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Otani K, Kimura R, Nagasawa N, Hayashi Y, Ohmiya S, Watanabe O, Khandaker I, Kimura H, Nishimura H. Phylogenomic Analyses of the Hemagglutinin-Neuraminidase ( HN) Gene in Human Parainfluenza Virus Type 4 Isolates in Japan. Microorganisms 2025; 13:384. [PMID: 40005750 PMCID: PMC11857914 DOI: 10.3390/microorganisms13020384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Revised: 01/30/2025] [Accepted: 02/01/2025] [Indexed: 02/27/2025] Open
Abstract
To better understand the phylogenomics of the hemagglutinin-neuraminidase (HN) gene and HN protein in human parainfluenza virus type 4 (HPIV4), we performed phylogenomic analyses using various bioinformatics methods. The main bioinformatics analyses included a time-scaled phylogeny, genetic distance assessments, and three-dimensional (3D) structure mapping of the HN protein with conformational epitope and selective pressure analyses. The time-scaled phylogenetic tree indicated that the most recent common ancestor of the HN gene emerged approximately 100 years ago. Additionally, the tree revealed two distinct clusters corresponding to HPIV4a and HPIV4b. The divergence times for the most recent common ancestors of the HN gene in HPIV4a and HPIV4b strains were estimated to be around 1993 and 1986, respectively. The evolutionary rates of the gene varied significantly between clusters, ranging from approximately 1.2 × 10-3 to 8.7 × 10-4 substitutions per site per year. Genetic distances within each cluster were relatively short (less than 0.04). Phylodynamic analyses demonstrated an increase in the genome population size around the year 2000. Structural analyses revealed that the active sites of the HN protein were located at the protein's head. Furthermore, the most conformational epitopes were located in adjacent active sites of the protein. These results suggested that reinfection may be unlikely to occur in the case of most HPIV4. Together, the HN gene and protein of HPIV4 strains isolated in Japan have undergone unique evolutionary changes. In addition, antibodies targeting the conformational epitopes of the HPIV4 HN protein may contribute to protection against the virus.
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Affiliation(s)
- Kanako Otani
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan; (S.O.); (O.W.); (I.K.)
| | - Ryusuke Kimura
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi-shi 371-8511, Japan;
- Advanced Medical Science Research Center, Gunma Paz University, Takasaki-shi 370-0006, Japan
| | - Norika Nagasawa
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Japan; (N.N.); (Y.H.)
| | - Yuriko Hayashi
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Japan; (N.N.); (Y.H.)
| | - Suguru Ohmiya
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan; (S.O.); (O.W.); (I.K.)
| | - Oshi Watanabe
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan; (S.O.); (O.W.); (I.K.)
| | - Irona Khandaker
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan; (S.O.); (O.W.); (I.K.)
- Department of Surgery, Trauma and Transfusion Medicine Research Center (TTMRC), University of Pittsburgh, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Hirokazu Kimura
- Advanced Medical Science Research Center, Gunma Paz University, Takasaki-shi 370-0006, Japan
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Japan; (N.N.); (Y.H.)
| | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan; (S.O.); (O.W.); (I.K.)
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Mizukoshi F, Kimura H, Sugimoto S, Kimura R, Nagasawa N, Hayashi Y, Hashimoto K, Hosoya M, Shirato K, Ryo A. Molecular Evolutionary Analyses of the Fusion Genes in Human Parainfluenza Virus Type 4. Microorganisms 2024; 12:1633. [PMID: 39203475 PMCID: PMC11356533 DOI: 10.3390/microorganisms12081633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 07/31/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
The human parainfluenza virus type 4 (HPIV4) can be classified into two distinct subtypes, 4a and 4b. The full lengths of the fusion gene (F gene) of 48 HPIV4 strains collected during the period of 1966-2022 were analyzed. Based on these gene sequences, the time-scaled evolutionary tree was constructed using Bayesian Markov chain Monte Carlo methods. A phylogenetic tree showed that the first division of the two subtypes occurred around 1823, and the most recent common ancestors of each type, 4a and 4b, existed until about 1940 and 1939, respectively. Although the mean genetic distances of all strains were relatively wide, the distances in each subtype were not wide, indicating that this gene was conserved in each subtype. The evolutionary rates of the genes were relatively low (4.41 × 10-4 substitutions/site/year). Moreover, conformational B-cell epitopes were predicted in the apex of the trimer fusion protein. These results suggest that HPIV4 subtypes diverged 200 years ago and the progenies further diverged and evolved.
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Affiliation(s)
- Fuminori Mizukoshi
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
| | - Hirokazu Kimura
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (Y.H.)
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi 377-0008, Gunma, Japan
- Department of Clinical Engineering, Faculty of Medical Technology, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan
| | - Satoko Sugimoto
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
- Research Center for Biosafety, Laboratory Animal and Pathogen Bank, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan
| | - Ryusuke Kimura
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi-shi 371-8511, Gunma, Japan;
| | - Norika Nagasawa
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (Y.H.)
| | - Yuriko Hayashi
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (Y.H.)
| | - Koichi Hashimoto
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima-shi 960-1295, Fukushima, Japan;
| | - Mitsuaki Hosoya
- Department of Perinatology and Pediatrics for Regional Medical Support, Fukushima Medical University, Fukushima-shi 960-1295, Fukushima, Japan;
| | - Kazuya Shirato
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
| | - Akihide Ryo
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
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Adachi H, Minagawa H, Hirose E, Nakamura N, Niimi H, Saito N, Ito M, Sato K, Yasui Y. Genetic Comparison of Human Parainfluenza Virus Type 3 Detected in Respiratory Samples from Patients with Encephalopathy and Airway Inflammation in Aichi Prefecture, Japan. Jpn J Infect Dis 2024; 77:155-160. [PMID: 38296544 DOI: 10.7883/yoken.jjid.2023.265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Human parainfluenza virus type 3 (HPIV-3, human respirovirus 3) is the second most frequently detected virus in lower respiratory tract infections in children after human respiratory syncytial virus (HRSV). HPIV-3, similar to related respiratory viruses such as HRSV and influenza virus, may cause encephalopathy; however, the relevance of HPIV-3 as a pathogenic factor in encephalopathy is unknown. We attempted to detect HPIV-1, HPIV-2, HPIV-3, HPIV-4, HRSV, and human metapneumovirus (HMPV) in 136 patients with encephalitis/encephalopathy or suspected encephalitis/encephalopathy during a 6-year period from 2014 to 2019. HPIV-3 was detected in 6 patients, followed by HRSV in 3 patients. The HPIV-3 strains detected were closely related to those detected in a patient with respiratory disease during the same period. Although HPIV-3 is less widely recognized than HRSV as a triggering virus of encephalopathy, our results suggest that HPIV-3 is as important as HRSV. Surveillance of the causative viruses of encephalopathy, including HPIV-3, would help clarify the causes of encephalopathy in Japan, as the cause is currently reported in less than half of cases in Japan.
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Affiliation(s)
- Hirokazu Adachi
- Laboratory of Virology, Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, Japan
| | - Hiroko Minagawa
- Laboratory of Virology, Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, Japan
| | - Emi Hirose
- Laboratory of Virology, Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, Japan
| | - Noriko Nakamura
- Laboratory of Virology, Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, Japan
| | - Hitomi Niimi
- Laboratory of Virology, Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, Japan
| | - Noriko Saito
- Laboratory of Virology, Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, Japan
| | - Miyabi Ito
- Laboratory of Virology, Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, Japan
| | - Katsuhiko Sato
- Laboratory of Virology, Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, Japan
| | - Yoshihiro Yasui
- Laboratory of Virology, Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, Japan
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Tran XD, Hoang VT, Goumballa N, Vu TN, Tran TK, Pham TD, Dao TL, Vu TT, Nguyen DC, Nguyen QT, Marty P, Gautret P. Viral and bacterial microorganisms in Vietnamese children with severe and non-severe pneumonia. Sci Rep 2024; 14:120. [PMID: 38167637 PMCID: PMC10761988 DOI: 10.1038/s41598-023-50657-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
To investigate potential respiratory pathogens in children with community-acquired pneumonia (CAP) and risk factors for severe disease. This prospective study was conducted among 467 children at the Thai Binh Paediatric Hospital, Vietnam between 1 July 2020 and 30 June 2021. Clinical data and laboratory results were collected. Twenty-four respiratory microorganisms were tested from nasopharyngeal swabs using real-time PCR. Logistical regression was used to estimate a factor's adjusted odd ratios of the severity of disease. Mean age of patients = 15.4 ± 13.3 months, 63.0% were male. Over 97% of patients had a positive PCR result. 87% of patients were positive for multiple (up to eight) microorganisms. Rhinovirus (46%), respiratory syncytial virus (RSV) (24%), enterovirus (17%), and parainfluenza viruses-3 (13%) were the most frequent viruses. H. influenzae (61%), S. pneumoniae (45%) and M. catarrhalis (30%) were the most common bacteria. 128 (27%) cases were classified as severe pneumonia. Presence of smokers at home (aOR 2.11, 95% CI 1.27-3.52, P value = 0.004), CRP level ≥ 50 mg/dL (aOR 6.11, 95% CI 3.86-9.68, P value < 0.0001), RSV (aOR 1.78, 95% CI 1.07-2.96, P value = 0.03) and H. influenzae (aOR 1.66, 95% CI 1.03-2.67, P value = 0.04) PCR detection associated with a higher risk of severe pneumonia; ,. Causative agents of pneumonia in children are complex. Children positive with RSV and H. influenzae need to be closely monitored to prevent severe pneumonia.
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Affiliation(s)
- Xuan Duong Tran
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, Marseille, France
| | - Van-Thuan Hoang
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Ndiaw Goumballa
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | | | | | - Thi Dung Pham
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Thi-Loi Dao
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Thi Thuy Vu
- Thai Binh Paediatric Hospital, Thai Binh, Vietnam
| | - Duy Cuong Nguyen
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Quoc Tien Nguyen
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Pierre Marty
- Inserm, C3M, Université Côte d'Azur, Nice Cedex 3, France
- Parasitologie-Mycologie, Centre Hospitalier Universitaire l'Archet, Nice Cedex 3, France
| | - Philippe Gautret
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam.
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, Marseille, France.
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Campelo FS, de Aguiar Cordeiro R, Moura FEA. The role of human bocavirus as an agent of community-acquired pneumonia in children under 5 years of age in Fortaleza, Ceará (Northeast Brazil). Braz J Microbiol 2022; 53:1915-1924. [PMID: 35933553 PMCID: PMC9679084 DOI: 10.1007/s42770-022-00806-1] [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: 04/25/2022] [Accepted: 07/21/2022] [Indexed: 01/13/2023] Open
Abstract
The human bocavirus (HBoV) is an agent of upper and lower respiratory infections, affecting mainly children under 5 years of age. Community-acquired pneumonia (CAP) is an important public health problem in developing countries, representing one of the main causes of hospitalizations and deaths in children. The aim of this study was to describe the prevalence of HBoV and the clinical and epidemiological characteristics in children diagnosed with CAP. For this purpose, nasopharyngeal aspirates were collected from 545 children aged 0 to 60 months diagnosed with CAP between January 2013 and December 2014 in a reference pediatric hospital in Fortaleza, Ceará, Brazil. The samples were subjected to PCR for detection of HBoV and parainfluenza 4 (PIV4) and indirect immunofluorescence for detection of respiratory syncytial virus (RSV), adenovirus (AdV), influenza A and B (FLU A and FLU B), and parainfluenza 1, 2, and 3 (PIV1, PIV2, PIV3). Clinically, most CAP were non-complicated (487/545; 89.3%); however, 10.7% (58/545) of children were treated in the ICU/resuscitation sector. Among the total samples analyzed, 359 (65.8%) were positive for at least one virus surveyed and 105 (19.2%) samples had two or more viruses. HBoV was detected in 87 samples (15.9%), being the second most prevalent virus. RSV, AdV, FLU A, FLU B, and PIV 1-3 were detected in 150 (27.5%), 45 (8.2%), 30 (5.5%), 3 (0.5%), and 131 (24%) samples, respectively. The age average was 12.1 months in children infected with HBoV, and the most frequent symptoms were dyspnea and cough. In addition, 90.6% of HboV-positive children received antibiotics as empirical treatment. HBoV did not show any circulation pattern; however, it seemed to be more frequent in the first half of the year, totaling 68.9% of the cases. HBoV is a frequent agent of pneumonia in the child population studied.
