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Hayashida K, Garcia A, Moonga LC, Sugi T, Takuya K, Kawase M, Kodama F, Nagasaka A, Ishiguro N, Takada A, Kajihara M, Nao N, Shingai M, Kida H, Suzuki Y, Hall WW, Sawa H, Yamagishi J. Field-deployable multiplex detection method of SARS-CoV-2 and influenza virus using loop-mediated isothermal amplification and DNA chromatography. PLoS One 2023; 18:e0285861. [PMID: 37192155 DOI: 10.1371/journal.pone.0285861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/03/2023] [Indexed: 05/18/2023] Open
Abstract
A novel multiplex loop-mediated isothermal amplification (LAMP) method combined with DNA chromatography was developed for the simultaneous detection of three important respiratory disease-causing viruses: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus, and influenza B virus. Amplification was performed at a constant temperature, and a positive result was confirmed by a visible colored band. An in-house drying protocol with trehalose was used to prepare the dried format multiplex LAMP test. Using this dried multiplex LAMP test, the analytical sensitivity was determined to be 100 copies for each viral target and 100-1000 copies for the simultaneous detection of mixed targets. The multiplex LAMP system was validated using clinical COVID-19 specimens and compared with the real-time qRT-PCR method as a reference test. The determined sensitivity of the multiplex LAMP system for SARS-CoV-2 was 71% (95% CI: 0.62-0.79) for cycle threshold (Ct) ≤ 35 samples and 61% (95% CI: 0.53-0.69) for Ct ≤40 samples. The specificity was 99% (95%CI: 0.92-1.00) for Ct ≤35 samples and 100% (95%CI: 0.92-1.00) for the Ct ≤40 samples. The developed simple, rapid, low-cost, and laboratory-free multiplex LAMP system for the two major important respiratory viral diseases, COVID-19 and influenza, is a promising field-deployable diagnosis tool for the possible future 'twindemic, ' especially in resource-limited settings.
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Affiliation(s)
- Kyoko Hayashida
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Alejandro Garcia
- UCD Centre for Experimental Pathogen Host Research, University College Dublin, Belfield, Ireland
| | - Lavel Chinyama Moonga
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Tatsuki Sugi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | | | | | | | - Nobuhisa Ishiguro
- Division of Infection Control, Hokkaido University Hospital, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Ayato Takada
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Masashi Shingai
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroshi Kida
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Ireland
- Global Virus Network, Baltimore, Maryland, United States of America
| | - Hirofumi Sawa
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
- Global Virus Network, Baltimore, Maryland, United States of America
| | - Junya Yamagishi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
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Eisen AKA, Gularte JS, Demoliner M, de Abreu Goés Pereira VM, Heldt FH, Filippi M, de Almeida PR, Hansen AW, Fleck JD, Spilki FR. Low circulation of Influenza A and coinfection with SARS-CoV-2 among other respiratory viruses during the COVID-19 pandemic in a region of southern Brazil. J Med Virol 2021; 93:4392-4398. [PMID: 33829531 PMCID: PMC8250881 DOI: 10.1002/jmv.26975] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/10/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022]
Abstract
With the arrival of coronavirus disease 2019 (COVID-19) in Brazil in February 2020, several preventive measures were taken by the population aiming to avoid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection including the use of masks, social distancing, and frequent hand washing then, these measures may have contributed to preventing infection also by other respiratory viruses. Our goal was to determine the frequencies of Influenza A and B viruses (FLUAV/FLUBV), human mastadenovirus C (HAdV-C), Enterovirus 68 (EV-68), and rhinovirus (RV) besides SARS-CoV-2 among hospitalized patients suspect of COVID-19 with cases of acute respiratory disease syndrome (ARDS) in the period of March to December 2020 and to detect possible coinfections among them. Nucleic acid detection was performed using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) in respiratory samples using naso-oropharyngeal swabs and bronchoalveolar lavage. A total of 418 samples of the 987 analyzed (42.3%) were positive for SARS-CoV-2, 16 (1.62%) samples were positive for FLUAV, no sample was positive for FLUBV or EV-68, 67 (6.78%) samples were positive for HAdV-C, 55 samples were positive for RV 1/2 (26.3%) and 37 for RV 2/2 (13.6%). Coinfections were also detected, including a triple coinfection with SARS-CoV-2, FLUAV, and HAdV-C. In the present work, a very low frequency of FLUV was reported among hospitalized patients with ARDS compared to the past years, probably due to preventive measures taken to avoid COVID-19 and the high influenza vaccination coverage in the region in which this study was performed.
