and Phylogenetic Analysis as Well as Seroepidemiology in Yamagata, Japan, between 1999 and 2018. Jpn J Infect Dis 2019; 72:211-223. [PMID: 30814463 DOI: 10.7883/yoken.jjid.2018.500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We introduced a microplate method for virus isolation in the Department of Microbiology, Yamagata Prefectural Institute of Public Health (YPIPH) in 1999 in Yamagata, Japan. We have since carried out longitudinal epidemiological studies on viral infectious diseases, particularly respiratory viruses, combining traditional technologies such as virus isolation and serological techniques and newly developed molecular methods. Here, we provide an overview of our activities at YPIPH between 1999 and 2018. During the study period, we observed emerging and re-merging diseases such as those caused by echovirus type 13, enterovirus D68, parechovirus-A3 (PeV-A3), and Saffold virus. With regard to PeV-A3, we proposed a new disease concept, "PeV-A3-associated myalgia/myositis." We also revealed the longitudinal epidemiologies of several viruses such as enterovirus A71 and coxsackievirus A16. To perform longitudinal epidemiological studies at any time in Yamagata, we established a system for stocking clinical specimens, viral isolates, complementary DNAs, and serum specimens. We have also pursued collaboration works with virology laboratories across Japan. We hope our experiences, findings, and research materials will further contribute to the development of countermeasures against viral infectious diseases and improvement in public health strategies in Yamagata, Japan, Asia, and around the world.
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Affiliation(s)
- Katsumi Mizuta
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
| | - Waka Tanaka
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
| | | | - Shizuka Tanaka
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
| | - Junji Seto
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
| | - Yoko Aoki
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
| | - Tatsuya Ikeda
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
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Sugai K, Kimura H, Miyaji Y, Tsukagoshi H, Yoshizumi M, Sasaki-Sakamoto T, Matsunaga S, Yamada Y, Kashiwakura JI, Noda M, Ikeda M, Kozawa K, Ryo A, Yoshihara S, Ogata H, Okayama Y. MIP-1α level in nasopharyngeal aspirates at the first wheezing episode predicts recurrent wheezing. J Allergy Clin Immunol 2015; 137:774-81. [PMID: 26494023 DOI: 10.1016/j.jaci.2015.08.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/11/2015] [Accepted: 08/21/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Respiratory virus-induced wheezing, such as that induced by respiratory syncytial virus (RSV) and human rhinovirus, is an important risk factor for recurrent wheezing and childhood asthma. However, no biomarkers for predicting recurrent wheezing have been identified. OBJECTIVE We searched for predictors of recurrent wheezing using nasopharyngeal aspirates obtained from patients during the first wheezing episode who were hospitalized with an acute lower respiratory tract illness. METHODS We enrolled 82 infants during the first wheezing episode (median age, 5.0 months) who were hospitalized for acute lower respiratory tract illness between August 2009 and June 2012 and followed these patients for 2.5 years. Nasopharyngeal aspirates and blood samples were obtained on the first day of hospitalization. Viral genomes were identified by using RT-PCR and sequencing. Levels of 33 cytokines, tryptase, IgE, anti-RSV IgE, and anti-RSV IgG were measured by using ELISAs or the Bio-Plex multiplex assay. Predictors of recurrent wheezing were examined by using a stepwise logistic regression model with backward elimination. RESULTS Sixty percent of the patients experienced recurrent wheezing episodes. One or more viruses were detected in the nasopharynxes of 93% of the patients during the first wheezing episode. IFN-γ, IL-2, IL-9, MIP-1α, and MIP-1β levels were significantly higher among patients with recurrent wheezing than among those without recurrent wheezing (P < .05 or .01). The stepwise model demonstrated that the MIP-1α level (odds ratio, 7.72; 95% CI, 1.50-39.77; P = .015) was the strongest independent predictor of the occurrence of recurrent wheezing. CONCLUSION An increased MIP-1α level in nasopharyngeal aspirates from patients with acute respiratory symptoms during the first wheezing episode caused by viral infections might predict recurrent wheezing.
