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Sugimoto S, Kawase M, Suwa R, Kume Y, Chishiki M, Ono T, Okabe H, Norito S, Hanaki KI, Hosoya M, Hashimoto K, Shirato K. Comparison of mutations in human parainfluenza viruses during passage in primary human bronchial/tracheal epithelial air-liquid interface cultures and cell lines. Microbiol Spectr 2024:e0116424. [PMID: 39078148 DOI: 10.1128/spectrum.01164-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 05/31/2024] [Indexed: 07/31/2024] Open
Abstract
Human parainfluenza virus (HPIV) causes respiratory infections, which are exacerbated in children and older people. Correct evaluation of viral characteristics is essential for the study of countermeasures. However, adaptation of viruses to cultured cells during isolation or propagation might select laboratory passage-associated mutations that modify the characteristics of the virus. It was previously reported that adaptation of HPIV3, but not other HPIVs, was avoided in human airway epithelia. To examine the influence of laboratory passage on the genomes of HPIV1-HPIV4, we evaluated the occurrence of mutations after passage in primary human bronchial/tracheal epithelial cell air-liquid interface (HBTEC-ALI) culture and conventional cultured cells (Vero cells expressing the transmembrane protease, serine 2, and normal Vero cells). The occurrence of mutations was significantly lower in HBTEC-ALI than in conventional culture. In HBTEC-ALI culture, most of the mutations were silent or remained at low variant frequency, resulting in less impact on the viral consensus sequence. In contrast, passage in conventional culture induced or selected genetic mutations at high frequency with passage-associated unique substitutions. High mutagenesis of hemagglutinin-neuraminidase was commonly observed in all four HPIVs, and mutations even occurred in a single passage. In addition, in HPIV1 and HPIV2, mutations in the large protein were more frequent. These results indicate that passage in HBTEC-ALI culture is more suitable than conventional culture for maintaining the original characteristics of clinical isolates in all four HPIVs, which can help with the understanding of viral pathogenesis. IMPORTANCE Adaptation of viruses to cultured cells can increase the risk of misinterpretation in virological characterization of clinical isolates. In human parainfluenza virus (HPIV) 3, it has been reported that the human airway epithelial and lung organoid models are preferable for the study of viral characteristics of clinical strains without mutations. Therefore, we analyzed clinical isolates of all four HPIVs for the occurrence of mutations after five laboratory passages in human bronchial/tracheal epithelial cell air-liquid interface (HBTEC-ALI) or conventional culture. We found a high risk of hemagglutinin-neuraminidase mutagenesis in all four HPIVs in conventional cultured cells. In addition, in HPIV1 and HPIV2, mutations of the large protein were also more frequent in conventional cultured cells than in HBTEC-ALI culture. HBTEC-ALI culture was useful for maintaining the original sequence and characteristics of clinical isolates in all four HPIVs. The present study contributes to the understanding of HPIV pathogenesis and antiviral strategies.
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Affiliation(s)
- Satoko Sugimoto
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
- Research Center for Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Miyuki Kawase
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Suwa
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yohei Kume
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Mina Chishiki
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Takashi Ono
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hisao Okabe
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Sakurako Norito
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Ken-Ichi Hanaki
- Research Center for Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Koichi Hashimoto
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Kazuya Shirato
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
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2
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Kawase M, Suwa R, Sugimoto S, Kakizaki M, Kume Y, Chishiki M, Ono T, Okabe H, Norito S, Ujike M, Hosoya M, Hashimoto K, Shirato K. Evidence of the simultaneous replications of active viruses in specimens positive for multiple respiratory viruses. Microbiol Spectr 2024; 12:e0192023. [PMID: 38051050 PMCID: PMC10783086 DOI: 10.1128/spectrum.01920-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/04/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Since the pandemic of coronavirus diseases 2019, the use of real-time PCR assay has become widespread among people who were not familiar with it in virus detection. As a result, whether a high real-time PCR value in one time test indicates virus transmissibly became a complicated social problem, regardless of the difference in assays and/or amplification conditions, the time and number of diagnostic test during the time course of infection. In addition, the multiple positives in the test of respiratory viruses further add to the confusion in the interpretation of the infection. To address this issue, we performed virus isolation using pediatric SARI (severe acute respiratory infections) specimens on air-liquid interface culture of human bronchial/tracheal epithelial cell culture. The result of this study can be a strong evidence that the specimens showing positivity for multiple agents in real-time PCR tests possibly contain infectious viruses.
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Affiliation(s)
- Miyuki Kawase
- Department of Virology III, National Institute of Infectious Disease, Gakuen, Musashimurayama, Tokyo, Japan
| | - Reiko Suwa
- Department of Virology III, National Institute of Infectious Disease, Gakuen, Musashimurayama, Tokyo, Japan
| | - Satoko Sugimoto
- Department of Virology III, National Institute of Infectious Disease, Gakuen, Musashimurayama, Tokyo, Japan
| | - Masatoshi Kakizaki
- Department of Virology III, National Institute of Infectious Disease, Gakuen, Musashimurayama, Tokyo, Japan
| | - Yohei Kume
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Mina Chishiki
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Takashi Ono
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Hisao Okabe
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Sakurako Norito
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Makoto Ujike
- Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Koichi Hashimoto
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Kazuya Shirato
- Department of Virology III, National Institute of Infectious Disease, Gakuen, Musashimurayama, Tokyo, Japan
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3
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Morales-Jadán D, Muslin C, Viteri-Dávila C, Coronel B, Castro-Rodríguez B, Vallejo-Janeta AP, Henríquez-Trujillo AR, Garcia-Bereguiain MA, Rivera-Olivero IA. Coinfection of SARS-CoV-2 with other respiratory pathogens in outpatients from Ecuador. Front Public Health 2023; 11:1264632. [PMID: 37965509 PMCID: PMC10641819 DOI: 10.3389/fpubh.2023.1264632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/04/2023] [Indexed: 11/16/2023] Open
Abstract
Worldwide, the COVID-19 pandemic caused by SARS-CoV-2 has enormously impacted healthcare systems, especially in low and middle-income countries. Coinfections with respiratory pathogens in COVID-19 patients may contribute to worse outcomes. This study identified the presence of 12 viral coinfections and pneumococcal carriers among individuals with SARS-CoV-2 infection in outpatient and community settings in Ecuador. From January 2020 to November 2021, 215 nasopharyngeal and nasal swabs were taken from individuals who reported symptoms of COVID-19 or had known exposure to someone with confirmed or suspected COVID-19. One hundred fifty-eight tested positive for SARS-CoV-2 by RT-qPCR and coinfections were detected in 12% (19/158) of SARS-CoV-2-positive patients; the most frequent coinfection was with influenza A virus at 4.4% (7/158; 95% CI: 1.2-7.6), followed by respiratory syncytial virus with 3.1% (5/158; 95% CI: 0.4-5.8), and finally rhinovirus and human coronavirus NL63 with 1.2% (2/158). Pneumococcal carriage was detected in 3.7% (6/158; 95% CI: 0.76-6.64) of SARS-CoV-2 cases. Influenza B, adenovirus, human metapneumovirus (HMPV), parainfluenza virus types 1, 2, and 3, and human coronavirus HKU1 were undetected. To our knowledge, this is the first study of coinfection of SARS-CoV-2 and respiratory pathogens performed on outpatients in Latin America. The high proportion of outpatients with viral coinfections reported in our cohort allows us to suggest that testing for SARS-CoV-2 and other common respiratory pathogens should be carried out to ensure accurate diagnoses, prompt patient treatment, and appropriate isolation.
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Affiliation(s)
| | - Claire Muslin
- One Health Research Group, Universidad de Las Américas, Quito, Ecuador
| | | | - Barbara Coronel
- One Health Research Group, Universidad de Las Américas, Quito, Ecuador
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4
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Nearly Complete Genome Sequences of 12 Types of Human Rhinoviruses Isolated from Pediatric Inpatients in Fukushima, Japan. Microbiol Resour Announc 2022; 11:e0052922. [PMID: 35862917 PMCID: PMC9387279 DOI: 10.1128/mra.00529-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We reported nearly complete genomic sequences of 12 serotypes of human rhinoviruses (HRVs) isolated from pediatric inpatients in Fukushima, Japan using an air-liquid interface culture of human bronchial tracheal epithelial cells. We found that various serotypes of HRV circulated locally and simultaneously from 2018 to 2021.
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Ten Nearly Complete Genome Sequences of Human Orthorubulavirus 4 Isolated from Pediatric Inpatients in Fukushima, Japan. Microbiol Resour Announc 2022; 11:e0041122. [PMID: 35678587 PMCID: PMC9302191 DOI: 10.1128/mra.00411-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We report 10 nearly complete genomic sequences of human orthorubulavirus 4, also called human parainfluenza virus 4 (HPIV4), isolated from pediatric inpatients with respiratory infections in Fukushima, Japan, by using an air-liquid interface culture of human bronchial and tracheal epithelial cells.