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Affiliation(s)
- Ana Karolina Antunes Eisen
- Laboratório de Microbiologia Molecular, Instituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Instituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Instituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | | | - Fágner Henrique Heldt
- Laboratório de Microbiologia Molecular, Instituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Instituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | - Paula Rodrigues de Almeida
- Laboratório de Microbiologia Molecular, Instituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular, Instituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular, Instituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
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3
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Melén K, Jalkanen P, Kukkonen JP, Partinen M, Nohynek H, Vuorela A, Vaarala O, Freitag TL, Meri S, Julkunen I. No evidence of autoimmunity to human OX 1 or OX 2 orexin receptors in Pandemrix-vaccinated narcoleptic children. J Transl Autoimmun 2020; 3:100055. [PMID: 32743535 PMCID: PMC7388359 DOI: 10.1016/j.jtauto.2020.100055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 04/15/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
Narcolepsy type 1, likely an immune-mediated disease, is characterized by excessive daytime sleepiness and cataplexy. The disease is strongly associated with human leukocyte antigen (HLA) DQB1∗06:02. A significant increase in the incidence of childhood and adolescent narcolepsy was observed after a vaccination campaign with AS03-adjuvanted Pandemrix influenza vaccine in Nordic and several other countries in 2010 and 2011. Previously, it has been suggested that a surface-exposed region of influenza A nucleoprotein, a structural component of the Pandemrix vaccine, shares amino acid residues with the first extracellular domain of the human OX2 orexin/hypocretin receptor eliciting the development of autoantibodies. Here, we analyzed, whether H1N1pdm09 infection or Pandemrix vaccination contributed to the development of autoantibodies to the orexin precursor protein or the OX1 or OX2 receptors. The analysis was based on the presence or absence of autoantibody responses against analyzed proteins. Entire OX1 and OX2 receptors or just their extracellular N-termini were transiently expressed in HuH7 cells to determine specific antibody responses in human sera. Based on our immunofluorescence analysis, none of the 56 Pandemrix-vaccinated narcoleptic patients, 28 patients who suffered from a laboratory-confirmed H1N1pdm09 infection or 19 Pandemrix-vaccinated controls showed specific autoantibody responses to prepro-orexin, orexin receptors or the isolated extracellular N-termini of orexin receptors. We also did not find any evidence for cell-mediated immunity against the N-terminal epitopes of OX2. Our findings do not support the hypothesis that the surface-exposed region of the influenza nucleoprotein A would elicit the development of an immune response against orexin receptors. No evidence of humoral immunity against human OX1 or OX2 orexin receptors. No cross-reactive antibodies between influenza virus NP and orexin receptors. No evidence for cell-mediated immunity against the N-terminal epitopes of OX2.
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Affiliation(s)
- Krister Melén
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland.,Expert Microbiology Unit, Finnish Institute for Health and Welfare, Mannerheimintie 166, 00300, Helsinki, Finland
| | - Pinja Jalkanen
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Jyrki P Kukkonen
- Department of Physiology and Department of Pharmacology, Institute of Biomedicine, Faculty of Medicine and Biochemistry and Cell Biology, Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Markku Partinen
- Helsinki Sleep Clinic, Vitalmed Research Centre Helsinki and Medicum, Faculty of Medicine, University of Helsinki, Finland
| | - Hanna Nohynek
- Infectious Disease Control and Vaccination Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Arja Vuorela
- Reseach Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki
| | - Outi Vaarala
- Reseach Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki
| | - Tobias L Freitag
- Department of Bacteriology and Immunology and Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Seppo Meri
- Department of Bacteriology and Immunology and Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ilkka Julkunen
