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Motoya T, Nagata N, Kashimura R, Ohashi K, Saito A, Osawa S, Goto K, Iwama S, Yanaoka T, Okayama K, Hirai S, Sugai T, Murakami K, Ishioka T, Ryo A, Katayama K, Kimura H. A Longitudinal Study on Enteric Virus Contamination in Bivalves along the Coast of Ibaraki Prefecture, Japan. J Food Prot 2021; 84:946-952. [PMID: 33411914 DOI: 10.4315/jfp-20-353] [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: 08/31/2020] [Accepted: 12/17/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT During the 2014 to 2018 seasons, we conducted a longitudinal study involving enteric virus surveillance in bivalves, including natural oysters and clams harvested in Ibaraki Prefecture, Japan. Some norovirus (NoV) contaminations were detected in natural oysters, whereas no enteric virus was found in clams. NoVs detected in oysters were of the genotypes GII.4 and GII.6, both of which are closely related genetically to the NoV strains prevalent in humans. We found low level of enteric virus contamination in bivalves collected along the coast of Ibaraki Prefecture. The possibility of food poisoning caused by these viruses appears low, and few cases of infectious disease have been observed in the surrounding area. The harvest timing was more related to contamination quantity than the harvest area in many enteric viruses. Our results highlight that contamination of bivalves by enteric viruses may depend upon the prevalence of human diarrhea and illness. HIGHLIGHTS
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Affiliation(s)
- Takumi Motoya
- Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan
| | - Noriko Nagata
- Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan
| | - Ryo Kashimura
- Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan
| | - Keiko Ohashi
- Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan
| | - Aoi Saito
- Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan
| | - Shuichi Osawa
- Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan
| | - Keiko Goto
- Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan
| | - Sadaki Iwama
- Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan
| | | | - Kaori Okayama
- Gunma Paz University Graduate School of Health Science, Gunma, Japan
| | - Shinichiro Hirai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshiyuki Sugai
- Division of Nursing Science, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Taisei Ishioka
- Faculty of Agriculture, Takasaki University of Health and Welfare, Gunma, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
| | - Hirokazu Kimura
- Gunma Paz University Graduate School of Health Science, Gunma, Japan.,Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
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Brahim Belhaouari D, Wurtz N, Grimaldier C, Lacoste A, Pires de Souza GA, Penant G, Hannat S, Baudoin JP, La Scola B. Microscopic Observation of SARS-Like Particles in RT-qPCR SARS-CoV-2 Positive Sewage Samples. Pathogens 2021; 10:516. [PMID: 33923138 PMCID: PMC8146039 DOI: 10.3390/pathogens10050516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022] Open
Abstract
The ongoing outbreak of novel coronavirus pneumonia (COVID-19) caused by SARS-CoV-2 infection has spread rapidly worldwide. The major transmission routes of SARS-CoV-2 are recognised as inhalation of aerosol/droplets and person-to-person contact. However, some studies have demonstrated that live SARS-CoV-2 can be isolated from the faeces and urine of infected patients, which can then enter the wastewater system. The currently available evidence indicates that the viral RNA present in wastewater may become a potential source of epidemiological data. However, to investigate whether wastewater may present a risk to humans such as sewage workers, we investigated whether intact particles of SARS-CoV-2 were observable and whether it was possible to isolate the virus in wastewater. Using a correlative strategy of light microscopy and electron microscopy (CLEM), we demonstrated the presence of intact and degraded SARS-like particles in RT-qPCR SARS-CoV-2-positive sewage sample collected in the city of Marseille. However, the viral infectivity assessment of SARS-CoV-2 in the wastewater was inconclusive, due to the presence of other viruses known to be highly resistant in the environment such as enteroviruses, rhinoviruses, and adenoviruses. Although the survival and the infectious risk of SARS-CoV-2 in wastewater cannot be excluded from our study, additional work may be required to investigate the stability, viability, fate, and decay mechanisms of SARS-CoV-2 thoroughly in wastewater.
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Affiliation(s)
- Djamal Brahim Belhaouari
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Clio Grimaldier
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
| | - Alexandre Lacoste
- Bataillon des Marins Pompiers de Marseille, 13003 Marseille, France;
| | - Gabriel Augusto Pires de Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Gwilherm Penant
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
| | - Sihem Hannat
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Jean-Pierre Baudoin
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
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Tarim EA, Karakuzu B, Oksuz C, Sarigil O, Kizilkaya M, Al-Ruweidi MKAA, Yalcin HC, Ozcivici E, Tekin HC. Microfluidic-based virus detection methods for respiratory diseases. EMERGENT MATERIALS 2021; 4:143-168. [PMID: 33786415 PMCID: PMC7992628 DOI: 10.1007/s42247-021-00169-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
With the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.
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Affiliation(s)
- E. Alperay Tarim
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Betul Karakuzu
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Cemre Oksuz
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Oyku Sarigil
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Melike Kizilkaya
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | | | | | - Engin Ozcivici
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - H. Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
- METU MEMS Center, Ankara, Turkey
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Higgins RR, Peci A, Cardona M, Gubbay JB. Validation of a Laboratory-Developed Triplex Molecular Assay for Simultaneous Detection of Gastrointestinal Adenovirus and Rotavirus in Stool Specimens. Pathogens 2020; 9:pathogens9050326. [PMID: 32349251 PMCID: PMC7281709 DOI: 10.3390/pathogens9050326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 01/31/2023] Open
Abstract
Enteric viral pathogens causing gastroenteritis include adenovirus and rotavirus, among others. Rotavirus is the leading cause of severe diarrhea in infants and young children worldwide. Among the adenoviruses known to cause gastroenteritis are those of species F (serotypes 40, 41). Here, we describe the development and validation of a laboratory-developed gastrointestinal triplex rRT-PCR (triplex) assay that targets adenovirus and rotavirus. Stool specimens were tested from patients across Ontario. Specimens were previously tested for adenovirus and/or rotavirus by electron microscopy (EM) or immunochromatographic test (ICT). Triplex sensitivity, specificity, positive and negative predictive values compared to Seegene assay (a commercial assay used here as the standard reference method) were 100%, 97.8%, 86.0%, 100% for adenovirus, and 99.1%, 98.4%, 96.3%. 99.6% for rotavirus, respectively. The triplex assay had a 95.2% and 97.3% overall percent agreements (OPAs) when compared to EM for adenovirus or rotavirus detection, respectively, and an OPA of 90.9% when compared to rotavirus ICT for rotavirus detection. Triplex assay exhibited similar performance to the Seegene assay for both adenovirus and rotavirus and detected more adenovirus and rotavirus than traditional testing methods. The high performance along with lower cost and reduced turnaround time makes the triplex assay a desirable testing method for a clinical microbiology laboratory.
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Affiliation(s)
- Rachel R. Higgins
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (A.P.); (M.C.); (J.B.G.)
- Correspondence: ; Tel.: +1-647-792-3440
| | - Adriana Peci
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (A.P.); (M.C.); (J.B.G.)
| | - Mark Cardona
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (A.P.); (M.C.); (J.B.G.)
| | - Jonathan B. Gubbay
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (A.P.); (M.C.); (J.B.G.)
