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Gadsby NJ, Musher DM. The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures. Clin Microbiol Rev 2022; 35:e0001522. [PMID: 36165783 PMCID: PMC9769922 DOI: 10.1128/cmr.00015-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
All modern advances notwithstanding, pneumonia remains a common infection with substantial morbidity and mortality. Understanding of the etiology of pneumonia continues to evolve as new techniques enable identification of already known organisms and as new organisms emerge. We now review the etiology of pneumonia (at present often called "community-acquired pneumonia") beginning with classic bacteriologic techniques, which identified Streptococcus pneumoniae as the overwhelmingly common cause, to more modern bacteriologic studies, which emphasize Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Enterobacteriaceae, Pseudomonas, and normal respiratory flora. Urine antigen detection is useful in identifying Legionella and pneumococcus. The low yield of bacteria in recent studies is due to the failure to obtain valid sputum samples before antibiotics are administered. The use of high-quality sputum specimens enables identification of recognized ("typical") bacterial pathogens as well as a role for commensal bacteria ("normal respiratory flora"). Nucleic acid amplification technology for viruses has revolutionized diagnosis, showing the importance of viral pneumonia leading to hospitalization with or without coinfecting bacterial organisms. Quantitative PCR study of sputum is in its early stages of application, but regular detection of high counts of bacterial DNA from organisms that are not seen on Gram stain or grown in quantitative culture presents a therapeutic dilemma. This finding may reflect the host microbiome of the respiratory tract, in which case treatment may not need to be given for them. Finally, host transcriptional signatures might enable clinicians to distinguish between viral and bacterial pneumonia, an important practical consideration.
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Affiliation(s)
- Naomi J. Gadsby
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Daniel M. Musher
- Michael E. DeBakey Veterans Administration Medical Center, Houston, Texas, USA
- Baylor College of Medicine, Houston, Texas, USA
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2
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Chattopadhyay K, Mandal M, Maiti DK. Smart Metal-Organic Frameworks for Biotechnological Applications: A Mini-Review. ACS APPLIED BIO MATERIALS 2021; 4:8159-8171. [PMID: 35005918 DOI: 10.1021/acsabm.1c00982] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this pandemic situation it is evident that viruses and bacteria, more specifically, multiple drug resistant (MDR) bacteria, endanger human civilization severely. It is high time to design smart weapons to combat these pathogens for the prevention and cure of allied ailments. Metal-organic frameworks (MOFs) are porous materials designed from metal ions or inorganic clusters and multidentate organic ligands. Due to some unique features like high porosity, tunable pore shape and size, numerous possible metal-ligand combinations, etc., MOFs are ideal candidates to design "smart biotechnological tools". MOFs construct promising fluorescence based biosensing platforms for detection of viruses. MOFs also exhibit excellent antibacterial activity due to their ability for sustained release of active biocidal agents. There are several reviews that summarize the antibacterial applications of MOFs, but the biosensing platforms based on MOFs for detection of viruses have scarcely been summarized. This review carefully covers both the aspects including virus detection (nucleic acid recognition and immunological detection) with underlying mechanisms as well as antibacterial application of MOFs and doped MOFs or composites. This review will deliver valuable information and references for designing new, smarter antimicrobial agents based on MOFs.
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Affiliation(s)
- Krishna Chattopadhyay
- Department of Chemistry, University of Calcutta, Kolkata 700009, India.,Post Graduate Department of Chemistry, Lady Brabourne College, Kolkata 700017, India
| | - Manas Mandal
- Department of Chemistry, Sree Chaitanya College, Habra, WB 743268, India.,Department of Chemistry, Jadavpur University, Kolkata, WB 700032, India
| | - Dilip Kumar Maiti
- Department of Chemistry, University of Calcutta, Kolkata 700009, India
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Dronina J, Samukaite-Bubniene U, Ramanavicius A. Advances and insights in the diagnosis of viral infections. J Nanobiotechnology 2021; 19:348. [PMID: 34717656 PMCID: PMC8556785 DOI: 10.1186/s12951-021-01081-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.
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Affiliation(s)
- Julija Dronina
- Laboratory of Nanotechnology, Department of Functional Materials and Electronics, Center for Physical Sciences and Technology, Sauletekio av. 3, Vilnius, Lithuania
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Urte Samukaite-Bubniene
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Arunas Ramanavicius
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania.