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Affiliation(s)
- Kazuko Sugai
- Department of Pediatrics, National Hospital Organization Fukuyama Medical Center, Hiroshima, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yumiko Miyaji
- Department of Pediatrics, National Hospital Organization Yokohama Medical Center, Yokohama, Japan
| | - Hiroyuki Tsukagoshi
- Department of Health Science, Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi, Japan
| | - Masakazu Yoshizumi
- Department of Health Science, Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi, Japan
| | - Tomomi Sasaki-Sakamoto
- Allergy and Immunology Group, Research Institute of Medical Science, Division of Medical Education Planning and Development, Nihon University School of Medicine, Tokyo, Japan
| | - Satoko Matsunaga
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yumi Yamada
- Yamada Gastroenterology Pediatric Clinic, Tochigi, Japan
| | - Jun-ichi Kashiwakura
- Laboratory for Allergic Disease, RCAI, RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Yokohama, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masanori Ikeda
- Department of Pediatrics, National Hospital Organization Fukuyama Medical Center, Hiroshima, Japan
| | - Kunihisa Kozawa
- Department of Health Science, Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | | | - Hiromitsu Ogata
- Center for Information Research, National Institute of Public Health, Saitama, Tokyo, Japan
| | - Yoshimichi Okayama
- Allergy and Immunology Group, Research Institute of Medical Science, Division of Medical Education Planning and Development, Nihon University School of Medicine, Tokyo, Japan.
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Nidaira M, Kuba Y, Saitoh M, Taira K, Maeshiro N, Mahoe Y, Kyan H, Takara T, Okano S, Kudaka J, Yoshida H, Oishi K, Kimura H. Molecular evolution of VP3, VP1, 3C(pro) and 3D(pol) coding regions in coxsackievirus group A type 24 variant isolates from acute hemorrhagic conjunctivitis in 2011 in Okinawa, Japan. Microbiol Immunol 2014; 58:227-38. [PMID: 24517637 DOI: 10.1111/1348-0421.12141] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/03/2014] [Accepted: 02/06/2014] [Indexed: 11/28/2022]
Abstract
A large acute hemorrhagic conjunctivitis (AHC) outbreak occurred in 2011 in Okinawa Prefecture in Japan. Ten strains of coxsackievirus group A type 24 variant (CA24v) were isolated from patients with AHC and full sequence analysis of the VP3, VP1, 3C(pro) and 3D(pol) coding regions performed. To assess time-scale evolution, phylogenetic analysis was performed using the Bayesian Markov chain Monte Carlo method. In addition, similarity plots were constructed and pairwise distance (p-distance) and positive pressure analyses performed. A phylogenetic tree based on the VP1 coding region showed that the present strains belong to genotype 4 (G4). In addition, the present strains could have divided in about 2010 from the same lineages detected in other countries such as China, India and Australia. The mean rates of molecular evolution of four coding regions were estimated at about 6.15 to 7.86 × 10(-3) substitutions/site/year. Similarity plot analyses suggested that nucleotide similarities between the present strains and a prototype strain (EH24/70 strain) were 0.77-0.94. The p-distance of the present strains was relatively short (<0.01). Only one positive selected site (L25H) was identified in the VP1 protein. These findings suggest that the present CA24v strains causing AHC are genetically related to other AHC strains with rapid evolution and emerged in around 2010.