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 2V8, Canada
- The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
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5
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Zhang J, Guan H, Zhao W, Zhang H, Wang W, Ling X, Xiao Y, Guo J, Huang Z, Xu Y, Zhang L, He Z, Zhou S, Kan B. Evaluation of the BioFire FilmArray Gastrointestinal Panel and Real-Time Polymerase Chain Reaction Assays for the Detection of Major Diarrheagenic Pathogens by a Multicenter Diarrheal Disease Surveillance Program in China. Foodborne Pathog Dis 2019; 16:788-798. [PMID: 31478765 DOI: 10.1089/fpd.2019.2642] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In the field of the detection of pathogens responsible for infectious diarrhea, multiplex nucleic acids detection technology has attracted attention due to its ability to simultaneously screen a wide range of pathogens, its simplicity to operate and a faster turnaround time. We conducted a three-center evaluation that compared the BioFire FilmArray gastrointestinal panel (FA GI) and real-time polymerase chain reaction (PCR) assays for the detection of pathogens from 462 clinical diarrhea specimens, and characterized the distribution of various pathogens that were analyzed. The sensitivity of FA GI was 100% for 13 pathogens and 93.8-98.3% for 4 pathogens, but low for Salmonella (60.5%) and adenovirus (88.9%). The sensitivity per pathogen of real-time PCR assays was lower than that observed with FA GI. The specificity of FA GI and real-time PCR assays per pathogen was greater than 94.5% and 99%, respectively. FA GI and real-time PCR assays detected ≥1 pathogen in 339 (73.4%) and 297 (64.3%) samples, respectively, and 324 (70.1%) samples were considered as positive according to the reference standard. Multiple pathogens were detected in 37.2% and 24.9% of samples by FA GI and real-time PCR assays, respectively. Norovirus GI/GII and Campylobacter were less associated with coinfections. The positive rates of some pathogens varied among the three regions of China. Molecular methods can help squickly identify the cause of diarrhea and provide valuable information for early diagnosis and optimal patient therapy.
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Affiliation(s)
- Jingyun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongxia Guan
- Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Wensui Zhao
- Shanghai Changning District Center for Disease Control and Prevention, Shanghai, China
| | - Hong Zhang
- Hunan Provincial Center for Disease Control and Prevention, Changsha City, China
| | - Wei Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xia Ling
- Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Yong Xiao
- Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Jiayin Guo
- Shanghai Changning District Center for Disease Control and Prevention, Shanghai, China
| | - Zheng Huang
- Shanghai Changning District Center for Disease Control and Prevention, Shanghai, China
| | - Yang Xu
- Shanghai Changning District Center for Disease Control and Prevention, Shanghai, China
| | - Ling Zhang
- Shanghai Changning District Center for Disease Control and Prevention, Shanghai, China
| | - Zixiang He
- Hunan Provincial Center for Disease Control and Prevention, Changsha City, China
| | - Shuaifeng Zhou
- Hunan Provincial Center for Disease Control and Prevention, Changsha City, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Guerrero NAS, Bello FJ. Comparative assessment of the replication efficiency of dengue, yellow fever, and chikungunya arboviruses in some insect and mammalian cell lines. Rev Soc Bras Med Trop 2019; 52:e20180511. [PMID: 31038623 DOI: 10.1590/0037-8682-0511-2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/22/2019] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Insect cell cultures play an essential role in understanding arboviral replication. However, the replicative efficiency of some of these viruses such as dengue (DENV), yellow fever (YFV), and chikungunya (CHIKV) in a new cellular substrate (Lulo) and in the other two recognized cell lines has not been comparatively assessed. METHODS Vero, C6/36, and Lulo cell lines were infected with DENV, YFV, and CHIKV. The viral progeny was quantified through plaque assays and quantitative reverse transcription-polymerase chain reaction, while for DENV2, the findings were confirmed by immunofluorescence antibody assay. RESULTS The higher DENV2 titer (from multiplicity of infection 0.001) was obtained on day four post-infection in C6/36 and on day six in Vero cells, while the Lulo cell line was almost impossible to infect under the same conditions. However, C6/36 showed the highest values of viral RNA production compared to Vero cells, while the quantification of the viral RNA in Lulo cells showed high levels of viral genomes, which had no correlation to the infectious viral particles. CONCLUSIONS C6/36 was the most efficient cell line in the alpha and flavivirus production, followed by Vero cells. Thus, Lulo cells may be a useful substrate to study the mechanisms by which cells evade viral replication.
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Affiliation(s)
- Nidya Alexandra Segura Guerrero
- Universidad Pedagógica y Tecnológica de Colombia, Faculty of Science, Laboratory of Medical and Forensic Entomology, Tunja, Colombia
| | - Felio Jesús Bello
- Universidad de La Salle, Faculty of Agricultural and Livestock Sciences, Program of Veterinary Medicine, Bogotá, Colombia
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Syed-Ab-Rahman SF, Carvalhais LC, Chua E, Xiao Y, Wass TJ, Schenk PM. Identification of Soil Bacterial Isolates Suppressing Different Phytophthora spp. and Promoting Plant Growth. FRONTIERS IN PLANT SCIENCE 2018; 9:1502. [PMID: 30405657 PMCID: PMC6201231 DOI: 10.3389/fpls.2018.01502] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/26/2018] [Indexed: 05/08/2023]
Abstract
Bacterial isolates obtained from the rhizosphere of Arabidopsis and a plantless compost potting mix was screened for anti-oomycete activity against Phytophthora capsici, Phytophthora citricola, Phytophthora palmivora, and Phytophthora cinnamomi. Three out of 48 isolates exhibited more than 65% inhibition against all tested Phytophthora species and were selected for further studies. These strains, named UQ154, UQ156, and UQ202, are closely related to Bacillus amyloliquefaciens, Bacillus velezensis, and Acinetobacter sp., respectively, based on 16S rDNA sequence analysis. The isolates were evaluated for their ability to fix nitrogen, solubilize phosphate, as well as for siderophore, indoleacetic acid, cell wall degrading enzymes and biofilm production. Their plant growth promoting activities were evaluated by measuring their effect on the germination percentage, root and shoot length, and seedling vigor of lettuce plants. All of these traits were significantly enhanced in plants grown from seeds inoculated with the isolates compared with control plants. Moreover, bacteria-inoculated P. capsici-infected chili plants exhibited improved productivity based on CO2 assimilation rates. Both real-time quantitative PCR and disease severity index revealed significant decreases in pathogen load in infected chili root tissues when plants were previously inoculated with the isolates. Biocontrol activity may result from the secretion of diketopiperazines as identified by Gas chromatography-mass spectrometry analysis of bacterial cultures' extracts. Collectively, this work demonstrates the potential of bacterial isolates to control Phytophthora infection and promote plant growth. They can, therefore be considered as candidate microbial biofertilizers and biopesticides.
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Affiliation(s)
- Sharifah Farhana Syed-Ab-Rahman
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lilia C. Carvalhais
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Elvis Chua
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yawen Xiao
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Taylor J. Wass
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Peer M. Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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Luzzati R, D'Agaro P, Busca A, Maurel C, Martellani F, Rosin C, Segat L, Gatti G, Mascarello M, Confalonieri M. Herpes simplex virus (HSV) pneumonia in the non-ventilated immunocompromised host: Burden and predictors. J Infect 2018; 78:127-133. [PMID: 30267802 DOI: 10.1016/j.jinf.2018.09.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/31/2018] [Accepted: 09/10/2018] [Indexed: 11/16/2022]
Abstract
OBJECTIVES To evaluate burden and predictors of HSV pneumonia among immunocompromised patients not undergoing invasive mechanical ventilation according to a tailored diagnostic algorithm. METHODS This prospective, observational study included immunocompromised adults with pneumonia non-responding to empirical antibiotic therapy. Bronchoalveolar lavage (BAL) specimens were cultured for bacteria, mycobacteria and fungi. Real-time PCR for Herpesviruses and other microorganisms were performed on BAL and other specimens. Cytological examination of BAL samples was carried out for identification of intranuclear inclusion bodies and immunohistochemical staining for HSV. RESULTS We enrolled 45 patients (mean age 64.6 years) from January 2015 to June 2016. Nineteen (42.2%) cases tested positive for HSV-1 PCR on BAL. According to our definitions, 11 (24.4%) patients had HSV-1 pneumonia with viral loads ranging between 103 copies/mL and 107 copies/mL. HSV-1 positive throat swab (OR 85.2, 95% CI 5.83-1245.1, P < 0.001) and solid organ transplant (SOT) (OR 53.3, 95% CI 1.37-2072.8, P < 0.03) as underlying condition were found to be independently associated with HSV pneumonia by multivariable analysis. CONCLUSIONS HSV pneumonia turned out to be relatively common and should be investigated especially in individuals with HSV positive throat swab and SOT. Interventional studies are needed to assess the real clinical impact of HSV pneumonia in immunocompromised patients.