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Hamamoto I, Takahashi H, Shimazaki N, Nakamura K, Mizuta K, Sato K, Nishimura H, Yamamoto N, Hasegawa H, Odagiri T, Tashiro M, Nobusawa E. Suitability of NIID-MDCK cells as a substrate for cell-based influenza vaccine development from the perspective of adventitious virus susceptibility. Microbiol Immunol 2022; 66:361-370. [PMID: 35545856 DOI: 10.1111/1348-0421.12985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/27/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022]
Abstract
The practical use of cell-based seasonal influenza vaccines is currently being considered in Japan. From the perspective of adventitious virus contamination, we assessed the suitability of NIID-MDCK cells (NIID-MDCK-Cs) as a safe substrate for the isolation of influenza viruses from clinical specimens. We first established a sensitive multiplex real-time PCR system to screen for 27 respiratory viruses and used it on 34 virus samples that were isolated by passaging influenza-positive clinical specimens in NIID-MDCK-Cs. Incidentally, the limit of detection of the system was 100 or fewer genome copies per reaction. In addition to influenza viruses, human enterovirus 68 (HEV-D68) genomes were detected in two samples after two or three passages in NIID-MDCK-Cs. To further investigate the susceptibility of NIID-MDCK-Cs to adventitious viruses, eight common respiratory viruses were subjected to passages in NIID-MDCK-Cs. The genome copy numbers of seven viruses other than parainfluenza 3 decreased below the limit of detection (LOD) by passage 4. By passaging in NIID-MDCK-Cs, the genome numbers of the input HEV-D68, 1 x 108 copies, declined to 102 at passage 3 and to under the LOD at passage 4, whereas those of the other six viruses were under the LOD by passage 3. These results implied that during the process of isolating influenza viruses with NIID-MDCK-Cs, contaminating viruses other than parainfluenza 3 can be efficiently removed by passages in NIID-MDCK-Cs. NIID-MDCK-Cs could be a safe substrate for isolating influenza viruses that can be used to develop cell-based influenza vaccine candidate viruses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Itsuki Hamamoto
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Hitoshi Takahashi
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Noriko Shimazaki
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Kazuya Nakamura
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Ko Sato
- Virus Research Center, Sendai Medical Center, National Hospital Organization, Sendai, Japan
| | - Hidekazu Nishimura
- Virus Research Center, Sendai Medical Center, National Hospital Organization, Sendai, Japan
| | - Norio Yamamoto
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan.,Department of Microbiology, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Hideki Hasegawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Takato Odagiri
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Masato Tashiro
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Eri Nobusawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
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7
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Kume Y, Hashimoto K, Chishiki M, Norito S, Suwa R, Ono T, Mochizuki I, Mashiyama F, Ishibashi N, Suzuki S, Sakuma H, Takahashi H, Takeda M, Shirato K, Hosoya M. Changes in virus detection in hospitalized children before and after the severe acute respiratory syndrome coronavirus 2 pandemic. Influenza Other Respir Viruses 2022; 16:837-841. [PMID: 35488324 PMCID: PMC9343337 DOI: 10.1111/irv.12995] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022] Open
Abstract
The impact of strengthening preventive measures against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection on the prevalence of respiratory viruses in children was examined. After the SARS‐CoV‐2 pandemic, the rate of multiple virus detection among hospitalized children decreased. Immediately after the SARS‐CoV‐2 pandemic, respiratory syncytial and parainfluenza viruses were rarely detected and subsequently reemerged. Human metapneumovirus and influenza virus were not consistently detected. Non‐enveloped viruses (bocavirus, rhinovirus, and adenovirus) were detected to some extent even after the pandemic. Epidemic‐suppressed infectious diseases may reemerge as susceptibility accumulates in the population and should continue to be monitored.
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Affiliation(s)
- Yohei Kume
- Department of Pediatrics, Fukushima Medical University, Fukushima, Japan
| | - Koichi Hashimoto
- Department of Pediatrics, Fukushima Medical University, Fukushima, Japan
| | - Mina Chishiki
- Department of Pediatrics, Fukushima Medical University, Fukushima, Japan
| | - Sakurako Norito
- Department of Pediatrics, Fukushima Medical University, Fukushima, Japan
| | - Reiko Suwa
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Takashi Ono
- Department of Pediatrics, Fukushima Medical University, Fukushima, Japan
| | - Izumi Mochizuki
- Department of Pediatrics, Ohara General Hospital, Fukushima, Japan
| | - Fumi Mashiyama
- Department of Pediatrics, Hoshi General Hospital, Koriyama, Japan
| | | | - Shigeo Suzuki
- Department of Pediatrics, Ohara General Hospital, Fukushima, Japan
| | - Hiroko Sakuma
- Department of Pediatrics, Hoshi General Hospital, Koriyama, Japan
| | - Hitoshi Takahashi
- Influenza and Respiratory Virus Research Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Makoto Takeda
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Kazuya Shirato
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, Fukushima Medical University, Fukushima, Japan
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Kume Y, Hashimoto K, Shirato K, Norito S, Suwa R, Chishiki M, Ono T, Mashiyama F, Mochizuki I, Sato M, Ishibashi N, Suzuki S, Sakuma H, Takahashi H, Takeda M, Hosoya M. Epidemiological and clinical characteristics of infections with seasonal human coronavirus and respiratory syncytial virus in hospitalized children immediately before the coronavirus disease 2019 pandemic. J Infect Chemother 2022; 28:859-865. [PMID: 35307263 PMCID: PMC8920880 DOI: 10.1016/j.jiac.2022.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 11/18/2022]
Abstract
Introduction Seasonal human coronavirus (HCoV)-229E, -NL63, -OC43, and -HKU1 are seasonal coronaviruses that cause colds in humans. However, the clinical characteristics of pediatric inpatients infected with HCoVs are unclear. This study aimed to compare and clarify the epidemiological and clinical features of HCoVs and respiratory syncytial virus (RSV), which commonly causes severe respiratory infections in children. Methods Nasopharyngeal swabs were collected from all pediatric inpatients with respiratory symptoms at two secondary medical institutions in Fukushima, Japan. Eighteen respiratory viruses, including RSV and four HCoVs, were detected via reverse transcription-polymerase chain reaction. Results Of the 1757 specimens tested, viruses were detected in 1272 specimens (72.4%), with 789 single (44.9%) and 483 multiple virus detections (27.5%). RSV was detected in 639 patients (36.4%) with no difference in clinical characteristics between RSV-A and RSV-B. HCoV was detected in 84 patients (4.7%): OC43, NL63, HKU1, and 229E in 25 (1.4%), 26 (1.5%), 23 (1.3%), and 16 patients (0.9%), respectively. Patients with HCoV monoinfection (n = 35) had a significantly shorter period from onset to hospitalization (median [interquartile range] days, 2 [1–4.5] vs. 4 [2–5]), significantly shorter hospitalization stays (4 [3–5] vs. 5 [4–6]), and more cases of upper respiratory infections (37.1% vs. 3.9%) and croup (17.1% vs. 0.3%) but less cases of lower respiratory infection (54.3% vs. 94.8%) than patients with RSV monoinfection (n = 362). Conclusion Seasonal HCoV-infected patients account for approximately 5% of children hospitalized for respiratory tract infections and have fewer lower respiratory infections and shorter hospital stays than RSV-infected patients.
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9
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Thirteen Nearly Complete Genome Sequences of Human Bocavirus 1 Isolated from Pediatric Inpatients in Fukushima, Japan. Microbiol Resour Announc 2022; 11:e0102721. [PMID: 35049344 PMCID: PMC8772594 DOI: 10.1128/mra.01027-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We report 13 genomic sequences of human bocavirus 1 isolated from pediatric inpatients in Fukushima, Japan, using an air-liquid interface culture of human bronchial tracheal epithelial cells. This work suggests the endemic circulation of a human bocavirus variant with a unique amino acid signature in Fukushima.
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10
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Nagasawa K, Ishiwada N. Disease burden of respiratory syncytial virus infection in the pediatric population in Japan. J Infect Chemother 2021; 28:146-157. [PMID: 34952776 DOI: 10.1016/j.jiac.2021.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/22/2021] [Accepted: 11/11/2021] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) is one of the most common causes of lower respiratory tract infections in children aged <5 years and is associated with long-term respiratory morbidities such as recurrent wheezing and asthma, decreased lung function, and allergic sensitization. The objective of this review was to evaluate the epidemiology and burden of RSV infection in the pediatric population in Japan. METHODS Studies indexed in PubMed and ICHUSHI databases during January 2010-December 2020 were manually reviewed. Data on proportion of RSV infections, seasonality, length of stay (LoS), mortality, medical expenses, and palivizumab use were extracted from the selected articles. RESULTS Ninety-three articles were included (PubMed, 64; ICHUSHI, 29). The proportion of patients/samples with an RSV infection was 5.5%-66.7%, and 6.0%-29.9% in the inpatient and outpatient departments, respectively. RSV infections generally occurred during autumn/winter; however, recently the peak has shifted to summer. The LoS was variable and depended on factors such as age, infection severity, wheezing, and RSV subgroups. Mortality rates varied from <1% to 19% depending on the infection severity. The average daily hospitalization and intensive care unit cost was JPY 34,548 while intensive care unit incurred an additional cost of JPY 541,293. Palivizumab was indicated for high-risk infants and 0%-3% of patients required hospitalization despite palivizumab use. CONCLUSIONS RSV imposes a significant burden on the Japanese healthcare system, suggesting a need to create awareness among caregivers of children, pregnant women and healthcare professionals to ensure early recognition of infection and adequate treatment or prophylaxis.
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Affiliation(s)
- Koo Nagasawa
- Division of Infectious Diseases, Chiba Children's Hospital, 579-1, Heta-cho, Midori-ku, Chiba 266-0007, Japan; Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2, Nitona-cho, Chuo-ku, Chiba 260-8717, Japan.
| | - Naruhiko Ishiwada
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba-shi, Chiba 260-8673, Japan
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11
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Mira-Iglesias A, Demont C, López-Labrador FX, Mengual-Chuliá B, García-Rubio J, Carballido-Fernández M, Tortajada-Girbés M, Mollar-Maseres J, Schwarz-Chavarri G, Puig-Barberà J, Díez-Domingo J. Role of age and birth month in infants hospitalized with RSV-confirmed disease in the Valencia Region, Spain. Influenza Other Respir Viruses 2021; 16:328-339. [PMID: 34821055 PMCID: PMC8818825 DOI: 10.1111/irv.12937] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 10/24/2021] [Indexed: 11/30/2022] Open
Abstract
Background RSV is the leading cause of hospital admissions in infants and the principal cause of bronchiolitis in young children. There is a lack of granular data on RSV‐associated hospitalization per season using laboratory confirmed results. Our current study addresses this issue and intends to fill this gap. Methods The study was conducted from 2014 through 2018, in 4 to 10 hospitals in the Valencia Region, Spain. Infants included in this study were admitted in hospital through the Emergency Department with a respiratory complaint and tested by RT‐PCR for RSV in a central laboratory. Results Incidence rates of RSV‐associated hospitalization varied by season and hospital. Overall, the highest incidence rates were observed in 2017/2018. RSV‐associated hospitalization was highest in infants below 3 months of age and in those born before or at the beginning of the RSV season. Almost 54% of total infants hospitalized with laboratory confirmed RSV were found to be born outside the season, from April to October. The RSV positivity rate by ICD‐10 discharged codes varied by season and age with results from 48% to 57% among LRI (J09‐J22). Conclusion The study was instrumental in bringing forth the time unpredictability of RSV epidemics, the critical impact of age, and the comparable distribution of RSV‐associated hospitalization in infants born on either side of the RSV season. These data could help in better characterization of the population that drives the healthcare burden and is crucial for the development of future immunization strategies, especially with upcoming vaccines in against RSV.