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland.,Turku University Hospital, Clinical Microbiology, Kiinamyllynkatu 10, 20520, Turku, Finland
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Nanopore Sequencing Reveals Novel Targets for Detection and Surveillance of Human and Avian Influenza A Viruses. J Clin Microbiol 2020; 58:JCM.02127-19. [PMID: 32132187 DOI: 10.1128/jcm.02127-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/25/2020] [Indexed: 12/24/2022] Open
Abstract
Accurate detection of influenza A virus (IAV) is crucial for patient management, infection control, and epidemiological surveillance. The World Health Organization and the Centers for Disease Control and Prevention have recommended using the M gene as the diagnostic gene target for reverse-transcription-PCR (RT-PCR). However, M gene RT-PCR has reduced sensitivity for recent IAV due to novel gene mutations. Here, we sought to identify novel diagnostic targets for the molecular detection of IAV using long-read third-generation sequencing. Direct nanopore sequencing from 18 nasopharyngeal specimens and one saliva specimen showed that the 5' and 3' ends of the PB2 gene and the entire NS gene were highly abundant. Primers selected for PB2 and NS genes were well matched with seasonal or avian IAV gene sequences. Our novel PB2 and NS gene real-time RT-PCR assays showed limits of detection similar to or lower than that of M gene RT-PCR and achieved 100% sensitivity and specificity in the detection of A(H1N1), A(H3N2), and A(H7N9) in nasopharyngeal and saliva specimens. For 10 patients with IAV detected by M gene RT-PCR conversion in sequentially collected specimens, NS and/or PB2 gene RT-PCR was positive in 2 (20%) of the initial specimens that were missed by M gene RT-PCR. In conclusion, we have shown that PB2 or NS gene RT-PCRs are suitable alternatives to the recommended M gene RT-PCR for diagnosis of IAV. Long-read nanopore sequencing facilitates the identification of novel diagnostic targets.
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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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Helanterä I, Janes R, Anttila VJ. Clinical efficacy of seasonal influenza vaccination: characteristics of two outbreaks of influenza A(H1N1) in immunocompromised patients. J Hosp Infect 2017; 99:169-174. [PMID: 29225054 DOI: 10.1016/j.jhin.2017.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/01/2017] [Indexed: 01/04/2023]
Abstract
BACKGROUND Influenza A(H1N1) causes serious complications in immunocompromised patients. The efficacy of seasonal vaccination in these patients has been questioned. AIM To describe two outbreaks of influenza A(H1N1) in immunocompromised patients. METHODS Two outbreaks of influenza A(H1N1) occurred in our institution: on the kidney transplant ward in 2014 including patients early after kidney or simultaneous pancreas-kidney transplantation, and on the oncology ward in 2016 including patients receiving chemotherapy for malignant tumours. Factors leading to these outbreaks and the clinical efficacy of seasonal influenza vaccination were analysed. FINDINGS Altogether 86 patients were exposed to influenza A(H1N1) during the outbreaks, among whom the seasonal influenza vaccination status was unknown in 10. Only three out of 38 vaccinated patients were infected with influenza A(H1N1), compared with 20 out of 38 unvaccinated patients (P = 0.02). The death of one out of 38 vaccinated patients was associated with influenza, compared with seven out of 38 unvaccinated patients (P = 0.06). Shared factors behind the two outbreaks included outdated facilities not designed for the treatment of immunosuppressed patients. Vaccination coverage among patients was low, between 40% and 70% despite vaccination being offered to all patients free of charge. Vaccination coverage of healthcare workers on the transplant ward was low (46%), but, despite high coverage on the oncology ward (92%), the outbreak occurred. CONCLUSION Seasonal influenza vaccination was clinically effective with both a reduced risk of influenza infection and a trend towards reduced mortality in these immunocompromised patients. Several possible causes were identified behind these two outbreaks, requiring continuous awareness in healthcare professionals to prevent further outbreaks.
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Affiliation(s)
- I Helanterä
- Transplantation and Liver Surgery, Helsinki University Hospital, Helsinki, Finland.