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Affiliation(s)
- Roberto Luzzati
- Infectious Diseases Unit, University Hospital of Trieste, Piazza dell'Ospitale 1, 34125 Trieste, Italy.
| | - Pierlanfranco D'Agaro
- Laboratory for Hygiene and Public Health, University Hospital of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Annalisa Busca
- Pulmonology Unit, University Hospital of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Cristina Maurel
- Infectious Diseases Unit, University Hospital of Trieste, Piazza dell'Ospitale 1, 34125 Trieste, Italy
| | - Fulvia Martellani
- Anatomy and Histopathology Unit, University Hospital of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Chiara Rosin
- Infectious Diseases Unit, University Hospital of Trieste, Piazza dell'Ospitale 1, 34125 Trieste, Italy
| | - Ludovica Segat
- Laboratory for Hygiene and Public Health, University Hospital of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Giuseppe Gatti
- Cardiosurgery Unit, University Hospital of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Marta Mascarello
- Infectious Diseases Unit, University Hospital of Trieste, Piazza dell'Ospitale 1, 34125 Trieste, Italy
| | - Marco Confalonieri
- Pulmonology Unit, University Hospital of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
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Ikonen N, Savolainen-Kopra C, Enstone JE, Kulmala I, Pasanen P, Salmela A, Salo S, Nguyen-Van-Tam JS, Ruutu P. Deposition of respiratory virus pathogens on frequently touched surfaces at airports. BMC Infect Dis 2018; 18:437. [PMID: 30157776 PMCID: PMC6116441 DOI: 10.1186/s12879-018-3150-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND International and national travelling has made the rapid spread of infectious diseases possible. Little information is available on the role of major traffic hubs, such as airports, in the transmission of respiratory infections, including seasonal influenza and a pandemic threat. We investigated the presence of respiratory viruses in the passenger environment of a major airport in order to identify risk points and guide measures to minimize transmission. METHODS Surface and air samples were collected weekly at three different time points during the peak period of seasonal influenza in 2015-16 in Finland. Swabs from surface samples, and air samples were tested by real-time PCR for influenza A and B viruses, respiratory syncytial virus, adenovirus, rhinovirus and coronaviruses (229E, HKU1, NL63 and OC43). RESULTS Nucleic acid of at least one respiratory virus was detected in 9 out of 90 (10%) surface samples, including: a plastic toy dog in the children's playground (2/3 swabs, 67%); hand-carried luggage trays at the security check area (4/8, 50%); the buttons of the payment terminal at the pharmacy (1/2, 50%); the handrails of stairs (1/7, 14%); and the passenger side desk and divider glass at a passport control point (1/3, 33%). Among the 10 respiratory virus findings at various sites, the viruses identified were: rhinovirus (4/10, 40%, from surfaces); coronavirus (3/10, 30%, from surfaces); adenovirus (2/10, 20%, 1 air sample, 1 surface sample); influenza A (1/10, 10%, surface sample). CONCLUSIONS Detection of pathogen viral nucleic acids indicates respiratory viral surface contamination at multiple sites associated with high touch rates, and suggests a potential risk in the identified airport sites. Of the surfaces tested, plastic security screening trays appeared to pose the highest potential risk, and handling these is almost inevitable for all embarking passengers.
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Affiliation(s)
- Niina Ikonen
- Department of Health Security, National Institute for Health and Welfare, P.O.Box 30, 00271 Helsinki, Finland
| | - Carita Savolainen-Kopra
- Department of Health Security, National Institute for Health and Welfare, P.O.Box 30, 00271 Helsinki, Finland
| | - Joanne E. Enstone
- School of Medicine, Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
| | - Ilpo Kulmala
- VTT Technical Research Centre of Finland Ltd, Espoo and Tampere, Finland
| | - Pertti Pasanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Anniina Salmela
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Satu Salo
- VTT Technical Research Centre of Finland Ltd, Espoo and Tampere, Finland
| | - Jonathan S. Nguyen-Van-Tam
- School of Medicine, Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
| | - Petri Ruutu
- Department of Health Security, National Institute for Health and Welfare, P.O.Box 30, 00271 Helsinki, Finland
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Zhang W, Fu J, Liu J, Wang H, Schiwon M, Janz S, Schaffarczyk L, von der Goltz L, Ehrke-Schulz E, Dörner J, Solanki M, Boehme P, Bergmann T, Lieber A, Lauber C, Dahl A, Petzold A, Zhang Y, Stewart AF, Ehrhardt A. An Engineered Virus Library as a Resource for the Spectrum-wide Exploration of Virus and Vector Diversity. Cell Rep 2018; 19:1698-1709. [PMID: 28538186 DOI: 10.1016/j.celrep.2017.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/12/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Adenoviruses (Ads) are large human-pathogenic double-stranded DNA (dsDNA) viruses presenting an enormous natural diversity associated with a broad variety of diseases. However, only a small fraction of adenoviruses has been explored in basic virology and biomedical research, highlighting the need to develop robust and adaptable methodologies and resources. We developed a method for high-throughput direct cloning and engineering of adenoviral genomes from different sources utilizing advanced linear-linear homologous recombination (LLHR) and linear-circular homologous recombination (LCHR). We describe 34 cloned adenoviral genomes originating from clinical samples, which were characterized by next-generation sequencing (NGS). We anticipate that this recombineering strategy and the engineered adenovirus library will provide an approach to study basic and clinical virology. High-throughput screening (HTS) of the reporter-tagged Ad library in a panel of cell lines including osteosarcoma disease-specific cell lines revealed alternative virus types with enhanced transduction and oncolysis efficiencies. This highlights the usefulness of this resource.
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Affiliation(s)
- Wenli Zhang
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China; Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Jing Liu
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China; Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Maren Schiwon
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Sebastian Janz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Lukas Schaffarczyk
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Lukas von der Goltz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Eric Ehrke-Schulz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Johannes Dörner
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Manish Solanki
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Philip Boehme
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Thorsten Bergmann
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Andre Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195-7720, USA
| | - Chris Lauber
- Institute for Medical Informatics and Biometry, Carl Gustav Carus, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Petzold
- Deep Sequencing, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China.
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Anja Ehrhardt
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany.
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Walter JM, Wunderink RG. Severe Respiratory Viral Infections: New Evidence and Changing Paradigms. Infect Dis Clin North Am 2017; 31:455-474. [PMID: 28687214 PMCID: PMC7347414 DOI: 10.1016/j.idc.2017.05.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lower respiratory tract infection is a leading cause of death in the United States. Advances in diagnostic testing have improved our ability to detect pathogens. Viral pathogens are important causal pathogens in immunocompetent patients. As the number of elderly adults and those with chronic medical conditions increases, the burden of viral respiratory infections will increase. Clinicians must be familiar with the characteristics of rhinovirus, human adenoviruses, respiratory syncytial virus, and human metapneumovirus. Major challenges include distinguishing true infection from asymptomatic carriage and characterizing patients admitted with severe lower respiratory tract infection who do not have a causative pathogen identified.
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Affiliation(s)
- James M Walter
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, 676 North St Clair Street, Arkes 14-000, Chicago, IL 60611, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, 676 North St Clair Street, Arkes 14-000, Chicago, IL 60611, USA.