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Affiliation(s)
- Minoru Nidaira
- Okinawa Prefectural Institute of Health and Environment, 2085 Ozato, Nanjo-Shi, Okinawa, 901-1202
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Nidaira M, Taira K, Kato T, Arakaki E, Kyan H, Takara T, Okano S, Kuba Y, Kudaka J, Noda M. Phylogenetic analysis of sapovirus detected from an outbreak of acute gastroenteritis on Ishigaki Island (Okinawa Prefecture, Japan) in 2012. Jpn J Infect Dis 2014; 67:141-3. [PMID: 24647263 DOI: 10.7883/yoken.67.141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Linder JE, Plachco TE, Libster R, Miller EK. Sequencing human rhinoviruses: direct sequencing versus plasmid cloning. J Virol Methods 2014; 211:64-9. [PMID: 25286177 DOI: 10.1016/j.jviromet.2014.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 09/17/2014] [Accepted: 09/24/2014] [Indexed: 01/08/2023]
Abstract
Human rhinoviruses (RV) are associated with the majority of viral respiratory illnesses in infants, children and adults. Over the last several years, researchers have begun to sequence the many different species and strains of RV in order to determine if certain species were associated with increased disease severity. There are a variety of techniques employed to prepare samples for sequencing. One method utilizes plasmid-cloning, which is expensive and takes several hours to complete. Recently, some investigators have instead used direct sequencing to sequence RV strains, allowing for omission of the time- and labor-intensive cloning step. This study formally compares and contrasts the sequencing results obtained from plasmid-cloning and direct Sanger sequencing of a 500 base pair PCR product covering the VP4/VP2 region of RV. A slightly longer sequence (by 65 base pairs on average) was obtained when specimens were plasmid-cloned, and the sequences were 86% similar. After trimming the extra base pairs from the cloned sequences, the sequences were 99.7% identical. Overall success of directly sequencing samples was similar to that of cloning, 5% on average failed for each technique. Therefore, in many instances, directly sequencing samples may be considered in lieu of the more expensive and time-consuming plasmid-cloning technique.
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Affiliation(s)
- Jodell E Linder
- Department of Pediatrics, Vanderbilt University School of Medicine, Medical Center North, Nashville, TN 37232, United States.
| | - Tatyana E Plachco
- Hospital de Pediatria SAMIC Prof. Dr. Juan P Garrahan, Buenos Aires, Argentina; Hospital Materno Infantil Ramon Sarda, Buenos Aires, Argentina.
| | | | - E Kathryn Miller
- Department of Pediatrics, Vanderbilt University School of Medicine, Medical Center North, Nashville, TN 37232, United States.
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Miyaji Y, Kobayashi M, Sugai K, Tsukagoshi H, Niwa S, Fujitsuka-Nozawa A, Noda M, Kozawa K, Yamazaki F, Mori M, Yokota S, Kimura H. Severity of respiratory signs and symptoms and virus profiles in Japanese children with acute respiratory illness. Microbiol Immunol 2014; 57:811-21. [PMID: 24117766 DOI: 10.1111/1348-0421.12102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/19/2013] [Accepted: 09/26/2013] [Indexed: 01/01/2023]
Abstract
Associations between the severity of respiratory signs and symptoms and the respiratory viruses identified in 214 Japanese children with acute respiratory illness (ARI) enrolled between January and December 2012 were studied. Respiratory rate, wheezing, cyanosis, and the use of accessory muscles were used as indices of respiratory severity and phylogenetic analysis of the viruses identified in these children was performed. Respiratory viruses such as respiratory syncytial virus (RSV), human rhinovirus (HRV), human parainfluenza virus (HPIV), and human metapneumovirus (HMPV) were prevalent, being detected in approximately 70% of the patients (151/214 patients). Co-detection of viruses occurred in about 9% of patients. RSV was identified more frequently in cases scored as moderate/severe than in those scored as mild (P < 0.05). Severity scores of patients with RSV were significantly higher than those of cases with HPIV. Moreover, severity scores in patients with mild disease and co-detections were higher than in those in whom only HPIV or adenovirus was detected. Phylogenetic analysis showed that many genotypes of HRV-A and -C with wide genetic divergence were associated with acute respiratory illness (ARI). On the other hand, only a limited number of genotypes of RSV were associated with ARI. HPIV and HMPV were associated with ARI at similar frequencies. These results suggest that different respiratory viruses with unique genetic characteristics can be found in patients with mild to severe ARI.