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Affiliation(s)
- Ainara Mira-Iglesias
- Área de Investigación en Vacunas, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Clarisse Demont
- RSV Medical Evidence Generation, Sanofi Pasteur, Lyon, France
| | - F Xavier López-Labrador
- Laboratorio de Virología, Área de Genómica y Salud. Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain.,Consorcio de Investigación Biomédica de Epidemiología y Salud Pública (CIBER-ESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Beatriz Mengual-Chuliá
- Laboratorio de Virología, Área de Genómica y Salud. Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Javier García-Rubio
- Área de Investigación en Vacunas, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Mario Carballido-Fernández
- Preventive Medicine, Hospital General Universitario de Castellón, Castellón de la Plana, Spain.,Medicine Department, Universidad CEU Cardenal Herrera, Castellón de la Plana, Spain
| | | | - Juan Mollar-Maseres
- Preventive Medicine, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Germán Schwarz-Chavarri
- Out-of-Hospital Family and Community Medicine, Hospital General Universitario de Alicante, Alicante, Spain
| | - Joan Puig-Barberà
- Área de Investigación en Vacunas, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Javier Díez-Domingo
- Área de Investigación en Vacunas, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
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- Área de Investigación en Vacunas, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
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Shirato K, Tomita Y, Katoh H, Yamada S, Fukushi S, Matsuyama S, Takeda M. Performance evaluation of real-time RT-PCR assays for detection of severe acute respiratory syndrome coronavirus-2 developed by the National Institute of Infectious Diseases, Japan. Jpn J Infect Dis 2021; 74:465-472. [PMID: 33642428 DOI: 10.7883/yoken.jjid.2020.1079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Soon after the December 2019 outbreak of coronavirus disease 2019 in Wuhan, China, a protocol for real-time RT-PCR assay detection of severe acute respiratory syndrome coronavirus (SARS-CoV-2) was established by the National Institute of Infectious Diseases (NIID) in Japan. The protocol used Charité's nucleocapsid (Sarbeco-N) and NIID's nucleocapsid (NIID-N2) assays. During the following months, SARS-CoV-2 spread causing a global pandemic, and a variety of SARS-CoV-2 sequences were registered to public databases, such as the Global Initiative on Sharing All Influenza Data (GISAID). In this study, we evaluated the newly developed S2 assay (NIID-S2) to replace the Sarbeco-N assay and the performance of NIID-N2 and NIID-S2 assays, referring mismatches in the primer/probe targeted region. We found the analytical sensitivity and specificity of the NIID-S2 set were comparable to the NIID-N2 assay, and the detection rate for clinical specimens was identical to that of the NIID-N2 assay. Furthermore, among available sequences (approximately 192,000), the NIID-N2 and NIID-S2 sets had 2.6% and 1.2% mismatched sequences, respectively, although most of these mismatches did not affect the amplification efficiency, with the exception of the 3' end of the NIID-N2 forward primer. These findings indicate that the previously developed NIID-N2 assay remains suitable for the detection SARS-CoV-2 with support of the newly developed NIID-S2 set.
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Affiliation(s)
- Kazuya Shirato
- Department of Virology III, National Institute of Infectious Disease, Japan
| | - Yuriko Tomita
- Department of Virology III, National Institute of Infectious Disease, Japan
| | - Hiroshi Katoh
- Department of Virology III, National Institute of Infectious Disease, Japan
| | - Souichi Yamada
- Departiment of Virology I, National Institute of Infectious Disease, Japan
| | - Shuetsu Fukushi
- Departiment of Virology I, National Institute of Infectious Disease, Japan
| | - Shutoku Matsuyama
- Department of Virology III, National Institute of Infectious Disease, Japan
| | - Makoto Takeda
- Department of Virology III, National Institute of Infectious Disease, Japan
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Liu K, Jing H, Chen Y, Zheng X, Jiang H, Kong D, Zheng Y, Chen S, Liu P, Jiang Y. Evaluation of TaqMan Array card (TAC) for the detection of 28 respiratory pathogens. BMC Infect Dis 2020; 20:820. [PMID: 33172401 PMCID: PMC7653217 DOI: 10.1186/s12879-020-05562-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Respiratory infections are a serious threat to human health. So, rapid detection of all respiratory pathogens can facilitate prompt treatment and prevent the deterioration of respiratory disease. Previously published primers and probes of the TaqMan array card (TAC) for respiratory pathogens are not sensitive to Chinese clinical specimens. This study aimed to develop and improve the TAC assay to detect 28 respiratory viral and bacterial pathogens in a Chinese population. Methods To improve the sensitivity, we redesigned the primers and probes, and labeled the probes with minor groove binders. The amplification efficiency, sensitivity, and specificity of the primers and probes were determined using target-gene containing standard plasmids. The detection performance of the TAC was evaluated on 754 clinical specimens and the results were compared with those from conventional methods. Results The performance of the TAC assay was evaluated using 754 clinical throat swab samples and the results were compared with those from gold-standard methods. The sensitivity and specificity were 95.4 and 96.6%, respectively. The lowest detection limit of the TAC was 10 to 100 copies/μL. Conclusions TAC is an efficient, accurate, and high-throughput approach to detecting multiple respiratory pathogens simultaneously and is a promising tool for the identification of pathogen outbreaks.
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Affiliation(s)
- Keke Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,Shandong Academy of Clinical Medicine, Shandong Provincial Hospital, Jinan, 250021, China
| | - Hongbo Jing
- Department of Laboratory Medicine, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Ying Chen
- School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Xin Zheng
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yvling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shuiping Chen
- Department of Laboratory Medicine, the Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China.
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
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14
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Komabayashi K, Matoba Y, Tanaka S, Seto J, Aoki Y, Ikeda T, Shimotai Y, Matsuzaki Y, Itagaki T, Mizuta K. Longitudinal epidemiology of human coronavirus OC43 in Yamagata, Japan, 2010-2017: Two groups based on spike gene appear one after another. J Med Virol 2020; 93:945-951. [PMID: 32720708 DOI: 10.1002/jmv.26361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/03/2020] [Accepted: 07/18/2020] [Indexed: 01/01/2023]
Abstract
Human coronavirus OC43 (HCoV-OC43) is divided into genotypes A to H based on genetic recombination including the spike (S) gene. To investigate the longitudinal transition of the phylogenetic feature of the HCoV-OC43 S gene in a community, phylogenetic analysis of the S1 region of the S gene was conducted using 208 strains detected in Yamagata during 2010 to 2017 with reference strains of the genotype. The S1 sequences were divisible into four groups: A to D. All Yamagata strains belonged to either group B or group D. In group B, 46 (90.2%) out of 51 Yamagata strains were clustered with those of genotype E reference strains (cluster E). In group D, 28 (17.8%) and 122 (77.7%) out of 157 Yamagata strains were clustered, respectively, with genotype F and genotype G reference strains. In cluster G, 28 strains formed a distinct cluster. Monthly distributions of HCoV-OC43 in Yamagata in 2010 to 2017 revealed that group B and group D appeared one after another. In group B, the cluster E strains were prevalent recurrently. In conclusion, epidemics of HCoV-OC43 in Yamagata, Japan might be attributable to two genetically different groups: group B showed a recurrent epidemic of strains belonging to a single phylogenetic cluster and group D showed epidemic strains belonging to multiple clusters.
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Affiliation(s)
- Kenichi Komabayashi
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Yohei Matoba
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Shizuka Tanaka
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Junji Seto
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Yoko Aoki
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Tatsuya Ikeda
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Yoshitaka Shimotai
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Yoko Matsuzaki
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | | | - Katsumi Mizuta
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
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15
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Clinical evaluation of fully automated molecular diagnostic system "Simprova" for influenza virus, respiratory syncytial virus, and human metapneumovirus. Sci Rep 2020; 10:13496. [PMID: 32782312 PMCID: PMC7419501 DOI: 10.1038/s41598-020-70090-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022] Open
Abstract
Influenza virus, respiratory syncytial virus, and human metapneumovirus commonly cause acute upper and lower respiratory tract infections, especially in children and the elderly. Although rapid antigen detection tests for detecting these infections have been introduced recently, these are less sensitive than nucleic acid amplification tests. More recently, highly sensitive point-of-care testings (POCTs) have been developed based on nucleic acid amplification tests, which are easy to use in clinical settings. In this study, loop-mediated isothermal amplification (LAMP)-based POCT “Simprova” to detect influenza A and B viruses, respiratory syncytial virus, and human metapneumovirus was developed. Simprova system is fully automated and does not require skilled personnel. In addition, positive results can be achieved faster than with PCR. In this study, the accuracy of the POCT was retrospectively analyzed using 241 frozen stocked specimens. Additionally, the usability of the Simprova at clinical sites was assessed in a prospective clinical study using 380 clinical specimens and compared to those of real-time PCR and rapid antigen detection test. The novel LAMP-based POCT demonstrated high sensitivity and specificity in characterizing clinical specimens from patients with influenza-like illnesses. The Simprova is a powerful tool for early diagnosis of respiratory viral infections in point-of-care settings.