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Affiliation(s)
- Felipe Serra Campelo
- Postgraduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, Brazil
| | - Rossana de Aguiar Cordeiro
- Postgraduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, Brazil ,Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, Brazil
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Oh DY, Biere B, Grenz M, Wolff T, Schweiger B, Dürrwald R, Reiche J. Virological Surveillance and Molecular Characterization of Human Parainfluenzavirus Infection in Children with Acute Respiratory Illness: Germany, 2015-2019. Microorganisms 2021; 9:1508. [PMID: 34361941 PMCID: PMC8307145 DOI: 10.3390/microorganisms9071508] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/24/2022] Open
Abstract
Human parainfluenza viruses (HPIVs) are important causes of respiratory illness, especially in young children. However, surveillance for HPIV is rarely performed continuously, and national-level epidemiologic and genetic data are scarce. Within the German sentinel system, to monitor acute respiratory infections (ARI), 4463 respiratory specimens collected from outpatients < 5 years of age between October 2015 and September 2019 were retrospectively screened for HPIV 1-4 using real-time PCR. HPIV was identified in 459 (10%) samples. HPIV-3 was the most common HPIV-type, with 234 detections, followed by HPIV-1 (113), HPIV-4 (61), and HPIV-2 (49). HPIV-3 was more frequently associated with age < 2 years, and HPIV-4 was more frequently associated with pneumonia compared to other HPIV types. HPIV circulation displayed distinct seasonal patterns, which appeared to vary by type. Phylogenetic characterization clustered HPIV-1 in Clades 2 and 3. Reclassification was performed for HPIV-2, provisionally assigning two distinct HPIV-2 groups and six clades, with German HPIV-2s clustering in Clade 2.4. HPIV-3 clustered in C1, C3, C5, and, interestingly, in A. HPIV-4 clustered in Clades 2.1 and 2.2. The results of this study may serve to inform future approaches to diagnose and prevent HPIV infections, which contribute substantially to ARI in young children in Germany.
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Affiliation(s)
- Djin-Ye Oh
- Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, National Influenza Centre, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Barbara Biere
- Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, National Influenza Centre, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Markus Grenz
- Consultant Laboratory for RSV, PIV and HMPV, Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Thorsten Wolff
- Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, National Influenza Centre, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Brunhilde Schweiger
- Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, National Influenza Centre, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Ralf Dürrwald
- Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, National Influenza Centre, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
| | - Janine Reiche
- Consultant Laboratory for RSV, PIV and HMPV, Unit 17, Department of Infectious Diseases, Influenza and Other Respiratory Viruses, Robert Koch Institute, Seestraße 10, D-13353 Berlin, Germany
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Gu YE, Park JY, Lee MK, Lim IS. Characteristics of human parainfluenza virus type 4 infection in hospitalized children in Korea. Pediatr Int 2020; 62:52-58. [PMID: 31705838 PMCID: PMC7167709 DOI: 10.1111/ped.14049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/09/2019] [Accepted: 11/07/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND The characteristics of human parainfluenza virus type 4 (hPIV4) infection are not thoroughly understood. We therefore clarified the characteristics of hPIV4 in Korea. METHOD From January 2013 to December 2017, children admitted with respiratory tract infection at the Department of Pediatrics in Chung-Ang University Hospital were enrolled in the study. Nasopharyngeal aspirate specimens were obtained from patients and tested for hPIV types by multiplex reverse transcription polymerase chain reaction. We retrospectively reviewed subject medical records, focusing on epidemiological and clinical characteristics. RESULTS Of the 12 423 NPA specimens, 8,406 were positive by multiplex reverse transcription polymerase chain reaction for nine respiratory viruses, and 1,018 were positive for one of the four types of hPIV: 1,018 specimens led to the detection of 1,029 hPIVs; 3ss (31.3%) were positive for hPIV1, 120 (11.7%) were positive for hPIV2, 356 (34.6%) were positive for hPIV3, and 231 (22.4%) were positive for hPIV4. Of the hPIV-positive patients, the mean age was 2.3 years (range, 0.1-12.7 years), 225 (97.4%) had no underlying disease, and 178 (77.1%) had a fever with a duration of 4.1 ± 2.3 days and a peak temperature of 39.0 ± 0.7 ℃. The most common diagnosis in hPIV4 infection was pneumonia (44.2%), followed by bronchiolitis (26.0%) and upper respiratory tract infection (24.3%). Only 2.2% of patients were diagnosed with croup. Although the most prevalent overall type of hPIV was hPIV3, hPIV4 generally caused acute respiratory tract infection in summer and early fall in an irregular annual pattern. CONCLUSIONS Human parainfluenza virus type 4 is an important common pathogen of respiratory tract infections in pediatric patients in Korea.
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Affiliation(s)
- Young E Gu
- Department of Pediatrics, Chung-Ang University College of Medicine, Seoul, Korea
| | - Ji Y Park
- Department of Pediatrics, Chung-Ang University College of Medicine, Seoul, Korea.,Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Mi K Lee
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - In S Lim
- Department of Pediatrics, Chung-Ang University College of Medicine, Seoul, Korea
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Abe N, Yasudo H, Fukano R, Nakamura T, Okada S, Wakiguchi H, Okazaki F, Shirabe K, Toda S, Okamoto R, Ouchi K, Ohga S, Hasegawa S. Multi-season analyses of causative pathogens in children hospitalized with asthma exacerbation. Pediatr Allergy Immunol 2019; 30:724-731. [PMID: 31251831 PMCID: PMC7167852 DOI: 10.1111/pai.13102] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND Respiratory viral and mycoplasma infections are associated with childhood asthma exacerbations. Here, we explored epidemiologic profile of causative pathogens and possible factors for exacerbation in a single center over a three-year period. METHODS Hospitalized asthmatic children with attack aged 6 months-17 years were recruited between 2012 and 2015 (n = 216). Nasopharyngeal mucosa cell samples were collected from the participants and examined by reverse transcription-polymerase chain reaction to detect rhinovirus (RV), respiratory syncytial virus (RSV), enterovirus (EV), parainfluenza virus (PIV), Mycoplasma pneumoniae, and others. Clinical features, laboratory data, asthma exacerbation intensity, and asthma severity were compared among participants. Epidemiologic profile of causative pathogens and possible factors for exacerbation were explored. RESULTS Viruses and/or Mycoplasma pneumoniae were detected in 75% of the participants. Rhinovirus (48%) was the most commonly detected virus in the participants with single infection, followed by RSV (6%). The median age at admission in the RV group was significantly higher than that in the RSV group. Insufficient asthma control and allergen sensitization were significantly related to RV-associated asthma exacerbation. There was no seasonality of pathogen types associated with asthma exacerbation although a sporadic prevalence of EV-D68 was observehinovirud. Rhinovirus were repeatedly detected in multiple admission cases. CONCLUSION Our three-year analysis revealed that patients with RV infection were significantly prone to repeated RV infection in the subsequent exacerbation and good asthma control could prevent RV-associated asthma development and exacerbation. Multiple-year monitoring allowed us to comprehend the profile of virus- and/or mycoplasma-induced asthma exacerbation.
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Affiliation(s)
- Nozomi Abe
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Hiroki Yasudo
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Reiji Fukano
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Tamaki Nakamura
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Seigo Okada
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Hiroyuki Wakiguchi
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Fumiko Okazaki
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Shoichi Toda
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Reiko Okamoto
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Kazunobu Ouchi
- Department of Pediatrics, Kawasaki Medical School, Kurashiki, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan.,Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shunji Hasegawa
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
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Farrag MA, Hamed ME, Amer HM, Almajhdi FN. Epidemiology of respiratory viruses in Saudi Arabia: toward a complete picture. Arch Virol 2019; 164:1981-1996. [PMID: 31139937 PMCID: PMC7087236 DOI: 10.1007/s00705-019-04300-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
Acute lower respiratory tract infection is a major health problem that affects more than 15% of the total population of Saudi Arabia each year. Epidemiological studies conducted over the last three decades have indicated that viruses are responsible for the majority of these infections. The epidemiology of respiratory viruses in Saudi Arabia is proposed to be affected mainly by the presence and mobility of large numbers of foreign workers and the gathering of millions of Muslims in Mecca during the Hajj and Umrah seasons. Knowledge concerning the epidemiology, circulation pattern, and evolutionary kinetics of respiratory viruses in Saudi Arabia are scant, with the available literature being inconsistent. This review summarizes the available data on the epidemiology and evolution of respiratory viruses. The demographic features associated with Middle East respiratory syndrome-related coronavirus infections are specifically analyzed for a better understanding of the epidemiology of this virus. The data support the view that continuous entry and exit of pilgrims and foreign workers with different ethnicities and socioeconomic backgrounds in Saudi Arabia is the most likely vehicle for global dissemination of respiratory viruses and for the emergence of new viruses (or virus variants) capable of greater dissemination.
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Affiliation(s)
- Mohamed A Farrag
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455QA6, Riyadh, 11451, Saudi Arabia
| | - Maaweya E Hamed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455QA6, Riyadh, 11451, Saudi Arabia
| | - Haitham M Amer
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455QA6, Riyadh, 11451, Saudi Arabia.
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10
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A method to identify respiratory virus infections in clinical samples using next-generation sequencing. Sci Rep 2019; 9:2606. [PMID: 30796243 PMCID: PMC6384955 DOI: 10.1038/s41598-018-37483-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 11/26/2018] [Indexed: 12/30/2022] Open
Abstract
Respiratory virus infections are very common. Such infections impose an enormous economic burden and occasionally lead to death. Furthermore, every few decades, respiratory virus pandemics emerge, putting the entire world population at risk. Thus, there is an urgent need to quickly and precisely identify the infecting agent in a clinical setting. However, in many patients with influenza-like symptoms (ILS) the identity of the underlying pathogen remains unknown. In addition, it takes time and effort to individually identify the virus responsible for the ILS. Here, we present a new next-generation sequencing (NGS)-based method that enables rapid and robust identification of pathogens in a pool of clinical samples without the need for specific primers. The method is aimed at rapidly uncovering a potentially common pathogen affecting many samples with an unidentified source of disease.
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11
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Thomazelli LM, Oliveira DBD, Durigon GS, Whitaker B, Kamili S, Berezin EN, Durigon EL. Human parainfluenza virus surveillance in pediatric patients with lower respiratory tract infections: a special view of parainfluenza type 4. JORNAL DE PEDIATRIA (VERSÃO EM PORTUGUÊS) 2018. [DOI: 10.1016/j.jpedp.2017.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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12
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Thomazelli LM, Oliveira DBLD, Durigon GS, Whitaker B, Kamili S, Berezin EN, Durigon EL. Human parainfluenza virus surveillance in pediatric patients with lower respiratory tract infections: a special view of parainfluenza type 4. J Pediatr (Rio J) 2018; 94:554-558. [PMID: 28963878 DOI: 10.1016/j.jped.2017.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE Characterize the role of human parainfluenza virus and its clinical features in Brazilian children under 2 years of age presenting with acute lower respiratory tract infections. METHODS Real-time assays were used to identify strains of human parainfluenza virus and other common respiratory viruses in nasopharyngeal aspirates. One thousand and two children presenting with acute lower respiratory tract illnesses were enrolled from February 2008 to August 2010. RESULTS One hundred and four (10.4%) patients were human parainfluenza virus positive, of whom 60 (57.7%) were positive for human parainfluenza virus-3, 30 (28.8%) for human parainfluenza virus-4, 12 (11.5%) for human parainfluenza virus-1, and two (1.9%) for human parainfluenza virus-2. Seven (6.7%) patients had more than one strain of human parainfluenza virus detected. The most frequent symptoms were tachypnea and cough, similar to other viral respiratory infections. Clinical manifestations did not differ significantly between human parainfluenza virus-1, -2, -3, and -4 infections. Human parainfluenza virus-1, -3, and -4 were present in the population studied throughout the three years of surveillance, with human parainfluenza virus-3 being the predominant type identified in the first two years. CONCLUSION Human parainfluenza viruses contribute substantially to pediatric acute respiratory illness (ARI) in Brazil, with nearly 30% of this contribution attributable to human parainfluenza virus-4.
