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Baumgarth N, Prieto AC, Luo Z, Kulaga H. B cells modulate lung antiviral inflammatory responses via the neurotransmitter acetylcholine. RESEARCH SQUARE 2024:rs.3.rs-4421566. [PMID: 38978583 PMCID: PMC11230464 DOI: 10.21203/rs.3.rs-4421566/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The rapid onset of innate immune defenses is critical for early control of viral replication in an infected host, yet it can also lead to irreversible tissue damage, especially in the respiratory tract. Intricate regulatory mechanisms must exist that modulate inflammation, while controlling the infection. Here, B cells expressing choline acetyl transferase (ChAT), an enzyme required for production of the metabolite and neurotransmitter acetylcholine (ACh) are identified as such regulators of the immediate early response to influenza A virus. Lung tissue ChAT + B cells are shown to interact with a7 nicotinic Ach receptor-expressing lung interstitial macrophages in mice within 24h of infection to control their production of TNFa, shifting the balance towards reduced inflammation at the cost of enhanced viral replication. Thus, innate-stimulated B cells are key participants of an immediate-early regulatory cascade that controls lung tissue damage after viral infection.
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An SH, Kim NY, Heo GB, Kang YM, Lee YJ, Lee KN. Development and evaluation of a multiplex real-time RT-PCR assay for simultaneous detection of H5, H7, and H9 subtype avian influenza viruses. J Virol Methods 2024; 327:114942. [PMID: 38670532 DOI: 10.1016/j.jviromet.2024.114942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
H5, H7 and H9 are the major subtypes of avian influenza virus (AIV) that cause economic losses in the poultry industry and sporadic zoonotic infection. Early detection of AIV is essential for preventing disease spread. Therefore, molecular diagnosis and subtyping of AIV via real-time RT-PCR (rRT-PCR) is preferred over other classical diagnostic methods, such as egg inoculation, RT-PCR and HI test, due to its high sensitivity, specificity and convenience. The singleplex rRT-PCRs for the Matrix, H5 and H7 gene used for the national surveillance program in Korea have been developed in 2017; however, these methods were not designed for multiplexing, and does not reflect the sequences of currently circulating strains completely. In this study, the multiplex H5/7/9 rRT-PCR assay was developed with sets of primers and probe updated or newly designed to simultaneously detect the H5, H7 and H9 genes. Multiplex H5/7/9 rRT-PCR showed 100% specificity without cross-reactivity with other subtypes of AIVs and avian disease-causing viruses or bacteria, and the limit of detection was 1-10 EID50/0.1 ml (50% egg infectious dose). Artificial mixed infections with the three different subtypes could be detected accurately with high analytical sensitivity even under highly biased relative molecular ratios by balancing the reactivities of each subtype by modifying the concentration of the primers and probes. The multiplex H5/7/9 rRT-PCR assay developed in this study could be a useful tool for large-scale surveillance programs for viral detection as well as subtyping due to its high specificity, sensitivity and robustness in discriminating viruses in mixed infections, and this approach would greatly decrease the time, cost, effort and chance of cross-contamination compared to the conventional method of testing three subtypes by different singleplex rRT-PCR methods in parallel or in series.
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Affiliation(s)
- Se-Hee An
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, South Korea
| | - Na-Yeong Kim
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, South Korea
| | - Gyeong-Beom Heo
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, South Korea
| | - Yong-Myung Kang
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, South Korea
| | - Youn-Jeong Lee
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, South Korea
| | - Kwang-Nyeong Lee
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, South Korea.
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Azeem S, Baroch J, Tewari D, Pabilonia KL, Killian M, Bradel-Tretheway B, Sun D, Ghorbani-Nezami S, Yoon KJ. Molecular Characterization of Non-H5 and Non-H7 Avian Influenza Viruses from Non-Mallard Migratory Waterbirds of the North American Flyways, 2006-2011. Pathogens 2024; 13:333. [PMID: 38668288 PMCID: PMC11054893 DOI: 10.3390/pathogens13040333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
The surveillance of migratory waterbirds (MWs) for avian influenza virus (AIV) is indispensable for the early detection of a potential AIV incursion into poultry. Surveying AIV infections and virus subtypes in understudied MW species could elucidate their role in AIV ecology. Oropharyngeal-cloacal (OPC) swabs were collected from non-mallard MWs between 2006 and 2011. OPC swabs (n = 1158) that molecularly tested positive for AIV (Cts ≤ 32) but tested negative for H5 and H7 subtypes were selected for virus isolation (VI). The selected samples evenly represented birds from all four North American flyways (Pacific, Central, Mississippi, and Atlantic). Eighty-seven low pathogenic AIV isolates, representing 31 sites in 17 states, were recovered from the samples. All isolates belonged to the North American lineage. The samples representing birds from the Central Flyway had the highest VI positive rate (57.5%) compared to those from the other flyways (10.3-17.2%), suggesting that future surveillance can focus on the Central Flyway. Of the isolates, 43.7%, 12.6%, and 10.3% were obtained from blue-winged teal, American wigeon, and American black duck species, respectively. Hatch-year MWs represented the majority of the isolates (70.1%). The most common H and N combinations were H3N8 (23.0%), H4N6 (18.4%), and H4N8 (18.4%). The HA gene between non-mallard and mallard MW isolates during the same time period shared 85.5-99.5% H3 identity and 89.3-99.7% H4 identity. Comparisons between MW (mallard and non-mallard) and poultry H3 and H4 isolates also revealed high similarity (79.0-99.0% and 88.7-98.4%), emphasizing the need for continued AIV surveillance in MWs.
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Affiliation(s)
- Shahan Azeem
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA; (S.A.); (D.S.)
- Institute of Microbiology, Faculty of Veterinary Science, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - John Baroch
- Wildlife Services, Animal & Plant Health Inspection Service (APHIS), United States Department of Agriculture (USDA), Fort Collins, CO 80526, USA
| | - Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA;
| | - Kristy L. Pabilonia
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA;
| | - Mary Killian
- National Veterinary Services Laboratories, Animal & Plant Health Inspection Service (APHIS), United States Department of Agriculture (USDA), Ames, IA 50010, USA;
| | - Birgit Bradel-Tretheway
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, USA;
| | - Dong Sun
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA; (S.A.); (D.S.)
| | - Sara Ghorbani-Nezami
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA
| | - Kyoung-Jin Yoon
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA
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Zhu X, Cai J, Wang Y, Liu X, Chen X, Wang H, Wu Z, Bao W, Fan H, Wu S. A High-Fat Diet Increases the Characteristics of Gut Microbial Composition and the Intestinal Damage Associated with Non-Alcoholic Fatty Liver Disease. Int J Mol Sci 2023; 24:16733. [PMID: 38069055 PMCID: PMC10706137 DOI: 10.3390/ijms242316733] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing annually, and emerging evidence suggests that the gut microbiota plays a causative role in the development of NAFLD. However, the role of gut microbiota in the development of NAFLD remains unclear and warrants further investigation. Thus, C57BL/6J mice were fed a high-fat diet (HFD), and we found that the HFD significantly induced obesity and increased the accumulation of intrahepatic lipids, along with alterations in serum biochemical parameters. Moreover, it was observed that the HFD also impaired gut barrier integrity. It was revealed via 16S rRNA gene sequencing that the HFD increased gut microbial diversity, which enriched Colidextribacter, Lachnospiraceae-NK4A136-group, Acetatifactor, and Erysipelatoclostridium. Meanwhile, it reduced the abundance of Faecalibaculum, Muribaculaceae, and Coriobacteriaceae-UCG-002. The predicted metabolic pathways suggest that HFD enhances the chemotaxis and functional activity of gut microbiota pathways associated with flagellar assembly, while also increasing the risk of intestinal pathogen colonization and inflammation. And the phosphotransferase system, streptomycin biosynthesis, and starch/sucrose metabolism exhibited decreases. These findings reveal the composition and predictive functions of the intestinal microbiome in NAFLD, further corroborating the association between gut microbiota and NAFLD while providing novel insights into its potential application in gut microbiome research for NAFLD patients.
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Affiliation(s)
- Xiaoyang Zhu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.Z.); (Y.W.); (X.L.); (X.C.); (H.W.); (Z.W.); (W.B.)
| | - Jiajia Cai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China;
| | - Yifu Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.Z.); (Y.W.); (X.L.); (X.C.); (H.W.); (Z.W.); (W.B.)
| | - Xinyu Liu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.Z.); (Y.W.); (X.L.); (X.C.); (H.W.); (Z.W.); (W.B.)
| | - Xiaolei Chen
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.Z.); (Y.W.); (X.L.); (X.C.); (H.W.); (Z.W.); (W.B.)
| | - Haifei Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.Z.); (Y.W.); (X.L.); (X.C.); (H.W.); (Z.W.); (W.B.)
| | - Zhengchang Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.Z.); (Y.W.); (X.L.); (X.C.); (H.W.); (Z.W.); (W.B.)
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.Z.); (Y.W.); (X.L.); (X.C.); (H.W.); (Z.W.); (W.B.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China;
| | - Hairui Fan
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.Z.); (Y.W.); (X.L.); (X.C.); (H.W.); (Z.W.); (W.B.)
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.Z.); (Y.W.); (X.L.); (X.C.); (H.W.); (Z.W.); (W.B.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China;
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Rector A, Bloemen M, Van Ranst M, Wollants E. Used paper tissues for pathogen identification in acute respiratory infection. J Med Virol 2023; 95:e29127. [PMID: 37772540 DOI: 10.1002/jmv.29127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023]
Abstract
During the Belgian winter and spring season 2022-2023, we investigated the potential of used paper tissue (UPT) as a noninvasive sampling method for the diagnosis of acute respiratory infections. Screening for respiratory pathogens was done using an in-house developed respiratory panel for simultaneous detection of 22 respiratory viruses and seven nonviral pathogens. The method allowed the identification and typing of respiratory pathogens in symptomatic individuals, as well as in collective samples taken at a community level. Pathogens that were identified in nasal swabs could also be detected in concurrent UPT from the same patient. In all cases that tested positive on an antigen-detection rapid diagnostic test, the corresponding virus could be detected in UPT. The collection of UPT could be useful in epidemiological surveillance of severe acute respiratory syndrome coronavirus 2 and other coronaviruses, as well as other respiratory pathogens such as influenzavirus, respiratory syncytial virus, entero/rhinoviruses including EV-D68, parainfluenzaviruses, and Streptococcus pneumoniae. Multiple respiratory pathogens could be detected in UPTs of collectivities, confirming its applicability for community testing. This is especially interesting for screening in nursing homes, centers for the disabled, schools or other settings were taking nasal or nasopharyngeal samples is cumbersome.
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Affiliation(s)
- Annabel Rector
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mandy Bloemen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Laboratory Medicine, National Reference Center Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Elke Wollants
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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Rector A, Bloemen M, Schiettekatte G, Maes P, Van Ranst M, Wollants E. Sequencing directly from antigen-detection rapid diagnostic tests in Belgium, 2022: a gamechanger in genomic surveillance? Euro Surveill 2023; 28:2200618. [PMID: 36862099 PMCID: PMC9983067 DOI: 10.2807/1560-7917.es.2023.28.9.2200618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
BackgroundLateral flow antigen-detection rapid diagnostic tests (Ag-RDTs) for viral infections constitute a fast, cheap and reliable alternative to nucleic acid amplification tests (NAATs). Whereas leftover material from NAATs can be employed for genomic analysis of positive samples, there is a paucity of information on whether viral genetic characterisation can be achieved from archived Ag-RDTs.AimTo evaluate the possibility of retrieving leftover material of several viruses from a range of Ag-RDTs, for molecular genetic analysis.MethodsArchived Ag-RDTs which had been stored for up to 3 months at room temperature were used to extract viral nucleic acids for subsequent RT-qPCR, Sanger sequencing and Nanopore whole genome sequencing. The effects of brands of Ag-RDT and of various ways to prepare Ag-RDT material were evaluated.ResultsSARS-CoV-2 nucleic acids were successfully extracted and sequenced from nine different brands of Ag-RDTs for SARS-CoV-2, and for five of these, after storage for 3 months at room temperature. The approach also worked for Ag-RDTs for influenza virus (n = 3 brands), as well as for rotavirus and adenovirus 40/41 (n = 1 brand). The buffer of the Ag-RDT had an important influence on viral RNA yield from the test strip and the efficiency of subsequent sequencing.ConclusionOur finding that the test strip in Ag-RDTs is suited to preserve viral genomic material, even for several months at room temperature, and therefore can serve as source material for genetic characterisation could help improve global coverage of genomic surveillance for SARS-CoV-2 as well as for other viruses.