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12
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Aetiology and Outcomes of Suspected Infections of the Central Nervous System in Children in Mbarara, Uganda. Sci Rep 2017; 7:2728. [PMID: 28578421 PMCID: PMC5457409 DOI: 10.1038/s41598-017-02741-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/19/2017] [Indexed: 11/24/2022] Open
Abstract
Infections of the central nervous system (CNS) are severe conditions, leading to neurological sequelae or death. Knowledge of the causative agents is essential to develop guidelines for case management in resource-limited settings. Between August 2009 and October 2012, we conducted a prospective descriptive study of the aetiology of suspected CNS infections in children two months to 12 years old, with fever and at least one sign of CNS involvement in Mbarara Hospital, Uganda. Children were clinically evaluated on admission and discharge, and followed-up for 6 months for neurological sequelae. Pathogens were identified from cerebrospinal fluid (CSF) and blood using microbiological and molecular methods. We enrolled 459 children. Plasmodium falciparum (36.2%) and bacteria in CSF (13.3%) or blood (3.3%) were the most detected pathogens. Viruses were found in 27 (5.9%) children. No pathogen was isolated in 207 (45.1%) children. Patterns varied by age and HIV status. Eighty-three (18.1%) children died during hospitalisation, and 23 (5.0%) during follow-up. Forty-one (13.5%) children had neurological sequelae at the last visit. While malaria remains the main aetiology in children with suspected CNS infections, no pathogen was isolated in many children. The high mortality and high rate of neurological sequelae highlight the need for efficient diagnosis.
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13
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Yoon H, Jhun BW, Kim SJ, Kim K. Clinical characteristics and factors predicting respiratory failure in adenovirus pneumonia. Respirology 2016; 21:1243-50. [PMID: 27301912 PMCID: PMC7169084 DOI: 10.1111/resp.12828] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 02/17/2016] [Accepted: 02/24/2016] [Indexed: 11/26/2022]
Abstract
Background and objective Limited data exist regarding factors predicting respiratory failure (RF) in non‐immunocompromised patients with adenovirus (AdV) pneumonia. Methods We described characteristics of AdV pneumonia (n = 91) versus non‐AdV pneumonia (n = 55) and compared clinico‐laboratory and radiological characteristics in patient groups categorized by RF. Results All 91 AdV pneumonia patients presented with acute respiratory symptoms and radiological infiltrations and had significantly lower levels of white blood cell counts and platelet counts compared with non‐AdV pneumonia. Of them, 67 patients had mild pneumonia without RF (non‐RF), 14 patients had no RF at admission but progressed to RF during hospitalization (progressed to RF) and 10 patients had RF at admission (initial RF). Initial monocyte percentage and absolute monocyte counts in RF patient groups (progressed to RF and initial RF) were significantly lower than those of non‐RF patients (both P < 0.001), and the differences among progressed to RF and initial RF patients were not significant. Chest computed tomography findings such as dominant pattern or distribution, clinical symptoms, and bacterial or viral co‐infections other than AdV were not discriminable between patients who had RF and those who did not. On univariate analysis, initial monocytopenia, multilobar infiltrations and pleural effusion were associated with RF. However, on multivariable analysis, only initial monocytopenia remained significant (P = 0.004) for predicting RF. Conclusion Our data suggest that initial monocytopenia may help to predict RF during the course of AdV pneumonia in non‐immunocompromised patients. We described the characteristics of adenovirus (AdV) pneumonia in non‐immunocompromised adult patients and evaluated factors predicting the occurrence of respiratory failure (RF). Our data suggest that initial monocytopenia may help to predict RF during an AdV pneumonia in non‐immunocompromised adult patients.
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Affiliation(s)
- Hee Yoon
- Department of Emergency Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Armed Forces Capital Hospital, Seongnam, Korea.
| | - Se Jin Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Armed Forces Capital Hospital, Seongnam, Korea
| | - Kang Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Burd EM, Hinrichs BH. Gastrointestinal Infections. MOLECULAR PATHOLOGY IN CLINICAL PRACTICE 2016. [PMCID: PMC7123654 DOI: 10.1007/978-3-319-19674-9_50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Establishing a specific etiology for gastrointestinal infections can be challenging because of the common clinical features and wide variety of causative microorganisms. In many cases, the etiologic agent cannot be determined using traditional diagnostic methods and may result in unnecessary antibiotic use or prolonged periods of illness. Molecular tests provide many advantages over traditional laboratory methods but, with the exception of a few analytes, are still largely in the developmental phase for gastrointestinal pathogens and are not widely used. The main advantages of molecular tests include increased sensitivity and the ability to detect agents which will not grow in culture. To test for all possible gastrointestinal pathogens at one time would require a large panel that would include a variety of bacterial, viral and parasitic agents. Challenges inherent in developing diagnostic molecular panels include ensuring that all variants of a particular microorganism can be detected as well as the rapid evolution of pathogens. In this chapter, the diagnostic merit of molecular tests as well as available tests will be presented for the major groups of gastrointestinal pathogens.
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15
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Molecular Diagnosis of Gastrointestinal Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch27] [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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16
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Throat and nasal swabs for molecular detection of respiratory viruses in acute pharyngitis. Virol J 2015; 12:178. [PMID: 26511714 PMCID: PMC4625558 DOI: 10.1186/s12985-015-0408-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Detection of specific respiratory viruses is important for surveillance programs, where nasopharyngeal or nasal swabs have traditionally been used. Our objective was to determine whether sampling with a throat swab provides incremental benefit-when used in conjunction with a nasal swab-to detect respiratory viruses among patients with acute pharyngitis in the outpatient setting. FINDINGS Among 83 university students with acute pharyngitis, we detected respiratory viruses with molecular assays on two samples collected per student: with a flocked nasal mid-turbinate swab and a rayon throat swab. Forty-eight (58 %) patients had virus-positive samples, with 49 virus positives detected by either swab (one patient had a dual viral co-infection). The most common viruses were rhinovirus, coronavirus, and influenza A virus. Specifically, 29 virus positives were detected by both swabs, 14 exclusively by the nasal swab, and six exclusively by the throat swab. The additional six virus positives detected by the throat swab corresponded to an absolute increase in viral detection of 7.1 % (95 % CI: 1.2-12.9 %); the specific viruses detected were four rhinoviruses and two coronaviruses. CONCLUSIONS The flocked nasal swab samples respiratory viruses well, even among patients whose primary complaint is a sore throat. The rayon throat swab has modest incremental value over and above using the flocked nasal mid-turbinate swab alone, which suggests that while throat swabs alone would not be adequate for respiratory viral surveillance, they may have value as a supplementary test.
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17
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Mölsä M, Hemmilä H, Rönkkö E, Virkki M, Nikkari S, Ziegler T. Molecular characterization of adenoviruses among finnish military conscripts. J Med Virol 2015; 88:571-7. [PMID: 26308159 DOI: 10.1002/jmv.24364] [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: 08/19/2015] [Indexed: 11/07/2022]
Abstract
Although adenoviruses were identified as important respiratory pathogens many years ago, little information is available concerning the prevalence of different adenovirus serotypes, which are circulating and causing epidemics in Finnish military training centers. Over a period of five years from 2008 to 2012, 3577 respiratory specimens were collected from military conscripts presenting with symptoms compatible with acute respiratory tract infection. Upon initial testing for certain respiratory viruses by real-time PCR, 837 of these specimens were identified as adenovirus-positive. For 672 of these specimens, the serotype of the adenovirus responsible was successfully determined by DNA sequencing. Serotypes 1, 2, 3, and 4 were detected in 1, 3, 181, and 487 samples, respectively. Adenovirus epidemics were observed during each year of this study. Based on these findings, adenovirus vaccination should be considered for military conscripts in the Finnish Defence Forces.