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Affiliation(s)
- Luciano M Thomazelli
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas, São Paulo, SP, Brazil.
| | | | - Giuliana S Durigon
- Irmandade da Santa Casa de Misericórdia de São Paulo, São Paulo, SP, Brazil
| | - Brett Whitaker
- Center for Disease Control and Prevention, Atlanta, United States
| | - Shifaq Kamili
- Center for Disease Control and Prevention, Atlanta, United States
| | - Eitan N Berezin
- Irmandade da Santa Casa de Misericórdia de São Paulo, São Paulo, SP, Brazil
| | - Edison L Durigon
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas, São Paulo, SP, Brazil
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13
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Álvarez-Argüelles ME, Rojo-Alba S, Pérez Martínez Z, Leal Negredo Á, Boga Riveiro JA, Alonso Álvarez MA, Rodríguez Súarez J, de Oña Navarro M, Melón García S. New clinical and seasonal evidence of infections by Human Parainfluenzavirus. Eur J Clin Microbiol Infect Dis 2018; 37:2211-2217. [PMID: 30143939 PMCID: PMC7088353 DOI: 10.1007/s10096-018-3363-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/17/2018] [Indexed: 11/30/2022]
Abstract
Human Parainfluenzaviruses (PIVs) account for a significant proportion of viral acute respiratory infections (ARIs) in children, and are also associated with morbidity and mortality in adults, including nosocomial infections. This work aims to describe PIV genotypes and their clinical and epidemiological distribution. Between December 2016 and December 2017, 6121 samples were collected, and submitted to viral culture and genomic quantification, specifically Parainfluenza 1–4 (PIV1–4), Influenza A and B, Respiratory Syncytial Virus (RSV) A and B, Adenovirus, Metapneumovirus, Coronavirus, Rhinovirus, and Enterovirus. Normalized viral load, as (log10) copies/103 cells, was calculated as virus Ct, determined by multiple qRT-PCR, as a function of the Ct of β-globin. PIV was confirmed in 268 cases (4.37%), and linked to both upper and lower respiratory tract disease, being more frequent in children than in adults (5.23 and 2.43%, respectively). PIV1 and PIV3 were most common (31 and 32.5%, of total PIV positive samples, respectively), with distribution being similar in children and adults, as was viral load. PIV type was correlated with seasonality: PIV3 being more frequent in winter and spring, PIV1 in summer, and PIV 4 in fall. No correlation between vial load and clinical severity was found. Novel findings were that PIV viral load was higher in fall than in other seasons, and PIV4, classically linked to mild respiratory symptoms, was circulating, in children and adults, at all levels of symptoms throughout the year.
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Affiliation(s)
- Marta E Álvarez-Argüelles
- Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain. .,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain.
| | - Susana Rojo-Alba
- Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Zulema Pérez Martínez
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain.,Morphology and Cellular Biology Department, Oviedo University, Oviedo, Spain
| | - Álvaro Leal Negredo
- Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - José Antonio Boga Riveiro
- Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | | | | | - María de Oña Navarro
- Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Santiago Melón García
- Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
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14
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Snoeck CJ, Ponghsavath V, Luetteke N, Kaufmann S, Sausy A, Samountry B, Jutavijittum P, Weber B, Muller CP. Etiology of viral respiratory infections in Northern Lao People's Democratic Republic. J Med Virol 2018; 90:1553-1558. [PMID: 29896913 PMCID: PMC7167017 DOI: 10.1002/jmv.25237] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/05/2018] [Indexed: 12/01/2022]
Abstract
In Lao People's Democratic Republic (PDR), acute respiratory infections overburden the health care system, but viral etiology, genetic diversity, and seasonality, especially in light of the introduction of influenza vaccination in the country, are poorly understood. From August 2010 to April 2011, 309 outpatients were recruited at the Luang Prabang Provincial Hospital covering highland Lao communities. Nasopharyngeal swabs were screened for the presence of 13 respiratory viruses. At least one virus was detected in 69.6% and dual/triple viral infections in 12.9%/1.9% of the patients. Influenza A and B viruses combined were the most frequently detected pathogens, followed by human adenovirus and respiratory syncytial virus (RSV). The other viruses were detected in less than 10% of the patients. Phylogenetic analyses on a representative set of RSV strains revealed that, while otherwise very rare, the RSV‐B CB1/THB genotype cocirculated with other common genotypes. A single wave of influenza virus and RSV activity was observed during the rainy season, providing further support to influenza vaccination before the onset of the rains. This study provides recommendations for influenza vaccination that still needs optimization and highlights the need for revised guidelines for treatment and prevention of respiratory infections in Lao PDR, as well as for increased surveillance efforts.
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Affiliation(s)
- Chantal J Snoeck
- Infectious Disease Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | | | - Nina Luetteke
- Infectious Disease Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | | | - Aurélie Sausy
- Infectious Disease Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Bounthome Samountry
- Department of Pathology, Faculty of Medicine, University of Health Sciences, Vientiane, Lao PDR
| | - Prapan Jutavijittum
- Department of Pathology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Claude P Muller
- Infectious Disease Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.,Lao-Lux-Laboratory, Institut Pasteur du Laos, Vientiane, Lao PDR.,Laboratoire National de Santé, Dudelange, Luxembourg
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15
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Thi Ty Hang V, Thi Han Ny N, My Phuc T, Thi Thanh Tam P, Thao Huong D, Dang Trung Nghia H, Tran Anh Vu N, Thi Hong Phuong P, Van Xang N, Dong N, Nhu Hiep P, Van Hung N, Tinh Hien T, Rabaa M, Thwaites GE, Baker S, Van Tan L, van Doorn H, VIZIONS consortium. Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam. Wellcome Open Res 2017; 2:80. [PMID: 29503874 PMCID: PMC5811805 DOI: 10.12688/wellcomeopenres.12429.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2017] [Indexed: 12/01/2024] Open
Abstract
BACKGROUND Acute respiratory infections (ARI) are among the leading causes of hospitalization in children ≤5 years old. Rapid diagnostics of viral pathogens is essential to avoid unnecessary antibiotic treatment, thereby slowing down antibiotic-resistance. We evaluated the diagnostic performance of the Luminex xTAG Respiratory Viral Panel FAST v2 against viral specific PCR as reference assays for ARI in Vietnam. METHODS Four hundred and forty two nose and throat swabs were collected in viral transport medium, and were tested with Luminex xTAG Respiratory Viral Panel FAST v2. Multiplex RT-PCR and single RT-PCR were used as references. Results: Overall, viral pathogens were detected in a total count of 270/294 (91.8%, 95% CI 88.1-94.7) by the Luminex among reference assays, whilst 112/6336 (1.8%, 95% CI, 1.4-2.1) of pathogens were detected by the Luminex, but not by reference assays. Frequency of pathogens detected by Luminex and reference assays was 379 and 292, respectively. The diagnostic yield was 66.7% (295/442, 95%CI 62.1-71.1%) for the Luminex assay and 54.1% (239/442, 95% CI, 49.3-58.8%) for reference assays. The Luminex kit had higher yields for all viruses except influenza B virus, respiratory syncytial virus, and human bocavirus. High agreements between both methods [mean (range): 0.91 (0.83-1.00)] were found for 10/15 viral agents. CONCLUSIONS The Luminex assay is a high throughput multiplex platform for rapid detection of common viral pathogens causing ARI. Although the current high cost may prevent Luminex assays from being widely used, especially in limited resource settings where ARI are felt most, its introduction in clinical diagnostics may help reduce unnecessary use of antibiotic prescription.
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Affiliation(s)
- Vu Thi Ty Hang
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Han Ny
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran My Phuc
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Thi Thanh Tam
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Dang Thao Huong
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho Dang Trung Nghia
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | | | - Nguyen Dong
- Khanh Hoa General Hospital, Khanh Hoa, Vietnam
| | | | | | - Tran Tinh Hien
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Maia Rabaa
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy E. Thwaites
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- The London School of Hygiene and Tropical Medicine, London, UK
| | - Le Van Tan
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - H.Rogier van Doorn
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- National Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - VIZIONS consortium
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Dong Thap General Hospital, Dong Thap, Vietnam
- Khanh Hoa General Hospital, Khanh Hoa, Vietnam
- Hue Central Hospital, Thua Thien - Hue, Vietnam
- Dak Lak General Hospital, Dak Lak, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- The London School of Hygiene and Tropical Medicine, London, UK
- National Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi, Vietnam
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16
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Thi Ty Hang V, Thi Han Ny N, My Phuc T, Thi Thanh Tam P, Thao Huong D, Dang Trung Nghia H, Tran Anh Vu N, Thi Hong Phuong P, Van Xang N, Dong N, Nhu Hiep P, Van Hung N, Tinh Hien T, Rabaa M, Thwaites GE, Baker S, Van Tan L, van Doorn H, VIZIONS consortium. Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam. Wellcome Open Res 2017; 2:80. [PMID: 29503874 PMCID: PMC5811805 DOI: 10.12688/wellcomeopenres.12429.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Acute respiratory infections (ARI) are among the leading causes of hospitalization in children ≤5 years old. Rapid diagnostics of viral pathogens is essential to avoid unnecessary antibiotic treatment, thereby slowing down antibiotic-resistance. We evaluated the diagnostic performance of the Luminex xTAG Respiratory Viral Panel FAST v2 against viral specific PCR as reference assays for ARI in Vietnam. METHODS Four hundred and forty two nose and throat swabs were collected in viral transport medium, and were tested with Luminex xTAG Respiratory Viral Panel FAST v2. Multiplex RT-PCR and single RT-PCR were used as references. Results: Overall, viral pathogens were detected in a total count of 270/294 (91.8%, 95% CI 88.1-94.7) by the Luminex among reference assays, whilst 112/6336 (1.8%, 95% CI, 1.4-2.1) of pathogens were detected by the Luminex, but not by reference assays. Frequency of pathogens detected by Luminex and reference assays was 379 and 292, respectively. The diagnostic yield was 66.7% (295/442, 95%CI 62.1-71.1%) for the Luminex assay and 54.1% (239/442, 95% CI, 49.3-58.8%) for reference assays. The Luminex kit had higher yields for all viruses except influenza B virus, respiratory syncytial virus, and human bocavirus. High agreements between both methods [mean (range): 0.91 (0.83-1.00)] were found for 10/15 viral agents. CONCLUSIONS The Luminex assay is a high throughput multiplex platform for rapid detection of common viral pathogens causing ARI. Although the current high cost may prevent Luminex assays from being widely used, especially in limited resource settings where ARI are felt most, its introduction in clinical diagnostics may help reduce unnecessary use of antibiotic prescription.