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Affiliation(s)
- Yumiko Miyaji
- Department of Pediatrics, National Hospital Organization Yokohama Medical Center, 3-60-2 Harajuku, Totsuka-ku, Yokohama, Kanagawa, 245-8575; Department of Pediatrics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004
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Mizuta K, Tsukagoshi H, Ikeda T, Aoki Y, Abiko C, Itagaki T, Nagano M, Noda M, Kimura H. Molecular evolution of the haemagglutinin-neuraminidase gene in human parainfluenza virus type 3 isolates from children with acute respiratory illness in Yamagata prefecture, Japan. J Med Microbiol 2014; 63:570-577. [PMID: 24464692 DOI: 10.1099/jmm.0.068189-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We conducted detailed genetic analyses of the haemagglutinin-neuraminidase (HN) gene in 272 human parainfluenza virus type 3 (HPIV3) isolates from children with acute respiratory illness during the period 2002-2009 in Yamagata prefecture, Japan. A phylogenetic tree reconstructed by the Bayesian Markov chain Monte Carlo method showed that the strains diversified at around 1946 and that the rate of molecular evolution was 1.10×10(-3) substitutions per site per year. Identity was high among the present strains (<90 %) and the pairwise-distances were short. Furthermore, we found four positive selection sites and some key amino acid substitutions in active/catalytic sites of the HN protein. The results suggest that the HN gene of HPIV3 in the present strains evolved rapidly, similarly to other virus genes such as the G gene of respiratory syncytial virus. However, the biological functions and detailed structures of the HN glycoprotein in some of these strains may have been altered.
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Affiliation(s)
- Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Tatsuya Ikeda
- Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
| | - Yoko Aoki
- Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
| | - Chieko Abiko
- Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
| | - Tsutomu Itagaki
- Yamanobe Pediatric Clinic, 2908-14 Yamanobe-machi, Higashimurayama-gun, Yamagata 990-0301, Japan
| | - Manami Nagano
- Technical Support, Life Technologies Japan Ltd, 4-2-8 Shibaura, Minato-ku, Tokyo 108-0023, Japan
| | - Masahiro Noda
- Infectious Diseases Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hirokazu Kimura
- Infectious Diseases Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
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Kiyota N, Kobayashi M, Tsukagoshi H, Ryo A, Harada S, Kusaka T, Obuchi M, Shimojo N, Noda M, Kimura H. Genetic analysis of human rhinovirus species A to C detected in patients with acute respiratory infection in Kumamoto prefecture, Japan 2011-2012. INFECTION GENETICS AND EVOLUTION 2013; 21:90-102. [PMID: 24200591 DOI: 10.1016/j.meegid.2013.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/25/2013] [Accepted: 10/26/2013] [Indexed: 10/26/2022]
Abstract
We performed detailed genetic analysis of the VP4/VP2 coding region in human rhinovirus species A to C (HRV-ABC) strains detected in patients with a variety of acute respiratory infections in Kumamoto, Japan in the period 2011-12. The phylogenetic tree and evolutionary timescale were obtained by the Bayesian Markov chain Monte Carlo method. Phylogenetic analyses showed that the present HRV-A, -B, and -C strains belonged to 25, 4, and 18 genotypes, respectively. Some new genotypes were confirmed as prevalent strains of HRV-C. An ancestor of the present HRV-ABCs could be dated back to about 20,000 years ago. The present HRV-A and -C strains have wide genetic divergence (pairwise distance >0.2) with rapid evolutionary rates (around 7 × 10(-4) to 4 × 10(-3)substitutions/site/year). Over 100 sites were found to be under negative selection, while no positively selected sites were found in the analyzed region. No evidence of recombination events was found in this region of the present strains. Our results indicate that the present HRV strains have rapidly evolved and subsequently diverged over a long period into multiple genotypes.
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Affiliation(s)
- Naoko Kiyota
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Uto-shi, Kumamoto 869-0425, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Uto-shi, Kumamoto 869-0425, Japan
| | - Takashi Kusaka
- Maternal Perinatal Center, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Masatsugu Obuchi
- Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-shi, Toyama 939-0363, Japan
| | - Naoki Shimojo
- Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.