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Affiliation(s)
- Annabel Rector
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Mandy Bloemen
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Gilberte Schiettekatte
- Center for Medical Analysis, Department of Molecular Biology and Immunology, Herentals, Belgium
| | - Piet Maes
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Marc Van Ranst
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium,University Hospitals Leuven, Department of Laboratory Medicine, National Reference Center for Respiratory Pathogens, Leuven, Belgium
| | - Elke Wollants
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
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Martín-Valls GE, Li Y, Díaz I, Cano E, Sosa-Portugal S, Mateu E. Diversity of respiratory viruses present in nasal swabs under influenza suspicion in respiratory disease cases of weaned pigs. Front Vet Sci 2022; 9:1014475. [PMID: 36337208 PMCID: PMC9627340 DOI: 10.3389/fvets.2022.1014475] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/29/2022] [Indexed: 11/15/2022] Open
Abstract
Respiratory diseases in weaned pigs are a common problem, with a complex etiology involving both viruses and bacteria. In the present study, we investigated the presence of eleven viruses in nasal swabs, collected from nurseries (55 cases) under the suspicion of swine influenza A virus (swIAV) and submitted by swine veterinarians for diagnosis. The other ten viruses included in the study were influenza B (IBV) and D (IDV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine respiratory coronavirus (PRCV), Porcine cytomegalovirus (PCMV), Porcine circovirus 2 (PCV2), 3 (PCV3) and 4 (PCV), Porcine parainfluenza 1 (PPIV1) and Swine orthopneumovirus (SOV). Twenty-six swIAV-positive cases and twenty-nine cases of swIAV-negative respiratory disease were primarily established. While IBV, IDV, PCV4 and PPIV1 were not found in any of the cases, PRCV, SOV, and PCMV were more likely to be found in swIAV-positive nurseries with respiratory disease (p < 0.05). Overall, PCV3, PRRSV, and PCMV were the most frequently detected agents at herd level. Taken individually, virus prevalence was: swIAV, 48.6%; PRCV, 48.0%; PRRSV, 31.6%; SOV, 33.8%; PCMV, 48.3%, PCV2, 36.0%; and PCV3, 33.0%. Moreover, low Ct values (<30) were common for all agents, except PCV2 and PCV3. When the correlation between pathogens was individually examined, the presence of PRRSV was negatively correlated with swIAV and PRCV, while was positively associated to PCMV (p < 0.05). Also, PRCV and SOV were positively correlated between them and negatively with PCMV. Besides, the analysis of suckling pig samples, collected in subclinically infected farrowing units under an influenza monitoring program, showed that circulation of PRCV, PCMV, SOV, and PCV3 started during the early weeks of life. Interestingly, in those subclinically infected units, none of the pathogens was found to be correlated to any other. Overall, our data may contribute to a better understanding of the complex etiology and epidemiology of respiratory diseases in weaners. This is the first report of SOV in Spain and shows, for the first time, the dynamics of this pathogen in swine farms.
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Affiliation(s)
- Gerard E. Martín-Valls
- Department de Sanitat i Anatomia Animals, Faculty of Veterinària, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- *Correspondence: Gerard E. Martín-Valls
| | - Yanli Li
- Department de Sanitat i Anatomia Animals, Faculty of Veterinària, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ivan Díaz
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Esmeralda Cano
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Silvana Sosa-Portugal
- Department de Sanitat i Anatomia Animals, Faculty of Veterinària, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Enric Mateu
- Department de Sanitat i Anatomia Animals, Faculty of Veterinària, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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Jiang XW, Huang TS, Xie L, Chen SZ, Wang SD, Huang ZW, Li XY, Ling WP. Development of a diagnostic assay by three-tube multiplex real-time PCR for simultaneous detection of nine microorganisms causing acute respiratory infections. Sci Rep 2022; 12:13306. [PMID: 35922526 PMCID: PMC9427838 DOI: 10.1038/s41598-022-15543-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Acute respiratory infections are widespread in vulnerable populations of all ages and are characterized by a variety of symptoms. The underlying infection can be caused by a multitude of microorganisms, including viruses and bacteria. Early detection of respiratory infections through rapid pathogen screening is vital in averting infectious respiratory disease epidemics. This study utilized a multiplex real-time PCR system to develop a three-tube reverse transcription-PCR (RT-PCR) assay, enabling simultaneously detect nine respiratory pathogens, including: influenza A and B, adenovirus, respiratory syncytial virus (RSV), Streptococcus pneumoniae, Legionella pneumophila, Haemophilus influenzae, Chlamydia pneumoniae, and Mycoplasma pneumoniae. This technique utilizes a one-step assay, with specifically designed TaqMan primer-probe sets combined in the same tube. This assay provided rapid and simplified detection of the nine prevalent pathogens, as well as increased sensitivity and reduced cross-contamination. This assay was evaluated using 25 related viral/bacterial strains as positive references, the other 25 irrelevant strains as negative controls, and clinical specimens from 179 patients. All positive strains were detected with no amplification of the non-target microorganism mixtures and the assay's detection limits ranged between 250-500 copies/ml (1.25-2.5 copies/reaction). A total of 167 (93.3%) samples tested positive for at least one of the pathogens identified; 109 of these samples were from patients confirmed to have RSV infections. The diagnostic accuracy of our assay was further confirmed by matching results from classical direct immunofluorescence assay and nucleotide sequencing. These data demonstrate the innovative multiplex real-time PCR assay as a promising alternative to the current approaches used for early screening of acute respiratory infections.
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Affiliation(s)
- Xi-Wen Jiang
- Research Institute, DAAN Gene Co., Ltd., No. 19 Xiangshan Road, Guangzhou, China.
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China.
| | - Tao-Sheng Huang
- Research Institute, DAAN Gene Co., Ltd., No. 19 Xiangshan Road, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Long Xie
- Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Si-Ze Chen
- Central Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- The Precise Therapy Engineering Technology Research Center of Guangdong Province for Esophageal Cancer, Guangzhou, China
| | - Shi-Dong Wang
- Research Institute, DAAN Gene Co., Ltd., No. 19 Xiangshan Road, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Zhi-Wen Huang
- Research Institute, DAAN Gene Co., Ltd., No. 19 Xiangshan Road, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Xin-Yu Li
- Research Institute, DAAN Gene Co., Ltd., No. 19 Xiangshan Road, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Wei-Ping Ling
- Research Institute, DAAN Gene Co., Ltd., No. 19 Xiangshan Road, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
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9
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Airborne Influenza A Virus Exposure in an Elementary School. Sci Rep 2020; 10:1859. [PMID: 32024882 PMCID: PMC7002614 DOI: 10.1038/s41598-020-58588-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/17/2020] [Indexed: 01/26/2023] Open
Abstract
Influenza contributes significantly to childhood morbidity and mortality. Given the magnitude of the school-aged child population, a sizeable proportion of influenza virus transmission events are expected to occur within school settings. However, influenza virus activity in schools is not well-understood, likely due to our limited ability to accurately monitor for respiratory viruses without disrupting the school environment. In this study, we evaluated the use of a bioaerosol sampling method to noninvasively detect and quantify airborne influenza A virus (IAV) densities in a public elementary school. Air samples were collected from multiple locations in the school, two days per week, throughout an eight-week sampling period during influenza season. Real-time RT-PCR targeting the IAV M gene revealed detectable IAV on five occasions in densities ranging from 2.0 × 10−1 to 1.9 × 104. No significant differences in IAV densities were related to student presence/absence. The majority of IAV-associated particles were ≤4 μm in diameter, and theoretical calculations indicate infectious thresholds after minutes of exposure. Our study represents the first identification and quantification of airborne influenza virus in an elementary school, and the results suggest that airborne IAV has the potential to circulate in schools during influenza season, in large enough doses known to cause infection.
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10
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Sun N, Wang Y, Yao X, Chen F, Gao D, Wang W, Li X. Visual signal generation for the detection of influenza viruses by duplex recombinase polymerase amplification with lateral flow dipsticks. Anal Bioanal Chem 2019; 411:3591-3602. [PMID: 31079175 DOI: 10.1007/s00216-019-01840-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022]
Abstract
We present a detailed study on visual detection of influenza viruses by duplex recombinase polymerase amplification (RPA) with lateral flow dipsticks (LFDs). The LFD consisted of two test lines and a control line, on which anti-fluorescein isothiocyanate antibodies, anti-digoxigenin antibodies, and biotinylated bovine serum albumin were immobilized, respectively. The performance of the LFD was evaluated with dual-labeled DNA amplicons. The results indicate that the detection of DNA amplicons by LFDs is specific and sensitive, with detection limits of 5.80 fmol for fluorescein isothiocyanate-labeled amplicons and 8.39 fmol for digoxigenin-labeled amplicons. We next developed a duplex RPA-LFD assay for simultaneous detection of influenza A virus and influenza B virus, and then optimized the parameters, including the reaction temperature, reaction time, and concentrations of primers and probes. Assessment of the specificity and sensitivity indicated that this assay is sensitive and specific for simultaneous detection of influenza viruses, with detection limits of 50 copies per reaction for influenza B virus and 500 copies per reaction for influenza A virus, without cross-reactivity with other pathogens. Compared with real-time PCR as a reference method to detect influenza viruses in clinical samples, the clinical sensitivity of the duplex RPA-LFD assay was 78.57% for influenza A virus and 87.50% for influenza B virus, with 100% specificity. In conclusion, the duplex RPA-LFD assay is a rapid, cost-effective, and sensitive method for the identification of influenza viruses.
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Affiliation(s)
- Ning Sun
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Ying Wang
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Xinyue Yao
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Fangfang Chen
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Deyu Gao
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Weiping Wang
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Xiaojun Li
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China. .,State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing, 210002, Jiangsu, China.
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11
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Circulation of influenza A and B in the Czech Republic from 2000-2001 to 2015-2016. BMC Infect Dis 2019; 19:160. [PMID: 30764763 PMCID: PMC6376715 DOI: 10.1186/s12879-019-3783-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 02/06/2019] [Indexed: 02/01/2023] Open
Abstract
Background To improve national influenza vaccination recommendations, additional data on influenza A and B virus circulation are needed. Here, we describe the circulation of influenza A and B in the Czech Republic during 16 seasons. Methods This was a retrospective analysis of data collected from the 2000–2001 to 2015–2016 influenza seasons by the Czech Republic national influenza surveillance network. Influenza was confirmed and viral isolates subtyped by virological assays followed by antigen detection or by reverse transcriptase-polymerase chain reaction. Results Of 16,940 samples collected, 5144 (30.4%) were influenza-positive. Influenza A represented 78.6% of positive cases overall and accounted for more than 55.0% of all influenza cases in every season, except for 2005–2006 (6.0%). Both A/H1N1 and A/H3N2 were detected in most seasons, except for 2001–2002 and 2003–2004 (only A/H3N2), and 2007–2008 and 2009–2010 (only A/H1N1). Influenza B represented 21.4% of positive cases overall (range, 0.0–94.0% per season). Both influenza B lineages were detected in three seasons, a single B lineage in 11, and no B strain in two. For the 11 seasons where influenza B accounted for ≥20% of positive cases, the dominant lineage was Yamagata in six and Victoria in four. In the remaining season, the two lineages co-circulated. For two seasons (2005–2006 and 2007–2008), the B lineage in the trivalent influenza vaccine did not match the dominant circulating B lineage. Conclusions In the Czech Republic, during the 2000–2001 to 2015–2016 influenza seasons, influenza virus circulation varied considerably. Although influenza A accounted for the most cases in almost all seasons, influenza B made a substantial, sometimes dominant, contribution to influenza disease.