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Affiliation(s)
- Vu Thi Ty Hang
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Han Ny
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran My Phuc
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Thi Thanh Tam
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Dang Thao Huong
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho Dang Trung Nghia
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | | | - Nguyen Dong
- Khanh Hoa General Hospital, Khanh Hoa, Vietnam
| | | | | | - Tran Tinh Hien
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Maia Rabaa
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy E. Thwaites
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- The London School of Hygiene and Tropical Medicine, London, UK
| | - Le Van Tan
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - H.Rogier van Doorn
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- National Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - VIZIONS consortium
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Dong Thap General Hospital, Dong Thap, Vietnam
- Khanh Hoa General Hospital, Khanh Hoa, Vietnam
- Hue Central Hospital, Thua Thien - Hue, Vietnam
- Dak Lak General Hospital, Dak Lak, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- The London School of Hygiene and Tropical Medicine, London, UK
- National Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi, Vietnam
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17
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Sato K, Watanabe O, Ohmiya S, Chiba F, Hayashi M, Suzuki T, Kawakami K, Nishimura H. Efficient isolation of human parainfluenza viruses 1 and 3 using MNT-1, a human malignant melanoma cell line system that exhibits an apparent cytopathic effect. Microbiol Immunol 2017; 60:801-805. [PMID: 27762443 DOI: 10.1111/1348-0421.12446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/06/2016] [Accepted: 10/18/2016] [Indexed: 11/28/2022]
Abstract
Isolation of human parainfluenza virus (HPIV) serotypes 1 and 3 from clinical specimens is not very efficient because of the lack of a cell culture system capable of inducing CPE. In this study, the utility of a melanoma cell line, MNT-1, that allows HPIV growth and displays CPE was demonstrated. In particularly, the efficiency of isolating HPIV1 and HPIV3 using MNT-1 was greater than for cell lines conventionally used for HPIV isolation. Our demonstrated efficacy of HPIV1 and HPIV3 isolation with apparent CPE using the MNT-1 cell culture system has the potential to improve virus isolation from clinical specimens.
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Affiliation(s)
- Ko Sato
- Virus Research Center, Clinical Research Division, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Sendai 983-8520, 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, Sendai 983-8520, Japan
| | - Suguru Ohmiya
- Virus Research Center, Clinical Research Division, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Sendai 983-8520, Japan
| | - Fumiko Chiba
- Virus Research Center, Clinical Research Division, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Sendai 983-8520, Japan
| | - Masahiro Hayashi
- Department of Dermatology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata 990-9985, Japan
| | - Tamio Suzuki
- Department of Dermatology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata 990-9985, 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, Sendai 983-8520, Japan
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18
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Essa S, Al-Tawalah H, AlShamali S, Al-Nakib W. The potential influence of human parainfluenza viruses detected during hospitalization among critically ill patients in Kuwait, 2013-2015. Virol J 2017; 14:19. [PMID: 28159006 PMCID: PMC5291994 DOI: 10.1186/s12985-017-0681-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/12/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The four types of human parainfluenza viruses (PIV) are important causes of community-acquired pneumonia, particularly in children; however, limited information exists about the incidence of PIV in critically ill patients. The aim of this study is to describe the spectrum, incidence and clinical features of PIV-associated infections diagnosed during the hospital stay of patients admitted to pediatric intensive care unit (PICU) and intensive care unit (ICU) of 5 medical centers across Kuwait. METHODS This was a population-based, retrospective study from 2013 to 2015. Specimens were analyzed by molecular methods. This analysis was performed using the database of Virology Unit, Mubarak Al-Kabeer Hospital. Data from 1510 admitted patients with suspected respiratory viral infections was extracted. RESULTS The database contained a total of 39 (2.6%) patients infected with PIV (53.8% male and 46.2% females) and 20 (51.3%) were under 1 year of age. The most frequently isolated type was type 3 (28, 71.8%) followed by type 1 (9, 23.1%). At admission the most common clinical diagnosis was pneumonia in 12 patients (30.8%, p < 0.05) followed by bronchiolitis in 10 patients (25.6%). CONCLUSION PIV plays an important yet unrecognized role in the outcomes of PIUC and ICU patients. Our results contribute to the limited epidemiologic data of PIV in PIUC and ICU in this region.
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Affiliation(s)
- Sahar Essa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait.
| | - Haya Al-Tawalah
- Ministry of Health, Sabah Hospital, Virology Unit, Kuwait City, Kuwait
| | | | - Widad Al-Nakib
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
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19
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Indumathi CP, Gunanasekaran P, Kaveri K, Arunagiri K, Mohana S, Sheriff AK, SureshBabu BV, Padmapriya P, Senthilraja R, Fathima G. Isolation & molecular characterization of human parainfluenza virus in Chennai, India. Indian J Med Res 2016; 142:583-90. [PMID: 26658594 PMCID: PMC4743346 DOI: 10.4103/0971-5916.171287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background & objectives: Human parainfluenza virus (HPIV) accounts for a significant proportion of lower respiratory tract infections in children as well as adults. This study was done to detect the presence of different subtypes of HPIV from patients having influenza like illness (ILI). Methods: Throat and nasal swabs from 232 patients with ILI who were negative for influenza viruses were tested by multiplex reverse transcription polymerase chain reaction(mRT-PCR) for the detection of human parainfluenza virus. All samples were inoculated in rhesus monkey kidney (LLC-MK2) cell line. Results: Of the 232 samples, 26(11.2%) were positive by mRT-PCR and nine (34.6%) showed cytopathic effect with syncytium formation for HPIV and all were HPIV-3 serotype, other serotypes like 1,2,4 were negative. The HPIV-3 strains (HN gene) were sequenced and analysed. Two novel mutations were identified at amino acid residues 295 and 297. Interpretation & conclusions: The mRT-PCR assay offers a rapid, sensitive and accurate diagnostic method for detection of HPIV which enables early detection and control. In our study there was a predominance of HPIV among 1-5 yr age group and the school going age group was less affected. Further studies need to be done to characterize HPIV isolated from different parts of the country.
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Affiliation(s)
| | | | - K Kaveri
- Department of Virology, King Institute of Preventive Medicine & Research, Chennai, India
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Ramezannia M, Hosseini SM, Fotouhi F, Khansarinejad B, Mazaheri V. Development of a multiplex real-time RT-PCR assay for detection of human parainfluenza viruses in patients with respiratory symptoms. Future Virol 2016. [DOI: 10.2217/fvl-2016-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: The human parainfluenza viruses (HPIVs) are common viral causes of both upper and lower respiratory tract infections in infants and children. The purpose of this study was to develop a real-time reverse transcription PCR assay to detect HPIVs in clinical specimens in a single test. Specimens: Specific primers and probes matched to conserved region of hemagglutinin–neuraminidase genes were designed. Clinical specimens were collected from hospitalized children of ≤5 years old. Results & conclusion: Of 230 specimens, 48 samples contained one of HPIV types 1–4. The most percentage of positive HPIVs belonged to HPIV2. HPIVs were found in fall, winter and spring but not in summer months. In conclusion, our in-house multiplex real-time reverse transcription PCR is a suitable technique for simultaneous detection of HPIVs in clinical samples.
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Affiliation(s)
- Mahboobeh Ramezannia
- Department of Influenza & Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran
| | - Seyed Masoud Hosseini
- Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran
| | - Fatemeh Fotouhi
- Department of Influenza & Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Behzad Khansarinejad
- Department of Microbiology & Immunology, Arak University of Medical Sciences, Arak, Iran
| | - Vahideh Mazaheri
- Department of Influenza & Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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Xiao NG, Duan ZJ, Xie ZP, Zhong LL, Zeng SZ, Huang H, Gao HC, Zhang B. Human parainfluenza virus types 1-4 in hospitalized children with acute lower respiratory infections in China. J Med Virol 2016; 88:2085-2091. [PMID: 27197630 PMCID: PMC7166804 DOI: 10.1002/jmv.24580] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2016] [Indexed: 11/09/2022]
Abstract
Human parainfluenza viruses (HPIVs) are an important cause of acute lower respiratory tract infections (ALRTIs). HPIV-4, a newly identified virus, has been associated with severe ALRTIs recently. A total of 771 nasopharyngeal aspirate samples were collected from hospitalized children between March 2010 and February 2011. HPIVs were detected by Nest-PCR, and other known respiratory viruses were detected by RT-PCR and PCR. All amplification products were sequenced. HPIVs were detected in 151 (19.58%) patients, of whom 28 (3.63%) were positive for HPIV-4, 12(1.55%) for HPIV-1, 4 (0.51%) for HPIV-2, and 107 (13.87%) for HPIV-3. Only three were found to be co-infected with different types of HPIVs. All HPIV-positive children were under 5 years of age, with the majority being less than 1 year. Only the detection rate of HPIV-3 had a significant statistical difference (χ2 = 29.648, P = 0.000) between ages. HPIV-3 and HPIV-4 were detected during the summer. Sixty (39.74%) were co-infected with other respiratory viruses, and human rhinovirus (HRV) was the most common co-infecting virus. The most frequent clinical diagnosis was bronchopneumonia, and all patients had cough; some patients who were infected with HPIV-3 and HPIV-4 had polypnea and cyanosis. No significant difference was found in clinical manifestations between those who were infected with HPIV-4 and HPIV-3. Two genotypes for HPIV-4 were prevalent, although HPIV-4a dominated. HPIV-4 is an important virus for children hospitalized with ALRTIs in China. HRV was the most common co-infecting virus. Two genotypes for HPIV-4 are prevalent, HPIV-4a dominated. J. Med. Virol. 88:2085-2091, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ni-Guang Xiao
- Department of Pediatrics, Hunan Provincial People's Hospital, Hunan Provincial, China
| | - Zhao-Jun Duan
- State Key Laboratory of Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Zhi-Ping Xie
- State Key Laboratory of Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Li-Li Zhong
- Department of Pediatrics, Hunan Provincial People's Hospital, Hunan Provincial, China
| | - Sai-Zhen Zeng
- Department of Pediatrics, Hunan Provincial People's Hospital, Hunan Provincial, China
| | - Han Huang
- Department of Pediatrics, Hunan Provincial People's Hospital, Hunan Provincial, China
| | - Han-Chun Gao
- State Key Laboratory of Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Bing Zhang
- Department of Pediatrics, Hunan Provincial People's Hospital, Hunan Provincial, China.
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Cho HJ, Hong SW, Kim HJ, Kwak YS. Development of a Multiplex PCR Method to Detect Fungal Pathogens for Quarantine on Exported Cacti. THE PLANT PATHOLOGY JOURNAL 2016; 32:53-7. [PMID: 26889115 PMCID: PMC4755675 DOI: 10.5423/ppj.nt.09.2015.0184] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 05/22/2023]
Abstract
Major diseases in grafted cacti have been reported and Fusarium oxysporum, Bipolaris cactivora, Phytophthora spp. and Collectotrichum spp. are known as causal pathogens. These pathogens can lead to plant death after infection. Therefore, some European countries have quarantined imported cacti that are infected with specific fungal pathogens. Consequently, we developed PCR detection methods to identify four quarantined fungal pathogens and reduce export rejection rates of Korean grafted cacti. The pathogen specific primer sets F.oF-F.oR, B.CF-B.CR, P.nF-P.nR, and P.cF-P.CR were tested for F. oxysporum, B. cactivora, P. nicotinae, and P. cactorum, respectively. The F.oF-F.oR primer set was designed from the Fusarium ITS region; the B.CF-B.CR and P.nF-P.nR primers respectively from Bipolaris and Phytophthora ITS1; and the P.cF-P.CR primer set from the Ypt1protein gene region. The quarantine fungal pathogen primer pairs were amplified to the specific number of base pairs in each of the following fungal pathogens: 210-bp (F. oxysporum), 510-bp (B. cactivora), 313-bp (P. nicotinae), and 447-bp (P. cactorum). The detection limit for the mono- and multiplex PCR primer sets was 0.1 ng of template DNA under in vitro conditions. Therefore, each primer set successfully diagnosed contamination of quarantine pathogens in export grafted cacti. Consequently, our methodology is a viable tool to screen contamination of the fungal pathogen in exported grafted cacti.