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Tsukagoshi H, Ishioka T, Noda M, Kozawa K, Kimura H. Molecular epidemiology of respiratory viruses in virus-induced asthma. Front Microbiol 2013; 4:278. [PMID: 24062735 PMCID: PMC3771312 DOI: 10.3389/fmicb.2013.00278] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/27/2013] [Indexed: 11/22/2022] Open
Abstract
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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Affiliation(s)
- Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences Gunma, Japan
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Molecular evolution of attachment glycoprotein (G) gene in human respiratory syncytial virus detected in Japan 2008-2011. INFECTION GENETICS AND EVOLUTION 2013; 18:168-73. [PMID: 23707845 DOI: 10.1016/j.meegid.2013.05.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 05/01/2013] [Accepted: 05/13/2013] [Indexed: 11/23/2022]
Abstract
We investigated the evolution of the C-terminal 3rd hypervariable region of G gene in the prevalent human respiratory syncytial virus (RSV) subgroups A (RSV-A) and B (RSV-B) in Japan in 2008-2011. Phylogenetic analysis and the evolutionary timescale was obtained by the Bayesian Markov Chain Monte Carlo method. All 38 RSV-A strains detected were classified into genotype NA1 and the 17 RSV-B strains detected belonged to genotypes BA and GB2. NA1 subdivided around 1998 in the present phylogenetic tree. Genotype BA subdivided around 1994. The evolutionary rates for RSV-A and RSV-B were estimated at 3.63×10⁻³ and 4.56×10⁻³ substitutions/site/year, respectively. The mean evolutionary rate of RSV-B was significantly faster than that of RSV-A during all seasons. The pairwise distance was relatively short (less than 0.06). In addition, some unique sites under positive selection were found. The results suggested that this region of the RSV strains rapidly evolved with some unique amino acid substitutions due to positive pressure.
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McIntyre CL, Knowles NJ, Simmonds P. Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types. J Gen Virol 2013; 94:1791-1806. [PMID: 23677786 PMCID: PMC3749525 DOI: 10.1099/vir.0.053686-0] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human rhinoviruses (HRVs) frequently cause mild upper respiratory tract infections and more severe disease manifestations such as bronchiolitis and asthma exacerbations. HRV is classified into three species within the genus Enterovirus of the family Picornaviridae. HRV species A and B contain 75 and 25 serotypes identified by cross-neutralization assays, although the use of such assays for routine HRV typing is hampered by the large number of serotypes, replacement of virus isolation by molecular methods in HRV diagnosis and the poor or absent replication of HRV species C in cell culture. To address these problems, we propose an alternative, genotypic classification of HRV-based genetic relatedness analogous to that used for enteroviruses. Nucleotide distances between 384 complete VP1 sequences of currently assigned HRV (sero)types identified divergence thresholds of 13, 12 and 13 % for species A, B and C, respectively, that divided inter- and intra-type comparisons. These were paralleled by 10, 9.5 and 10 % thresholds in the larger dataset of >3800 VP4 region sequences. Assignments based on VP1 sequences led to minor revisions of existing type designations (such as the reclassification of serotype pairs, e.g. A8/A95 and A29/A44, as single serotypes) and the designation of new HRV types A101–106, B101–103 and C34–C51. A protocol for assignment and numbering of new HRV types using VP1 sequences and the restriction of VP4 sequence comparisons to type identification and provisional type assignments is proposed. Genotypic assignment and identification of HRV types will be of considerable value in the future investigation of type-associated differences in disease outcomes, transmission and epidemiology.
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Affiliation(s)
- Chloe L McIntyre
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH15 9RG, UK
| | - Nick J Knowles
- Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Peter Simmonds
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH15 9RG, UK