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Shirato K, Nao N, Matsuyama S, Takeda M, Kageyama T. An Ultra-Rapid Real-Time RT-PCR Method Using the PCR1100 to Detect Severe Acute Respiratory Syndrome Coronavirus-2. Jpn J Infect Dis 2020; 74:29-34. [PMID: 32611983 DOI: 10.7883/yoken.jjid.2020.324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Wuhan, China, in December 2019, has rapidly spread worldwide. SARS-CoV-2 is usually detected via real-time reverse-transcription polymerase chain reaction (RT-PCR). However, the increase in specimen load in institutions/hospitals necessitates a simpler detection system. Here, we present an ultra-rapid, real-time RT-PCR assay for SARS-CoV-2 detection using PCR1100 device. Although PCR1100 tests only one specimen at a time, the amplification period is less than 20 min and the sensitivity and specificity match those of conventional real-time RT-PCR performed on large instruments. The method is potentially helpful when daily multiple SARS-CoV-2 testing is needed, for example to confirm virus-free status prior to patient discharge.
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Affiliation(s)
- Kazuya Shirato
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, Japan
| | - Naganori Nao
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, Japan
| | - Shutoku Matsuyama
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, Japan
| | - Makoto Takeda
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, Japan
| | - Tsutomu Kageyama
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
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17
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Takagi Y, Imamura T, Endo S, Hayashi K, Akiyama S, Ikuta Y, Kawaguchi T, Sumita T, Katori T, Hashino M, Saito S, Odagiri T, Oba K, Kuroda M, Kageyama T. Neurogenic pulmonary edema following febrile status epilepticus in a 22-month-old infant with multiple respiratory virus co-detection: a case report. BMC Infect Dis 2020; 20:388. [PMID: 32487032 PMCID: PMC7266127 DOI: 10.1186/s12879-020-05115-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 05/24/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Neurogenic pulmonary edema is a rare but serious complication of febrile status epilepticus in children. Comprehensive screening for viral pathogens is seldomly performed in the work-up of febrile children. CASE PRESENTATION A 22-month-old girl presented with her first episode of febrile status epilepticus, after which she developed acute pulmonary edema and respiratory failure. After the termination of seizure activity, the patient was intubated and managed on mechanical ventilation in the emergency room. The resolution of respiratory failure, as well as the neurological recovery, was achieved 9 h after admission, and the patient was discharged 6 days after admission without any complications. Molecular biological diagnostic methods identified the presence of human coronavirus HKU1, influenza C virus, and human parainfluenza virus 2 from the patient's nasopharyngeal specimens. CONCLUSIONS Neurogenic pulmonary edema following febrile status epilepticus was suspected to be the etiology of our patient's acute pulmonary edema and respiratory failure. Timely seizure termination and rapid airway and respiratory intervention resulted in favorable outcomes of the patient. Molecular biological diagnostic methods identified three respiratory viruses; however, their relevance and association with clinical symptoms remain speculative.
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Affiliation(s)
- Yoshie Takagi
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
- Department of Emergency Medicine and Critical Care, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
| | - Takeaki Imamura
- Department of Emergency Medicine and Critical Care, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo, Aoba, Sendai, 980-8575, Japan
| | - Shota Endo
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
| | - Kenta Hayashi
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
| | - Satoka Akiyama
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
| | - Yoji Ikuta
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
| | - Takahiro Kawaguchi
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
| | - Tomoko Sumita
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
| | - Tatsuo Katori
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
| | - Masanori Hashino
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Shinji Saito
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Takato Odagiri
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo, 187-8510, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Tsutomu Kageyama
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan.
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18
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Kazuya S, Nao N, Matsuyama S, Kageyama T. Ultra-Rapid Real-Time RT-PCR Method for Detecting Middle East Respiratory Syndrome Coronavirus Using a Mobile PCR Device, PCR1100. Jpn J Infect Dis 2019; 73:181-186. [PMID: 31875608 DOI: 10.7883/yoken.jjid.2019.400] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) is usually diagnosed through highly sensitive and specific genetic tests such as real-time reverse transcription polymerase chain reaction (RT-PCR). Currently, two real-time RT-PCR assays targeting the upE and ORF1a regions of the MERS-CoV genome are widely used, and these are the standard assays recommended by the World Health Organization (WHO). The MERS outbreaks to date suggest that rapid diagnosis and subsequent isolation of infected patients, particularly superspreaders, are critical for containment. However, conventional real-time RT-PCR assays require large laboratory instruments, and amplification takes approximately 2 h. These disadvantages limit rapid diagnosis. Here, an ultra-rapid real-time RT-PCR test was established comprising a multiplex assay for upE and ORF1a running on a mobile PCR1100 device. As few as five copies of the MERS-CoV RNA can be detected within 20 min using the standard WHO assays in the mobile PCR device, with the sensitivity and specificity being similar to those of a conventional real-time PCR instrument such as the LightCyler, thereby enabling timely intervention to control MERS-CoV infection.
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Affiliation(s)
- Shirato Kazuya
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases
| | - Naganori Nao
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases
| | - Shutoku Matsuyama
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases
| | - Tsutomu Kageyama
- Influenza Virus Research Center, National Institute of Infectious Diseases
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19
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Kanbayashi D, Kaida A, Hirai Y, Yamamoto SP, Fujimori R, Okada M, Kubo H, Iritani N. An Epidemic of Hand, Foot, and Mouth Disease Caused by Coxsackievirus A6 in Osaka City, Japan, in 2017. Jpn J Infect Dis 2019; 72:334-336. [PMID: 31061358 DOI: 10.7883/yoken.jjid.2018.532] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The second largest epidemic of hand, foot, and mouth disease since 1982 occurred in 2017, which involved 6,173 cases in Osaka City, Japan. The main causative agent was coxsackievirus A6 (CV-A6). Phylogenetic analysis revealed that the detected CV-A6 strains belonged to genetic groups A3 and A4 in clade A.
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Affiliation(s)
| | | | | | | | - Ryoko Fujimori
- Osaka City Public Health Bureau, Osaka City Health Center
| | - Megumi Okada
- Osaka City Public Health Bureau, Osaka City Health Center
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20
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Takayama I, Nakauchi M, Takahashi H, Oba K, Semba S, Kaida A, Kubo H, Saito S, Nagata S, Odagiri T, Kageyama T. Development of real-time fluorescent reverse transcription loop-mediated isothermal amplification assay with quenching primer for influenza virus and respiratory syncytial virus. J Virol Methods 2019; 267:53-58. [PMID: 30831121 PMCID: PMC7113748 DOI: 10.1016/j.jviromet.2019.02.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/31/2019] [Accepted: 02/28/2019] [Indexed: 12/20/2022]
Abstract
Influenza virus and respiratory syncytial virus cause acute upper and lower respiratory tract infections, especially in children and the elderly. Early treatment for these infections is thought to be important, so simple and sensitive detection methods are needed for use at clinical sites. Therefore, in this study, real-time reverse transcription loop-mediated isothermal amplification assays with quenching primer for influenza virus and respiratory syncytial virus were developed. Evaluation of a total of 113 clinical specimens compared to real-time RT-PCR assays showed that the novel assays could distinguish between the types and subtypes of influenza virus and respiratory syncytial virus and had 100% diagnostic specificity. The diagnostic sensitivity of each assay exceeded 85.0% and the assays showed sufficient clinical accuracy. Furthermore, positive results could be obtained in around 15 min using the novel assays in cases with high concentrations of virus. The developed assays should be useful for identifying influenza virus and respiratory syncytial virus cases not only in experimental laboratories but also in hospital and quarantine laboratories.
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Affiliation(s)
- Ikuyo Takayama
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Mina Nakauchi
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hitoshi Takahashi
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira-shi, Tokyo 187-0002, Japan
| | - Shohei Semba
- Eiken Chemical Co. Ltd., 4-19-9 Taito, Taito-ku, Tokyo 110-8408, Japan
| | - Atsushi Kaida
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Hideyuki Kubo
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Shinji Saito
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Shiho Nagata
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Takato Odagiri
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Tsutomu Kageyama
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.
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21
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Saito S, Takayama I, Nakauchi M, Nagata S, Oba K, Odagiri T, Kageyama T. Development and evaluation of a new real-time RT-PCR assay for detecting the latest H9N2 influenza viruses capable of causing human infection. Microbiol Immunol 2019; 63:21-31. [PMID: 30599081 PMCID: PMC6590187 DOI: 10.1111/1348-0421.12666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 12/25/2022]
Abstract
The H9N2 subtype of avian influenza A viruses (AIV) has spread among domestic poultry and wild birds worldwide. H9N2 AIV is sporadically transmitted to humans from avian species. A total of 42 laboratory‐confirmed cases of non‐fatal human infection with the Eurasian Y280 and G1 lineages have been reported in China, Hong Kong, Bangladesh and Egypt since 1997. H9N2 AIV infections in poultry have become endemic in Asia and the Middle East and are a major source of viral internal genes for other AIV subtypes, such that continuous monitoring of H9N2 AIV is recommended. In this study, a new, one‐step, real‐time RT‐PCR assay was developed to detect two major Eurasian H9 lineages of AIV capable of causing human infection. The sensitivity of this assay was determined using in vitro‐transcribed RNA, and the detection limit was approximately 3 copies/reaction. In this assay, no cross‐reactivity was observed against RNA from H1–15 subtypes of influenza A viruses, influenza B viruses and other viral respiratory pathogens. In addition, this assay could detect the H9 hemagglutinin (HA) gene from artificially reconstituted clinical samples spiked with H9N2 virus without any non‐specific reactions. Therefore, this assay is highly sensitive and specific for H9 HA detection. The assay is useful both for diagnostic purposes in cases of suspected human infection with influenza H9N2 viruses and for the surveillance of both avian and human influenza viruses.