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Affiliation(s)
- Hyun ji Cho
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701,
Korea
| | - Seong Won Hong
- Department of Plant Medicine and Research Institute of Life Science, Gyeongsang National University, Jinju 660-701,
Korea
| | - Hyun-ju Kim
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Suwon 443-400,
Korea
| | - Youn-Sig Kwak
- Department of Plant Medicine and Research Institute of Life Science, Gyeongsang National University, Jinju 660-701,
Korea
- Corresponding author. Phone) +82-55-772-1922, FAX) +82-55-772-1929, E-mail)
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Cebey-López M, Herberg J, Pardo-Seco J, Gómez-Carballa A, Martinón-Torres N, Salas A, Martinón-Sánchez JM, Gormley S, Sumner E, Fink C, Martinón-Torres F, GENDRES network. Viral Co-Infections in Pediatric Patients Hospitalized with Lower Tract Acute Respiratory Infections. PLoS One 2015; 10:e0136526. [PMID: 26332375 PMCID: PMC4558027 DOI: 10.1371/journal.pone.0136526] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/04/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Molecular techniques can often reveal a broader range of pathogens in respiratory infections. We aim to investigate the prevalence and age pattern of viral co-infection in children hospitalized with lower tract acute respiratory infection (LT-ARI), using molecular techniques. METHODS A nested polymerase chain reaction approach was used to detect Influenza (A, B), metapneumovirus, respiratory syncytial virus (RSV), parainfluenza (1-4), rhinovirus, adenovirus (A-F), bocavirus and coronaviruses (NL63, 229E, OC43) in respiratory samples of children with acute respiratory infection prospectively admitted to any of the GENDRES network hospitals between 2011-2013. The results were corroborated in an independent cohort collected in the UK. RESULTS A total of 204 and 97 nasopharyngeal samples were collected in the GENDRES and UK cohorts, respectively. In both cohorts, RSV was the most frequent pathogen (52.9% and 36.1% of the cohorts, respectively). Co-infection with multiple viruses was found in 92 samples (45.1%) and 29 samples (29.9%), respectively; this was most frequent in the 12-24 months age group. The most frequently observed co-infection patterns were RSV-Rhinovirus (23 patients, 11.3%, GENDRES cohort) and RSV-bocavirus / bocavirus-influenza (5 patients, 5.2%, UK cohort). CONCLUSION The presence of more than one virus in pediatric patients admitted to hospital with LT-ARI is very frequent and seems to peak at 12-24 months of age. The clinical significance of these findings is unclear but should warrant further analysis.
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Affiliation(s)
- Miriam Cebey-López
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Jethro Herberg
- Section of Paediatrics, Division of Infectious Disease, Imperial College of London, South Kensington Campus, London, United Kingdom
| | - Jacobo Pardo-Seco
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Alberto Gómez-Carballa
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Nazareth Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - José María Martinón-Sánchez
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Stuart Gormley
- Section of Paediatrics, Division of Infectious Disease, Imperial College of London, South Kensington Campus, London, United Kingdom
| | - Edward Sumner
- Micropathology Ltd., University of Warwick Science Park, Coventry, United Kingdom
| | - Colin Fink
- Micropathology Ltd., University of Warwick Science Park, Coventry, United Kingdom
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
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Shatizadeh S, Yavarian J, Rezaie F, Mahmoodi M, Naseri M, Mokhtari Azad T. Epidemiological and clinical evaluation of children with respiratory virus infections. Med J Islam Repub Iran 2014; 28:102. [PMID: 25664303 PMCID: PMC4301222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 01/28/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Respiratory viruses are the leading cause of respiratory tract infections among children and are responsible for causing morbidity and mortality worldwide. This study was performed to detect viruses in children with respiratory infections and describe their epidemiology and clinical characteristics. METHODS In this descriptive cross sectional study, throat swabs and wash specimens from 202 children younger than six years of age with diagnosis of a respiratory tract infection from a total of 897 specimens were evaluated using multiplex PCR method. RESULTS Respiratory viruses were detected in 92 children: respiratory synsytial virus, 16.8%; influenza virus, 5.4%; parainfluenza virus, 8.4%; adenovirus, 14.4% and human metapneumo virus 0.49% with male predominance and higher distribution in children younger than 1 year of age with preference in the cold months of year. The clinical presentations of all detected viruses were almost similar. CONCLUSION In the present study, nine different respiratory viruses were detected. RSV causes the great majority of respiratory virus infections in children. There was no significant difference in epidemiologic patterns of these viruses in comparison to other studies.
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Affiliation(s)
- Somayeh Shatizadeh
- 1. MSc, PhD student of Virology, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Jila Yavarian
- 2. MD, PhD, Assistant Professor of Virology, Department of virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Farhad Rezaie
- 3. PhD, Assistant Professor of Virology, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mahmood Mahmoodi
- 4. PhD, Professor, Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Maryam Naseri
- 5. MSc, Master of Science in virology, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Talat Mokhtari Azad
- 6. DVM, MPH, PhD, Professor of Virology, Department of virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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25
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Bialasiewicz S, McVernon J, Nolan T, Lambert SB, Zhao G, Wang D, Nissen MD, Sloots TP. Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing. BMC Infect Dis 2014; 14:275. [PMID: 24885416 PMCID: PMC4038074 DOI: 10.1186/1471-2334-14-275] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 04/11/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Human Parainfluenza viruses are a common cause of both upper and lower respiratory tract infections, particularly in children. Of the four Parainfluenza virus serotypes, Parainfluenza 4 is least well characterised from both the clinical, epidemiological and genetic perspectives. METHODS Flocked nose or throat swabs from a previous study investigating viral prevalence in community-based adults suffering from influenza like illness were used as the basis for this study. Samples in which no virus was detected using a 16 viral respiratory pathogen real-time PCR panel were barcoded and pyrosequenced using the Roche 454 GS FLX Titanium chemistry. The sequences were analysed using the VirusHunter bioinformatic pipeline. Sanger sequencing was used to complete the detected Parainfluenza 4 coding region. RESULTS A variant Parainfluenza 4 subtype b strain (QLD-01) was discovered in an otherwise healthy adult who presented with influenza like illness. Strain QLD-01 shared genomic similarities with both a and b subtypes. The extent of divergence of this genome from the 5 available whole Parainfluenza 4 genomes impacted the predicted binding efficiencies of the majority of published Parainfluenza 4 PCR assays. CONCLUSIONS These findings further support a possible role for Parainfluenza 4 in the aetiology of adult respiratory disease within the community setting, and highlight the caution needed to be used in designing PCR assays from limited sequence information or in using proprietary commercial PCR assays.
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Affiliation(s)
- Seweryn Bialasiewicz
- Queensland Children’s Medical Research Institute, The University of Queensland, Brisbane, Qld, Australia
- Queensland Paediatric Infectious Diseases Laboratory, The Royal Children’s Hospital, Brisbane, Qld, Australia
- Sir Albert Sakzewski Virus Research Centre, Building C28, Back Rd, Herston, QLD 4029, Australia
| | - Jodie McVernon
- Murdoch Children’s Research Institute & Melbourne School of Population Health, The University of Melbourne, Parkville, Vic, Australia
| | - Terry Nolan
- Murdoch Children’s Research Institute & Melbourne School of Population Health, The University of Melbourne, Parkville, Vic, Australia
| | - Stephen B Lambert
- Queensland Children’s Medical Research Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Guoyan Zhao
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael D Nissen
- Queensland Children’s Medical Research Institute, The University of Queensland, Brisbane, Qld, Australia
- Queensland Paediatric Infectious Diseases Laboratory, The Royal Children’s Hospital, Brisbane, Qld, Australia
| | - Theo P Sloots
- Queensland Children’s Medical Research Institute, The University of Queensland, Brisbane, Qld, Australia
- Queensland Paediatric Infectious Diseases Laboratory, The Royal Children’s Hospital, Brisbane, Qld, Australia
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Park KS, Yang MH, Lee CK, Song KJ. Genetic analysis of human parainfluenza viruses circulating in Korea, 2006. J Med Virol 2014; 86:1041-7. [PMID: 24464425 DOI: 10.1002/jmv.23890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2014] [Indexed: 01/20/2023]
Abstract
Human parainfluenza viruses (HPIV) are important causes of respiratory tract infections in young children. To characterize the molecular epidemiology of an HPIV outbreak occurring in Korea during 2006, genetic analysis of 269 cell culture isolates from HPIV-infected children, was conducted using nested reverse transcription-PCR (RT-PCR). HPIV-1 was detected in 70.3% of tested samples (189/269). The detection rate of HPIV-2 and HPIV-3 was 1.5% (4/269) and 9.3% (25/269), respectively. Mixed HPIV-1, -2 and -3 infections were detected in 19.0% (51/269): HPIV-1 and HPIV-2 in 15, HPIV-1 and HPIV-3 in 26, HPIV-2 and HPIV-3 in 6, and HPIV-1, -2 and -3 in 4. Of these positive samples for three different types HIPV-1, -2, and -3, two each representative strains were selected, the full length of hemagglutinin-neuraminidase (HN) gene for HPIV was amplified by RT-PCR, and sequenced. Multiple alignment analysis, based on reference sequence of HPIV-1, -2, and -3 strains available in GenBank, showed that the identity of nucleotide and deduced amino acid sequences was 92.4-97.6% and 92.7-97.9%, respectively, for HPIV-1, 88.5-99.8% and 88.6-100% for HPIV-2, and 96.3-99.5% and 95.0-99.3% for HPIV-3, respectively. Phylogenetic analysis showed that HPIV-1, -2, and -3 strains identified in this study were closely related among the strains in the same type with no significant genetic variability. These results show that HPIV of multiple imported sources was circulating in Korea.
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Affiliation(s)
- Kwang Sook Park
- Department of Microbiology, The Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, Korea University, Seoul, Korea
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Yano T, Fukuta M, Maeda C, Akachi S, Matsuno Y, Yamadera M, Kobayashi A, Nagai Y, Kusuhara H, Kobayashi T, Amano H, Nishinaka T, Ochiai H, Watanabe M, Nakamura H, Suga S, Ihara T. Epidemiological Investigation and Seroprevalence of Human Parainfluenza Virus in Mie Prefecture in Japan during 2009^|^ndash;2013. Jpn J Infect Dis 2014. [DOI: 10.7883/yoken.67.506] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Roy Mukherjee T, Chanda S, Mullick S, De P, Dey‐Sarkar M, Chawla‐Sarkar M. Spectrum of respiratory viruses circulating in eastern India: prospective surveillance among patients with influenza-like illness during 2010-2011. J Med Virol 2013; 85:1459-65. [PMID: 23765782 PMCID: PMC7166942 DOI: 10.1002/jmv.23607] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2013] [Indexed: 11/07/2022]
Abstract
In developing countries, viruses causing respiratory disease are a major concern of public health. During January 2010-December 2011, 2,737 patients with acute respiratory infection from the outpatient departments as well as patients admitted to hospitals were screened for different respiratory viruses. Nasal and or throat swabs were collected and transported to the laboratory where initial screening of influenza A and influenza B viruses was performed. The samples were tested further for influenza C virus, parainfluenza viruses 1-4, human rhinovirus, metapneumovirus and respiratory syncytial virus by conventional RT- PCR. The study revealed that the majority of the patients were under 5 years of age; both due to their higher susceptibility to respiratory infections and presentation to hospitals. Out of 2,737 patients enrolled in this study, 59% were found positive for one or more respiratory viruses. Influenza B infection was detected in 12% of patients followed by influenza A (11.7%), respiratory syncytial virus (7.1%), parainfluenza virus-2 (6%), metapneumovirus (3%), parainfluenza virus-3 (1%), parainfluenza virus-4 (0.6%), parainfluenza virus-1 (0.3%), influenza C (0.2%) and human rhinovirus (0.2%). Distinct seasonal infection was observed only for influenza A and influenza B viruses.