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12
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Sun N, Wang W, Wang J, Yao X, Chen F, Li X, Yinglei Y, Chen B. Reverse transcription recombinase polymerase amplification with lateral flow dipsticks for detection of influenza A virus and subtyping of H1 and H3. Mol Cell Probes 2018; 42:25-31. [PMID: 30394299 PMCID: PMC7127182 DOI: 10.1016/j.mcp.2018.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 12/29/2022]
Abstract
Three reverse transcription recombinase polymerase amplification assays with lateral flow dipsticks (RT-RPA-LFD) were developed for identification of the matrix and hemagglutinin (HA) genes to detect influenza A virus and distinguish subtypes H1 and H3. Assessment of the assays' specificity showed that there was no cross-reactivity with other targets. Their limits of detection were 123.6 copies per reaction for the matrix gene, 677.1 copies per reaction for the H1 HA gene, and 112.2 copies/reaction for the H3 HA gene. Of 111 samples tested by RT-RPA-LFD assays, 27 were positive for influenza A virus, 14 were positive for H1, and 10 were positive for H3. Compared to the results obtained from real-time RT-PCR assays, the sensitivity of RT-RPA-LFD assays was 75%, 93.33% and 71.43% for the matrix, H1, and H3, with 100% specificity. The sensitivity of RT-RPA-LFD assays is lower than that of real-time RT-PCR, comparable or better than that of conventional RT-PCR, and much better than that of RIDTs. In conclusion, these assays offer an efficient and reliable tool for identification and subtyping of influenza A virus (subtype H1 and H3) in the resource-limited setting.
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Affiliation(s)
- Ning Sun
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Weiping Wang
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Jie Wang
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Xinyue Yao
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Fangfang Chen
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Xiaojun Li
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China; State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing, China.
| | - Yi Yinglei
- Shanghai Institute of Biological Products Co., Ltd, Shanghai, China
| | - Bo Chen
- Ningbo Health BioMed Co., Ltd, Ning Bo, China
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13
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Kim Y, Chang KO. Protein disulfide isomerases as potential therapeutic targets for influenza A and B viruses. Virus Res 2018; 247:26-33. [PMID: 29382552 PMCID: PMC5831498 DOI: 10.1016/j.virusres.2018.01.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 01/17/2018] [Accepted: 01/21/2018] [Indexed: 01/03/2023]
Abstract
Seasonal flu as well as potential pandemic flu outbreaks continuously underscores the importance of the preventive and therapeutic measures against influenza viruses. During screening of natural and synthetic small molecules against influenza A and B virus, we identified juniferdin as a highly effective inhibitor against both viruses in cells. Since juniferdin is known to inhibit protein disulfide isomerases (PDIs), multiple PDI inhibitors were tested against these viruses. Among PDI inhibitors, 16F16, PACMA31, isoquercetin, epigallocatechin-3-gallate or nitazoxanide significantly reduced the replication of influenza A and B viruses in MDCK and A549 cells. Furthermore, siRNAs specific to three PDI family members (PDI1, PDIA3 or PDIA4) also significantly reduced the replication of influenza A and B viruses in cells. These results suggest that PDIs may serve as excellent targets for the development of new anti-influenza drugs.
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Affiliation(s)
- Yunjeong Kim
- Department of Pathobiology and Preventive Medicine, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Kyeong-Ok Chang
- Department of Pathobiology and Preventive Medicine, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
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14
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Development and application of a triplex real-time PCR assay for the simultaneous detection of avian influenza virus subtype H5, H7 and H9. J Virol Methods 2017; 252:49-56. [PMID: 29129489 DOI: 10.1016/j.jviromet.2017.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/25/2017] [Accepted: 11/09/2017] [Indexed: 11/21/2022]
Abstract
Avian influenza virus (AIV), especially subtypes H5, H7 and H9, has contributed to enormous economic losses and poses a potential pandemic threat to global human public health. Early screening of suspected cases is key to controlling the spread of AIVs. In this study, an accurate, rapid, and triplex real-time polymerase chain reaction (PCR) assay was developed for the simultaneous detection of AIV subtypes H5, H7 and H9. The sensitivity of the real-time PCR was at least 100 times higher than that of the conventional PCR, with a detection limit of 50 copies and an EID50 of 1 (50% egg infections dose) for the H5, H7, and H9 subtypes. The lack of cross-reaction with other avian respiratory viruses suggested that the real-time PCR assay was highly specific. The reproducibility of the assay was confirmed using plasmids containing targets genes. Furthermore, 362 clinical field samples were evaluated. Subtypes H5, H7 and H9 were detected in 102 (28.18%) samples by real-time PCR and in 35 (9.67%) samples by conventional virus isolation. These results indicate that the triplex real-time PCR assay has good sensitivity, specificity and reproducibility and that it might be useful for laboratory surveillance and rapid diagnosis of the H5, H7 and H9 subtypes of influenza A viruses.
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15
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Savage HP, Yenson VM, Sawhney SS, Mousseau BJ, Lund FE, Baumgarth N. Blimp-1-dependent and -independent natural antibody production by B-1 and B-1-derived plasma cells. J Exp Med 2017; 214:2777-2794. [PMID: 28698287 PMCID: PMC5584113 DOI: 10.1084/jem.20161122] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 04/27/2017] [Accepted: 06/08/2017] [Indexed: 11/04/2022] Open
Abstract
Natural antibodies contribute to tissue homeostasis and protect against infections. They are secreted constitutively without external antigenic stimulation. The differentiation state and regulatory pathways that enable continuous natural antibody production by B-1 cells, the main cellular source in mice, remain incompletely understood. Here we demonstrate that natural IgM-secreting B-1 cells in the spleen and bone marrow are heterogeneous, consisting of (a) terminally differentiated B-1-derived plasma cells expressing the transcriptional regulator of differentiation, Blimp-1, (b) Blimp-1+, and (c) Blimp-1neg phenotypic B-1 cells. Blimp-1neg IgM-secreting B-1 cells are not simply intermediates of cellular differentiation. Instead, they secrete similar amounts of IgM in wild-type and Blimp-1-deficient (PRDM-1ΔEx1A) mice. Blimp-1neg B-1 cells are also a major source of IgG3. Consequently, deletion of Blimp-1 changes neither serum IgG3 levels nor the amount of IgG3 secreted per cell. Thus, the pool of natural antibody-secreting B-1 cells is heterogeneous and contains a distinct subset of cells that do not use Blimp-1 for initiation or maximal antibody secretion.
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Affiliation(s)
- Hannah P Savage
- Graduate Group in Immunology, University of California, Davis, Davis, CA.,Center for Comparative Medicine, University of California, Davis, Davis, CA
| | - Vanessa M Yenson
- Center for Comparative Medicine, University of California, Davis, Davis, CA
| | - Sanjam S Sawhney
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Betty J Mousseau
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Frances E Lund
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Nicole Baumgarth
- Graduate Group in Immunology, University of California, Davis, Davis, CA .,Center for Comparative Medicine, University of California, Davis, Davis, CA.,Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA
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16
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Walz PH, Newcomer BW, Riddell KP, Scruggs DW, Cortese VS. Virus detection by PCR following vaccination of naive calves with intranasal or injectable multivalent modified-live viral vaccines. J Vet Diagn Invest 2017; 29:628-635. [PMID: 28545321 DOI: 10.1177/1040638717709039] [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] [Indexed: 11/16/2022] Open
Abstract
We evaluated duration of PCR-positive results following administration of modified-live viral (MLV) vaccines to beef calves. Twenty beef calves were randomly assigned to either group 1 and vaccinated intranasally with a MLV vaccine containing bovine alphaherpesvirus 1 (BoHV-1), bovine respiratory syncytial virus (BRSV), and bovine parainfluenza virus 3 (BPIV-3), or to group 2 and vaccinated subcutaneously with a MLV vaccine containing bovine viral diarrhea virus 1 and 2 (BVDV-1, -2), BoHV-1, BRSV, and BPIV-3. Deep nasopharyngeal swabs (NPS) and transtracheal washes (TTW) were collected from all calves, and whole blood was collected from group 2 calves and tested by PCR. In group 1, the proportions of calves that tested PCR-positive to BVDV, BoHV-1, BRSV, and BPIV-3 on any sample at any time were 0%, 100%, 100%, and 10%, respectively. In group 1 calves, 100% of calves became PCR-positive for BoHV-1 by day 3 post-vaccination and 100% of calves became PCR-positive for BRSV by day 7 post-vaccination. In group 2, the proportions of calves that tested positive to BVDV, BoHV-1, BRSV, and BPIV-3 on any sample at any time were 50%, 40%, 10%, and 0%, respectively. All threshold cycle (Ct) values were >30 in group 2 calves, irrespective of virus; however, Ct values <25 were observed in group 1 calves from PCR-positive results for BoHV-1 and BRSV. All calves were PCR-negative for all viruses after day 28. Following intranasal MLV viral vaccination, PCR results and Ct values for BRSV and BoHV-1 suggest that attempts to differentiate vaccine virus from natural infection is unreliable.
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Affiliation(s)
- Paul H Walz
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz, Newcomer, Riddell).,Zoetis Inc., Florham Park, NJ (Cortese, Scruggs)
| | - Benjamin W Newcomer
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz, Newcomer, Riddell).,Zoetis Inc., Florham Park, NJ (Cortese, Scruggs)
| | - Kay P Riddell
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz, Newcomer, Riddell).,Zoetis Inc., Florham Park, NJ (Cortese, Scruggs)
| | - Daniel W Scruggs
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz, Newcomer, Riddell).,Zoetis Inc., Florham Park, NJ (Cortese, Scruggs)
| | - Victor S Cortese
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz, Newcomer, Riddell).,Zoetis Inc., Florham Park, NJ (Cortese, Scruggs)
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17
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Seleka M, Treurnicht FK, Tempia S, Hellferscee O, Mtshali S, Cohen AL, Buys A, McAnerney JM, Besselaar TG, Pretorius M, von Gottberg A, Walaza S, Cohen C, Madhi SA, Venter M. Epidemiology of influenza B/Yamagata and B/Victoria lineages in South Africa, 2005-2014. PLoS One 2017; 12:e0177655. [PMID: 28542324 PMCID: PMC5444647 DOI: 10.1371/journal.pone.0177655] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/01/2017] [Indexed: 12/29/2022] Open
Abstract
Background Studies describing the epidemiology of influenza B lineages in South Africa are lacking. Methods We conducted a prospective study to describe the circulation of influenza B/Victoria and B/Yamagata lineages among patients of all ages enrolled in South Africa through three respiratory illness surveillance systems between 2005 and 2014: (i) the Viral Watch (VW) program enrolled outpatients with influenza-like illness (ILI) from private healthcare facilities during 2005–2014; (ii) the influenza-like illnesses program enrolled outpatients in public healthcare clinics (ILI/PHC) during 2012–2014; and (iii) the severe acute respiratory illnesses (SARI) program enrolled inpatients from public hospitals during 2009–2014. Influenza B viruses were detected by virus isolation during 2005 to 2009 and by real-time reverse transcription polymerase chain reaction from 2009–2014. Clinical and epidemiological characteristics of patients hospitalized with SARI and infected with different influenza B lineages were also compared using unconditional logistic regression. Results Influenza viruses were detected in 22% (8,706/39,804) of specimens from patients with ILI or SARI during 2005–2014, of which 24% (2,087) were positive for influenza B. Influenza B viruses predominated in all three surveillance systems in 2010. B/Victoria predominated prior to 2011 (except 2008) whereas B/Yamagata predominated thereafter (except 2012). B lineages co-circulated in all seasons, except in 2013 and 2014 for SARI and ILI/PHC surveillance. Among influenza B-positive SARI cases, the detection of influenza B/Yamagata compared to influenza B/Victoria was significantly higher in individuals aged 45–64 years (adjusted odds ratio [aOR]: 4.2; 95% confidence interval [CI]: 1.1–16.5) and ≥65 years (aOR: 12.2; 95% CI: 2.3–64.4) compared to children aged 0–4 years, but was significantly lower in HIV-infected patients (aOR: 0.4; 95% CI: 0.2–0.9). Conclusion B lineages co-circulated in most seasons except in 2013 and 2014. Hospitalized SARI cases display differential susceptibility for the two influenza B lineages, with B/Victoria being more prevalent among children and HIV-infected persons.