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Affiliation(s)
- Markos Mölsä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Heidi Hemmilä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Esa Rönkkö
- National Institute for Health and Welfare (THL), Virology Unit, Helsinki, Finland
| | - Maria Virkki
- Päijät-Häme Social and Health Care Group, Lahti, Finland
| | - Simo Nikkari
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Thedi Ziegler
- National Institute for Health and Welfare (THL), Virology Unit, Helsinki, Finland.,Research Center for Child Psychiatry, University of Turku, Turku, Finland
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18
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Detrait M, De Prophetis S, Delville JP, Komuta M. Fulminant isolated adenovirus hepatitis 5 months after haplo-identical HSCT for AML. Clin Case Rep 2015; 3:802-5. [PMID: 26509010 PMCID: PMC4614643 DOI: 10.1002/ccr3.347] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 06/25/2015] [Accepted: 07/29/2015] [Indexed: 11/12/2022] Open
Abstract
The principal limitation of allogeneic hematopoietic stem cell transplantation except relapse remains the transplant-related mortality (TRM). In addition to graft-versus-host disease (GvHD), infections contribute to TRM in many patients. We describe herein a case of an adult patient presenting 5 months after haplo-identical transplantation an isolated fulminant hepatitis due to adenovirus.
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Affiliation(s)
- Marie Detrait
- Onco-Hematology Department, Notre-Dame Hospital, Grand Hopital De Charleroi Charleroi, Belgium ; Bone Marrow Transplantation Program, Hematology Department, CHU de Nancy, Hôpitaux de Brabois Vandoeuvre les Nancy, France
| | - Stephanie De Prophetis
- Onco-Hematology Department, Notre-Dame Hospital, Grand Hopital De Charleroi Charleroi, Belgium
| | - Jean-Pierre Delville
- Onco-Hematology Department, Notre-Dame Hospital, Grand Hopital De Charleroi Charleroi, Belgium
| | - Mina Komuta
- Division of Pathology, Hepatology, Cliniques Universitaires St-Luc, UCL Brussels, Belgium
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Yu X, Kou Y, Xia D, Li J, Yang X, Zhou Y, He X. Human respiratory syncytial virus in children with lower respiratory tract infections or influenza-like illness and its co-infection characteristics with viruses and atypical bacteria in Hangzhou, China. J Clin Virol 2015. [PMID: 26209367 PMCID: PMC7185398 DOI: 10.1016/j.jcv.2015.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is the most important viral pathogen in children. However, its epidemic patterns and co-infection characteristics are not fully understood. OBJECTIVES We attempted to determine the level of genetic variation of RSV, and describe the prevalence and co-infection characteristics of RSV in Hangzhou during two epidemic seasons. STUDY DESIGN Single respiratory samples from 1820 pediatric patients were screened for RSV and genotyped by RT-PCR and sequencing. In all RSV positive specimens, we screened for viruses and atypical bacteria. Demographic and clinical information was recorded and analyzed. RESULTS A total of 34.5% and 3.8% of samples from acute lower respiratory tract infections (ALRI) and influenza-like illness (ILI) were positive for RSV, respectively. Phylogenetic analysis revealed that 61.1% of the selected 167 RSV strains were NA1, 31.1% were BA, 3.6% were ON1, 2.4% were CB1, and 1.8% were NA3. A new genotype, BA11 was identified, which comprised 98.1% of BA strains in this study, while the rest were BA10. A total of 36.4% and 9.1% of RSV-positive children with ALRI and ILI respectively were found to be co-infected. Rhinovirus was the most common additional respiratory virus, followed by human metapneumovirus. Except for fever, no significant differences in other clinical presentation between the RSV mono-infection and co-infection groups were observed. CONCLUSIONS The circulating RSV strains had high genetic variability with RSV-B showing a more local pattern. In ALRI cases, co-infection of RSV with other viruses or atypical bacteria has no significant effect on the clinical presentation except fever.
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Affiliation(s)
- Xinfen Yu
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China.
| | - Yu Kou
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Daozong Xia
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jun Li
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Xuhui Yang
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Yinyan Zhou
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaoyan He
- Microbiology Laboratory, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
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Kim SJ, Kim K, Park SB, Hong DJ, Jhun BW. Outcomes of early administration of cidofovir in non-immunocompromised patients with severe adenovirus pneumonia. PLoS One 2015; 10:e0122642. [PMID: 25875735 PMCID: PMC4398328 DOI: 10.1371/journal.pone.0122642] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/23/2015] [Indexed: 11/29/2022] Open
Abstract
The benefits of treatment with antiviral therapy for severe adenovirus (AdV) pneumonia are not well established. We described the clinical characteristics and treatment outcomes of early cidofovir treatment of severe AdV pneumonia in non-immunocompromised patients. We retrospectively reviewed the medical records of all patients diagnosed with severe AdV pneumonia between 2012 and 2014. A total of seven non-immunocompromised patients with severe AdV pneumonia were identified, and all isolates typed (n = 6) were human AdV-B55. All patients had progressive respiratory failure with lobar consolidation with or without patchy ground glass opacity. Three patients required vasopressors and mechanical ventilation. All patients had abnormal laboratory findings including: leukopenia, thrombocytopenia, or elevated liver enzymes. After admission, all patients received antiviral therapy with cidofovir, and the median time from admission to cidofovir administration was 48 h and median the time from onset of symptoms to cidofovir administration was 7.1 days. After cidofovir administration, complete symptomatic improvement occurred after a median of 12 days and radiographic resolution occurred after a median of 21 days. Consequently, all patients completely improved without complications. Our data suggest that early administration of cidofovir in the course of treatment for respiratory failure as a result of AdV pneumonia in non-immunocompromised patients could be a treatment strategy worth considering, especially in cases of HAdV-55 infection.
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Affiliation(s)
- Se Jin Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Armed Forces Capital Hospital, Seong-nam, Gyeonggi province, South Korea
| | - Kang Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Armed Forces Capital Hospital, Seong-nam, Gyeonggi province, South Korea
| | - Sung Bum Park
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Armed Forces Capital Hospital, Seong-nam, Gyeonggi province, South Korea
| | - Duck Jin Hong
- Department of Laboratory Medicine, The Armed Forces Capital Hospital, Seong-nam, Gyeonggi province, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Armed Forces Capital Hospital, Seong-nam, Gyeonggi province, South Korea
- * E-mail:
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Outbreak of coinfection with human metapneumovirus and measles virus resulting in the death of a child at a hospital in China. Am J Infect Control 2015; 43:365-7. [PMID: 25690877 PMCID: PMC7115315 DOI: 10.1016/j.ajic.2015.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 12/31/2014] [Accepted: 01/06/2015] [Indexed: 12/02/2022]
Abstract
Two children with different digestive diseases were admitted to the gastroenterology department of a children's hospital in Hangzhou, Zhejiang Province, China, in May 2010. They manifested successively acute lower respiratory tract infection symptoms during their stay in the hospital. The epidemiologic and experimental evidence supports that one child acquired nosocomial coinfection with measles virus and human metapneumovirus from another child while they shared the same ward. An outbreak with nosocomial coinfection of human metapneumovirus and measles virus. Misdiagnosis of one patient caused misplacement at a ward for gastroenterology disease. Misdiagnosis of the patient caused acquired nosocomial coinfection of measles virus and human metapneumovirus in a second patient. Diagnosis accuracy is key to the prevention of nosocomial measles infection.