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4
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Ahn SJ, Baek YH, Lloren KKS, Choi WS, Jeong JH, Antigua KJC, Kwon HI, Park SJ, Kim EH, Kim YI, Si YJ, Hong SB, Shin KS, Chun S, Choi YK, Song MS. Rapid and simple colorimetric detection of multiple influenza viruses infecting humans using a reverse transcriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic platform. BMC Infect Dis 2019; 19:676. [PMID: 31370782 PMCID: PMC6669974 DOI: 10.1186/s12879-019-4277-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 07/11/2019] [Indexed: 01/15/2023] Open
Abstract
Background In addition to seasonal influenza viruses recently circulating in humans, avian influenza viruses (AIVs) of H5N1, H5N6 and H7N9 subtypes have also emerged and demonstrated human infection abilities with high mortality rates. Although influenza viral infections are usually diagnosed using viral isolation and serological/molecular analyses, the cost, accessibility, and availability of these methods may limit their utility in various settings. The objective of this study was to develop and optimized a multiplex detection system for most influenza viruses currently infecting humans. Methods We developed and optimized a multiplex detection system for most influenza viruses currently infecting humans including two type B (both Victoria lineages and Yamagata lineages), H1N1, H3N2, H5N1, H5N6, and H7N9 using Reverse Transcriptional Loop-mediated Isothermal Amplification (RT-LAMP) technology coupled with a one-pot colorimetric visualization system to facilitate direct determination of results without additional steps. We also evaluated this multiplex RT-LAMP for clinical use using a total of 135 clinical and spiked samples (91 influenza viruses and 44 other human infectious viruses). Results We achieved rapid detection of seasonal influenza viruses (H1N1, H3N2, and Type B) and avian influenza viruses (H5N1, H5N6, H5N8 and H7N9) within an hour. The assay could detect influenza viruses with high sensitivity (i.e., from 100 to 0.1 viral genome copies), comparable to conventional RT-PCR-based approaches which would typically take several hours and require expensive equipment. This assay was capable of specifically detecting each influenza virus (Type B, H1N1, H3N2, H5N1, H5N6, H5N8 and H7N9) without cross-reactivity with other subtypes of AIVs or other human infectious viruses. Furthermore, 91 clinical and spiked samples confirmed by qRT-PCR were also detected by this multiplex RT-LAMP with 98.9% agreement. It was more sensitive than one-step RT-PCR approach (92.3%). Conclusions Results of this study suggest that our multiplex RT-LAMP assay may provide a rapid, sensitive, cost-effective, and reliable diagnostic method for identifying recent influenza viruses infecting humans, especially in locations without access to large platforms or sophisticated equipment. Electronic supplementary material The online version of this article (10.1186/s12879-019-4277-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Su Jeong Ahn
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Yun Hee Baek
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Khristine Kaith S Lloren
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Won-Suk Choi
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Ju Hwan Jeong
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Khristine Joy C Antigua
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Hyeok-Il Kwon
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Su-Jin Park
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Eun-Ha Kim
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Young-Il Kim
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Young-Jae Si
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea
| | - Seung Bok Hong
- Department of Clinical Laboratory Science, Chungbuk Health and Science University, Cheongju, Republic of Korea
| | - Kyeong Seob Shin
- Departments of Laboratory Medicine, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
| | - Sungkun Chun
- Department of Physiology, Chonbuk National University Medical School, Jeonju, 54907, Republic of Korea
| | - Young Ki Choi
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea.
| | - Min-Suk Song
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Chungdae-ro 1, Seowon-Ku, Cheongju, 28644, Republic of Korea.
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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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6
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Akashi Y, Suzuki H, Ueda A, Hirose Y, Hayashi D, Imai H, Ishikawa H. Analytical and clinical evaluation of a point-of-care molecular diagnostic system and its influenza A/B assay for rapid molecular detection of the influenza virus. J Infect Chemother 2019; 25:578-583. [PMID: 30905631 DOI: 10.1016/j.jiac.2019.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/28/2019] [Accepted: 02/26/2019] [Indexed: 12/29/2022]
Abstract
Recently, rapid molecular detection systems have been used for point-of-care testing for the diagnosis of influenza worldwide. Here, we evaluated the performance of the cobas Liat system and the cobas Influenza A/B assay (Liat) using fresh nasopharyngeal samples collected from a Japanese population between December 2017 and February 2018. The performance of the examination was compared with that of antigen testing and a conventional polymerase chain reaction (nested-PCR) method. A total of 159 patients were included in this study, and 77 tested positive using Liat. The concordance rate between Liat and nested PCR was 97.5%. The median time between the ordering of testing and completion of molecular analyses using Liat was 30 min (interquartile range: 28-35 min). The overall sensitivity and specificity of antigen testing were 57.1% and 100%, respectively. The duration from symptom onset to examination did not alter antigen testing sensitivity. The current study demonstrates the high performance of Liat for the rapid molecular identification of the influenza virus.