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Affiliation(s)
- Shinji Saito
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Ikuyo Takayama
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Mina Nakauchi
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Shiho Nagata
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, 8-1-1 Hanakoganei, Kodaira, Tokyo 187-8510, Japan
| | - Takato Odagiri
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Tsutomu Kageyama
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
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22
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Nakauchi M, Takayama I, Takahashi H, Semba S, Saito S, Kubo H, Kaida A, Oba K, Nagata S, Odagiri T, Kageyama T. Development of real-time fluorescent reverse transcription loop-mediated isothermal amplification assays for rhinovirus detection. J Med Virol 2019; 91:1232-1238. [PMID: 30735248 PMCID: PMC7166982 DOI: 10.1002/jmv.25427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 02/04/2023]
Abstract
Human rhinoviruses (RVs) belong to the genus Enterovirus of the family Picornaviridae, and are classified into RV-A, -B, and -C species. Two assays were developed to detect RVs by a real-time fluorescent reverse transcription loop-mediated isothermal amplification method: one was designed based on the 5'-untranslated regions (UTRs) of RV-A and -B, and the other was designed based on the 5'-UTR of RV-C. The competence of both assays for the diagnosis of RV infection was tested using isolated viruses and compared with real-time reverse transcription polymerase chain reaction assays on clinical specimens. Neither assay demonstrated cross-reactivity with other tested enteroviruses, and they detected 19 out of 21 tested RV-As and seven out of eight tested RV-Cs. The specificity of the assays was 100% for the detection of RVs and their sensitivity for RV-A and RV-C was 86.3% and 77.3%, respectively, on clinical specimens by the combined use of both assays. Considering that both developed assays were highly specific and detected the majority of recently circulating RVs, they are helpful for the diagnosis of RV infection. Consequently, the results generated by these assays will enhance the surveillance of respiratory illness and the study of the roles of RVs associated with clinical features and disease severity.
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Affiliation(s)
- Mina Nakauchi
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Ikuyo Takayama
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Hitoshi Takahashi
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Shohei Semba
- Eiken Chemical Co, Ltd, Taito, Taito-ku, Tokyo, Japan
| | - Shinji Saito
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Hideyuki Kubo
- Division of Microbiology, Osaka Institute of Public Health, Tojo-cho, Tennoji-ku, Osaka, Japan
| | - Atsushi Kaida
- Division of Microbiology, Osaka Institute of Public Health, Tojo-cho, Tennoji-ku, Osaka, Japan
| | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, Hanakoganei, Kodaira-shi, Tokyo, Japan
| | - Shiho Nagata
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Takato Odagiri
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Tsutomu Kageyama
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
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Liu GS, Niu PH, Zhao SC, Lu RJ, Tan WJ. Detection of six common human paramyxoviruses in patients with acute febrile respiratory symptoms using a novel multiplex real-time RT-PCR assay. J Med Virol 2018; 91:564-569. [PMID: 30358912 PMCID: PMC7167037 DOI: 10.1002/jmv.25350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/18/2018] [Indexed: 11/16/2022]
Abstract
Human metapneumovirus (hMPV), respiratory syncytial virus type A (RSV‐A), RSV‐B, and human parainfluenza viruses 1, 2, and 3 (HPIV‐1, HPIV‐2, and HPIV‐3) are common respiratory paramyxoviruses. Here, we developed a two‐tube triplex one‐step real‐time reverse‐transcription polymerase chain reaction (real‐time RT‐PCR) and evaluated its performance using clinical samples. The data showed that this novel assay was 100% consistent with the monoplex real‐time RT‐PCR assay (in‐house), which was superior to the commercial routine multiplex‐ligation‐NAT‐based assay. Meanwhile, the clinical nasopharyngeal swabs of 471 patients with the acute febrile respiratory syndrome (AFRS) were analyzed using the established method. The results showed that 52 (11.7%) cases were positive for paramyxovirus. Among them, HPIVs and RSV‐A had the highest detection rate. The age and seasonal distribution of human paramyxovirus infection were analyzed. In conclusion, we developed a novel multiplex real‐time RT‐PCR assay for the rapid detection of six common human paramyxoviruses, which were dominant in patients with AFRS in Qinghai. We developed a novel multiplex real‐time RT‐PCR assay for the rapid detection of six common human paramyxoviruses for patients with AFRS in Qinghai. This method provides a new approach with a higher quality of performance (accuracy, speed, and higher sensitivity) for the detection of common respiratory paramyxoviruses in clinical specimens. The method is more specimen‐ and time‐ saving and more cost‐effective, without compromising quality, compared with monoplex real time RT PCR and commercial routine multiplex ligation‐NAT‐based RF 22.
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Affiliation(s)
- Gao-Shan Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Key Laboratory of Medical Virology, Biotech Center for Viral Disease Emergency, Beijing, China
| | - Pei-Hua Niu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Key Laboratory of Medical Virology, Biotech Center for Viral Disease Emergency, Beijing, China
| | - Sheng-Cang Zhao
- Center for Disease Control and Prevention of Qinghai Province, Department of Virus Detection, Xining, China
| | - Rou-Jian Lu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Key Laboratory of Medical Virology, Biotech Center for Viral Disease Emergency, Beijing, China
| | - Wen-Jie Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Key Laboratory of Medical Virology, Biotech Center for Viral Disease Emergency, Beijing, China
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Abstract
Influenza virus infections are a leading cause of morbidity and mortality worldwide. This is due in part to the continual emergence of new viral variants and to synergistic interactions with other viruses and bacteria. There is a lack of understanding about how host responses work to control the infection and how other pathogens capitalize on the altered immune state. The complexity of multi-pathogen infections makes dissecting contributing mechanisms, which may be non-linear and occur on different time scales, challenging. Fortunately, mathematical models have been able to uncover infection control mechanisms, establish regulatory feedbacks, connect mechanisms across time scales, and determine the processes that dictate different disease outcomes. These models have tested existing hypotheses and generated new hypotheses, some of which have been subsequently tested and validated in the laboratory. They have been particularly a key in studying influenza-bacteria coinfections and will be undoubtedly be useful in examining the interplay between influenza virus and other viruses. Here, I review recent advances in modeling influenza-related infections, the novel biological insight that has been gained through modeling, the importance of model-driven experimental design, and future directions of the field.
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Affiliation(s)
- Amber M Smith
- University of Tennessee Health Science CenterMemphisTNUSA
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25
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Pathogen Clearance and New Respiratory Tract Infections Among Febrile Children in Zanzibar Investigated With Multitargeting Real-Time Polymerase Chain Reaction on Paired Nasopharyngeal Swab Samples. Pediatr Infect Dis J 2018; 37:643-648. [PMID: 29889810 DOI: 10.1097/inf.0000000000001876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND New molecular methods have revealed frequent and often polymicrobial respiratory infections in children in low-income settings. It is not known whether presence of multiple pathogens is due to prolonged infections or to frequent exposure. The aim of this study was to analyze short-term pathogen clearance from nasopharynx and the rate of new respiratory tract infections in febrile preschool children. METHODS Children (n = 207) with uncomplicated acute febrile illness 2-59 months of age presenting to a health center in Zanzibar, Tanzania, April-July 2011, were included. Paired nasopharyngeal swab samples, collected at enrolment and after 14 days, were analyzed by multiple real-time polymerase chain reaction for Adenovirus, bocavirus, Bordetella pertussis, Chlamydophila pneumoniae, Coronaviruses, Enterovirus, influenza A and B virus, metapneumovirus, measles virus, Mycoplasma pneumoniae, parainfluenza virus, Parechovirus, respiratory syncytial virus and Rhinovirus. An age-matched and geographically matched healthy control group (n = 166) underwent nasopharyngeal sampling on 1 occasion. RESULTS At baseline, 157/207 (76%) patients had at least 1 pathogen detected, in total 199 infections. At follow-up (day 14), 162/199 (81%) of these infections were not detected, including >95% of the previously detected infections with Enterovirus, influenza A virus, influenza B virus, metapneumovirus or parainfluenza virus. Still 115 (56%) children were positive for at least 1 pathogen at follow-up, of which 95/115 (83%) were not found at baseline. Detection of influenza B on day 14 was significantly associated with fever during follow-up. CONCLUSION The results suggest that children with acute febrile illness in Zanzibar rapidly clear respiratory tract infections but frequently acquire new infections within 14 days.
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Shirato K, Semba S, El-Kafrawy SA, Hassan AM, Tolah AM, Takayama I, Kageyama T, Notomi T, Kamitani W, Matsuyama S, Azhar EI. Development of fluorescent reverse transcription loop-mediated isothermal amplification (RT-LAMP) using quenching probes for the detection of the Middle East respiratory syndrome coronavirus. J Virol Methods 2018; 258:41-48. [PMID: 29763640 PMCID: PMC7113683 DOI: 10.1016/j.jviromet.2018.05.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/09/2018] [Accepted: 05/10/2018] [Indexed: 11/24/2022]
Abstract
Fluorescent RT-LAMP assays using quenching probes for MERS-CoV were developed. Quenching probe (QProbe) can solve the problem in turbidity monitoring mechanism. Only primer-derived signal can be monitored specifically by QProbes. Two primer sets were developed to enable to confirm MERS case by RT-LAMP only. Both sets were highly specific and sensitive in comparison with real-time RT-PCR.