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22
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Evaluation of anatomically designed flocked rectal swabs for molecular detection of enteric pathogens in children admitted to hospital with severe gastroenteritis in Botswana. J Clin Microbiol 2014; 52:3922-7. [PMID: 25165077 DOI: 10.1128/jcm.01894-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Two-hundred eighty matched bulk stool and anatomically designed flocked rectal swab samples were collected from children admitted to the hospital with acute diarrhea in Botswana. Their parents were asked about the acceptability of the swab collection method compared with bulk stool sampling. All samples underwent identical testing with a validated 15-target (9 bacterial, 3 viral, and 3 parasite) commercial multiplex PCR assay. The flocked swabs had a 12% higher yield for bacterial pathogen targets (241 versus 212; P = 0.003) compared with that of stool samples, as well as similar yields for viral targets (110 versus 113; P = 0.701) and parasite targets (59 versus 65; P = 0.345). One hundred sixty-four of the flocked swab-stool pairs were also tested with separate laboratory-developed bacterial and viral multiplex assays, and the flocked rectal swabs had a performance that was similar to that seen with commercial assay testing. Almost all parents/guardians found the swabs acceptable. Flocked rectal swabs significantly facilitate the molecular diagnosis of diarrheal disease in children.
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23
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Lee CY, Wu MC, Ho CL, Lai CC, Chou TY, Chan YJ. Design and application of a real-time polymerase chain for the detection and subsequent characterization of respiratory adenoviral infections. J Med Virol 2014; 86:2128-33. [PMID: 24916449 DOI: 10.1002/jmv.23940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2014] [Indexed: 11/06/2022]
Abstract
Human adenoviruses (HADVs) comprise at least 54 types and cause a wide spectrum of respiratory tract infections; early diagnosis and epidemiological monitoring of HADV infections requires a rapid and sensitive assay. The use of a real-time polymerase chain reaction (PCR) assay was evaluated with one set of in-house designed primers for respiratory adenoviral infections. The assay was first validated by detecting successfully 6 representative types and 100 clinical isolates. A concomitant prospective surveillance of viral aetiology using conventional cultures and PCR assays in 160 febrile children with acute respiratory tract symptoms was conducted between May 2010 and July 2011. Viral aetiologies were confirmed in 72 (45%) cases using conventional cultures, including 51 adenoviral infections. The concordance between the real-time PCR and culture was good (Kappa = 0.94), and two additional culture-negative adenovirus infections were identified. During the study period (January 2011), an adenoviral community epidemic occurred. Adenovirus B3 was the predominant type in this epidemic (69.8%), followed by C2 (5.7%), C1 (5.7%), C5 (1.9%), E4 (1.9%), C6 (1.9%), F41 (1.9%), and 4 unclassified species C (7.5%). Significantly prolonged duration of fever (>5 days), higher leukocyte counts, higher neutrophil counts, and higher C-reactive protein levels were in the adenoviral infected group (n = 53, P < 0.001), compared with the non-adenoviral infected group (n = 107). In conclusion, this in-house real-time PCR is capable of detecting adenoviral respiratory infections of various types in children; and patients with adenoviral aetiology suffered from more severe clinical manifestations.
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Affiliation(s)
- Chun-Yi Lee
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
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24
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Lee L, Ison M. Diarrhea caused by viruses in transplant recipients. Transpl Infect Dis 2014; 16:347-58. [DOI: 10.1111/tid.12212] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 12/11/2013] [Accepted: 12/21/2013] [Indexed: 01/25/2023]
Affiliation(s)
- L.Y. Lee
- Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago Illinois USA
- Northwestern University Transplant Outcomes Research Collaborative; Northwestern University Feinberg School of Medicine; Chicago Illinois USA
| | - M.G. Ison
- Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago Illinois USA
- Northwestern University Transplant Outcomes Research Collaborative; Northwestern University Feinberg School of Medicine; Chicago Illinois USA
- Division of Infectious Diseases Northwestern University Feinberg School of Medicine; Chicago Illinois USA
- Division of Organ Transplantation; Northwestern University Feinberg School of Medicine; Chicago Illinois USA
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Ni W, Le Guiner C, Moullier P, Snyder RO. Development and utility of an internal threshold control (ITC) real-time PCR assay for exogenous DNA detection. PLoS One 2012; 7:e36461. [PMID: 22570718 PMCID: PMC3343023 DOI: 10.1371/journal.pone.0036461] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 04/06/2012] [Indexed: 12/28/2022] Open
Abstract
Sensitive and specific tests for detecting exogenous DNA molecules are useful for infectious disease diagnosis, gene therapy clinical trial safety, and gene doping surveillance. Taqman real-time PCR using specific sequence probes provides an effective approach to accurately and quantitatively detect exogenous DNA. However, one of the major challenges in these analyses is to eliminate false positive signals caused by either non-targeted exogenous or endogenous DNA sequences, or false negative signals caused by impurities that inhibit PCR. Although multiplex Taqman PCR assays have been applied to address these problems by adding extra primer-probe sets targeted to endogenous DNA sequences, the differences between targets can lead to different detection efficiencies. To avoid these complications, a Taqman PCR-based approach that incorporates an internal threshold control (ITC) has been developed. In this single reaction format, the target sequence and ITC template are co-amplified by the same primers, but are detected by different probes each with a unique fluorescent dye. Sample DNA, a prescribed number of ITC template molecules set near the limit of sensitivity, a single pair of primers, target probe and ITC probe are added to one reaction. Fluorescence emission signals are obtained simultaneously to determine the cycle thresholds (Ct) for amplification of the target and ITC sequences. The comparison of the target Ct with the ITC Ct indicates if a sample is a true positive for the target (i.e. Ct less than or equal to the ITC Ct) or negative (i.e. Ct greater than the ITC Ct). The utility of this approach was demonstrated in a nonhuman primate model of rAAV vector mediated gene doping in vivo and in human genomic DNA spiked with plasmid DNA.
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Affiliation(s)
- Weiyi Ni
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | | | - Philippe Moullier
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
- Laboratoire de Thérapie Génique, INSERM UMR1089, IRT UN, Nantes, France
| | - Richard O. Snyder
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
- Laboratoire de Thérapie Génique, INSERM UMR1089, IRT UN, Nantes, France
- Center of Excellence for Regenerative Health Biotechnology, University of Florida, Alachua, Florida, United States of America
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McMinn BR, Cashdollar JL, Grimm AC, Fout GS. Evaluation of the celite secondary concentration procedure and an alternate elution buffer for the recovery of enteric adenoviruses 40 and 41. J Virol Methods 2012; 179:423-8. [DOI: 10.1016/j.jviromet.2011.11.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 09/27/2011] [Accepted: 11/09/2011] [Indexed: 11/25/2022]
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Real-time qualitative PCR for 57 human adenovirus types from multiple specimen sources. J Clin Microbiol 2011; 50:766-71. [PMID: 22170906 DOI: 10.1128/jcm.05629-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human adenoviruses (HAdVs) are ubiquitous double-stranded DNA viruses that cause a wide array of diseases in humans including pharyngitis, pneumonia, gastroenteritis, hemorrhagic cystitis, and keratoconjunctivitis. They also cause life-threatening opportunistic infections in immunocompromised individuals and are responsible for outbreaks in certain populations. Diagnosis is traditionally by cell culture or antigen detection methods. However, some HAdVs can take up to 4 weeks to isolate, and diarrheagenic types 40 and 41 will not grow in routine cell culture. Therefore, the goal of this study was to design a rapid, real-time PCR assay to detect all known 57 HAdV types from multiple different specimen sources. Primers and fluorescence resonance energy transfer hybridization probes were designed to target a 185-bp region of the penton base gene of HAdV. The analytical sensitivity was determined to be 10 copies/μl for HAdV types showing exact primer/probe homology in specimen matrix. Using whole-virus strains, the analytical sensitivity for representative HAdV types ranged from 10(-1) to 10(3) 50% tissue culture infective dose (TCID(50))/ml. The assay demonstrated 100% sensitivity and 99% specificity. This real-time PCR assay provides a rapid method for the detection of all 57 known HAdV types from respiratory specimens, blood, stool, urine, and ocular swabs.