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Affiliation(s)
| | - Shampa Chanda
- National Institute of Cholera and Enteric DiseasesBeliaghata, KolkataIndia
| | - Satarupa Mullick
- National Institute of Cholera and Enteric DiseasesBeliaghata, KolkataIndia
| | - Papiya De
- National Institute of Cholera and Enteric DiseasesBeliaghata, KolkataIndia
| | - Malay Dey‐Sarkar
- National Institute of Cholera and Enteric DiseasesBeliaghata, KolkataIndia
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Villaran MV, García J, Gomez J, Arango AE, Gonzales M, Chicaiza W, Alemán W, Lorenzana de Rivera I, Sanchez F, Aguayo N, Kochel TJ, Halsey ES. Human parainfluenza virus in patients with influenza-like illness from Central and South America during 2006-2010. Influenza Other Respir Viruses 2013; 8:217-27. [PMID: 24286248 PMCID: PMC4186470 DOI: 10.1111/irv.12211] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2013] [Indexed: 11/29/2022] Open
Abstract
Background Human parainfluenza viruses (HPIVs) are common viral causes of community-acquired pneumonia, particularly in children. The four types of HPIV have world-wide distribution; however, limited information exists about the epidemiological profile of HPIV in Latin-America. Objective Provide epidemiologic and phylogenetic information about HPIVs that circulated in Latin America between 2006 and 2010 to better characterize the extent and variability of this respiratory virus in the region. Methods Oropharyngeal swabs, demographic data and clinical characteristics were obtained from individuals with influenza-like illness in 10 Latin-American countries between 2006–2010. Specimens were analyzed with culture and molecular methods. Results A total of 30 561 individuals were enrolled; 991 (3·2%) were HPIV positive. Most infected participants were male (53·7%) and under 5 years of age (68·7%). The HPIV type most frequently isolated was HPIV-3 (403, 40·7%). In 66/2007 (3·3%) hospitalized individuals, HPIV was identified. The most frequent symptoms at enrollment were cough and rhinorrhea. We identified certain patterns for HPIV-1, -2 and -3 in specific cities. Phylogenetic analysis revealed a homogeneous distribution in the region. Conclusions In the current scenario, no vaccine or treatment is available for this pathogen. Our results contribute to the scarce epidemiologic and phylogenetic information of HPIV in the region that could support the development of specific management.
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Frost HM, Robinson CC, Dominguez SR. Epidemiology and clinical presentation of parainfluenza type 4 in children: a 3-year comparative study to parainfluenza types 1-3. J Infect Dis 2013; 209:695-702. [PMID: 24133181 PMCID: PMC3923541 DOI: 10.1093/infdis/jit552] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background. Human parainfluenza viruses (HPIVs) are among the most common causes of respiratory tract infections in children. Little is known about the epidemiology and clinical presentation of HPIV type 4. Methods. A retrospective chart review and comparison of patients positive for HPIV types 1–4 by multiplex polymerase chain reaction between 2009 and 2012 at Children's Hospital Colorado was performed. Patients who had only direct fluorescent antibody testing performed or concurrent viral infections were excluded. Results. Of 11 533 samples, 752 (6.5%) were positive for HPIV. After exclusion criteria, 316 samples were included in the study. HPIV-4 had year-round prevalence with biennial peaks in odd-numbered years. HPIV-4 and HPIV-3 had similar clinical presentations. 50.8% and 51.5% of patients with HPIV-3–4 had hypoxia compared to 20.3% and 33.3% of patients with HPIV-1–2 (P < .01). HPIV-1 (23.6%) and HPIV-2 (24.2%) were more associated with stridor than HPIV-3 (6.6%) and HPIV-4 (0%) (P < .01). No patients with HPIV-4 had croup. Patients with HPIV-4 had similar lengths of stay and mortality as those with HPIV-1–3. Conclusions. This is the first large-scale analysis of HPIV-4 clinical and epidemiologic features. HPIV-4 was most similar to HPIV-3 in clinical presentation. HPIV-4 had year-round prevalence with peaks in the autumn of odd-numbered years. HPIV-4 is a common respiratory pathogen capable of causing significant morbidity in children.
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Affiliation(s)
- Holly M Frost
- Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado
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Chan KH, Yan MK, To KKW, Lau SK, Woo PC, Cheng VCC, Li WS, Chan JFW, Tse H, Yuen KY. Use of the human colorectal adenocarcinoma (Caco-2) cell line for isolating respiratory viruses from nasopharyngeal aspirates. J Med Virol 2013; 85:874-9. [PMID: 23508913 PMCID: PMC7167083 DOI: 10.1002/jmv.23538] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2013] [Indexed: 12/24/2022]
Abstract
The human colorectal adenocarcinoma‐derived Caco‐2 cell line was evaluated as a means isolating common respiratory viruses from nasopharyngeal aspirates for the diagnosis of respiratory diseases. One hundred eighty‐nine direct immunofluorescence positive nasopharyngeal aspirates obtained from patients with various viral respiratory diseases were cultured in the presence of Caco‐2 cells or the following conventional cell lines: LLC‐MK2, MDCK, HEp‐2, and A549. Caco‐2 cell cultures effectively propagated the majority (84%) of the viruses present in nasopharyngeal aspirate samples compared with any positive cultures obtained using the panel cells (78%) or individual cell line MDCK (38%), HEp‐2 (21%), LLC‐MK2 (27%), or A549 (37%) cell lines. The differences against individual cell line were statistically significant (P = < 0.000001). Culture in Caco‐2 cells resulted in the isolation of 85% (36/42) of viruses which were not cultivated in conventional cell lines. By contrast, 80% (24/30) of viruses not cultivated in Caco‐2 cells were isolated using the conventional panel. The findings indicated that Caco‐2 cells were sensitive to a wide range of viruses and can be used to culture a broad range of respiratory viruses. J. Med. Virol. 85:874–879, 2013. © 2013 Wiley Periodicals, Inc.
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Affiliation(s)
- K H Chan
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong, Hong Kong Special Administrative Region, China.
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Litwin CM, Bosley JG. Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center. Arch Virol 2013; 159:65-72. [PMID: 23881085 PMCID: PMC7086932 DOI: 10.1007/s00705-013-1794-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/11/2013] [Indexed: 12/25/2022]
Abstract
Respiratory tract infections (RTIs) are a leading cause of mortality and morbidity. Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). We hypothesize that the availability of rapid, multiplex PCR diagnostics will provide better clinical care and new insights into the etiology and clinical spectrum of RTIs. We conducted a retrospective analysis of the incidence of respiratory pathogens at a 500-bed adult and 154-bed pediatric hospital tertiary care center. A total of 939 specimens from patients with an age range of 5 days to 91 years (median, 2 years) were tested by a multiplex respiratory pathogen PCR from November 14, 2011 to November 13, 2012. Sixty-five percent of specimens were positive for at least one pathogen. As the age of the patient increased, the positivity rate for the PCR decreased proportionately. Rhinoviruses/enteroviruses (Rhino/Entero) were the most prevalent (34.3 %) followed by RSV (19.2 %) and hMPV (6.2 %). Twelve percent of the positive samples were positive for multiple analytes, with Rhino/Entero and RSV being the most common combination. The peak months were September and May for Rhino/Entero infections, January for RSV and February for coronavirus. hMPV peaked 2 months after RSV, as has been observed recently in other studies. Multiplex PCR provides rapid diagnostic information that can be used to make knowledgeable clinical decisions and potentially reduce the use of antibiotics. Active respiratory PCR surveillance could also predict seasonal respiratory epidemics to allow for adequate planning of additional infection control measures.
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Affiliation(s)
- Christine M Litwin
- Department of Pathology, Medical College of Georgia, Georgia Regents University, 1120 15th St., Augusta, GA, 30912, USA,
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Sentilhes AC, Choumlivong K, Celhay O, Sisouk T, Phonekeo D, Vongphrachanh P, Brey P, Buchy P. Respiratory virus infections in hospitalized children and adults in Lao PDR. Influenza Other Respir Viruses 2013; 7:1070-8. [PMID: 23796419 PMCID: PMC4634274 DOI: 10.1111/irv.12135] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2013] [Indexed: 11/26/2022] Open
Abstract
Background Acute respiratory infections are an important cause of morbidity and mortality worldwide, with a major burden of disease in developing countries. The relative contribution of viruses in acute lower respiratory infections (ALRI) is, however, poorly documented in Lao PDR. Objective The objective of this study is to investigate the etiology of ALRI in patients of all ages in two hospitals of Laos. Methods Multiplex PCR/RT‐PCR methods were used to target 18 major common respiratory viruses. Between August 2009 and October 2010, samples from 292 patients presenting with ALRI were collected. Results and conclusion Viruses were detected in 162 (55%) samples. In 48% (140/292) of the total ALRI cases, a single virus was detected while coinfections were observed in 8% (22/292) of the samples. The most frequent viruses were rhinovirus/enterovirus (35%), human respiratory syncytial virus (26%), and influenza viruses (13%). Parainfluenza viruses were detected in 9%, adenovirus in 6%, human metapneumovirus in 4%, coronaviruses (229E, NL63, OC43, HKU1) in 4%, and bocavirus in 3% of ALRI specimens. Most viral infections occurred in patients below 5 years of age. The distribution of viruses varied according to age‐groups. No significant correlation was observed between the severity of the disease and the age of patients or the virus species. This study provides the description of viral etiology among patients presenting with ALRI in Lao PDR. Additional investigations are required to better understand the clinical role of the different viruses and their seasonality in Laos.
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Affiliation(s)
- Anne-Charlotte Sentilhes
- National Center for Laboratory and Epidemiology, Vientiane, Lao PDR; Virology Unit, Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia; Institut Pasteur in Laos, Réseau International des Instituts Pasteur, Vientiane, Lao PDR
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Kadmon G, Levy I, Mandelboim M, Nahum E, Stein J, Dovrat S, Schonfeld T. Polymerase-chain-reaction-based diagnosis of viral pulmonary infections in immunocompromised children. Acta Paediatr 2013; 102:e263-8. [PMID: 23421914 PMCID: PMC7159754 DOI: 10.1111/apa.12207] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 12/01/2022]
Abstract
Aim Viral pneumonia is a serious complication in immunocompromised children. Its aetiology is difficult to identify owing to the limitations of conventional microbiological tests. The aim of this study was to determine whether polymerase chain reaction (PCR) assays for respiratory viruses increase the diagnostic yield of bronchoalveolar lavage (BAL) in immunocompromised children. Methods BAL samples obtained from immunocompromised children hospitalized with pneumonia were processed for respiratory viruses by viral culture, rapid antigen test and PCR (for CMV, adenovirus, influenza, parainfluenza, herpesvirus, RSV and hMPV). Results The study group included 42 patients (mean age 7.2 ± 5.1 years) with 50 episodes of clinical pneumonia (50 BAL samples). Forty viral pathogens were identified in 30 episodes (60%). PCR increased the diagnostic rate by fourfold (75% identified by PCR alone, p < 0.0001). When viral culture and rapid antigen test were used as the gold standard, PCR was found to have high sensitivity (86–100% when assessed) and specificity (80–96%). The PCR results prompted the initiation of specific antiviral therapy and the avoidance of unnecessary antibiotic treatment in 17 (34%) episodes. Conclusion PCR‐based diagnosis from BAL may increase the rate of pathogen detection in immunocompromised children, decrease the time to diagnosis and spare patients unnecessary antimicrobial treatment.