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Kiyota N, Kushibuchi I, Kobayashi M, Tsukagoshi H, Ryo A, Nishimura K, Hirata-Saito A, Harada S, Arakawa M, Kozawa K, Noda M, Kimura H. Genetic analysis of the VP4/VP2 coding region in human rhinovirus species C in patients with acute respiratory infection in Japan. J Med Microbiol 2013; 62:610-617. [DOI: 10.1099/jmm.0.049072-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Naoko Kiyota
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Izumi Kushibuchi
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Koichi Nishimura
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Asumi Hirata-Saito
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Mika Arakawa
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
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Tomkinson N, Wenlock M, McCrae C. Selection of a screening panel of rhinoviral serotypes. Bioorg Med Chem Lett 2012; 22:7494-8. [DOI: 10.1016/j.bmcl.2012.10.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/03/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
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Levofloxacin inhibits rhinovirus infection in primary cultures of human tracheal epithelial cells. Antimicrob Agents Chemother 2012; 56:4052-61. [PMID: 22585227 DOI: 10.1128/aac.00259-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Respiratory virus infections, including infections with rhinoviruses (RVs), are related to exacerbations of chronic obstructive pulmonary disease (COPD). A new quinolone antibiotic, levofloxacin (LVFX), has been used to treat bacterial infections that cause COPD exacerbations as well as bacterial infections that are secondary to viral infection in COPD patients. However, the inhibitory effects of LVFX on RV infection and RV infection-induced airway inflammation have not been studied. We examined the effects of LVFX on type 14 rhinovirus (RV14) (a major human RV) infection of human tracheal epithelial cells pretreated with LVFX. LVFX pretreatment reduced the RV14 titer, the level of cytokines in the supernatant, the amount of RV14 RNA in the cells after RV14 infection, and the cells' susceptibility to RV14 infection. LVFX pretreatment decreased the mRNA level of intercellular adhesion molecule 1 (ICAM-1), a receptor for RV14, in the cells and the concentration of the soluble form of ICAM-1 in the supernatant before RV14 infection. LVFX pretreatment also decreased the number and the fluorescence intensity of the acidic endosomes from which RV14 RNA enters the cytoplasm. LVFX pretreatment inhibited the activation of nuclear factor κB proteins, including p50 and p65, in nuclear extracts. LVFX pretreatment did not reduce the titers of RV2 (a minor human RV) but reduced the titers of RV15 (a major human RV). These results suggest that LVFX inhibits major-group rhinovirus infections in part by reducing ICAM-1 expression levels and the number of acidic endosomes. LVFX may also modulate airway inflammation in rhinoviral infections.
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15
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Yoshida A, Kiyota N, Kobayashi M, Nishimura K, Tsutsui R, Tsukagoshi H, Hirano E, Yamamoto N, Ryo A, Saitoh M, Harada S, Inoue O, Kozawa K, Tanaka R, Noda M, Okabe N, Tashiro M, Mizuta K, Kimura H. Molecular epidemiology of the attachment glycoprotein (G) gene in respiratory syncytial virus in children with acute respiratory infection in Japan in 2009/2010. J Med Microbiol 2012; 61:820-829. [PMID: 22383445 DOI: 10.1099/jmm.0.041137-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study performed a detailed genetic analysis of the glycoprotein (G) gene of respiratory syncytial virus (RSV) detected in 50 Japanese children with acute respiratory infection (ARI) in the 2009/2010 season. A phylogenetic tree constructed by the neighbour-joining method showed that 34 and 16 of the RSV strains could be classified into subgroups A and B, respectively. Strains belonging to subgroups A and B were further subdivided into GA2 and BA, respectively. The nucleotide and deduced amino acid sequence identities were relatively high among these strains (>90%). The deduced amino acid sequences implied that a relatively high frequency of amino acid substitutions occurred in the C-terminal 3rd hypervariable region of the G protein in these strains. In addition, some positively selected sites were estimated. The results suggest that RSV with genotypes GA2 and BA was associated with ARI in Japanese children in 2009/2010.