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Affiliation(s)
- Mpho Seleka
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Florette K. Treurnicht
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- * E-mail:
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johanneburg, South Africa
| | - Senzo Mtshali
- Sequencing Core Facility, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Adam L. Cohen
- Global Influenza Program, World Health Organization (WHO), Geneva, Switzerland
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Johanna M. McAnerney
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Terry G. Besselaar
- Global Influenza Program, World Health Organization (WHO), Geneva, Switzerland
| | - Marthi Pretorius
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johanneburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A. Madhi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Marietjie Venter
- Zoonoses Research Unit, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
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18
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Granados A, Peci A, McGeer A, Gubbay JB. Influenza and rhinovirus viral load and disease severity in upper respiratory tract infections. J Clin Virol 2016; 86:14-19. [PMID: 27893998 DOI: 10.1016/j.jcv.2016.11.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND The role of viral load in respiratory viral infection is unclear. It is proposed that the viral load of some, but not all respiratory viruses correlate with disease severity. OBJECTIVES We aimed to determine if an association exists between viral loads among patients in ambulatory settings, compared to those requiring hospitalization/intensive care unit (ICU) admission with influenza A/H3N2, influenza B, or human rhinovirus (HRV); we also explored the impact of age, gender and co-detection of Streptococcus pneumoniae on patient setting. We hypothesized that hospitalized/ICU patients have higher respiratory virus viral loads compared to ambulatory (e.g. walk-in clinics, family practices)/ER patients. STUDY DESIGN We quantified viral load by in-house real-time RT-PCR in 774 nasopharyngeal swabs with influenza A/H3N2, or B or HRV viruses from various patient settings in Ontario, Canada. RESULTS Mean viral load (log10 copies/ml) of influenza A/H3N2 (6.94) was higher than influenza B (4.96) and HRV (5.58) (p<0.0001). Influenza A/H3N2 viral loads were highest in infants and the elderly; however, increased A/H3N2 viral loads were not associated with hospitalization/ICU admission compared to swabs collected in ambulatory/ER settings. Influenza B viral loads were higher in patients in hospital/ICU settings compared to those in ambulatory settings (OR 1.28, 95% CI 1.11-1.47). HRV viral loads did not differ by age (p=0.67) or setting (p=0.54); there was no association between S. pneumoniae colonization and setting for any virus. CONCLUSION When compared to ambulatory/ER patients, viral load was higher in hospitalized/ICU patients with influenza B, but not influenza A or HRV.
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Affiliation(s)
- Andrea Granados
- Public Health Ontario, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | | | - Allison McGeer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Mount Sinai Hospital, Toronto, ON, Canada; Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Jonathan B Gubbay
- Public Health Ontario, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; The Hospital for Sick Children, Toronto, ON, Canada
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19
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Wu C, Wang MH, Lu X, Chong KC, He J, Yau CY, Hui M, Cheng X, Yang L, Zee BCY, Zhang R, He ML. Concurrent epidemics of influenza A/H3N2 and A/H1N1pdm in Southern China: A serial cross-sectional study. J Infect 2015; 72:369-76. [PMID: 26747013 DOI: 10.1016/j.jinf.2015.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/25/2015] [Accepted: 12/26/2015] [Indexed: 02/05/2023]
Abstract
OBJECTIVES This study aimed to elucidate the antibody response pattern of multiple influenza subtypes through a 4-year serological study of a general population in Shenzhen, Southern China. METHODS A serial cross-sectional serological survey was conducted at eight time points between 2009 and 2012. A total number of 5876 subjects were recruited from all age groups. The influenza subtypes tested were A/H1N1, A/H3N2, B/Yamagata, B/Victoria, and A/H1N1pdm. Genetic sequencing and phylogenetic analysis were performed on 127 H3 genes and 28 H1pdm genes. RESULTS We found concurrent epidemics of A/H3N2 and A/H1N1pdm with simultaneous peak times at March 2011. A/H3N2 was the dominant subtype. Ten residue substitutions (S61N, T64I, K78E, K160N, N161S, A214S, T228A, A229V, V239I, N294K, and N328S) were found in the H3 gene that might underlie its epidemic. The elderly group showed an antibody response cycle that was weaker in magnitude and slower in peak time than in younger groups. CONCLUSIONS The study provides a broad transmission picture and epidemiological characteristics of the major flu subtypes. The findings suggest that it may be necessary to include the A/H1N1pdm strain to the current trivalent or quadrivalent vaccine design. The delayed antibody response cycle in the elderly group indicates the need for better protection of elderly people that might be achieved by an earlier vaccination at a higher dose.
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Affiliation(s)
- Chunli Wu
- Major Infectious Disease Control Key Laboratory, The Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Maggie Haitian Wang
- Division of Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China; The CUHK Shenzhen Research Institute, Shenzhen, China
| | - Xing Lu
- Major Infectious Disease Control Key Laboratory, The Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ka Chun Chong
- Division of Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China; The CUHK Shenzhen Research Institute, Shenzhen, China
| | - Jason He
- College of Letter and Science, University of California at Berkeley, CA, USA
| | - Chun-Yip Yau
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mark Hui
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiaowen Cheng
- Major Infectious Disease Control Key Laboratory, The Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Li Yang
- Division of Digestive Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Benny Chung-Ying Zee
- Division of Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China; The CUHK Shenzhen Research Institute, Shenzhen, China
| | - Renli Zhang
- Major Infectious Disease Control Key Laboratory, The Shenzhen Center for Disease Control and Prevention, Shenzhen, China.
| | - Ming-Liang He
- The CUHK Shenzhen Research Institute, Shenzhen, China; Stanley Ho Center for Emerging Infectious Diseases, and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, China; Department of Biomedical Science, The City University of Hong Kong, Hong Kong SAR, China.
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Miller LC, Crawford KK, Lager KM, Kellner SG, Brockmeier SL. Evaluation of two real-time polymerase chain reaction assays for Porcine epidemic diarrhea virus (PEDV) to assess PEDV transmission in growing pigs. J Vet Diagn Invest 2015; 28:20-9. [PMID: 26699519 DOI: 10.1177/1040638715621949] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In April 2013, a Porcine epidemic diarrhea virus (PEDV) epidemic began in the United States. As part of the response, real-time reverse transcription polymerase chain reaction (RT-PCR) assays to detect PEDV were developed by several veterinary diagnostic laboratories. Our study evaluated RT-PCR PEDV assays that detect the N gene (gN) and S gene (gS) for their ability to detect PEDV infection and the transmission potential of pigs experimentally exposed to PEDV. Detection limits and quantification cycle (Cq) values of real-time RT-PCR were assayed for PEDV samples and positive controls for both gN and gS. The limit of detection for the gN assay was 10(-6) (mean Cq: 39.82 ± 0.30) and 10(-5) (mean Cq: 39.39 ± 0.72) for the gS assay with PEDV strain USA/Colorado/2013. Following recommended guidelines, rectal swabs (n = 1,064) were tested; 354 samples were positive by gN assay and 349 samples were positive by gS assay (Cq ≤ 34.99), 710 samples were negative by gN assay and 715 were negative by gS assay (Cq > 34.99) of which 355 and 344 were "undetermined" (i.e., undetected within a threshold of 40 RT-PCR cycles, by gN and gS assays, respectively). The coefficient of variation (intra-assay variation) ranged from 0.00% to 2.65% and interassay variation had an average of 2.75%. PEDV could be detected in rectal swabs from all pigs for ~2 weeks postinfection at which time the prevalence began to decrease until all pigs were RT-PCR negative by 5 weeks postinfection. Our study demonstrated that RT-PCR assays functioned well to detect PEDV and that the gN assay was slightly better.
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Affiliation(s)
- Laura C Miller
- U.S. Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA
| | - Kimberly K Crawford
- U.S. Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA
| | - Kelly M Lager
- U.S. Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA
| | - Steven G Kellner
- U.S. Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA
| | - Susan L Brockmeier
- U.S. Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA
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Sultankulova KT, Chervyakova OV, Kozhabergenov NS, Shorayeva KA, Strochkov VM, Orynbayev MB, Sandybayev NT, Sansyzbay AR, Vasin AV. Comparative evaluation of effectiveness of IAVchip DNA microarray in influenza A diagnosis. ScientificWorldJournal 2014; 2014:620580. [PMID: 25548788 PMCID: PMC4274914 DOI: 10.1155/2014/620580] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/22/2014] [Accepted: 09/28/2014] [Indexed: 01/30/2023] Open
Abstract
The paper describes comparative evaluation of IAVchip DNA microarray, reverse transcription PCR (RT-PCR), and real-time RT-PCR versus virus isolation in chicken embryos and shows their diagnostic effectiveness in detection and subtyping of influenza A virus. The tests were evaluated with use of 185 specimens from humans, animals, and birds. IAVchip DNA microarray demonstrates higher diagnostic effectiveness (99.45%) in early influenza A diagnosis as compared to the real-time PCR (98.38%) and RT-PCR (96.22%), thus showing its clear superiority. Diagnostic sensitivity of IAVchip DNA microarray (100%) exceeds the same of RT-PCR (95.95%) and real-time RT-PCR (97.96%) in the range of estimated confidence intervals. IAVchip DNA microarray and real-time RT-PCR displayed equal diagnostic specificity (98.85%), while diagnostic specificity of RT-PCR was 96.40%. IAVchip DNA microarray has an advantage over the other tests for influenza A diagnosis and virus identification as a more rapid method that allows performing simultaneous detection and subtyping of about tens of specimens within one experiment during 8-10 hours. The developed IAVchip DNA microarray is a general test tool that enables identifying simultaneously 16 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes of influenza A virus and also to screen the influenza A viruses from humans, animals, and birds by M and NP genes.
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Affiliation(s)
- K. T. Sultankulova
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - O. V. Chervyakova
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - N. S. Kozhabergenov
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - K. A. Shorayeva
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - V. M. Strochkov
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - M. B. Orynbayev
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - N. T. Sandybayev
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - A. R. Sansyzbay
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - A. V. Vasin
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popov Street 15/17, Saint Petersburg 197376, Russia
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Nikitin N, Petrova E, Trifonova E, Karpova O. Influenza virus aerosols in the air and their infectiousness. Adv Virol 2014; 2014:859090. [PMID: 25197278 PMCID: PMC4147198 DOI: 10.1155/2014/859090] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/11/2014] [Accepted: 07/25/2014] [Indexed: 12/15/2022] Open
Abstract
Influenza is one of the most contagious and rapidly spreading infectious diseases and an important global cause of hospital admissions and mortality. There are some amounts of the virus in the air constantly. These amounts is generally not enough to cause disease in people, due to infection prevention by healthy immune systems. However, at a higher concentration of the airborne virus, the risk of human infection increases dramatically. Early detection of the threshold virus concentration is essential for prevention of the spread of influenza infection. This review discusses different approaches for measuring the amount of influenza A virus particles in the air and assessing their infectiousness. Here we also discuss the data describing the relationship between the influenza virus subtypes and virus air transmission, and distribution of viral particles in aerosol drops of different sizes.