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Affiliation(s)
- Gili Kadmon
- Pediatric Intensive Care Unit; Schneider Children's Medical Center of Israel; Petach Tikva Israel
| | - Itzhak Levy
- Infectious Diseases Unit; Schneider Children's Medical Center of Israel; Petach Tikva Israel
| | - Michal Mandelboim
- Sackler Faculty of Medicine; Central Virology Laboratory; Ministry of Health; Chaim Sheba Medical Center; Tel Aviv University; Tel Hashomer Tel Aviv Israel
| | - Elhanan Nahum
- Pediatric Intensive Care Unit; Schneider Children's Medical Center of Israel; Petach Tikva Israel
| | - Jerry Stein
- Department of Hematology-Oncology; Schneider Children's Medical Center of Israel; Petach Tikva Israel
| | - Sara Dovrat
- Sackler Faculty of Medicine; Central Virology Laboratory; Ministry of Health; Chaim Sheba Medical Center; Tel Aviv University; Tel Hashomer Tel Aviv Israel
| | - Tommy Schonfeld
- Pediatric Intensive Care Unit; Schneider Children's Medical Center of Israel; Petach Tikva Israel
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Couturier MR, Barney T, Alger G, Hymas WC, Stevenson JB, Hillyard D, Daly JA. Evaluation of the FilmArray® Respiratory Panel for clinical use in a large children's hospital. J Clin Lab Anal 2013; 27:148-54. [PMID: 23424157 PMCID: PMC6807554 DOI: 10.1002/jcla.21576] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 12/20/2012] [Indexed: 11/17/2022] Open
Abstract
Background Respiratory pathogens are a leading cause of hospital admission and traditional detection methods are time consuming and insensitive. Multiplex molecular detection methods have recently been investigated in hope of replacing these traditional techniques with rapid panel‐based testing. Objectives This study evaluated the FilmArray®Respiratory Panel ([FARP], Idaho Technology Inc., Salt Lake City, UT) as a replacement for direct fluorescent antibody (DFA) testing in a pediatric hospital. Methods Eleven of the 21 FARP analytes (Adenovirus, Bordetella pertussis, human Metapneumovirus, Influenza A, Influenza A H1N1 2009, Influenza B, Parainfluenza [1, 2, & 3], Respiratory Syncytial Virus, and rhinovirus) were evaluated using nasopharyngeal specimens. Positive samples were pooled in groups of 5. Samples identified by reference methods as positive for respiratory pathogens were used for the majority of positive samples. DFA was the reference method for ten analytes; LuminexTM xTAG Respiratory Virus Panel (RVP) was the reference method for rhinovirus. Discrepant results were resolved by positive culture and fluorescent antibody stain and/or laboratory‐developed real‐time polymerase chain reaction (PCR) assays (LDT). Results The agreement for most analytes was in concordance with the established reference methods with the exception of Adenovirus. Additionally, the FARP detected several pathogens not previously detected by DFA, and most were confirmed by LDT. Several DFA‐positive analytes were confirmed as true‐negatives by the FARP and LDT. Conclusion FARP overall performed better than DFA with the exception of Adenovirus, making the FARP an attractive alternative to laboratories looking to replace DFA with a rapid, user‐friendly, multiplex molecular assay. J. Clin. Lab. Anal. 27:148–154, 2013. © 2013 Wiley Periodicals, Inc.
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Nguyen AP, Downard KM. Proteotyping of the Parainfluenza Virus with High-Resolution Mass Spectrometry. Anal Chem 2013; 85:1097-105. [DOI: 10.1021/ac302962u] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- An P. Nguyen
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006,
Australia
| | - Kevin M. Downard
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006,
Australia
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Alquezar-Planas DE, Mourier T, Bruhn CAW, Hansen AJ, Vitcetz SN, Mørk S, Gorodkin J, Nielsen HA, Guo Y, Sethuraman A, Paxinos EE, Shan T, Delwart EL, Nielsen LP. Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing. Sci Rep 2013; 3:2468. [PMID: 24002378 PMCID: PMC3760282 DOI: 10.1038/srep02468] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/26/2013] [Indexed: 11/13/2022] Open
Abstract
Molecular detection of viruses has been aided by high-throughput sequencing, permitting the genomic characterization of emerging strains. In this study, we comprehensively screened 500 respiratory secretions from children with upper and/or lower respiratory tract infections for viral pathogens. The viruses detected are described, including a divergent human parainfluenza virus type 4 from GS FLX pyrosequencing of 92 specimens. Complete full-genome characterization of the virus followed, using Single Molecule, Real-Time (SMRT) sequencing. Subsequent "primer walking" combined with Sanger sequencing validated the RS platform's utility in viral sequencing from complex clinical samples. Comparative genomics reveals the divergent strain clusters with the only completely sequenced HPIV4a subtype. However, it also exhibits various structural features present in one of the HPIV4b reference strains, opening questions regarding their lifecycle and evolutionary relationships among these viruses. Clinical data from patients infected with the strain, as well as viral prevalence estimates using real-time PCR, is also described.
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Affiliation(s)
- David E. Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Department of Virology, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Christian A. W. Bruhn
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Anders J. Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Sarah Nathalie Vitcetz
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Søren Mørk
- Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark
| | | | - Yan Guo
- Pacific Biosciences, Menlo Park, California, USA
| | | | | | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute (SHVRI), Chinese Academy of Agricultural Sciences (CAAS)
- Blood Systems Research Institute, San Francisco, California
| | - Eric L. Delwart
- Blood Systems Research Institute, San Francisco, California
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - Lars P. Nielsen
- Department of Virology, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
- Department of Clinical Microbiology, Odense University Hospital, Denmark
- Aalborg University, Department of Health Sciences, Aalborg, Denmark
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Albuquerque MCM, Varella RB, Santos N. Acute respiratory viral infections in children in Rio de Janeiro and Teresópolis, Brazil. Rev Inst Med Trop Sao Paulo 2012; 54:249-55. [PMID: 22983287 DOI: 10.1590/s0036-46652012000500003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 05/31/2012] [Indexed: 11/22/2022] Open
Abstract
The frequency of viral pathogens causing respiratory infections in children in the cities of Rio de Janeiro and Teresópolis was investigated. Nasal swabs from children with acute respiratory illnesses were collected between March 2006 and October 2007. Specimens were tested for viral detection by conventional (RT)-PCR and/or real time PCR. Of the 205 nasal swabs tested, 64 (31.2%) were positive for at least one of the viral pathogens. Single infections were detected in 56 samples, 50 of those were caused by RNA viruses: 33 samples tested positive for rhinovirus, five for influenza A, five for metapneumovirus, four for coronavirus and, three for respiratory syncytial virus. For the DNA viruses, five samples were positive for bocavirus and one for adenovirus. Co-infections with these viruses were detected in eight samples. Our data demonstrate a high frequency of viral respiratory infections, emphasizing the need for a more accurate diagnosis particularly for the emerging respiratory viruses. The fact that the emerging respiratory viruses were present in 9.2% of the tested samples suggests that these viruses could be important respiratory pathogens in the country.
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Affiliation(s)
- Maria Carolina M Albuquerque
- Departament of Virology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Mao N, Ji Y, Xie Z, Wang H, Wang H, An J, Zhang X, Zhang Y, Zhu Z, Cui A, Xu S, Shen K, Liu C, Yang W, Xu W. Human parainfluenza virus-associated respiratory tract infection among children and genetic analysis of HPIV-3 strains in Beijing, China. PLoS One 2012; 7:e43893. [PMID: 22937119 PMCID: PMC3429441 DOI: 10.1371/journal.pone.0043893] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Accepted: 07/27/2012] [Indexed: 11/30/2022] Open
Abstract
The relevance of human parainfluenza viruses (HPIVs) to the epidemiology of acute respiratory infections (ARI) in China is unclear. From May 2008 to September 2010, 443 nasopharyngeal aspirates (NPAs) from hospitalized pediatric patients (age from 1 to 93 months) in Beijing were collected and screened for HPIVs and other common respiratory viruses by real-time RT-PCR. Sixty-two of 443 samples were positive for HPIVs with 4 positive for HPIV-2 and 58 positive for HPIV-3, indicating that HPIV-3 was the predominant virus present during the study period. A phylogenetic tree based on all the available HN (hemagglutinin-neuraminidase) sequences of HPIV-3 indicated that three distinct clusters (A,B, and C) were circulating with some temporal and regional clustering. Cluster C was further divided into sub-clusters, C1, C2, C3 and C4. HPIV-3 from Beijing isolates belonged to sub-cluster C3, and were grouped with the isolates from two Provinces of China and the neighboring country of Japan. Genetic analysis based on entire HN gene revealed that the HPIV-3 isolates from Beijing were highly similar with 97.2%-100% identity at the nucleotide level and these could be divided into two closely related lineages, C3a and C3b. These findings suggested that there was co-circulation of multiple lineages of HPIV-3 in the Beijing region during the study period. This is the first study to describe the epidemiology and molecular characterization of HPIVs in China.
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Affiliation(s)
- Naiying Mao
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yixin Ji
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhengde Xie
- Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Huanhuan Wang
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Neurobiology, Taishan Medical College, Taian, Shandong, China
| | - Huiling Wang
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Junjing An
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinxin Zhang
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Yan Zhang
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhen Zhu
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Aili Cui
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Songtao Xu
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kunling Shen
- Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Chunyan Liu
- Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Weizhong Yang
- Office for Disease Control and Emergency Response, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- World Health Organization Regional Office for the Western Pacific Regional Reference Measles Lab and State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Puppe W, Weigl J, Gröndahl B, Knuf M, Rockahr S, von Bismarck P, Aron G, Niesters HGM, Osterhaus ADME, Schmitt HJ. Validation of a multiplex reverse transcriptase PCR ELISA for the detection of 19 respiratory tract pathogens. Infection 2012; 41:77-91. [PMID: 22847627 PMCID: PMC7100787 DOI: 10.1007/s15010-012-0298-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 06/30/2012] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Since acute respiratory tract infections inflict a high burden of disease in children worldwide, a multiplex reverse transcription polymerase chain reaction combined with a microwell hybridization assay (m-RT-PCR-ELISA) to detect 19 different respiratory pathogens was developed and validated. METHODS A total of 430 respiratory specimens were retrospectively tested in parallel by both the advanced 19-valent m-RT-PCR-ELISA as well as by culture or individual RT-PCR assays used in clinical routine. RESULTS The mean (median) sensitivity of the m-RT-PCR-ELISA in the retrospective test was 93.3% (95.1%; range 83.3-100 %), and the mean (median) specificity was 99.8 and 100 % (range 98.6-100 %), respectively. The mean positive predictive value was 99.3 % (range 93.4-100 %) and the mean negative predictive value was 95.3 % (range 98.4-100 %). Feasibility and clinical value of the 19-valent method was prospectively shown on 16,231 incoming clinical specimens from patients between 0 and 16 years of age with acute respiratory tract infections admitted to pediatric hospitals or private practices from October 2003 to June 2010 in three regions in Germany (Kiel, Mainz, Freiburg; Freiburg to June 2007 only). At least one microorganism was detected in 10,765 of 16,231 (66.3 %) clinical specimens: 5,044 RV, 1,999 RSV, 1,286 AV, 944 EV, 737 seasonal IVA, 173 pandemic IVA H1N1-2009, 899 MPV, 518 CV, 383 PIV3, 268 PIV1, 259 Mpn, 205 IVB, 164 PIV2, 144 PIV4, 103 Bp, 29 Cpn and 29 Bpp, while reovirus and Lpn were not present in these specimens from a pediatric population. More than one organism could be detected in 13.4 % of the specimens. CONCLUSIONS The m-RT-PCR-ELISA evaluated here improves the spectrum for diagnosing respiratory infections and is a feasible instrument for individual diagnostic and epidemiological studies.