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Affiliation(s)
- Ayako Yoshida
- Aomori Prefectural Institute of Public Health and Environment, 1-1-1 Higashitsukurimichi, Aomori-shi, Aomori 030-8566, Japan
| | - Naoko Kiyota
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Kurisaki-machi, Uto-shi, Kumamoto 869-0425, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Koichi Nishimura
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Kurisaki-machi, Uto-shi, Kumamoto 869-0425, Japan
| | - Rika Tsutsui
- Aomori Prefectural Institute of Public Health and Environment, 1-1-1 Higashitsukurimichi, Aomori-shi, Aomori 030-8566, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Eiko Hirano
- Fukui Prefectural Institute of Public Health and Environmental Science, 39-4 Harame-cho, Fukui-shi, Fukui 910-8551, Japan
| | - Norio Yamamoto
- Influenza Virus Research Center and Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Mika Saitoh
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Kurisaki-machi, Uto-shi, Kumamoto 869-0425, Japan
| | - Osamu Inoue
- Aomori Prefectural Institute of Public Health and Environment, 1-1-1 Higashitsukurimichi, Aomori-shi, Aomori 030-8566, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Ryota Tanaka
- Department of Surgery, Institute of Medical Sciences, Kyorin University, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Nobuhiko Okabe
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Masato Tashiro
- Influenza Virus Research Center and Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.,Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
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16
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Clinical characteristics and genetic variability of human rhinovirus in Mexico. Viruses 2012; 4:200-10. [PMID: 22470832 PMCID: PMC3315212 DOI: 10.3390/v4020200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/17/2012] [Accepted: 01/17/2012] [Indexed: 12/19/2022] Open
Abstract
Human rhinovirus (HRV) is a leading cause of acute respiratory infection (ARI) in young children and infants worldwide and has a high impact on morbidity and mortality in this population. Initially, HRV was classified into two species: HRV-A and HRV-B. Recently, a species called HRV-C and possibly another species, HRV-D, were identified. In Mexico, there is little information about the role of HRV as a cause of ARI, and the presence and importance of species such as HRV-C are not known. The aim of this study was to determine the clinical characteristics and genetic variability of HRV in Mexican children. Genetic characterization was carried out by phylogenetic analysis of the 5'-nontranslated region (5'-NTR) of the HRV genome. The results show that the newly identified HRV-C is circulating in Mexican children more frequently than HRV-B but not as frequently as HRV-A, which was the most frequent species. Most of the cases of the three species of HRV were in children under 2 years of age, and all species were associated with very mild and moderate ARI.
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17
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Mizuta K, Saitoh M, Kobayashi M, Tsukagoshi H, Aoki Y, Ikeda T, Abiko C, Katsushima N, Itagaki T, Noda M, Kozawa K, Ahiko T, Kimura H. Detailed genetic analysis of hemagglutinin-neuraminidase glycoprotein gene in human parainfluenza virus type 1 isolates from patients with acute respiratory infection between 2002 and 2009 in Yamagata prefecture, Japan. Virol J 2011; 8:533. [PMID: 22152158 PMCID: PMC3295729 DOI: 10.1186/1743-422x-8-533] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 12/13/2011] [Indexed: 11/25/2022] Open
Abstract
Background Human parainfluenza virus type 1 (HPIV1) causes various acute respiratory infections (ARI). Hemagglutinin-neuraminidase (HN) glycoprotein of HPIV1 is a major antigen. However, the molecular epidemiology and genetic characteristics of such ARI are not exactly known. Recent studies suggested that a phylogenetic analysis tool, namely the maximum likelihood (ML) method, may be applied to estimate the evolutionary time scale of various viruses. Thus, we conducted detailed genetic analyses including homology analysis, phylogenetic analysis (using both the neighbor joining (NJ) and ML methods), and analysis of the pairwise distances of HN gene in HPIV1 isolated from patients with ARI in Yamagata prefecture, Japan. Results A few substitutions of nucleotides in the second binding site of HN gene were observed among the present isolates. The strains were classified into two major clusters in the phylogenetic tree by the NJ method. Another phylogenetic tree constructed by the ML method showed that the strains diversified in the late 1980s. No positively selected sites were found in the present strains. Moreover, the pairwise distance among the present isolates was relatively short. Conclusions The evolution of HN gene in the present HPIV1 isolates was relatively slow. The ML method may be a useful phylogenetic method to estimate the evolutionary time scale of HPIV and other viruses.