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Affiliation(s)
- Nikolai Nikitin
- Department of Virology, Lomonosov Moscow State University, 1/12 Leninskie Gory, Moscow 119234, Russia
| | - Ekaterina Petrova
- Department of Virology, Lomonosov Moscow State University, 1/12 Leninskie Gory, Moscow 119234, Russia
| | - Ekaterina Trifonova
- Department of Virology, Lomonosov Moscow State University, 1/12 Leninskie Gory, Moscow 119234, Russia
| | - Olga Karpova
- Department of Virology, Lomonosov Moscow State University, 1/12 Leninskie Gory, Moscow 119234, Russia
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Ratnamohan VM, Taylor J, Zeng F, McPhie K, Blyth CC, Adamson S, Kok J, Dwyer DE. Pandemic clinical case definitions are non-specific: multiple respiratory viruses circulating in the early phases of the 2009 influenza pandemic in New South Wales, Australia. Virol J 2014; 11:113. [PMID: 24942807 PMCID: PMC4076060 DOI: 10.1186/1743-422x-11-113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/10/2014] [Indexed: 11/23/2022] Open
Abstract
Background During the early phases of the 2009 pandemic, subjects with influenza-like illness only had laboratory testing specific for the new A(H1N1)pdm09 virus. Findings Between 25th May and 7th June 2009, during the pandemic CONTAIN phase, A(H1N1)pdm09 virus was detected using nucleic acid tests in only 56 of 1466 (3.8%) samples meeting the clinical case definition required for A(H1N1)pdm09 testing. Two hundred and fifty-five randomly selected A(H1N1)pdm09 virus-negative samples were tested for other respiratory viruses using a real-time multiplex PCR assay. Of the 255 samples tested, 113 (44.3%) had other respiratory viruses detected: rhinoviruses 63.7%, seasonal influenza A 17.6%, respiratory syncytial virus 7.9%, human metapneumovirus 5.3%, parainfluenzaviruses 4.4%, influenza B virus 4.4%, and enteroviruses 0.8%. Viral co-infections were present in 4.3% of samples. Conclusions In the very early stages of a new pandemic, limiting testing to only the novel virus will miss other clinically important co-circulating respiratory pathogens.
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Affiliation(s)
| | | | | | | | | | | | | | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia.
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Chen Y, Liu T, Cai L, Du H, Li M. A one-step RT-PCR array for detection and differentiation of zoonotic influenza viruses H5N1, H9N2, and H1N1. J Clin Lab Anal 2014; 27:450-60. [PMID: 24218127 DOI: 10.1002/jcla.21627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 04/30/2013] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Rapid and comprehensive pathogen identification is crucial in zoonotic influenza diagnosis. METHODS By optimizing the design of primers and probes and reverse-transcriptase polymerase chain reaction (RT-PCR) conditions, we achieved simultaneous detection of multiple influenza and zoonotic influenza viruses, including H1N1, H5N1, and H9N2 strains, in a one-step, quantitative real-time RT-PCR array (rRT-PCR array) of RNA from multiple influenza strains utilizing a single set of conditions for RT-PCR amplification. The target sequences from all targeted zoonotic influenza viruses were cloned into recombinant RNA virus particles, which were used to evaluate sensitivity, specificity, and reproducibility of the zoonotic influenza viruses RT-PCR array. RESULTS The detection limit of the array was shown to be between 10(0) and 10(1) copies per reaction, and the standard curve demonstrated a linear range from 10 to 10(6) copies. Thus, the analytical sensitivity of this zoonotic influenza viruses RT-PCR array is 10-100 times higher than conventional RT-PCR. Specificity of the one-step zoonotic influenza viruses RT-PCR array was verified by comparison of results obtained with retroviral-like particles (RVPs), which contained RNA from isolates of seasonal influenza viruses, zoonotic influenza viruses, and other pathogens known to cause acute respiratory disease. CONCLUSION The high sensitivity, rapidity, reproducibility, and specificity of this zoonotic influenza viruses rRT-PCR array has been verified as being sufficient to detect the presence of multiple zoonotic influenza viruses in a single assay. The zoonotic influenza viruses RT-PCR array might provide rapid identification of emergent zoonotic influenza viruses strains during influenza outbreaks and disease surveillance initiatives.
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Affiliation(s)
- Yao Chen
- School of Biotechnology, Southern Medical University, Guangzhou, People's Republic of China
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25
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Pletz MW, Terkamp C, Schumacher U, Rohde G, Schütte H, Welte T, Bals R. Vitamin D deficiency in community-acquired pneumonia: low levels of 1,25(OH)2 D are associated with disease severity. Respir Res 2014; 15:53. [PMID: 24766747 PMCID: PMC4046524 DOI: 10.1186/1465-9921-15-53] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/22/2014] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES We aimed to explore the association between vitamin D levels and the severity, mortality and microbiological etiology of community-acquired pneumonia. METHODS Vitamin D levels (both, the reservoir form 25-OH and the activated form 1,25-OH2) of 300 randomly selected patients with community-acquired pneumonia due to pre-specified pathogens included in the German competence network (CAPNETZ) study were measured. Prior to statistical analysis, values of 25-OH and 1,25-OH2 were power-transformed to achieve parametric distribution. All further analyses were performed with seasonally and age adjusted values. RESULTS There was only a modest (Spearman Coefficient 0.38) positive correlation between 25-OH and 1,25-OH2. For 1,25-OH2 but not 25-OH, the general linear model revealed a significant inverse correlation between serum concentration and CURB score (p = 0.011). Liver and respiratory co-morbidity were associated with significantly lower 25-OH values and renal co-morbidity with significantly lower 1,25-OH2 values. No significant differences of 1,25-OH2 or 25-OH between different pathogens (influenza virus, Legionella spp., Streptococcus pneumoniae) were detected. CONCLUSION For 1,25-OH2, we found a significant and independent (controlled for age, season and pathogen) negative correlation to pneumonia severity. Therefore, supplementation of non-activated vitamin D to protect from pneumonia may be non-sufficient in patients that have a decreased capacity to hydroxylate 25-OH to 1,25-OH2.
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Affiliation(s)
- Mathias W Pletz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Erlanger Allee 101, 07740 Jena, Germany
- CAPNETZ Foundation, Hannover, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Christoph Terkamp
- Department of Gastroenterology and Hepatology, Hannover Medical School, Hannover, Germany
| | - Ulrike Schumacher
- Center for Clinical Studies, Jena University Hospital, Jena, Germany
| | - Gernot Rohde
- Department of Respiratory Medicine, Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
- CAPNETZ Foundation, Hannover, Germany
| | - Hartwig Schütte
- Department of Respiratory Medicine, Charite, Berlin, Germany
- CAPNETZ Foundation, Hannover, Germany
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- CAPNETZ Foundation, Hannover, Germany
| | - Robert Bals
- Department of Internal Medicine V – Pneumology, Medical Centre of the Saarland University, Homburg, Germany
- CAPNETZ Foundation, Hannover, Germany
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26
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Incorporation of a proteotyping approach using mass spectrometry for surveillance of influenza virus in cell-cultured strains. J Clin Microbiol 2013; 52:725-35. [PMID: 24226917 DOI: 10.1128/jcm.02315-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The reemergence of deadly pandemic influenza virus strains has necessitated the development of improved methods for rapid detection and subtyping of influenza viruses that will enable more strains to be characterized at the molecular level. Representative circulating strains of human influenza viruses from primary clinical specimens were grown in cell culture, purified through polyethylene glycol precipitation, proteolytically digested with an endoproteinase, and analyzed and identified by high-resolution mass spectrometry using unique signature peptides that are characteristic of type A H1N1 and H3N2 and type B influenza viruses. This proteotyping approach enabled circulating strains of type A influenza virus to be typed and subtyped, cocirculating seasonal and pandemic H1N1 viruses to be differentiated, and the lineage of type B viruses to be determined through single-ion detection by high-resolution mass spectrometry. Results were obtained using virus titers comparable to those used in reverse transcription (RT)-PCR assays with clinical specimens grown in cell cultures. The methodology represents a more rapid and direct approach than RT-PCR and can be integrated into existing procedures currently used for the surveillance of emerging pandemic and seasonal influenza viruses.
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27
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Enan KA, Nabeshima T, Kubo T, Buerano CC, El Hussein ARM, Elkhidir IM, Khalil EAG, Morita K. Survey of causative agents for acute respiratory infections among patients in Khartoum-State, Sudan, 2010-2011. Virol J 2013; 10:312. [PMID: 24160894 PMCID: PMC3831848 DOI: 10.1186/1743-422x-10-312] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 10/21/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This study was carried out to determine causative agents of acute respiratory illness of patients in Khartoum State, Sudan. METHODS Four hundred patients experiencing respiratory infections within January-March 2010 and January-March 2011 were admitted at Khartoum Hospital and had their throat swab samples subjected to multiplex real-time RT-PCR to detect influenza viruses (including subtypes) and other viral agents. Isolation, nucleotide sequence and phylogenetic analysis on some influenza viruses based on the HA gene were done. RESULTS Out of 400 patients, 66 were found to have influenza viruses (35, 27, 2, and 2 with types A, B, C, and A and B co-infections, respectively). Influenza viruses were detected in 28, 33 and 5 patients in the age groups <1, 1-10, and 11-30 years old, respectively but none in the 31-50 years old group. Out of 334 patients negative for influenza viruses, 27, 14, and 2 were positive for human respiratory syncytial virus, rhinovirus and adenovirus, respectively. Phylogenetic tree on influenza A (H1N1) pdm09 subtype shows that Sudan strains belong to the same clade and are related to those strains from several countries such as USA, Japan, Italy, United Kingdom, Germany, Russia, Greece, Denmark, Taiwan, Turkey and Kenya. Seasonal A H3 subtypes have close similarity to strains from Singapore, Brazil, Canada, Denmark, USA and Nicaragua. For influenza B, Sudan strains belong to two different clades, and just like influenza A (H1N1) pdm09 and A H3 subtypes, seem to be part of worldwide endemic population (Kenya, USA, Brazil, Russia, Taiwan and Singapore). CONCLUSIONS In Sudan, the existence of respiratory viruses in patients with acute respiratory infection was confirmed and characterized for the first time by using molecular techniques.