Clinical detection of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) in patients is achieved using genetic diagnostic methods, such as real-time RT-PCR assay. Previously, we developed a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of MERS-CoV [Virol J. 2014. 11:139]. Generally, amplification of RT-LAMP is monitored by the turbidity induced by precipitation of magnesium pyrophosphate with newly synthesized DNA. However, this mechanism cannot completely exclude the possibility of unexpected reactions. Therefore, in this study, fluorescent RT-LAMP assays using quenching probes (QProbes) were developed specifically to monitor only primer-derived signals. Two primer sets (targeting nucleocapsid and ORF1a sequences) were constructed to confirm MERS cases by RT-LAMP assay only. Our data indicate that both primer sets were capable of detecting MERS-CoV RNA to the same level as existing genetic diagnostic methods, and that both were highly specific with no cross-reactivity observed with other respiratory viruses. These primer sets were highly efficient in amplifying target sequences derived from different MERS-CoV strains, including camel MERS-CoV. In addition, the detection efficacy of QProbe RT-LAMP was comparable to that of real-time RT-PCR assay using clinical specimens from patients in Saudi Arabia. Altogether, these results indicate that QProbe RT-LAMP assays described here can be used as powerful diagnostic tools for rapid detection and surveillance of MERS-CoV infections.
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Affiliation(s)
- Kazuya Shirato
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Disease, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan.
| | - Shohei Semba
- Eiken Chemical Co., Ltd., 4-19-9 Taito, Taito-ku, Tokyo 110-8408, Japan
| | - Sherif A El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed M Tolah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ikuyo Takayama
- Influenza virus Research Center, National Institute of Infectious Disease, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Tsutomu Kageyama
- Influenza virus Research Center, National Institute of Infectious Disease, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Tsugunori Notomi
- Eiken Chemical Co., Ltd., 4-19-9 Taito, Taito-ku, Tokyo 110-8408, Japan
| | - Wataru Kamitani
- Laboratory of Clinical Research on Infectious Diseases, Department of Pathogen Molecular Biology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shutoku Matsuyama
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Disease, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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27
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Zhou J, Peng Y, Peng X, Gao H, Sun Y, Xie L, Zhong L, Duan Z, Xie Z, Cao Y. Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China. Influenza Other Respir Viruses 2018; 12:279-286. [PMID: 29266860 PMCID: PMC5820417 DOI: 10.1111/irv.12535] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2017] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). We aimed to assay the correlation between viral load and clinical characteristics of HBoV and HMPV with LRTI in Changsha, China. METHODS Nasopharyngeal aspirates (NPAs) from children with LRTI were collected. Real-time PCR was used to screen HBoV and HMPV. Analyses were performed using SPSS 16.0 software. RESULTS Pneumonia was the most frequent diagnosis. There was no significant difference between HBoV- and HMPV-positive patients in age (P = .506) or hospitalization duration (P = .280); 24.1% and 18.2% were positive for HBoV and HMPV. HBoV infections peaked in summer (32.2%), and HMPV infections peaked in winter (28.9%). The HBoV-positive patients had a shorter hospitalization duration than the HBoV-negative patients (P = .021), and the HMPV-positive patients had a higher prevalence of fever than the HMPV-negative patients (P = .002). The HBoV viral load was significantly higher among patients aged <1 year (P = .006). The mean HBoV and HMPV viral loads were not significantly different between patients with single infections and coinfections. Patients infected with HBoV only were older than those coinfected with HBoV and other respiratory viruses (P = .005). No significant difference was found in the clinical characteristics of patients infected with HMPV only and those coinfected with HMPV and other respiratory viruses. CONCLUSION Pneumonia was the most frequent diagnosis caused by HBoV and HMPV. Neither HBoV nor HMPV viral load was correlated with disease severity.
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Affiliation(s)
- Jie‐ying Zhou
- Department of Laboratory MedicalThe First People's Hospital of Hunan ChenzhouChenzhouChina
- Key Laboratory for Medical VirologyMinistry of HealthNational Institute for Viral Disease Control and Prevention, ChinaCenter for Disease ControlBeijingChina
- Department of Laboratory MedicalThe First Affiliated Hospital of Hunan Normal UniversityChangshaChina
| | - Ying Peng
- Key Laboratory for Medical VirologyMinistry of HealthNational Institute for Viral Disease Control and Prevention, ChinaCenter for Disease ControlBeijingChina
- Department of PaediatricsThe First Affiliated Hospital of Hunan Normal UniversityChangshaChina
| | - Xiao‐you Peng
- Department of Laboratory MedicalThe First People's Hospital of Hunan ChenzhouChenzhouChina
| | - Han‐chun Gao
- Key Laboratory for Medical VirologyMinistry of HealthNational Institute for Viral Disease Control and Prevention, ChinaCenter for Disease ControlBeijingChina
| | - Ya‐ping Sun
- Yuhang District Center for Disease Control and PreventionHangzhouChina
| | - Le‐yun Xie
- Department of PaediatricsThe First Affiliated Hospital of Hunan Normal UniversityChangshaChina
| | - Li‐li Zhong
- Department of PaediatricsThe First Affiliated Hospital of Hunan Normal UniversityChangshaChina
| | - Zhao‐jun Duan
- Key Laboratory for Medical VirologyMinistry of HealthNational Institute for Viral Disease Control and Prevention, ChinaCenter for Disease ControlBeijingChina
| | - Zhi‐ping Xie
- Key Laboratory for Medical VirologyMinistry of HealthNational Institute for Viral Disease Control and Prevention, ChinaCenter for Disease ControlBeijingChina
| | - You‐de Cao
- Department of Laboratory MedicalThe First Affiliated Hospital of Hunan Normal UniversityChangshaChina
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Shirato K, Kawase M, Matsuyama S. Wild-type human coronaviruses prefer cell-surface TMPRSS2 to endosomal cathepsins for cell entry. Virology 2017; 517:9-15. [PMID: 29217279 PMCID: PMC7112029 DOI: 10.1016/j.virol.2017.11.012] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 11/15/2022]
Abstract
Human coronaviruses (HCoVs) enter cells via two distinct pathways: the endosomal pathway using cathepsins to activate spike protein and the cell-surface or early endosome pathway using extracellular proteases such as transmembrane protease serine 2 (TMPRSS2). We previously reported that clinical isolates of HCoV-229E preferred cell-surface TMPRSS2 to endosomal cathepsin for cell entry, and that they acquired the ability to use cathepsin L by repeated passage in cultured cells and were then able to enter cells via the endosomal pathway. Here, we show that clinical isolates of HCoV-OC43 and -HKU1 preferred the cell-surface TMRRSS2 to endosomal cathepsins for cell entry, similar to HCoV-229E. In addition, the cell-culture-adapted HCoV-OC43 lost the ability to infect and replicate in air-liquid interface cultures of human bronchial tracheal epithelial cells. These results suggest that circulating HCoVs in the field generally use cell-surface TMPRSS2 for cell entry, not endosomal cathepsins, in human airway epithelial cells. Clinical isolates of HCoV-OC43 and -HKU1 were isolated from ALI-cultured HBTE cells. Clinical isolates of HCoVs preferred the TMRRSS2 to cathepsins for cell entry. Cell culture adapted HCoV-OC43 lost the ability to replicate in HBTE-ALI culture.
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Affiliation(s)
- Kazuya Shirato
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan.
| | - Miyuki Kawase
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Shutoku Matsuyama
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
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29
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Sato K, Watanabe O, Ohmiya S, Chiba F, Suzuki A, Okamoto M, Younghuang J, Hata A, Nonaka H, Kitaoka S, Nagai Y, Kawamura K, Hayashi M, Kumaki S, Suzuki T, Kawakami K, Nishimura H. Efficient isolation of human metapneumovirus using MNT-1, a human malignant melanoma cell line with early and distinct cytopathic effects. Microbiol Immunol 2017; 61:497-506. [PMID: 28940687 DOI: 10.1111/1348-0421.12542] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/23/2017] [Accepted: 09/16/2017] [Indexed: 01/30/2023]
Abstract
Isolation of human metapneumovirus (HMPV) from clinical specimens is currently inefficient because of the lack of a cell culture system in which a distinct cytopathic effect (CPE) occurs. The cell lines LLC-MK2, Vero and Vero E6 are used for isolation of HMPV; however, the CPE in these cell lines is subtle and usually requires a long observation period and sometimes blind passages. Thus, a cell line in which an early and distinct CPE occurs following HMPV inoculation is highly desired by clinical virology laboratories. In this study, it was demonstrated that, in the human malignant melanoma cell line MNT-1, obvious syncytium formation occurs shortly after inoculation with HMPV-positive clinical specimens. In addition, the growth and efficiency of isolation of HMPV were greater using MNT-1 than using any other conventional cell line. Addition of this cell line to our routine viral isolation system for clinical specimens markedly enhanced isolation frequency, allowing isolation-based surveillance. MNT-1 has the potential to facilitate clinical and epidemiological studies of HMPV.