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Affiliation(s)
- W Puppe
- Pediatric Infectious Diseases, Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Schwanenweg 20, 24105, Kiel, Germany
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Ustun C, Slabý J, Shanley RM, Vydra J, Smith AR, Wagner JE, Weisdorf DJ, Young JAH. Human parainfluenza virus infection after hematopoietic stem cell transplantation: risk factors, management, mortality, and changes over time. Biol Blood Marrow Transplant 2012; 18:1580-8. [PMID: 22531491 DOI: 10.1016/j.bbmt.2012.04.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 04/17/2012] [Indexed: 11/16/2022]
Abstract
Human parainfluenza viruses (HPIVs) are uncommon, yet high-risk pathogens after hematopoietic stem cell transplant (HCT). We evaluated 5178 pediatric and adult patients undergoing HCT between 1974 and 2010 to determine the incidence, risk factors, response to treatment, and outcome of HPIV infection as well as any change in frequency or character of HPIV infection over time. HPIV was identified in 173 patients (3.3%); type 3 was most common (66%). HPIV involved upper respiratory tract infection (URTI; 57%), lower respiratory tract infection (LRTI; 9%), and both areas of the respiratory tract (34%), at a median of 62 days after transplantation. In more recent years, HPIV has occurred later after HCT, whereas the proportion with nosocomial infection and mortality decreased. Over the last decade, HPIV was more common in older patients and in those receiving reduced intensity conditioning (RIC). RIC was a significant risk factor for later (beyond day +30). HPIV infections, and this association was strongest in patients with URTI. HCT using a matched unrelated donor (MURD), mismatched related donor (MMRD), age 10 to 19 years, and graft-versus-host disease (GVHD) were all risk factors for HPIV infections. LRTI, early (<30 days), age 10 to 19 years, MMRD, steroid use, and coinfection with other pathogens were risk factors for mortality. The survival of patients with LRTI, especially very early infections, was poor regardless of ribavirin treatment. HPIV incidence remains low, but may have delayed onset associated with RIC regimens and improving survival. Effective prophylaxis and treatment for HPIV are needed.
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Affiliation(s)
- Celalettin Ustun
- Division of Hematology-Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
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Detection of human bocaviruses 1 to 4 from nasopharyngeal swab samples collected from patients with respiratory tract infections. J Clin Microbiol 2012; 50:2118-21. [PMID: 22442328 DOI: 10.1128/jcm.00098-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human bocaviruses (HBoV) 1, 2, 3, and 4 (HBoV1-4) were detected in 132 (15.5%), 5 (0.6%), 3 (0.4%), and 5 (0.6%) of 850 nasopharyngeal swab samples collected from children with respiratory tract infections, respectively. Out of the 145 HBoV1-4-positive samples, 62 (42.8%) were codetected with other respiratory viruses.
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[Pneumonia as a result of infection with parainfluenza virus type 4 and thrombotic thrombocytopenic purpura]. Med Intensiva 2011; 36:235. [PMID: 21683478 PMCID: PMC7131695 DOI: 10.1016/j.medin.2011.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 05/03/2011] [Indexed: 11/21/2022]
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Molecular Detection of Respiratory Viruses. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ren L, Gonzalez R, Xie Z, Xiong Z, Liu C, Xiang Z, Xiao Y, Li Y, Zhou H, Li J, Yang Q, Zhang J, Chen L, Wang W, Vernet G, Paranhos-Baccalà G, Shen K, Wang J. Human parainfluenza virus type 4 infection in Chinese children with lower respiratory tract infections: a comparison study. J Clin Virol 2011; 51:209-12. [PMID: 21636318 PMCID: PMC7185386 DOI: 10.1016/j.jcv.2011.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 04/13/2011] [Accepted: 05/02/2011] [Indexed: 11/25/2022]
Abstract
BACKGROUND Human parainfluenza viruses (HPIVs) are a leading cause of acute respiratory tract infections (ARTIs). Although HPIV-4 has been associated with mild ARTIs for years, recent investigations have also associated HPIV-4 infection with severe respiratory syndromes and with outbreaks of ARTIs in children. OBJECTIVES To characterize the role of HPIV-4 and its clinical features in children with acute lower respiratory tract infections (ALRTIs) in Beijing, China. STUDY DESIGN Nasopharyngeal aspirates were collected from 2009 hospitalized children with ALRTIs between March 2007 and April 2010. RT-PCR and PCR analyses were used to identify HPIV types and other known respiratory viruses. RESULTS HPIVs were detected in 246 (12.2%) patients, of whom 25 (10.2%) were positive for HPIV-4, 11 (4.5%) for HPIV-2, 51 (20.7%) for HPIV-1, 151 (61.4%) for HPIV-3, and 8 (3.3%) were co-detected with different types of HPIVs. Like HPIV-3, HPIV-4 was detected in spring, summer, and late fall over the study period. Seasonal incidence varied for HPIV-1 and -2. The median patient age was 20 months for HPIV-4 infections and 7-11 months for HPIV-1, -2, and -3 infections, but the clinical manifestations did not differ significantly between HPIV-1, -2, -3, and -4 infections. Moreover, co-detection of HPIV-4 (44%) with other respiratory viruses was lower than that of HPIV-1 (62.7%), HPIV-2 (63.6%), and HPIV-3 (72.7%). CONCLUSIONS HPIV-4 plays an important role in Chinese paediatric ALRTIs. The epidemiological and clinical characteristics reported here improve our understanding of the pathogenesis associated with HPIV-4.
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Affiliation(s)
- Lili Ren
- State Key Laboratory for Molecular Virology and Genetic Engineering and Dr. Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, China
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Comparison of two multiplex methods for detection of respiratory viruses: FilmArray RP and xTAG RVP. J Clin Microbiol 2011; 49:2449-53. [PMID: 21508156 DOI: 10.1128/jcm.02582-10] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We compared the FilmArray RP (Idaho Technology, Inc., Salt Lake City, UT) and the xTAG RVP (Luminex Corporation, Toronto, Canada) multiplex respiratory virus PCR methods for the detection of respiratory viruses in a set of 200 patient specimens frozen at -70 °C after standard viral culture and antigen detection methods were done. Both systems detected between 40 to 50% more viruses than traditional methods, primarily rhinoviruses and human metapneumovirus. The FilmArray RP detected significantly more total viruses either alone or as part of mixed infections than the xTAG RVP, as well as an additional 21.6% more respiratory syncytial viruses. The xTAG RVP requires 5 to 6 h with 2.5 to 3 h of hands-on time, while the FilmArray RP takes about an hour with 3 to 5 min of hands-on time, making it much easier to perform.
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Myocarditis caused by human parainfluenza virus in an immunocompetent child initially associated with 2009 influenza A (H1N1) virus. J Clin Microbiol 2011; 49:2072-3. [PMID: 21411596 DOI: 10.1128/jcm.02638-10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The association between respiratory viruses and myocarditis has hardly ever been described. We report a case of acute myocarditis in an immunocompetent child associated with the presence of parainfluenza virus type 3 infection, in a context of recent influenza illness, confirmed by molecular and serological studies.
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Zappa A, Canuti M, Frati E, Pariani E, Perin S, Ruzza ML, Farina C, Podestà A, Zanetti A, Amendola A, Tanzi E. Co-circulation of genetically distinct human metapneumovirus and human bocavirus strains in young children with respiratory tract infections in Italy. J Med Virol 2011; 83:156-64. [PMID: 21108354 PMCID: PMC7166789 DOI: 10.1002/jmv.21940] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The discovery of human Metapneumovirus (hMPV) and human Bocavirus (hBoV) identified the etiological causes of several cases of acute respiratory tract infections in children. This report describes the molecular epidemiology of hMPV and hBoV infections observed following viral surveillance of children hospitalized for acute respiratory tract infections in Milan, Italy. Pharyngeal swabs were collected from 240 children ≤3 years of age (130 males, 110 females; median age, 5.0 months; IQR, 2.0–12.5 months) and tested for respiratory viruses, including hMPV and hBoV, by molecular methods. hMPV‐RNA and hBoV‐DNA positive samples were characterized molecularly and a phylogenetical analysis was performed. PCR analysis identified 131/240 (54.6%) samples positive for at least one virus. The frequency of hMPV and hBoV infections was similar (8.3% and 12.1%, respectively). Both infections were associated with lower respiratory tract infections: hMPV was present as a single infectious agent in 7.2% of children with bronchiolitis, hBoV was associated with 18.5% of pediatric pneumonias and identified frequently as a single etiological agent. Genetically distinct hMPV and hBoV strains were identified in children examined with respiratory tract infections. Phylogenetic analysis showed an increased prevalence of hMPV genotype A (A2b sublineage) compared to genotype B (80% vs. 20%, respectively) and of the hBoV genotype St2 compared to genotype St1 (71.4% vs. 28.6%, respectively). Interestingly, a shift in hMPV infections resulting from A2 strains has been observed in recent years. In addition, the occurrence of recombination events between two hBoV strains with a breakpoint located in the VP1/VP2 region was identified. J. Med. Virol. 83:156–164, 2011. © 2010 Wiley‐Liss, Inc.
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Affiliation(s)
- Alessandra Zappa
- Department of Public Health-Microbiology-Virology, University of Milan, Milan, Italy
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Buecher C, Mardy S, Wang W, Duong V, Vong S, Naughtin M, Vabret A, Freymuth F, Deubel V, Buchy P. Use of a multiplex PCR/RT-PCR approach to assess the viral causes of influenza-like illnesses in Cambodia during three consecutive dry seasons. J Med Virol 2010; 82:1762-72. [PMID: 20827775 PMCID: PMC7166949 DOI: 10.1002/jmv.21891] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Acute respiratory infections are a major cause of mortality and morbidity worldwide. Using multiplex PCR/RT‐PCR methods for the detection of 18 respiratory viruses, the circulation of those viruses during 3 consecutive dry seasons in Cambodia was described. Among 234 patients who presented with influenza‐like illness, 35.5% were positive for at least one virus. Rhinoviruses (43.4%), parainfluenza (31.3%) viruses and coronaviruses (21.7%) were the most frequently detected viruses. Influenza A virus, parainfluenza virus 4 and SARS‐coronavirus were not detected during the study period. Ninety apparently healthy individuals were included as controls and 10% of these samples tested positive for one or more respiratory viruses. No significant differences were observed in frequency and in virus copy numbers for rhinovirus detection between symptomatic and asymptomatic groups. This study raises questions about the significance of the detection of some respiratory viruses, especially using highly sensitive methods, given their presence in apparently healthy individuals. The link between the presence of the virus and the origin of the illness is therefore unclear. J. Med. Virol. 82:1762–1772, 2010. © 2010 Wiley‐Liss, Inc.
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Molecular detection of respiratory viruses in clinical specimens from children with acute respiratory disease in Iran. Pediatr Infect Dis J 2010; 29:931-3. [PMID: 20879092 DOI: 10.1097/inf.0b013e3181e2062e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Viruses are the most common causes of respiratory tract infections in children. The implementation of rapid virology assays can identify the most common pathogens involved. This study was undertaken on Iranian children less than 6 years old with respiratory infection. METHODS A total of 202 specimens were tested for the presence of 9 respiratory viruses by developing 3 multiplex reverse transcription-polymerase chain reaction and 1 uniplex polymerase chain reaction assays. RESULTS Viral pathogens were detected in 92 samples (45.5%) with 5.4% having dual infections. Overall, respiratory syncytial virus was the most frequently identified virus (16.8%), followed by adenovirus (14.4%), influenza A virus (4.9%), parainfluenza virus-3 (4.4%), parainfluenza virus-1 (2.9%), and both influenza B virus and hMPV (0.49). CONCLUSIONS Respiratory tract infection is a frequent cause of pediatric morbidity and mortality and a common reason for admission in acute care hospitals and outpatients visits. Appropriate diagnostic testing is important for specific diagnosis at an early stage of the illness because of the similarity in clinical presentation of patients with different viral infections caused by several respiratory pathogens.
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