| | - R Janes
- Department of Oncology, Helsinki University Hospital, Helsinki, Finland
| | - V-J Anttila
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
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Etiology of acute respiratory disease in fattening pigs in Finland. Porcine Health Manag 2017; 3:19. [PMID: 28852568 PMCID: PMC5568250 DOI: 10.1186/s40813-017-0065-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background The objective of our study was to clinically and etiologically investigate acute outbreaks of respiratory disease in Finland. Our study also aimed to evaluate the clinical use of various methods in diagnosing respiratory infections under field conditions and to describe the antimicrobial resistance profile of the main bacterial pathogen(s) found during the study. Methods A total of 20 case herds having finishing pigs showing acute respiratory symptoms and eight control herds showing no clinical signs suggesting of respiratory problems were enrolled in the study. Researchers visited each herd twice, examining and bleeding 20 pigs per herd. In addition, nasal swab samples were taken from 20 pigs and three pigs per case herd were necropsied during the first visit. Serology was used to detect Actinobacillus pleuropneumoniae (APP), swine influenza virus (SIV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine respiratory coronavirus (PRCV) and Mycoplasma hyopneumoniae antibodies. Polymerase chain reaction (PCR) was used to investigate the presence of porcine circovirus type 2 (PCV2) in serum and SIV in the nasal and lung samples. Pathology and bacteriology, including antimicrobial resistance determination, were performed on lung samples obtained from the field necropsies. Results According to the pathology and bacteriology of the lung samples, APP and Ascaris suum were the main causes of respiratory outbreaks in 14 and three herds respectively, while the clinical signs in three other herds had a miscellaneous etiology. SIV, APP and PCV2 caused concurrent infections in certain herds but they were detected serologically or with PCR also in control herds, suggesting possible subclinical infections. APP was isolated from 16 (80%) case herds. Marked resistance was observed against tetracycline for APP, some resistance was detected against trimethoprim/sulfamethoxazole, ampicillin and penicillin, and no resistance against florfenicol, enrofloxacin, tulathromycin or tiamulin was found. Serology, even from paired serum samples, gave inconclusive results for acute APP infection diagnosis. Conclusions APP was the most common cause for acute respiratory outbreaks in our study. SIV, A. suum, PCV2 and certain opportunistic bacteria were also detected during the outbreaks; however, viral pathogens appeared less important than bacteria. Necropsies supplemented with microbiology were the most efficient diagnostic methods in characterizing the studied outbreaks.
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8
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Protein profiling of nasopharyngeal aspirates of hospitalized and outpatients revealed cytokines associated with severe influenza A(H1N1)pdm09 virus infections: A pilot study. Cytokine 2016; 86:10-14. [DOI: 10.1016/j.cyto.2016.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/04/2016] [Accepted: 07/05/2016] [Indexed: 12/19/2022]
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9
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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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10
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Helanterä I, Anttila VJ, Lappalainen M, Lempinen M, Isoniemi H. Outbreak of Influenza A(H1N1) in a Kidney Transplant Unit-Protective Effect of Vaccination. Am J Transplant 2015; 15:2470-4. [PMID: 25943587 DOI: 10.1111/ajt.13285] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/05/2015] [Accepted: 02/24/2015] [Indexed: 01/25/2023]
Abstract
Seasonal influenza vaccination is recommended for patients with end-stage renal disease (ESRD), despite suggested inferior efficacy among these patients. We characterize an outbreak of influenza A(H1N1) in a kidney transplant unit. Altogether 23 patients were treated on the ward for postoperative care after kidney transplantation during the outbreak. After the first positive case, all patients were tested with nasopharyngeal swab tests and 7 patients were diagnosed with influenza A(H1N1). Altogether 17/23 patients had received adequate seasonal influenza vaccination, of whom 2/17 tested positive for influenza (one asymptomatic, one with mild cough). Five of six unvaccinated patients were diagnosed with influenza A(H1N1); 3/5 suffered from severe respiratory failure and were treated with ventilator support in the ICU, but all died due to acute respiratory distress syndrome, whereas 2/5 suffered from mild viral pneumonitis and recovered fully. The risk of influenza infection and mortality was significantly increased in unvaccinated patients (odds ratio 37.5 [95% CI 2.7-507.5, p = 0.01] and 6.7 [95% CI 2.3-18.9, p = 0.003], respectively). Influenza A(H1N1) had a high mortality in our cohort of nonvaccinated immunosuppressed patients early after kidney transplantation. None of the vaccinated patients developed serious disease, supporting the role of vaccination also for ESRD patients.