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Affiliation(s)
- Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
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18
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Arakawa M, Okamoto-Nakagawa R, Toda S, Tsukagoshi H, Kobayashi M, Ryo A, Mizuta K, Hasegawa S, Hirano R, Wakiguchi H, Kudo K, Tanaka R, Morita Y, Noda M, Kozawa K, Ichiyama T, Shirabe K, Kimura H. Molecular epidemiological study of human rhinovirus species A, B and C from patients with acute respiratory illnesses in Japan. J Med Microbiol 2011; 61:410-419. [PMID: 22016561 DOI: 10.1099/jmm.0.035006-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent studies suggest that human rhinovirus species A, B and C (HRV-ABCs) may be associated with both the common cold and severe acute respiratory illnesses (ARIs) such as bronchiolitis, wheezy bronchiolitis and pneumonia. However, the state and molecular epidemiology of these viruses in Japan is not fully understood. This study detected the genomes of HRV-ABCs from Japanese patients (92 cases, 0-36 years old, mean±sd 3.5±5.0 years) with various ARIs including upper respiratory infection, bronchiolitis, wheezy bronchiolitis, croup and pneumonia between January and December 2010. HRV-ABCs were provisionally type assigned from the pairwise distances among the strains. On phylogenetic trees based on the nucleotide sequences of the VP4/VP2 coding region, HRV-A, -B and -C were provisionally assigned to 14, 2 and 12 types, respectively. The present HRV-A and -C strains had a wide genetic diversity (>30 % divergence). The interspecies distances were 0.230±0.063 (mean±sd, HRV-A), 0.218±0.048 (HRV-B) and 0.281±0.105 (HRV-C), based on nucleotide sequences, and 0.075±0.036 (HRV-A), 0.049±0.022 (HRV-B) and 0.141±0.064 (HRV-C) at the deduced amino acid level. Furthermore, HRV-A and -C were the predominant species and were detected throughout the seasons. The results suggested that HRV-A and -C strains have a wide genetic divergence and are associated with various ARIs in Japan.
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Affiliation(s)
- Mika Arakawa
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Reiko Okamoto-Nakagawa
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi-shi, Yamaguchi 753-082, Japan
| | - Shoichi Toda
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi-shi, Yamaguchi 753-082, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, Yamagata-shi, Yamagata 990-0031, Japan
| | - Shunji Hasegawa
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube-shi, Yamaguchi 755-8505, Japan
| | - Reiji Hirano
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube-shi, Yamaguchi 755-8505, Japan
| | - Hiroyuki Wakiguchi
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube-shi, Yamaguchi 755-8505, Japan
| | - Keiko Kudo
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube-shi, Yamaguchi 755-8505, Japan
| | - Ryota Tanaka
- Department of Surgery, Kyorin University, School of Medicine, Mitaka-shi, Tokyo 181-8611, Japan
| | - Yukio Morita
- Department of Nutritional Science, Tokyo Kasei University, Itabashi-ku, Tokyo 173-8602, Japan
| | - Masahiro Noda
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Takashi Ichiyama
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube-shi, Yamaguchi 755-8505, Japan
| | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi-shi, Yamaguchi 753-082, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.,Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
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A molecular epidemiological study of respiratory viruses detected in Japanese children with acute wheezing illness. BMC Infect Dis 2011; 11:168. [PMID: 21663657 PMCID: PMC3123215 DOI: 10.1186/1471-2334-11-168] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 06/10/2011] [Indexed: 11/28/2022] Open
Abstract
Background Recent studies strongly suggest that some respiratory viruses are associated with the induction of acute wheezing and/or exacerbation of bronchial asthma. However, molecular epidemiology of these viruses is not exactly known. Methods Using PCR technology, we attempted to detect various respiratory viruses from 115 Japanese children. Furthermore, the detected viruses were subjected to homology, pairwise distance, and phylogenetic analysis. Results Viruses were detected from 99 (86.1%) patients. Respiratory syncytial virus (RSV) alone and human rhinovirus (HRV) alone were detected in 47 (40.9%) and 36 (31.3%) patients, respectively. Both RSV and HRV were detected in 14 (12.2%) patients. Human metapneumovirus (HMPV) alone and human parainfluenza virus (HPIV) alone were detected in 1 (0.9%) patient each, respectively. Homology and phylogenetic analyses showed that the RSV and HRV strains were classified into genetically diverse species or subgroups. In addition, RSV was the dominant virus detected in patients with no history of wheezing, whereas HRV was dominant in patients with a history of wheezing. Conclusions The results suggested that these genetically diverse respiratory viruses, especially RSV and HRV, might be associated with wheezing in Japanese children.
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Itagaki T, Abiko C, Ikeda T, Aoki Y, Seto J, Mizuta K, Ahiko T, Tsukagoshi H, Nagano M, Noda M, Mizutani T, Kimura H. Sequence and phylogenetic analyses of Saffold cardiovirus from children with exudative tonsillitis in Yamagata, Japan. ACTA ACUST UNITED AC 2010; 42:950-2. [DOI: 10.3109/00365548.2010.496791] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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