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Affiliation(s)
- Khalid A Enan
- Central Laboratory, Ministry of Science and Technology, P.O. Box 7099, Khartoum, Sudan
| | - Takeshi Nabeshima
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Toru Kubo
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Corazon C Buerano
- Department of Molecular Epidemiology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | | | - Isam M Elkhidir
- Department of Microbiology and Parasitology, Faculty of Medicine, University of Khartoum, P.O. Box 8067, Khartoum, Sudan
| | - Eltahir AG Khalil
- Institute of Endemic Diseases, University of Khartoum, P.O. Box 45235, Khartoum, Sudan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
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28
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Wu CL, Lu J, Wang MH, Lv X, Chen Y, Kung HF, Zee B, Cheng XW, He ML. Cross sectional survey of influenza antibodies before and during the 2009 pandemic in Shenzhen, China. PLoS One 2013; 8:e53847. [PMID: 23382854 PMCID: PMC3558489 DOI: 10.1371/journal.pone.0053847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 12/05/2012] [Indexed: 01/08/2023] Open
Abstract
Much information is available for the 2009 H1N1 influenza immunity response, but little is known about the antibody change in seasonal influenza before and during the novel influenza A pandemic. In this study, we conducted a cross-sectional serological survey of 4 types of major seasonal influenza in March and September 2009 on a full range of age groups, to investigate seasonal influenza immunity response before and during the outbreak of the sH1N1 influenza in Shenzhen – the largest migration city in China. We found that the 0–5 age group had an increased antibody level for all types of seasonal influenza during the pandemic compared to the pre-outbreak level, in contrast with almost all other age groups, in which the antibody level decreased. Also, distinct from the antibodies of A/H3N2, B/Yamagata and B/Victoria that decreased significantly during the 2009 H1N1 pandemic, the antibody of A/H1N1 showed no statistical difference from the pre-outbreak level. The results suggest that the antibodies against the 2009 sH1N1 cross-reacted with seasonal H1N1. Moreover, the 0–5 age group was under attack by both seasonal and 2009 H1N1 influenza during the pandemic, hence vaccination merely against a new strain of flu might not be enough to protect the youngest group.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antibodies, Viral/immunology
- Antibodies, Viral/isolation & purification
- Child
- Child, Preschool
- China
- Cross Reactions/immunology
- Cross-Sectional Studies
- Disease Outbreaks
- Female
- Hemagglutination Inhibition Tests
- Humans
- Infant
- Infant, Newborn
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/pathogenicity
- Influenza, Human/immunology
- Influenza, Human/pathology
- Influenza, Human/virology
- Male
- Middle Aged
- Pandemics
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Affiliation(s)
- Chun-Li Wu
- The Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Juan Lu
- Southern Medical University, Guangzhou, China
- Stanley Ho Center for Emerging Infectious Diseases, School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Maggie Haitian Wang
- Division of Biostatistics, School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Xing Lv
- The Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ying Chen
- Stanley Ho Center for Emerging Infectious Diseases, School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Hsiang-fu Kung
- Stanley Ho Center for Emerging Infectious Diseases, School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Benny Zee
- Division of Biostatistics, School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiao-wen Cheng
- The Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ming-Liang He
- Stanley Ho Center for Emerging Infectious Diseases, School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- * E-mail:
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Niang MN, Dosseh A, Ndiaye K, Sagna M, Gregory V, Goudiaby D, Hay A, Diop OM. Sentinel surveillance for influenza in Senegal, 1996-2009. J Infect Dis 2013; 206 Suppl 1:S129-35. [PMID: 23169958 DOI: 10.1093/infdis/jis576] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Data on influenza in tropical and resource-limited countries are scarce. In this study we present results from 14 years of influenza surveillance in Senegal, one of the few tropical countries in Africa from which longitudinal data are available. METHODS From 1996 to 2009, we collected respiratory specimens from outpatients presenting with influenza-like illness at 13 facilities in order to investigate the epidemiology of seasonal influenza and the characteristics of the circulating influenza viruses. Specimens were tested for influenza using viral isolation and/or reverse-transcription polymerase chain reaction (RT-PCR). RESULTS From 1996 to 2009, specimens were obtained from 9176 patients; 1233 (13%) were influenza-positive by virus isolation and/or RT-PCR. Among positive samples, 958 (77%) were influenza A, 268 (22%) influenza B, and 7 (1%) influenza type C; of influenza A viruses, 619 (65%) were A(H3) and 339 (35%) A(H1), of which 13 (1%) were identified as H1N2. The proportion positive was similar for children <15 years, young adults 16-35 years, and adults 36-55 years (15%), but lower for persons >55 years (9%). Although influenza A(H1), A(H3), and B all circulated during most years, influenza A(H3N2) predominated during 9 of the 14 years. Influenza activity consistently peaked during the rainy season (July-September). Phylogenetic analysis showed that viruses circulating in Senegal were similar to contemporary viruses circulating elsewhere in the world. CONCLUSIONS Our data confirm that influenza is prevalent in Senegal, occurs in seasonal epidemics, and contributes to the burden of respiratory diseases in all age groups.
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Cheng X, Tan Y, He M, Lam TTY, Lu X, Viboud C, He J, Zhang S, Lu J, Wu C, Fang S, Wang X, Xie X, Ma H, Nelson MI, Kung HF, Holmes EC, Cheng J. Epidemiological dynamics and phylogeography of influenza virus in southern China. J Infect Dis 2012; 207:106-14. [PMID: 22930808 DOI: 10.1093/infdis/jis526] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Understanding the epidemiological dynamics of influenza virus is central to surveillance and vaccine strain selection. It has been suggested that tropical and subtropical regions represent the global source of influenza epidemics. However, our understanding of the epidemiological dynamics of influenza virus in these regions is limited by a relative lack of long-term data. METHODS We analyzed epidemiological and virological data on influenza recorded over a period of 15 years from the metropolitan city of Shenzhen in subtropical southern China. We used wavelet analysis to determine the periodicity of influenza epidemics and molecular phylogeographic analysis to investigate the role of Shenzhen and southern China in the global evolution of influenza virus. RESULTS We show that southern China is unlikely to represent an epicenter of global influenza activity, because activity in Shenzhen is characterized by significant annual cycles, multiple viral introductions every year, limited persistence across epidemic seasons, and viruses that generally are not positioned on the trunk of the global influenza virus phylogeny. CONCLUSIONS We propose that novel influenza viruses emerge and evolve in multiple geographic localities and that the global evolution of influenza virus is complex and does not simply originate from a southern Chinese epicenter.
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Affiliation(s)
- Xiaowen Cheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
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Optimization of one-step duplex real-time RT-PCR for detection of influenza and respiratory syncytial virus in nasopharyngeal aspirates. J Virol Methods 2012; 186:189-92. [PMID: 22796284 DOI: 10.1016/j.jviromet.2012.07.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/28/2012] [Accepted: 07/04/2012] [Indexed: 11/20/2022]
Abstract
Viruses are major contributors to acute respiratory infection-related morbidity and mortality worldwide. The influenza (IF) viruses and human respiratory syncytial virus (RSV) play a particularly important role in the etiology of acute respiratory infections. This study sought to standardize a one-step duplex real-time RT-PCR technique to optimize diagnosis of IFA/IFB and RSVA/RSVB infection. Viral RNA was extracted with the commercially available QIAamp Mini Kit according to manufacturer instructions. RT-PCR was performed with primers to the matrix protein gene of IFA, the hemagglutinin gene of IFB and the N gene of RSVA and RSVB. The limits of detection were 1 copy/μL for IFA, 10 copies/μL for IFB, 5 copies/μL for RSVA, and 250 copies/μL for RSVB. The specificity of RT-PCR was determined by comparison against a panel of several respiratory pathogens. RT-PCR and indirect immunofluorescence (IIF) were compared in a sample of 250 nasopharyngeal aspirates (NPAs) collected during the year 2010. RT-PCR was more sensitive than IIF and able to detect viral co-infections. In summary, RT-PCR optimized for IFA/IFB and RSVA/RSVB is sensitive and specific for these viral agents and is therefore useful for assessment of the etiology of respiratory infections, whether for clinical or epidemiological purposes.
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Janjua NZ, Skowronski DM, De Serres G, Dickinson J, Crowcroft NS, Taylor M, Winter AL, Hottes TS, Fonseca K, Charest H, Drews SJ, Sabaiduc S, Bastien N, Li Y, Gardy JL, Petric M. Estimates of influenza vaccine effectiveness for 2007-2008 from Canada's sentinel surveillance system: cross-protection against major and minor variants. J Infect Dis 2012; 205:1858-68. [PMID: 22492921 DOI: 10.1093/infdis/jis283] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To estimate influenza vaccine effectiveness (VE) for the 2007-2008 season and assess the sentinel surveillance system in Canada for monitoring virus evolution and impact on VE. METHODS Nasal/nasopharyngeal swabs and epidemiologic details were collected from patients presenting to a sentinel physician within 7 days of influenza-like illness onset. Cases tested positive for influenza A/B virus by real-time polymerase chain reaction; controls tested negative. Hemagglutination inhibition (HI) and gene sequencing explored virus relatedness to vaccine. VE was calculated as 1 minus the odds ratio for influenza in vaccinated versus nonvaccinated participants, with adjustment for confounders. RESULTS Of 1425 participants, 21% were vaccinated. Influenza virus was detected in 689 (48%), of which isolates from 663 were typed/subtyped: 189 (29%) were A/H1, 210 (32%) were A/H3, and 264 (40%) were B. Of A/H1N1 isolates, 6% showed minor HI antigenic mismatch to vaccine, with greater variation based on genetic identity. All A/H3N2 isolates showed moderate antigenic mismatch, and 98% of influenza B virus isolates showed major lineage-level mismatch to vaccine. Adjusted VE for A/H1N1, A/H3N2, and B components was 69% (95% confidence interval [CI], 44%-83%), 57% (95% CI, 32%-73%), and 55% (95% CI, 32%-70%), respectively, with an overall VE of 60% (95% CI, 45%-71%). CONCLUSIONS Detailed antigenic and genotypic analysis of influenza viruses was consistent with epidemiologic estimates of VE showing cross-protection. A routine sentinel surveillance system that combines detailed virus and VE monitoring annually, as modeled in Canada, may guide improved vaccine selection and protection.
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Nguyen VT, Nimse SB, Song KS, Kim J, Ta VT, Sung HW, Kim T. HPAI 9G DNAChip: discrimination of highly pathogenic influenza virus genes. Chem Commun (Camb) 2012; 48:4582-4. [PMID: 22456544 DOI: 10.1039/c2cc30709j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The HPAI 9G DNAChip discriminates the single nucleotide polymorphism of H5N1, H5N1 (K), and H5N3 in a 60:1 ratio. It allows the simultaneous detection of highly pathogenic avian influenza viruses with a signal to background ratio of 200 and 100% target-specific hybridization in 30 min at 25 °C.
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Affiliation(s)
- Van-Thuan Nguyen
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 200-702, Korea
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A comparison of self-report and health care provider data to assess surveillance definitions of influenza-like illness in outpatients. Canadian Journal of Public Health 2012. [PMID: 22338332 DOI: 10.1007/bf03404072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
OBJECTIVE Several surveillance definitions of influenza-like illness (ILI) have been proposed, based on the presence of symptoms. Symptom data can be obtained from patients, medical records, or both. Past research has found that agreements between health record data and self-report are variable depending on the specific symptom. Therefore, we aimed to explore the implications of using data on influenza symptoms extracted from medical records, similar data collected prospectively from outpatients, and the combined data from both sources as predictors of laboratory-confirmed influenza. METHODS Using data from the Hutterite Influenza Prevention Study, we calculated: 1) the sensitivity, specificity and predictive values of individual symptoms within surveillance definitions; 2) how frequently surveillance definitions correlated to laboratory-confirmed influenza; and 3) the predictive value of surveillance definitions. RESULTS Of the 176 participants with reports from participants and medical records, 142 (81%) were tested for influenza and 37 (26%) were PCR positive for influenza. Fever (alone) and fever combined with cough and/or sore throat were highly correlated with being PCR positive for influenza for all data sources. ILI surveillance definitions, based on symptom data from medical records only or from both medical records and self-report, were better predictors of laboratory-confirmed influenza with higher odds ratios and positive predictive values. DISCUSSION The choice of data source to determine ILI will depend on the patient population, outcome of interest, availability of data source, and use for clinical decision making, research, or surveillance.
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Li YC, Peng SZ, Chen HM, Zhang FX, Xu PP, Xie JH, He JJ, Chen JN, Lai XP, Su ZR. Oral administration of patchouli alcohol isolated from Pogostemonis Herba augments protection against influenza viral infection in mice. Int Immunopharmacol 2012; 12:294-301. [PMID: 22193241 DOI: 10.1016/j.intimp.2011.12.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 12/03/2011] [Accepted: 12/07/2011] [Indexed: 12/17/2022]
Abstract
Seasonal influenza A infection results in considerable morbidity and mortality. The limited efficacy of available therapeutic strategies stresses the need for development and study of new molecules against influenza virus (IFV). Patchouli alcohol (PA), the major chemical constituent of Pogostemonis Herba, was previously found to strongly inhibit influenza H1N1 replication in vitro. In the present study, the in vivo anti-IFV effect of PA was investigated. In a mouse model infected with lethal levels of FM1, oral administration of PA (20 mg/kg to 80 mg/kg) for 7 d post IFV infection significantly increased the survival rate and survival time. For IFV infection at nonlethal levels, the quantity of IFV in the lungs 5 d after infection was significantly reduced after PA (20 mg/kg to 80 mg/kg) administration. Anti-IFV IgA, IgM, and IgG titers in serum on day 6 were significantly higher in the PA-treated group than the IFV-control group. Anti-IFV immune response augmentation was further confirmed by the elevated production of CD3+, CD4+, and CD8+ T cell levels in blood. Furthermore, the levels of inflammatory cytokines, including TNF-alpha, IL-10 and IFN-gamma in serum of mice, were regulated. Lung inflammation was reduced significantly after PA administration, and the effect may be mediated, at least in part, by regulating the lung levels of inflammatory cytokines. Thus, oral administration of PA appears to be able to augment protection against IFV infection in mice via enhancement of host immune responses, and attenuation of systemic and pulmonary inflammatory responses.