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Low-dose penile SIVmac251 exposure of rhesus macaques infected with adenovirus type 5 (Ad5) and then immunized with a replication-defective Ad5-based SIV gag/pol/nef vaccine recapitulates the results of the phase IIb step trial of a similar HIV-1 vaccine. J Virol 2011; 86:2239-50. [PMID: 22156519 DOI: 10.1128/jvi.06175-11] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The Step Trial showed that the MRKAd5 HIV-1 subtype B Gag/Pol/Nef vaccine did not protect men from HIV infection or reduce setpoint plasma viral RNA (vRNA) levels but, unexpectedly, it did modestly enhance susceptibility to HIV infection in adenovirus type 5 (Ad5)-seropositive, uncircumcised men. As part of the process to understand the results of the Step Trial, we designed a study to determine whether rhesus macaques chronically infected with a host-range mutant Ad5 (Ad5hr) and then immunized with a replication defective Ad5 SIVmac239 Gag/Pol/Nef vaccine were more resistant or susceptible to SIV infection than unimmunized rhesus macaques challenged with a series of escalating dose penile exposures to SIVmac 251. The Ad5 SIV vaccine induced CD8(+) T cell responses in 70% of the monkeys, which is similar to the proportion of humans that responded to the vaccine in the Step Trial. However, the vaccine did not protect vaccinated animals from penile SIV challenge. At the lowest SIV exposure dose (10(3) 50% tissue culture infective doses), 2 of 9 Ad5-seropositive animals immunized with the Ad5 SIV vaccine became infected compared to 0 of 34 animals infected in the other animal groups (naive animals, Ad5-seropositive animals immunized with the empty Ad5 vector, Ad5-seronegative animals immunized with the Ad5 SIV vaccine, and Ad5-seronegative animals immunized with the empty Ad5 vector). Penile exposure to more concentrated virus inocula produced similar rates of infection in all animal groups. Although setpoint viral loads were unaffected in Step vaccinees, the Ad5 SIV-immunized animals had significantly lower acute-phase plasma vRNA levels compared to unimmunized animals. Thus, the results of the nonhuman primate (NHP) study described here recapitulate the lack of protection against HIV acquisition seen in the Step Trial and suggest a greater risk of infection in the Ad5-seropositive animals immunized with the Ad5 SIV vaccine. Further studies are necessary to confirm the enhancement of virus acquisition and to discern associated mechanisms.
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Aw TG, Rose JB. Detection of pathogens in water: from phylochips to qPCR to pyrosequencing. Curr Opin Biotechnol 2011; 23:422-30. [PMID: 22153035 PMCID: PMC7126744 DOI: 10.1016/j.copbio.2011.11.016] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 10/30/2011] [Accepted: 11/11/2011] [Indexed: 12/24/2022]
Abstract
Waterborne pathogens pose a significant threat to human health and a proper assessment of microbial water quality is important for decision making regarding water infrastructure and treatment investments and eventually to provide early warning of disease, particularly given increasing global disasters associated with severe public health risks. Microbial water quality monitoring has undergone tremendous transition in recent years, with novel molecular tools beginning to offer rapid, high-throughput, sensitive and specific detection of a wide spectrum of microbial pathogens that challenge traditional culture-based techniques. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ‘molecular revolution’ are at present emerging rapidly as tools of pathogen detection and discovery. Future challenges lie in integrating these molecular tools with concentration techniques and bioinformatics platforms for unbiased guide of pathogen surveillance in water and developing standardized protocols.
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Affiliation(s)
- Tiong Gim Aw
- Department of Fisheries and Wildlife, 13 Natural Resources, Michigan State University, East Lansing, MI 48824, United States.
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Couch RB, Atmar RL, Franco LM, Quarles JM, Niño D, Wells JM, Arden N, Cheung S, Belmont JW. Prior infections with seasonal influenza A/H1N1 virus reduced the illness severity and epidemic intensity of pandemic H1N1 influenza in healthy adults. Clin Infect Dis 2011; 54:311-7. [PMID: 22075792 PMCID: PMC3258274 DOI: 10.1093/cid/cir809] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background. A new influenza A/H1N1 (pH1N1) virus emerged in April 2009, proceeded to spread worldwide, and was designated as an influenza pandemic. A/H1N1 viruses had circulated in 1918–1957 and 1977–2009 and were in the annual vaccine during 1977–2009. Methods. Serum antibody to the pH1N1 and seasonal A/H1N1 viruses was measured in 579 healthy adults at enrollment (fall 2009) and after surveillance for illness (spring 2010). Subjects reporting with moderate to severe acute respiratory illness had illness and virus quantitation for 1 week; evaluations for missed illnesses were conducted over holiday periods and at the spring 2010 visit. Results. After excluding 66 subjects who received pH1N1 vaccine, 513 remained. Seventy-seven had reported with moderate to severe illnesses; 31 were infected with pH1N1 virus, and 30 with a rhinovirus. Determining etiology from clinical findings was not possible, but fever and prominent myalgias favored influenza and prominent rhinorrhea favored rhinovirus. Tests of fall and spring antibody indicated pH1N1 infection of 23% had occurred, with the rate decreasing with increasing anti-pH1N1 antibody; a similar pattern was seen for influenza-associated illness. A reducing frequency of pH1N1 infections was also seen with increasing antibody to the recent seasonal A/H1N1 virus (A/Brisbane/59/07). Preexisting antibody to pH1N1 virus, responses to a single vaccine dose, a low infection-to-illness ratio, and a short duration of illness and virus shedding among those with influenza indicated presence of considerable preexisting immunity to pH1N1 in the population. Conclusions. The 2009 A/H1N1 epidemic among healthy adults was relatively mild, most likely because of immunity from prior infections with A/H1N1 viruses.
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Affiliation(s)
- Robert B Couch
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA.
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Evaluation and verification of the Seeplex Diarrhea-V ACE assay for simultaneous detection of adenovirus, rotavirus, and norovirus genogroups I and II in clinical stool specimens. J Clin Microbiol 2011; 49:3154-62. [PMID: 21775550 DOI: 10.1128/jcm.00599-11] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Acute viral gastroenteritis is an intestinal infection that can be caused by several different viruses. Here we describe the evaluation and verification of Seeplex Diarrhea-V ACE (Seeplex DV), a novel commercial multiplex reverse transcription-PCR (RT-PCR) assay that detects 5 diarrheal pathogens, including adenovirus, rotavirus, norovirus genogroup I (GI) and GII, and astrovirus. We describe a retrospective study of 200 clinical specimens of which 177 were stool specimens previously tested for the presence of gastrointestinal viruses by electron microscopy (EM) and/or real-time RT-PCR (rRT-PCR). The remaining 23 specimens comprised other human pathogens of viral or bacterial origin. Discordant norovirus GI and GII results were resolved using a commercial kit; discordant adenovirus and rotavirus results were resolved using a home brew multiplex rRT-PCR assay. Diagnostic sensitivities and specificities were calculated before and after discordant analysis. After discordant analysis, estimated diagnostic sensitivities were 100% for adenovirus, rotavirus, and norovirus GI and 97% for norovirus GII. Diagnostic specificities after discordant analysis were 100% for adenovirus, rotavirus, and norovirus GI and 99.4% for norovirus GII. The 95% limits of detection were 31, 10, 2, and 1 genome equivalent per reaction for adenovirus, rotavirus, and norovirus GI and GII, respectively. The results demonstrate that the Seeplex DV assay is sensitive, specific, convenient, and reliable for the simultaneous detection of several viral pathogens directly in specimens from patients with gastroenteritis. Importantly, this novel multiplex PCR assay enabled the identification of viral coinfections in 12 (6.8%) stool specimens.