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Affiliation(s)
- Ko Sato
- Virus Research Center, Clinical Research Division, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Japan
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Oshi Watanabe
- Virus Research Center, Clinical Research Division, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Japan
| | - Suguru Ohmiya
- Virus Research Center, Clinical Research Division, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Japan
| | - Fumiko Chiba
- Virus Research Center, Clinical Research Division, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Japan
| | - Akira Suzuki
- Virus Research Center, Clinical Research Division, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Japan
| | - Michiko Okamoto
- Virus Research Center, Clinical Research Division, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Japan
| | - Jiang Younghuang
- Tauns Laboratories, 761-1 Kamishima, Izunokuni, Shizuoka 410-2325, Japan
| | - Akihiro Hata
- Tauns Laboratories, 761-1 Kamishima, Izunokuni, Shizuoka 410-2325, Japan
| | - Hiroyuki Nonaka
- Tauns Laboratories, 761-1 Kamishima, Izunokuni, Shizuoka 410-2325, Japan
| | - Setsuko Kitaoka
- Department of Pediatrics, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Sendai 983-8520, Japan
| | - Yukio Nagai
- Nagai Pediatric Clinic, 1-25-10 Miyagino, Miyagino-ku, Sendai, 983-0045, Japan
| | - Kazuhisa Kawamura
- Kawamura Children's Clinic, 1-16-1 Takamatsu, Aoba-ku, Sendai 981-0907, Japan
| | - Masahiro Hayashi
- Department of Dermatology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata 990-9585, Japan
| | - Satoru Kumaki
- Department of Pediatrics, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Sendai 983-8520, Japan
| | - Tamio Suzuki
- Department of Dermatology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata 990-9585, Japan
| | - Kazuyoshi Kawakami
- Department of Medical Microbiology, Mycology and Immunology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Japan
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30
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Kaida A, Iritani N, Yamamoto SP, Kanbayashi D, Hirai Y, Togawa M, Amo K, Kohdera U, Nishigaki T, Shiomi M, Asai S, Kageyama T, Kubo H. Distinct genetic clades of enterovirus D68 detected in 2010, 2013, and 2015 in Osaka City, Japan. PLoS One 2017; 12:e0184335. [PMID: 28902862 PMCID: PMC5597212 DOI: 10.1371/journal.pone.0184335] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 08/22/2017] [Indexed: 12/23/2022] Open
Abstract
The first upsurge of enterovirus D68 (EV-D68), a causative agent of acute respiratory infections (ARIs), in Japan was reported in Osaka City in 2010. In this study, which began in 2010, we surveyed EV-D68 in children with ARIs and analyzed sequences of EV-D68 strains detected. Real-time PCR of 19 respiratory viruses or subtypes of viruses, including enterovirus, was performed on 2,215 specimens from ARI patients (<10 years of age) collected between November 2010 and December 2015 in Osaka City, Japan. EV-D68 was identified in 18 enterovirus-positive specimens (n = 4 in 2013, n = 1 in 2014, and n = 13 in 2015) by analysis of viral protein 1 (VP1) or VP4 sequences, followed by a BLAST search for similar sequences. All EV-D68 strains were detected between June and October (summer to autumn), except for one strain detected in 2014. A phylogenetic analysis of available VP1 sequences revealed that the Osaka strains detected in 2010, 2013, and 2015 belonged to distinct clusters (Clades C, A, and B [Subclade B3], respectively). Comparison of the 5' untranslated regions of these viruses showed that Osaka strains in Clades A, B (Subclade B3), and C commonly had deletions at nucleotide positions 681-703 corresponding to the prototype Fermon strain. Clades B and C had deletions from nucleotide positions 713-724. Since the EV-D68 epidemic in 2010, EV-D68 re-emerged in Osaka City, Japan, in 2013 and 2015. Results of this study indicate that distinct clades of EV-D68 contributed to re-emergences of this virus in 2010, 2013, and 2015 in this limited region.
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Affiliation(s)
- Atsushi Kaida
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
- * E-mail:
| | - Nobuhiro Iritani
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Seiji P. Yamamoto
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Daiki Kanbayashi
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yuki Hirai
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | | | - Kiyoko Amo
- Osaka City General Hospital, Osaka, Japan
| | | | | | | | | | - Tsutomu Kageyama
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideyuki Kubo
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
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31
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Kanbayashi D, Kaida A, Yamamoto SP, Hirai Y, Kubo H, Fujimori R, Hakui N, Hirokawa H, Iritani N. Impact of Coxsackievirus A6 emergence on hand, foot, and mouth disease epidemic in Osaka City, Japan. J Med Virol 2017; 89:2116-2121. [PMID: 28771766 DOI: 10.1002/jmv.24905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/27/2017] [Indexed: 11/11/2022]
Abstract
Hand, foot, and mouth disease (HFMD) is an acute febrile illness characterized by fever; sore throat; and vesicular eruptions on the hands, feet, and oral mucosa. Until 2010, HFMD was predominantly associated with enterovirus (EV) A71 and coxsackievirus (CV) A16 in Japan. In 2011, CV-A6 emerged as a primary causative agent, causing the largest HFMD epidemic in Japan since 1981. Since then, CV-A6 has caused large HFMD epidemics every 2 years. The phylogenetic analysis of complete Viral Protein 1 (VP1) sequences revealed that most CV-A6 strains detected from 2011 to 2015 in Osaka City were classified into a different clade compared with CV-A6 strains detected from 1999 until 2009. The majority of CV-A6 strains detected in 2011 and most CV-A6 strains detected from 2013 to 2015 were mainly divided into two distinct genetic groups. Each epidemic strain carried unique amino acid substitutions in the presumed DE, EF, and GH loops of the VP1 protein that is exposed on the surface of the virion. There is a possibility that the appearance of substitutions on the surface of the virion and an accumulation of a susceptible population are significant factors in recent HFMD epidemics.
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Affiliation(s)
- Daiki Kanbayashi
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Tennoji-ku, Osaka, Japan.,Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan
| | - Atsushi Kaida
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Tennoji-ku, Osaka, Japan
| | - Seiji P Yamamoto
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Tennoji-ku, Osaka, Japan.,Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, Japan
| | - Yuki Hirai
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Tennoji-ku, Osaka, Japan
| | - Hideyuki Kubo
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Tennoji-ku, Osaka, Japan
| | - Ryoko Fujimori
- Osaka City Public Health, Bureau Osaka City Health Center, Abeno-ku, Osaka, Japan
| | - Noritaka Hakui
- Osaka City Public Health, Bureau Osaka City Health Center, Abeno-ku, Osaka, Japan
| | - Hidetetsu Hirokawa
- Osaka City Public Health, Bureau Osaka City Health Center, Abeno-ku, Osaka, Japan
| | - Nobuhiro Iritani
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Tennoji-ku, Osaka, Japan
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Fernandes-Matano L, Monroy-Muñoz IE, Angeles-Martínez J, Sarquiz-Martinez B, Palomec-Nava ID, Pardavé-Alejandre HD, Santos Coy-Arechavaleta A, Santacruz-Tinoco CE, González-Ibarra J, González-Bonilla CR, Muñoz-Medina JE. Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico. PLoS One 2017; 12:e0176298. [PMID: 28467515 PMCID: PMC5415110 DOI: 10.1371/journal.pone.0176298] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/07/2017] [Indexed: 01/10/2023] Open
Abstract
Background Acute respiratory infections are the leading cause of morbidity and mortality worldwide. Although a viral aetiological agent is estimated to be involved in up to 80% of cases, the majority of these agents have never been specifically identified. Since 2009, diagnostic and surveillance efforts for influenza virus have been applied worldwide. However, insufficient epidemiological information is available for the many other respiratory viruses that can cause Acute respiratory infections. Methods This study evaluated the presence of 14 non-influenza respiratory viruses in 872 pharyngeal exudate samples using RT-qPCR. All samples met the operational definition of a probable case of an influenza-like illness or severe acute respiratory infection and had a previous negative result for influenza by RT-qPCR. Results The presence of at least one non-influenza virus was observed in 312 samples (35.8%). The most frequent viruses were rhinovirus (RV; 33.0%), human respiratory syncytial virus (HRSV; 30.8%) and human metapneumovirus (HMPV; 10.6%). A total of 56 cases of co-infection (17.9%) caused by 2, 3, or 4 viruses were identified. Approximately 62.5% of all positive cases were in children under 9 years of age. Conclusion In this study, we identified 13 non-influenza respiratory viruses that could occur in any season of the year. This study provides evidence for the prevalence and seasonality of a wide range of respiratory viruses that circulate in Mexico and constitute a risk for the population. Additionally, our data suggest that including these tests more widely in the diagnostic algorithm for influenza may reduce the use of unnecessary antibiotics, reduce the hospitalisation time, and enrich national epidemiological data with respect to the infections caused by these viruses.
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Affiliation(s)
| | - Irma Eloísa Monroy-Muñoz
- Laboratorio de Genómica, Departamento de Genética y Genómica Humana, Instituto Nacional de Perinatología “Isidro Espinosa de los Reyes”. Ciudad de México, México
| | - Javier Angeles-Martínez
- Laboratorio de Genómica, Departamento de Biología Molecular, Instituto Nacional de Cardiología “Ignacio Chávez”. Ciudad de México, México
| | - Brenda Sarquiz-Martinez
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Iliana Donají Palomec-Nava
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Hector Daniel Pardavé-Alejandre
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Andrea Santos Coy-Arechavaleta
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Clara Esperanza Santacruz-Tinoco
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Joaquín González-Ibarra
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Cesar Raúl González-Bonilla
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - José Esteban Muñoz-Medina
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
- * E-mail:
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Gamiño‐Arroyo AE, Moreno‐Espinosa S, Llamosas‐Gallardo B, Ortiz‐Hernández AA, Guerrero ML, Galindo‐Fraga A, Galán‐Herrera JF, Prado‐Galbarro FJ, Beigel JH, Ruiz‐Palacios GM, Noyola DE. Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico. Influenza Other Respir Viruses 2017; 11:48-56. [PMID: 27439650 PMCID: PMC5155644 DOI: 10.1111/irv.12414] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a leading etiological agent of acute respiratory tract infections and hospitalizations in children. However, little information is available regarding RSV infections in Latin American countries, particularly among adult patients. OBJECTIVE To describe the epidemiology of RSV infection and to analyze the factors associated with severe infections in children and adults in Mexico. METHODS Patients ≥1 month old, who presented with an influenza-like illness (ILI) to six hospitals in Mexico, were eligible for participation in the study. Multiplex reverse-transcriptase polymerase chain reaction identified viral pathogens in nasal swabs from 5629 episodes of ILI. Patients in whom RSV was detected were included in this report. RESULTS Respiratory syncytial virus was detected in 399 children and 171 adults. RSV A was detected in 413 cases and RSV B in 163, including six patients who had coinfection with both subtypes; 414 (72.6%) patients required hospital admission, including 96 (16.8%) patients that required admission to the intensive care unit. Coinfection with one or more respiratory pathogens other than RSV was detected in 159 cases. Young age (in children) and older age (in adults) as well as the presence of some underlying conditions were associated with more severe disease. CONCLUSIONS This study confirms that RSV is an important respiratory pathogen in children in Mexico. In addition, a substantial number of cases in adults were also detected highlighting the relevance of this virus in all ages. It is important to identify subjects at high risk of complications who may benefit from current or future preventive interventions.