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Affiliation(s)
- I Helanterä
- Department of Transplant and Liver Surgery, Helsinki University Central Hospital, Helsinki, Finland
| | - V-J Anttila
- Department of Infectious Diseases, Helsinki University Central Hospital, Helsinki, Finland
| | - M Lappalainen
- Department of Virology, Helsinki University Central Hospital, Helsinki, Finland
| | - M Lempinen
- Department of Transplant and Liver Surgery, Helsinki University Central Hospital, Helsinki, Finland
| | - H Isoniemi
- Department of Transplant and Liver Surgery, Helsinki University Central Hospital, Helsinki, Finland
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11
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Syrjänen RK, Jokinen J, Ziegler T, Sundman J, Lahdenkari M, Julkunen I, Kilpi TM. Effectiveness of pandemic and seasonal influenza vaccines in preventing laboratory-confirmed influenza in adults: a clinical cohort study during epidemic seasons 2009-2010 and 2010-2011 in Finland. PLoS One 2014; 9:e108538. [PMID: 25265186 PMCID: PMC4180439 DOI: 10.1371/journal.pone.0108538] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 08/26/2014] [Indexed: 11/20/2022] Open
Abstract
Background One dose of pandemic influenza vaccine Pandemrix (GlaxoSmithKline) was offered to the entire population of Finland in 2009–10. We conducted a prospective clinical cohort study to determine the vaccine effectiveness in preventing febrile laboratory-confirmed influenza infection during the influenza season 2009–10 and continued the study in 2010–11. Methods In total, 3,518 community dwelling adults aged 18–75 years living in Tampere city were enrolled. The participants were not assigned to any vaccination regimen, but they could participate in the study regardless of their vaccination status or intention to be vaccinated with the pandemic or seasonal influenza vaccine. They were asked to report if they received Pandemrix in 2009–10 and/or trivalent influenza vaccine in 2010–11. Vaccinations were verified from medical records. The participants were instructed to report all acute symptoms of respiratory tract infection with fever (at least 38°C) and pneumonias to the study staff. Nasal and oral swabs were obtained within 5–7 days after symptom onset and influenza-specific RNA was identified by reverse transcription polymerase chain reaction. Results In 2009–10, the estimated vaccine effectiveness was 81% (95%CI 30–97). However, the vaccine effectiveness could not be estimated reliably, because only persons in prioritized groups were vaccinated before/during the first pandemic wave and many participants were enrolled when they already had the symptoms of A(H1N1)pdm09 influenza infection. In 2010–11, 2,276 participants continued the follow-up. The vaccine effectiveness, adjusted for potential confounding factors was 81% (95%CI 41–96) for Pandemrix only and 88% (95%CI 63–97) for either Pandemrix or trivalent influenza vaccine 2010–11 or both, respectively. Conclusion Vaccination with an AS03-adjuvanted pandemic vaccine in 2009–10 was still effective in preventing A(H1N1)pdm09 influenza during the following epidemic season in 2010–11. Trial Registration ClinicalTrials.gov NCT01024725. NCT01206114.
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Affiliation(s)
- Ritva K. Syrjänen
- Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Tampere, Finland
- * E-mail:
| | - Jukka Jokinen
- Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
| | - Thedi Ziegler
- Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
| | - Jonas Sundman
- Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
| | - Mika Lahdenkari
- Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
| | - Ilkka Julkunen
- Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
| | - Terhi M. Kilpi
- Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
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Abstract
Influenza viruses cause recurring epidemic outbreaks every year associated with high morbidity and mortality. Despite extensive research and surveillance efforts to control influenza outbreaks, the primary mitigation treatment for influenza is the development of yearly vaccine mixes targeted for the most prevalent virus strains. Consequently, the focus of many detection technologies has evolved toward accurate identification of subtype and understanding the evolution and molecular determinants of novel and pathogenic forms of influenza. The recent availability of potential antiviral treatments are only effective if rapid and accurate diagnostic tests for influenza epidemic management are available; thus, early detection of influenza infection is still important for prevention, containment, patient management, and infection control. This review discusses the current and emerging technologies for detection and strain identification of influenza virus and their specific gene targets, as well as their implications in patient management.