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Tong HI, Lu Y. Effective detection of human adenovirus in Hawaiian waters using enhanced PCR methods. Virol J 2011; 8:57. [PMID: 21303549 PMCID: PMC3045892 DOI: 10.1186/1743-422x-8-57] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 02/08/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The current criteria for recreational water quality evaluation are primarily based on measurements of fecal indicator bacteria growth. However, these criteria often fail to predict the presence of waterborne human pathogenic viruses. To explore the possibility of direct use of human enteric viruses as improved human fecal contamination indicators, human adenovirus (HAdV) was tested as a model in this study. FINDINGS In order to establish a highly sensitive protocol for effective detection of HAdV in aquatic environments, sixteen published PCR primer sets were re-optimized and comparatively evaluated. Primer sets nehex3deg/nehex4deg, ADV-F/ADV-R, and nested PCR primer sets hex1deg/hex2deg and nehex3deg/nehex4deg were identified to be the most sensitive ones, with up to 1,000 fold higher detection sensitivity compared to other published assays. These three PCR protocols were successfully employed to detect HAdV in both treated and untreated urban wastewaters, and also in 6 of 16 recreational water samples collected around the island of Oahu, Hawaii. CONCLUSIONS Findings from this study support the possible use of enteric viruses for aquatic environmental monitoring, specifically for the essential routine monitoring of Hawaiian beach waters using the optimized PCR protocol to detect HAdV at certain water sites to ensure a safe use of recreational waters.
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Affiliation(s)
- Hsin-I Tong
- Departments of Public Health Sciences and Microbiology, University of Hawaii, Honolulu, Hawaii 96822, USA
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Artieda J, Montes M, Vicente D, Martínez C, Piñeiro L, Mendiola J. [Outbreak of follicular conjunctivitis caused by adenovirus in a geriatric centre]. Enferm Infecc Microbiol Clin 2010; 28:690-3. [PMID: 20952102 DOI: 10.1016/j.eimc.2010.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 03/26/2010] [Accepted: 04/09/2010] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Adenovirus serotype 4a is a respiratory virus that occasionally causes conjunctivitis. This paper describes an outbreak of follicular conjunctivitis that occurred in a geriatric centre. MATERIAL AND METHODS Outbreak description and epidemiological research through a survey. For the microbiological study conjunctival swabs were collected using viral and bacterial transport media. Adenovirus was detected by real-time polymerase chain reaction. The serotype was determined by sequencing of a fragment of the hexon and E1 genes. RESULTS In autumn 2008 an outbreak of follicular conjunctivitis caused by adenovirus serotype 4a was detected. Twenty three percent 23% (69/300) of residents and 5% (9/180) of workers in a geriatric centre in Gipuzkoa were affected. The clinical symptoms were of prolonged duration (11±5 days). The temporal association of the cases suggested transmission from person to person. The sanitary measures established (asepsis and frequent hand washing, cleaning and disinfection of objects and surfaces) were effective, interrupting the transmission of the disease within a short period of time. CONCLUSION Rapid detection, identification of the causative agent and implementing appropriate control measures can significantly reduce the impact on both health and economic costs of these outbreaks.
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Affiliation(s)
- Juncal Artieda
- Departamento de Salud del Gobierno Vasco, Donostia-San Sebastián, Gipuzkoa, España
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Abstract
Adenovirus (AdV) infections are very common in the general pediatric population. The delayed clearance in young persons imposes a threat to immunocompromised patients after hematopoietic stem cell transplantation (HSCT), who can reactivate the virus, resulting in life-threatening disseminated disease. Although a definitive cure requires adequate immune reconstitution, 2 approaches appear to be feasible and effective to improve the outcomes of AdV infections. Strict monitoring with AdV quantitative polymerase chain reaction followed by preemptive treatment with low-dose (1 mg/kg) cidofovir 3 times a week, is effective in most cases to bridge the severely immunocompromised period shortly after HSCT, with acceptable toxicity rates. For centers who have the access, AdV-specific cytotoxic T cells can be the other important cornerstone of anti-AdV therapy with promising results so far. Methods to positively influence the reconstitution of the immune system after HSCT and optimizing new and currently available cellular immunotherapies will make HSCT safer against the threat of AdV infection/reactivation and associated disease.
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Multiplexed Luminex xMAP assay for detection and identification of five adenovirus serotypes associated with epidemics of respiratory disease in adults. J Clin Microbiol 2010; 48:2217-22. [PMID: 20410343 DOI: 10.1128/jcm.00029-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several serotypes of human adenovirus (HAdV) cause acute respiratory disease (ARD) among healthy adults, sometimes generating broad outbreaks with high attack rates and occasional fatalities. Timely serotype identification provides valuable epidemiological information and significantly contributes to prevention (vaccination) strategies. The prevalence of specific serotypes causing ARD varies geographically. HAdV-3, HAdV-4, HAdV-7, HAdV-14, and HAdV-21 are the serotypes most commonly found in adult populations in the Western Hemisphere. Unfortunately, conventional serotype identification is a tedious process which can take a week or longer. For this reason, new molecular methods for serotype identification are needed. Commercially available rapid antigen and PCR assays for the detection of HAdV are universal but do not distinguish between the different serotypes. We describe the development of a sensitive and specific multiplex assay capable of identifying serotypes 3, 4, 7, 14, and 21. Two sets of primers were used for nonspecific (universal) PCR amplification, and serotype-specific probes coupled to Luminex tags were used for target-specific extension (TSE). PCR and TSE primers were designed using known hexon gene sequences of HAdV. The TSE products of HAdV-3, HAdV-4, HAdV-7, HAdV-14, and HAdV-21 were correctly identified using the Luminex xMAP fluid microsphere-based array system. No cross-reactivity with other respiratory pathogens or other HAdV serotypes was observed. This multiplexed assay can be expanded to include more serotypes and will allow broad and rapid detection and identification of adenoviral serotypes in a high-throughput environment.
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Abstract
Adenovirus plays a significant role in respiratory tract disease in pediatric and adult patients. It has been linked to outbreaks and epidemics in various patient populations, resulting in considerable morbidity and mortality. In this article, we discuss the epidemiology, pathogenesis, respiratory tract illnesses and complications, and roles of potential treatment options. The role of the past oral adenovirus vaccine and the military implications of its withdrawal from routine use in military recruits is discussed as well.
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Affiliation(s)
- Anjali N Kunz
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20184, USA,
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Dina J, Nguyen E, Gouarin S, Petitjean J, Parienti JJ, Nimal D, Brouard J, Freymuth F, Vabret A. Development of duplex real-time PCR for detection of two DNA respiratory viruses. J Virol Methods 2009; 162:119-25. [PMID: 19654024 PMCID: PMC7112853 DOI: 10.1016/j.jviromet.2009.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 07/21/2009] [Accepted: 07/27/2009] [Indexed: 01/29/2023]
Abstract
A method was developed for the detection and quantitation of HAdV (human adenovirus) and HBoV (human bocavirus) based on a duplex real-time PCR, the AB PCR, using a Smartcycler instrument. A control real-time PCR was carried out on albumin DNA to standardise the non-homogenous respiratory samples. No cross-reactivity was observed with viruses or bacteria that could be found in the respiratory tract. The diagnosis rate using the AB PCR on clinical samples was 10.7%: 3.4% for HBoV detection, 6.9% for HAdV detection and 0.3% double detection HBoV-HAdV. The clinical and epidemiological characteristics of the HAdV- and HBoV-infected patients were evaluated. In the HAdV-positive group and the HBoV-positive group the samples were classified according to the severity of the disease. The HAdV viral load did not appear to be linked to the severity of the disease. Conversely, the difference between the two HBoV groups, severe and non-severe, was significant statistically when the comparison was based on the viral load (P=0.006) or after adjustment of the viral load to the number of cells in the samples (P=0.02).
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Affiliation(s)
- Julia Dina
- Department of Virology, University Hospital of Caen, Avenue Georges Clemenceau, 14033 Caen Cedex, France.
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