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Affiliation(s)
- Yu-Cui Li
- College of Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, PR China
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Applicability of a sensitive duplex real-time PCR assay for identifying B/Yamagata and B/Victoria lineages of influenza virus from clinical specimens. Appl Microbiol Biotechnol 2011; 93:797-805. [PMID: 22113559 DOI: 10.1007/s00253-011-3710-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/24/2011] [Accepted: 11/05/2011] [Indexed: 10/15/2022]
Abstract
Type B influenza virus is one of the major epidemic strains and responsible for considerable mortality and morbidity. Rapidly and accurately identifying different influenza B virus lineages, i.e., B/Yamagata (B/Y) and B/Victoria (B/V), is desirable during the flu season. However, the available rapid techniques lack sensitivity, and the usual methods for identifying influenza viruses require expansion of virus in tissue culture or embryonated hen's eggs. Thus, we developed several sets of primer pairs that were able to detect and distinguish B/Y and B/V in a single real-time PCR assay. Used in conjunction with two sets of specific primers that exhibited purine at 3' end of at least one primer targeting on HA gene of B/Y and B/V lineages allows us to accurately identify approximately 10(2) copies per microliter for B/Y and B/V with intra- and inter-assay coefficient of variation (CV) <4%. When it was used to test 17,765 throat swab specimens obtained in the 2006-2010 influenza surveillance season, this method was comparable to hemagglutination inhibition assay in detection, typing and subtyping of influenza viruses with 100% true-negative (specificity) and 100% true-positive (sensitivity). Taken together, this method provides sensitive and robust tool for routine diagnosis and on-time epidemiological examination for WHO decisions on vaccine composition.
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Eggers M, Roth B, Schweiger B, Schmid M, Gregersen JP, Enders M. Comparison of the novel ResPlex III assay and existing techniques for the detection and subtyping of influenza virus during the influenza season 2006-2007. Eur J Clin Microbiol Infect Dis 2011; 31:1257-65. [PMID: 22012658 PMCID: PMC3346937 DOI: 10.1007/s10096-011-1437-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 09/22/2011] [Indexed: 11/15/2022]
Abstract
Influenza virus is a major cause of disease worldwide. The accurate detection and further subtyping of influenza A viruses are important for epidemiologic surveillance, and subsequent comprehensive characterization of circulating influenza viruses is essential for the selection of an optimal vaccine composition. ResPlex III is a new multiplex reverse transcriptase polymerase chain reaction (RT-PCR)-based method for detecting, typing, and subtyping influenza virus in clinical specimens. The ResPlex III assay was compared with other methods with respect to sensitivity and accuracy, using 450 clinical specimens obtained from subjects throughout Germany during the 2006–2007 influenza season. Samples were analyzed for the presence of influenza virus in Madin-Darby canine kidney (MDCK) cells by rapid cell culture using peroxidase staining and conventional cell culture confirmed by hemagglutination inhibition assay, a rapid diagnostic assay (Directigen Flu A+B test; BD Diagnostic Systems, Heidelberg, Germany), in-house real-time RT-PCR (RRT-PCR), and ResPlex III (Qiagen, Hilden, Germany). ResPlex III had the highest sensitivity for detecting influenza virus in clinical specimens, followed by in-house RRT-PCR (96% compared with ResPlex III). Conventional cell culture in MDCK cells, rapid culture, and quick test assays were substantially less sensitive (55%, 72%, and 39%, respectively). Virus subtyping results were identical using ResPlex III and the standard virological subtyping method, hemagglutination inhibition. ResPlex III is a quick, accurate, and sensitive assay for detecting and typing influenza A and B viruses and subtyping influenza A viruses in clinical specimens, and might be considered for a supplemental role in worldwide seasonal and pandemic influenza surveillance.
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Affiliation(s)
- M Eggers
- Laboratory Prof. G. Enders and Partner & Institute of Virology, Infectious Diseases and Epidemiology e.V., Rosenbergstrasse 85, 70193, Stuttgart, Germany.
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Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. PLoS One 2011; 6:e24471. [PMID: 21935413 PMCID: PMC3173375 DOI: 10.1371/journal.pone.0024471] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/11/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The aim of this study was to analyse the genetic patterns of Hemagglutinin (HA) genes of influenza A strains circulating on Corsica Island during the 2006-2009 epidemic seasons and the 2009-2010 pandemic season. METHODS Nasopharyngeal samples from 371 patients with influenza-like illness (ILI) were collected by General Practitioners (GPs) of the Sentinelles Network through a randomised selection routine. RESULTS Phylogenetic analysis of HA revealed that A/H3N2 strains circulating on Corsica were closely related to the WHO recommended vaccine strains in each analyzed season (2006-2007 to 2008-2009). Seasonal Corsican influenza A/H1N1 isolated during the 2007-2008 season had drifted towards the A/Brisbane/59/2007 lineage, the A/H1N1 vaccine strain for the 2008-2009 season. The A/H1N1 2009 (A/H1N1pdm) strains isolated on Corsica Island were characterized by the S220T mutation specific to clade 7 isolates. It should be noted that Corsican isolates formed a separate sub-clade of clade 7 as a consequence of the presence of the fixed substitution D222E. The percentages of the perfect match vaccine efficacy, estimated by using the p(epitope) model, against influenza viruses circulating on Corsica Island varied substantially across the four seasons analyzed, and tend to be highest for A/H1N1 compared with A/H3N2 vaccines, suggesting that cross-immunity seems to be stronger for the H1 HA gene. CONCLUSION The molecular analysis of the HA gene of influenza viruses that circulated on Corsica Island between 2006-2010 showed for each season the presence of a dominant lineage characterized by at least one fixed mutation. The A/H3N2 and A/H1N1pdm isolates were characterized by multiples fixation at antigenic sites. The fixation of specific mutations at each outbreak could be explained by the combination of a neutral phenomenon and a founder effect, favoring the presence of a dominant lineage in a closed environment such as Corsica Island.
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Yazawa K, Kurokawa M, Obuchi M, Li Y, Yamada R, Sadanari H, Matsubara K, Watanabe K, Koketsu M, Tuchida Y, Murayama T. Anti-influenza virus activity of tricin, 4',5,7-trihydroxy-3',5'-dimethoxyflavone. Antivir Chem Chemother 2011; 22:1-11. [PMID: 21860068 DOI: 10.3851/imp1782] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND We examined the anti-influenza virus activity of tricin, 4',5,7-trihydroxy-3',5'-dimethoxyflavone, against five viruses: A/Solomon islands/3/2006 (H1N1), A/Hiroshima/52/2005 (H3N2), A/California/07/2009 (H1N1pdm), A/Narita/1/2009 (H1N1pdm) and B/Malaysia/2506/2004 strains in vitro and against A/PR/8/34 virus in vivo. METHODS The effect of tricin was studied by an infectious virus yield reduction assay. The anti-influenza virus mechanism of the tricin was examined by western blot analysis, real-time reverse transcriptase PCR analysis, haemagglutination inhibition (HI) assay and neuraminidase (NA) inhibition assay. The anti-influenza virus efficacy of tricin was further examined in a murine influenza virus infection model. RESULTS Tricin of 3.3 to 30 μM significantly reduced seasonal A (H1N1), (H3N2) viruses, novel A (H1N1pdm) virus, as well as B virus in a dose-dependent manner. The 50% effective concentrations of tricin were 3.4 μM for seasonal A (H3N2) virus, 4.9 μM for B virus and 8.2 μM for A/Narita (H1N1pdm) virus. Tricin decreased the expression of haemagglutinin (HA) protein and matrix (M) protein, and messenger RNA expression of HA and M of influenza virus in the infected cells. Tricin exhibited little or no effects on influenza virus HI and NA activities. In the mouse infection model, tricin was significantly effective in reducing body weight loss, and also effective in prolonging survival times of infected mice. CONCLUSIONS Tricin was indicated to possess anti-influenza virus activity and to ameliorate body weight loss and survival rate of influenza-A-virus-infected mice. Tricin is a novel compound with potential anti-influenza virus activity in vitro and in vivo.
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Affiliation(s)
- Kurumi Yazawa
- Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Hokuriku University, Kanazawa, Japan
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Schnepf N, Resche-Rigon M, Chaillon A, Scemla A, Gras G, Semoun O, Taboulet P, Molina JM, Simon F, Goudeau A, LeGoff J. High burden of non-influenza viruses in influenza-like illness in the early weeks of H1N1v epidemic in France. PLoS One 2011; 6:e23514. [PMID: 21858150 PMCID: PMC3157400 DOI: 10.1371/journal.pone.0023514] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 07/19/2011] [Indexed: 11/18/2022] Open
Abstract
Background Influenza-like illness (ILI) may be caused by a variety of pathogens. Clinical observations are of little help to recognise myxovirus infection and implement appropriate prevention measures. The limited use of molecular tools underestimates the role of other common pathogens. Objectives During the early weeks of the 2009–2010 flu pandemic, a clinical and virological survey was conducted in adult and paediatric patients with ILI referred to two French University hospitals in Paris and Tours. Aims were to investigate the different pathogens involved in ILI and describe the associated symptoms. Methods H1N1v pandemic influenza diagnosis was performed with real time RT-PCR assay. Other viral aetiologies were investigated by the molecular multiplex assay RespiFinder19®. Clinical data were collected prospectively by physicians using a standard questionnaire. Results From week 35 to 44, endonasal swabs were collected in 413 patients. Overall, 68 samples (16.5%) were positive for H1N1v. In 13 of them, other respiratory pathogens were also detected. Among H1N1v negative samples, 213 (61.9%) were positive for various respiratory agents, 190 in single infections and 23 in mixed infections. The most prevalent viruses in H1N1v negative single infections were rhinovirus (62.6%), followed by parainfluenza viruses (24.2%) and adenovirus (5.3%). 70.6% of H1N1v cases were identified in patients under 40 years and none after 65 years. There was no difference between clinical symptoms observed in patients infected with H1N1v or with other pathogens. Conclusion Our results highlight the high frequency of non-influenza viruses involved in ILI during the pre-epidemic period of a flu alert and the lack of specific clinical signs associated with influenza infections. Rapid diagnostic screening of a large panel of respiratory pathogens may be critical to define and survey the epidemic situation and to provide critical information for patient management.