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Affiliation(s)
- Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, U. S. Naval Research Laboratory, 4555 Overlook Avenue, S. W., Code 6900, Washington, DC, 20375, USA
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Nokireki T, Laine T, London L, Ikonen N, Huovilainen A. The first detection of influenza in the Finnish pig population: a retrospective study. Acta Vet Scand 2013; 55:69. [PMID: 24047612 PMCID: PMC3850993 DOI: 10.1186/1751-0147-55-69] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 09/10/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Swine influenza is an infectious acute respiratory disease of pigs caused by influenza A virus. We investigated the time of entry of swine influenza into the Finnish pig population. We also describe the molecular detection of two types of influenza A (H1N1) viruses in porcine samples submitted in 2009 and 2010.This retrospective study was based on three categories of samples: blood samples collected for disease monitoring from pigs at major slaughterhouses from 2007 to 2009; blood samples from pigs in farms with a special health status taken in 2008 and 2009; and diagnostic blood samples from pigs in farms with clinical signs of respiratory disease in 2008 and 2009. The blood samples were tested for influenza A antibodies with an antibody ELISA. Positive samples were further analyzed for H1N1, H3N2, and H1N2 antibodies with a hemagglutination inhibition test. Diagnostic samples for virus detection were subjected to influenza A M-gene-specific real-time RT-PCR and to pandemic influenza A H1N1-specific real-time RT-PCR. Positive samples were further analyzed with RT-PCRs designed for this purpose, and the PCR products were sequenced and sequences analyzed phylogenetically. RESULTS In the blood samples from pigs in special health class farms producing replacement animals and in diagnostic blood samples, the first serologically positive samples originated from the period July-August 2008. In samples collected for disease monitoring, < 0.1%, 0% and 16% were positive for antibodies against influenza A H1N1 in the HI test in 2007, 2008, and 2009, respectively. Swine influenza A virus of avian-like H1N1 was first detected in diagnostic samples in February 2009. In 2009 and 2010, the avian-like H1N1 virus was detected on 12 and two farms, respectively. The pandemic H1N1 virus (A(H1N1)pdm09) was detected on one pig farm in 2009 and on two farms in 2010. CONCLUSIONS Based on our study, swine influenza of avian-like H1N1 virus was introduced into the Finnish pig population in 2008 and A(H1N1)pdm09 virus in 2009. The source of avian-like H1N1 infection could not be determined. Cases of pandemic H1N1 in pigs coincided with the period when the A(H1N1)pdm09 virus was spread in humans in Finland.
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Melén K, Partinen M, Tynell J, Sillanpää M, Himanen SL, Saarenpää-Heikkilä O, Hublin C, Olsen P, Ilonen J, Nohynek H, Syrjänen R, Kilpi T, Vuorela A, Kirjavainen T, Vaarala O, Julkunen I. No serological evidence of influenza A H1N1pdm09 virus infection as a contributing factor in childhood narcolepsy after Pandemrix vaccination campaign in Finland. PLoS One 2013; 8:e68402. [PMID: 23950869 PMCID: PMC3738560 DOI: 10.1371/journal.pone.0068402] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/28/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Narcolepsy cataplexy syndrome, characterised by excessive daytime sleepiness and cataplexy, is strongly associated with a genetic marker, human leukocyte antigen (HLA) DQB1*06:02. A sudden increase in the incidence of childhood narcolepsy was observed after vaccination with AS03-adjuvanted Pandemrix influenza vaccine in Finland at the beginning of 2010. Here, we analysed whether the coinciding influenza A H1N1pdm pandemic contributed, together with the Pandemrix vaccination, to the increased incidence of childhood narcolepsy in 2010. The analysis was based on the presence or absence of antibody response against non-structural protein 1 (NS1) from H1N1pdm09 virus, which was not a component of Pandemrix vaccine. METHODS Non-structural (NS) 1 proteins from recombinant influenza A/Udorn/72 (H3N2) and influenza A/Finland/554/09 (H1N1pdm09) viruses were purified and used in Western blot analysis to determine specific antibody responses in human sera. The sera were obtained from 45 patients who fell ill with narcolepsy after vaccination with AS03-adjuvanted Pandemrix at the end of 2009, and from controls. FINDINGS Based on quantitative Western blot analysis, only two of the 45 (4.4%) Pandemrix-vaccinated narcoleptic patients showed specific antibody response against the NS1 protein from the H1N1pdm09 virus, indicating past infection with the H1N1pdm09 virus. Instead, paired serum samples from patients, who suffered from a laboratory confirmed H1N1pdm09 infection, showed high levels or diagnostic rises (96%) in H1N1pdm virus NS1-specific antibodies and very high cross-reactivity to H3N2 subtype influenza A virus NS1 protein. CONCLUSION Based on our findings, it is unlikely that H1N1pdm09 virus infection contributed to a sudden increase in the incidence of childhood narcolepsy observed in Finland in 2010 after AS03-adjuvanted Pandemrix vaccination.
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Affiliation(s)
- Krister Melén
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland.