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Affiliation(s)
| | | | | | | | - M. Lourdes Guerrero
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | - Arturo Galindo‐Fraga
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | - Juan F. Galán‐Herrera
- Mexico Emerging Infectious Diseases Clinical Research Network Coordinating CenterMexico CityMexico
| | | | - John H. Beigel
- Leidos Biomedical, Frederick, MD, in support of the National Institutes of Allergy and Infectious Diseases, National Institutes of HealthBethesdaMDUSA
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A novel primer set for improved direct gene sequencing of human bocavirus genotype-1 from clinical samples. J Virol Methods 2015; 228:108-13. [PMID: 26658621 DOI: 10.1016/j.jviromet.2015.11.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/27/2015] [Accepted: 11/29/2015] [Indexed: 02/07/2023]
Abstract
Human bocavirus genotype (HBoV-1) is a parvovirus associated with respiratory tract infections in children with different degrees of severity. The current study intended to improve the direct gene sequencing of the HBoV-1 using a newly developed primer set. Screening the presence of human bocavirus infection among in-patients children suffering from lower respiratory tract infections was another aim of the current study. Nasopharyngeal swab samples from in-patients children suffering from lower respiratory tract infections were examined. The real-time polymerase chain reaction was used for the initial screening as a highly sensitive method to detect the HBoV. Genotyping of real-time positive samples was attempted by direct sequencing of PCR amplicons using NP, VP1/2 and the newly developed VP/NC primers. HBoV-1 was present in 56.8% of the examined children. The newly developed primer set successfully amplified all real-time PCR positive samples, however, the other primer pairs did not reliably detect real-time PCR positive samples. The gene sequences of the detected HBoV-1 showed conserved sequences to each other with a low rate of discrepancies. The high rate of infection and the similarity between the detected strains strongly suggest nosocomial infections.
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Aktürk H, Sütçü M, Badur S, Törün SH, Çıtak A, Erol OB, Somer A, Salman N. Evaluation of epidemiological and clinical features of influenza and other respiratory viruses. Turk Arch Pediatr 2015; 50:217-25. [PMID: 26884691 DOI: 10.5152/turkpediatriars.2015.2827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 09/28/2015] [Indexed: 11/22/2022]
Abstract
AIM In our study, we aimed to clinically and epidemiologically evaluate respiratory tract infections the viral agents of which were detected by molecular methods and to compare influenza and other respiratory tract viruses in this context. MATERIAL AND METHODS The records of 178 patients aged above 2 years who presented to pediatric emergency outpatient clinic with fever and respiratory tract infection findings between December 2013 and April 2014 were examined retrospectively. RESULTS At least one respiratory tract pathogen was detected by polymerase chain reaction in 78.6% (n=140) of the patients: influenza A 33.5%, influenza B 16.4%, respiratory syncytial virus 9.2%, adenovirus 7.8%, rhinovirus 7.1%, coronavirus 7.1%, human metapneumovirus 5.7%, human bocavirus 5.7%, parainfluenza virus 3.5%, coinfection 2.8%. The mean age of the patients was 6.3±3.6 years. Sixty-nine patients (49.2%) were aged between 2 and 5 years. Seventy-one patients (50.7%) were aged 5 years and above. Upper respiratory tract infection was found with a rate of 65.7% and lower respiratory tract infection was found with a rate of 34.2%. It was observed that the distribution of respiratory tract viruses showed variance by age groups. Influenza A infection was observed with the highest rate in both age groups. Influenza B was the second leading agent (p=0.008) above the age of 5 years and respiratory syncytial virus was the second leading agent in the 2-5 year age group (p=0.003). Influenza viruses were detected in 55.9% of 118 patients who were found to be compatible with the definition of "influenza-like illness" specified in the Center for Disease Control and Prevention guidelines and other viral agenst were detected in 44%. No difference could be found between the clinical pictures and radiological findings caused by influenza and other respiratory tract viruses. CONCLUSIONS In this study, it was concluded that influenza and other respiratory viruses can not be differentiated definitely by clinical and radiological findings, though there are some differences.
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Affiliation(s)
- Hacer Aktürk
- Department of Pediatrics, Division of Pediatric Infection, İstanbul University İstanbul Faculty of Medicine, İstanbul, Turkey
| | - Murat Sütçü
- Department of Pediatrics, Division of Pediatric Infection, İstanbul University İstanbul Faculty of Medicine, İstanbul, Turkey
| | - Selim Badur
- Department of Microbiology, Division of Virology, İstanbul University İstanbul Faculty of Medicine, İstanbul, Turkey
| | - Selda Hançerli Törün
- Department of Pediatrics, Division of Pediatric Infection, İstanbul University İstanbul Faculty of Medicine, İstanbul, Turkey
| | - Agop Çıtak
- Department of Pediatrics, Division of Pediatric Emergency and Intensive Care, İstanbul University İstanbul Faculty of Medicine, İstanbul, Turkey
| | - Oğuz Bülent Erol
- Department of Radiology, İstanbul University İstanbul Faculty of Medicine, İstanbul, Turkey
| | - Ayper Somer
- Department of Pediatrics, Division of Pediatric Infection, İstanbul University İstanbul Faculty of Medicine, İstanbul, Turkey
| | - Nuran Salman
- Department of Pediatrics, Division of Pediatric Infection, İstanbul University İstanbul Faculty of Medicine, İstanbul, Turkey
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Yamamoto SP, Kaida A, Naito T, Hosaka T, Miyazato Y, Sumimoto SI, Kohdera U, Ono A, Kubo H, Iritani N. Human parechovirus infections and child myositis cases associated with genotype 3 in Osaka City, Japan, 2014. J Med Microbiol 2015; 64:1415-1424. [PMID: 26358716 DOI: 10.1099/jmm.0.000167] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human parechovirus (HPeV) infects humans early in life and typically causes asymptomatic or mild diseases such as gastrointestinal and respiratory illness but sometimes leads to more serious consequences in neonates and young infants. In 2014, we detected HPeV from 38 patients by real-time reverse transcription-PCR in Osaka City, Japan, and 33 HPeV strains were genotyped based on their VP1 sequences. HPeV genotype 3 (HPeV-3) was the most prevalent and accounted for 22 cases (66.7%) followed by nine HPeV-1 (27.3%), one HPeV-2 (3.0%) and one HPeV-4 (3.0%). Phylogenetic analysis revealed that detected HPeV-3 strains were divided into three genetically distinct groups. One was characterized by a novel single amino acid deletion mutation at the N terminus of the 2A protein as well as the VP1 sequence, whereas the others were closely related to HPeV-3 strains detected in Japan in either 2008 or 2011. These HPeV-3 groups were detected from patients with various symptoms including three myositis cases. Recent papers have demonstrated that HPeV-3 was the aetiological agent for epidemic myalgia exclusively among adults from Yamagata Prefecture in Japan. Here, we provide clinical details and episodes of three myositis patients including an adult and two children in Osaka City, Japan. Our results suggest that HPeV-3 is a causative agent of myositis not only in adults but also in children.
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Affiliation(s)
- Seiji P Yamamoto
- Osaka City Institute of Public Health and Environmental Sciences, Osaka 543-0026, Japan
| | - Atsushi Kaida
- Osaka City Institute of Public Health and Environmental Sciences, Osaka 543-0026, Japan
| | | | | | | | | | | | - Atsushi Ono
- Osaka Saiseikai Izuo Hospital, Osaka 551-0032, Japan
| | - Hideyuki Kubo
- Osaka City Institute of Public Health and Environmental Sciences, Osaka 543-0026, Japan
| | - Nobuhiro Iritani
- Osaka City Institute of Public Health and Environmental Sciences, Osaka 543-0026, Japan
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Kaida A, Kubo H, Iritani N, Yamamoto SP, Hase A, Takakura KI, Kageyema T. Frequent respiratory viral infections in a young child in a 27-month follow-up study. JMM Case Rep 2014; 1:e003020. [PMID: 28663808 PMCID: PMC5415931 DOI: 10.1099/jmmcr.0.003020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/26/2014] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Viruses are major aetiological agents of acute respiratory infection in young children. Although many studies have reported detection and analysis of respiratory viruses in sporadic cases, there have been few follow-up studies of individuals. The purpose of this study was to investigate the frequency of respiratory viral infections in a young child and to examine the duration of viral genome detection in clinical specimens. CASE PRESENTATION A total of 284 nasal swabs were collected during symptomatic (196 specimens) and asymptomatic (88 specimens) periods of respiratory symptoms from a young female child (from 4 months to 31 months of age, who was admitted to a nursery school at 9 months). Multiplex real-time PCR for 19 respiratory viruses or subtypes was performed. One hundred and ninety-eight of the tested specimens were virus positive (69.7 %) (symptomatic periods, 149/196, 76.0 %; asymptomatic periods, 49/88, 55.7 %). Rhinovirus was the most frequently detected (26 times). Long durations of detection were observed for human coronavirus NL63 (30 days), rhinovirus (28 days) and human bocavirus 1 (22 days). CONCLUSION Young children living in a group context have a high risk of respiratory virus infections, especially rhinovirus. In some instances, viral genomes were detectable for about 1 month by PCR.
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Affiliation(s)
- Atsushi Kaida
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Hideyuki Kubo
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Nobuhiro Iritani
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Seiji P Yamamoto
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Atsushi Hase
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Koh-Ichi Takakura
- Department of Biological Resources Management, School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone-City, Shiga 522-8533, Japan
| | - Tsutomu Kageyema
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama-shi, Tokyo 208-0011, Japan
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