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Affiliation(s)
- Nathalie Schnepf
- Université Paris Diderot, Sorbonne Paris Cité, Microbiology Department, Saint-Louis Hospital, APHP, Paris, France
- François Rabelais University, Microbiology Department, Bretonneau Hospital, CHRU Tours, France
| | - Matthieu Resche-Rigon
- Université Paris Diderot, Sorbonne Paris Cité, Biostatistics Department, Saint-Louis Hospital, APHP, Paris, France
| | - Antoine Chaillon
- François Rabelais University, Microbiology Department, Bretonneau Hospital, CHRU Tours, France
| | - Anne Scemla
- Université Paris Diderot, Sorbonne Paris Cité, Infectious Diseases Department, Saint-Louis Hospital, APHP, Paris, France
| | - Guillaume Gras
- Internal Medicine and Infectious Diseases Departement, Bretonneau Hospital, CHRU Tours, France
| | - Oren Semoun
- Université Paris Diderot, Sorbonne Paris Cité, Biostatistics Department, Saint-Louis Hospital, APHP, Paris, France
| | - Pierre Taboulet
- Emergency Department, Saint-Louis Hospital, APHP, Paris, France
| | - Jean-Michel Molina
- Université Paris Diderot, Sorbonne Paris Cité, Infectious Diseases Department, Saint-Louis Hospital, APHP, Paris, France
| | - François Simon
- Université Paris Diderot, Sorbonne Paris Cité, Microbiology Department, Saint-Louis Hospital, APHP, Paris, France
- Inserm U941, Institut Universitaire d'Hématologie, Paris, France
| | - Alain Goudeau
- François Rabelais University, Microbiology Department, Bretonneau Hospital, CHRU Tours, France
| | - Jérôme LeGoff
- Université Paris Diderot, Sorbonne Paris Cité, Microbiology Department, Saint-Louis Hospital, APHP, Paris, France
- Inserm U941, Institut Universitaire d'Hématologie, Paris, France
- * E-mail:
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Longjam N, Deb R, Sarmah AK, Tayo T, Awachat VB, Saxena VK. A Brief Review on Diagnosis of Foot-and-Mouth Disease of Livestock: Conventional to Molecular Tools. Vet Med Int 2011; 2011:905768. [PMID: 21776357 PMCID: PMC3135314 DOI: 10.4061/2011/905768] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/25/2011] [Accepted: 04/20/2011] [Indexed: 12/31/2022] Open
Abstract
Foot-and-mouth disease (FMD) is one of the highly contagious diseases of domestic animals. Effective control of this disease needs sensitive, specific, and quick diagnostic tools at each tier of control strategy. In this paper we have outlined various diagnostic approaches from old to new generation in a nutshell. Presently FMD diagnosis is being carried out using techniques such as Virus Isolation (VI), Sandwich-ELISA (S-ELISA), Liquid-Phase Blocking ELISA (LPBE), Multiplex-PCR (m-PCR), and indirect ELISA (DIVA), and real time-PCR can be used for detection of antibody against nonstructural proteins. Nucleotide sequencing for serotyping, microarray as well as recombinant antigen-based detection, biosensor, phage display, and nucleic-acid-based diagnostic are on the way for rapid and specific detection of FMDV. Various pen side tests, namely, lateral flow, RT-LAMP, Immunostrip tests, and so forth. are also developed for detection of the virus in field condition.
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Affiliation(s)
- Neeta Longjam
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati 781022, India
| | - Rajib Deb
- Division of Animal Biotechnology, Indian Veterinary Research Institute (IVRI), Izatnagar 243122, India
| | - A. K. Sarmah
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati 781022, India
| | - Tilling Tayo
- Division of Animal Nutrition, Indian Veterinary Research Institute (IVRI), Izatnagar 243122, India
| | - V. B. Awachat
- Division of Poultry Science, Central Avian Research Institute (CARI), Izatnagar 243122, India
| | - V. K. Saxena
- Division of Veterinary Biochemistry and Physiology, Central Sheep and Wool Research Institute (CSWRI), Avikanagar, India
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Molecular Detection of Respiratory Viruses. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Influenza viruses continue to be a major cause of respiratory tract infection, resulting in substantial morbidity and mortality throughout the world. Accurate and rapid differential diagnosis of influenza virus infections, particularly associated with zoonotic infections, is important for public health actions, patient management, and treatment. Real-time PCR is widely considered the gold standard for molecular detection of influenza viruses owing to its high assay specificity, extreme detection sensitivity, and wide linear dynamic range. This protocol describes the use of a real-time RT-PCR assay for identification of influenza A and B viruses, detection of H5 subtype viruses, and an internal control, in a multiplexed, single-tube format. The inclusion of an internal bacteriophage control allows the efficiency of the extraction and amplification process to be monitored, so that false-negative results may be avoided. The primers and probe sets in this multiplex assay have been validated with a panel of influenza A viruses of different subtypes (including swine influenza viruses), and influenza B viruses, and specificity further confirmed with non-related respiratory viruses.
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Roa PL, Catalán P, Giannella M, de Viedma DG, Sandonis V, Bouza E. Comparison of real-time RT-PCR, shell vial culture, and conventional cell culture for the detection of the pandemic influenza A (H1N1) in hospitalized patients. Diagn Microbiol Infect Dis 2011; 69:428-31. [DOI: 10.1016/j.diagmicrobio.2010.11.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 11/10/2010] [Accepted: 11/12/2010] [Indexed: 10/18/2022]
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Hagan KA, Reedy CR, Uchimoto ML, Basu D, Engel DA, Landers JP. An integrated, valveless system for microfluidic purification and reverse transcription-PCR amplification of RNA for detection of infectious agents. LAB ON A CHIP 2011; 11:957-61. [PMID: 21152489 DOI: 10.1039/c0lc00136h] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We describe the first miniaturized device capable of the front-end sample preparation essential for detecting RNA-based infectious agents. The microfluidic device integrates sample purification and reverse transcription PCR (RT-PCR) amplification for the identification and detection of influenza A. The device incorporates a chitosan-based RNA binding phase for the completely aqueous isolation of nucleic acids, avoiding the PCR inhibitory effects of guanidine and isopropanol used in silica-based extraction methods. The purified nucleic acids and the reagents needed for single-step RT-PCR amplification are fluidically mobilized simultaneously to a PCR chamber. Utilizing infrared (IR)-mediated heating allowed for a > 5-fold decrease in RT-PCR analysis time compared to a standard thermal cycling protocol used in a conventional thermal cycler. Influenza A virus [A/PR/8/34 (H1N1)] was used as a simulant in this study for virus-based infectious and biowarfare agents with RNA genomes, and was successfully detected in a mock nasal swab sample at clinically relevant concentrations. Following on-chip purification, a fragment specific to the influenza A nucleoprotein gene was first amplified via RT-PCR amplification using IR-mediated heating to achieve more rapid heating and cooling rates. This was initially accomplished on a two-chip system to optimize the SPE and RT-PCR, and then translated to an integrated SPE-RT-PCR device.
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Affiliation(s)
- Kristin A Hagan
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA 22904, USA
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Houspie L, De Coster S, Keyaerts E, Narongsack P, De Roy R, Talboom I, Sisk M, Maes P, Verbeeck J, Van Ranst M. Exhaled breath condensate sampling is not a new method for detection of respiratory viruses. Virol J 2011; 8:98. [PMID: 21375748 PMCID: PMC3059288 DOI: 10.1186/1743-422x-8-98] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 03/04/2011] [Indexed: 11/24/2022] Open
Abstract
Background Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. Methods In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. Results Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. Conclusion Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.
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Affiliation(s)
- Lieselot Houspie
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Catholic University of Leuven, Minderbroedersstraat 10, B3000 Leuven, Belgium.
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Thaitrong N, Liu P, Briese T, Lipkin WI, Chiesl TN, Higa Y, Mathies RA. Integrated capillary electrophoresis microsystem for multiplex analysis of human respiratory viruses. Anal Chem 2010; 82:10102-9. [PMID: 21114282 PMCID: PMC3076062 DOI: 10.1021/ac1020744] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We developed a two-layer, four-channel polymerase chain reaction (PCR)-capillary electrophoresis microdevice that integrates nucleic acid amplification, sample cleanup and concentration, capillary electrophoretic separation, and detection for multiplex analysis of four human respiratory viral pathogens, influenza A, influenza B, coronavirus OC43, and human metapneumovirus. Biotinylated and fluorescently labeled double-stranded (ds) deoxyribonucleic acid (DNA) amplification products are generated in a 100 nL PCR reactor incorporating an integrated heater and a temperature sensor. After amplification, the products are captured and concentrated in a cross-linked acrylamide gel capture matrix copolymerized with acrydite-functionalized streptavidin-capture agents. Thermal dehybridization releases the fluorescently labeled DNA strand for capillary electrophoresis injection, separation, and detection. Using plasmid standards containing the viral genes of interest, each target can be detected starting from as few as 10 copies/reactor. When a two-step reverse transcription PCR amplification is employed, the device can detect ribonucleic acid (RNA) analogues of all four viral targets with detection limits in the range of 25-100 copies/reactor. The utility of the microdevice for analyzing samples from nasopharyngeal swabs is demonstrated. When size-based separation is combined with four-color detection, this platform provides excellent product discrimination, making it readily extendable to higher-order multiplex assays. This portable microsystem is also suitable for performing automated assays in point-of-care diagnostic applications.
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Affiliation(s)
- Numrin Thaitrong
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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Deyde VM, Sampath R, Garten RJ, Blair PJ, Myers CA, Massire C, Matthews H, Svoboda P, Reed MS, Pohl J, Klimov AI, Gubareva LV. Genomic signature-based identification of influenza A viruses using RT-PCR/electro-spray ionization mass spectrometry (ESI-MS) technology. PLoS One 2010; 5:e13293. [PMID: 20967258 PMCID: PMC2953491 DOI: 10.1371/journal.pone.0013293] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 09/16/2010] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The emergence and rapid spread of the 2009 H1N1 pandemic influenza A virus (H1N1pdm) in humans highlights the importance of enhancing the capability of existing influenza surveillance systems with tools for rapid identification of emerging and re-emerging viruses. One of the new approaches is the RT-PCR electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology, which is based on analysis of base composition (BC) of RT-PCR amplicons from influenza "core" genes. Combination of the BC signatures represents a "genomic print" of an influenza A virus. METHODOLOGY/PRINCIPAL FINDINGS Here, 757 samples collected between 2006 and 2009 were tested, including 302 seasonal H1N1, 171 H3N2, 7 swine triple reassortants, and 277 H1N1pdm viruses. Of the 277 H1N1pdm samples, 209 were clinical specimens (throat, nasal and nasopharyngeal swabs, nasal washes, blood and sputum). BC signatures for the clinical specimen from one of the first cases of the 2009 pandemic, A/California/04/2009, confirmed it as an unusual, previously unrecognized influenza A virus, with "core" genes related to viruses of avian, human and swine origins. Subsequent analysis of additional 276 H1N1pdm samples revealed that they shared the genomic print of A/California/04/2009, which differed from those of North American swine triple reassortant viruses, seasonal H1N1 and H3N2 and other viruses tested. Moreover, this assay allowed distinction between "core" genes of co-circulating groups of seasonal H1N1, such as clades 2B, 2C, and their reassortants with dual antiviral resistance to adamantanes and oseltamivir. CONCLUSIONS/SIGNIFICANCE The RT-PCR/ESI-MS assay is a broad range influenza identification tool that can be used directly on clinical specimens for rapid and accurate detection of influenza virus genes. The assay differentiates the H1N1pdm from seasonal and other nonhuman hosts viruses. Although not a diagnostic tool, this assay demonstrates its usefulness and robustness in influenza virus surveillance and detection of novel and unusual viruses with previously unseen genomic prints.
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Affiliation(s)
- Varough M. Deyde
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rangarajan Sampath
- Genomics & Computational Biology, Ibis Biosciences, Carlsbad, California, United States of America
| | - Rebecca J. Garten
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Patrick J. Blair
- Naval Respiratory Disease Laboratory, Naval Health Research Center, San Diego, California, United States of America
| | - Christopher A. Myers
- Naval Respiratory Disease Laboratory, Naval Health Research Center, San Diego, California, United States of America
| | - Christian Massire
- Genomics & Computational Biology, Ibis Biosciences, Carlsbad, California, United States of America
| | - Heather Matthews
- Genomics & Computational Biology, Ibis Biosciences, Carlsbad, California, United States of America
| | - Pavel Svoboda
- Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Matthew S. Reed
- Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jan Pohl
- Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alexander I. Klimov
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Larisa V. Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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