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Kumpu M, Lehtoranta L, Roivainen M, Rönkkö E, Ziegler T, Söderlund-Venermo M, Kautiainen H, Järvenpää S, Kekkonen R, Hatakka K, Korpela R, Pitkäranta A. The use of the probiotic Lactobacillus rhamnosus GG and viral findings in the nasopharynx of children attending day care. J Med Virol 2013; 85:1632-8. [PMID: 23794458 DOI: 10.1002/jmv.23623] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2013] [Indexed: 01/23/2023]
Abstract
Limited data are available on the effects of probiotics on the nasopharyngeal presence of respiratory viruses in children attending day care. In this substudy of a randomized, double-blinded, placebo-controlled 28-week intervention study, nasopharyngeal swab samples were collected, on visits to a physician due to symptoms of infection, from children receiving control milk (N = 97) and children receiving the same milk supplemented with probiotic Lactobacillus rhamnosus GG (N = 97). The presence of 14 respiratory viruses was assessed by PCR methods, and viral findings were compared with symptom prevalences in the intervention groups. Rhinovirus was identified in 28.6% of 315 swab samples, followed by respiratory syncytial virus (12.4%), parainfluenza virus 1 (12.1%), enterovirus (8.9%), influenza A(H1N1)pdm09 (7.9%), human bocavirus 1 (3.8%), parainfluenza virus 2 (3.2%), adenovirus (2.9%), and influenza A(H3N2) (0.6%). The children in the probiotic group had less days with respiratory symptoms per month than the children in the control group (6.48 [95% CI 6.28-6.68] vs. 7.19 [95% CI 6.98-7.41], P < 0.001). Probiotic intervention did not reduce significantly the occurrence of the examined respiratory viruses, or have an effect on the number of respiratory symptoms observed at the time of a viral finding. Rhinovirus, respiratory syncytial virus, and parainfluenza virus 1 were the most common respiratory viruses in symptomatic children. Children receiving Lactobacillus rhamnosus GG had fewer days with respiratory symptoms than children in the control group, although probiotic intervention was not effective in reducing the amount of viral findings or the respiratory symptoms associated with viral findings.
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Smura T, Kakkola L, Blomqvist S, Klemola P, Parsons A, Kallio-Kokko H, Savolainen-Kopra C, Kainov DE, Roivainen M. Molecular evolution and epidemiology of echovirus 6 in Finland. INFECTION GENETICS AND EVOLUTION 2013; 16:234-47. [DOI: 10.1016/j.meegid.2013.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/10/2013] [Accepted: 02/05/2013] [Indexed: 12/30/2022]
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Detection of influenza A viruses with a portable real-time PCR instrument. J Virol Methods 2012; 181:188-91. [DOI: 10.1016/j.jviromet.2012.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 02/03/2012] [Accepted: 02/13/2012] [Indexed: 11/23/2022]
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Jokela P, Piiparinen H, Mannonen L, Auvinen E, Lappalainen M. Performance of the Luminex xTAG Respiratory Viral Panel Fast in a clinical laboratory setting. J Virol Methods 2012; 182:82-6. [PMID: 22465255 PMCID: PMC7119588 DOI: 10.1016/j.jviromet.2012.03.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 03/11/2012] [Accepted: 03/14/2012] [Indexed: 11/29/2022]
Abstract
The aim of the study was to develop a real-time RT-PCR for the detection of enteroviruses (EVs) and rhinoviruses (RVs) and to assess the performance of the xTAG RVP Fast assay in comparison to a direct fluorescent assay (DFA), a real-time RT-PCR assay for the detection of respiratory syncytial virus (RSV) and human metapneumovirus (hMPV), and the EV/RV RT-PCR assay developed in this study. The performance of the RVP Fast assay was assessed in the analysis of 373 nasopharyngeal samples. For the viruses of the DFA panel, detection rates of 27.6% and 23.8% were obtained by RVP and DFA, respectively, in analysis of a set of 297 samples collected in 2009–2010. These results show statistically significant superiority of the RVP Fast assay (P = 0.049). For RSV, hMPV, EV, and RV, detection rates of 48.0% and 45.2% were achieved by RVP and RT-PCR, respectively. For individual targets, increased detection of EV/RV (P = 0.043) and decreased detection of influenza A virus (P = 0.004) by RVP in comparison to real-time RT-PCR was observed. The results of the present study imply the need to adjust the InfA component of the RVP Fast assay to also cover the InfA(H1N1) 2009 virus.
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Affiliation(s)
- Pia Jokela
- Department of Virology, Haartman Institute, University of Helsinki, FIN-00014 Helsinki, Finland.
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