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Affiliation(s)
- Yusaku Akashi
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Ibaraki, 305-8558, Japan; Department of Clinical Laboratory Medicine, Tsukuba Medical Center Hospital, Ibaraki, 305-8558, Japan.
| | - Hiromichi Suzuki
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Ibaraki, 305-8558, Japan; Department of Clinical Laboratory Medicine, Tsukuba Medical Center Hospital, Ibaraki, 305-8558, Japan.
| | - Atsuo Ueda
- Department of Clinical Laboratory, Tsukuba Medical Center Hospital, Ibaraki, 305-8558, Japan.
| | - Yumi Hirose
- Department of General Medicine and Primary Care, Tsukuba Medical Center Hospital, Ibaraki, 305-8558, Japan.
| | - Daisuke Hayashi
- Department of Pediatrics, Tsukuba Medical Center Hospital, Ibaraki, 305-8558, Japan.
| | - Hironori Imai
- Department of Pediatrics, Tsukuba Medical Center Hospital, Ibaraki, 305-8558, Japan.
| | - Hiroichi Ishikawa
- Department of Respiratory Medicine, Tsukuba Medical Center Hospital, Ibaraki, 305-8558, Japan.
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7
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Abstract
New surveillance methods employing mass spectrometry (MS) have been developed to characterize the influenza virus and, by extension, other biopathogens at the molecular level. The structure and antigenicity of protein antigens on the surface of the viral capsid are screened in a single step employing the immunoproteomics MS-based approach. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) coupled to gel electrophoresis is used both to identify viral antigens and screen their antigenicity. Evidence that antigen-antibody complexes, and protein complexes more generally, can survive on conventional MALDI targets has allowed both the primary structure and antigenicity of viral strains to be rapidly screened and protein epitopes to be identified with molecular precision. The approach should aid in future screening of the virus and assist in the development of immunogenic peptide constructs as alternative treatments to vaccination over the whole inactivated virus. The assay adds to the repertoire of mass spectrometric approaches for examining antigen-antibody interactions, in particular, and protein complexes, in general, without the need to immobilize, tag, or recover either component.
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Affiliation(s)
- Kevin M Downard
- Infectious Disease Responses Laboratory, POWCS, Medicine, University of New South Wales, Sydney, NSW, Australia.
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Rastogi M, Singh SK. Advances in Molecular Diagnostic Approaches for Biothreat Agents. DEFENSE AGAINST BIOLOGICAL ATTACKS 2019. [PMCID: PMC7123646 DOI: 10.1007/978-3-030-03071-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The advancement in Molecular techniques has been implicated in the development of sophisticated, high-end diagnostic platform and point-of-care (POC) devices for the detection of biothreat agents. Different molecular and immunological approaches such as Immunochromatographic and lateral flow assays, Enzyme-linked Immunosorbent assays (ELISA), Biosensors, Isothermal amplification assays, Nucleic acid amplification tests (NAATs), Next Generation Sequencers (NGS), Microarrays and Microfluidics have been used for a long time as detection strategies of the biothreat agents. In addition, several point of care (POC) devices have been approved by FDA and commercialized in markets. The high-end molecular platforms like NGS and Microarray are time-consuming, costly, and produce huge amount of data. Therefore, the future prospects of molecular based technique should focus on developing quick, user-friendly, cost-effective and portable devices against biological attacks and surveillance programs.
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9
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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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10
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Abstract
The plaque assay is an essential method for quantification of infectious virus titer. Cells infected with virus particles are overlaid with a viscous substrate. A suitable incubation period results in the formation of plaques, which can be fixed and stained for visualization. Here, we describe a method for measuring Chikungunya virus (CHIKV) titers via virus plaque assays.
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Affiliation(s)
- Parveen Kaur
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 5 Science Drive 2, Singapore, 117597, Singapore
| | - Regina Ching Hua Lee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 5 Science Drive 2, Singapore, 117597, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 5 Science Drive 2, Singapore, 117597, Singapore.
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11
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Song S, Ha K, Guk K, Hwang SG, Choi JM, Kang T, Bae P, Jung J, Lim EK. Colorimetric detection of influenza A (H1N1) virus by a peptide-functionalized polydiacetylene (PEP-PDA) nanosensor. RSC Adv 2016. [DOI: 10.1039/c6ra06689e] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We developed a peptide-functionalized polydiacetylene nanosensor for pH1N1 virus detection with the naked eye.
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Affiliation(s)
- Sinae Song
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
| | - Kab Ha
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
| | - Kyeonghye Guk
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
- Major of Nanobiotechnology and Bioinformatics
| | - Seul-Gee Hwang
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
- Major of Nanobiotechnology and Bioinformatics
| | - Jong Min Choi
- BioNano Health Guard Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon
- Republic of Korea
| | - Taejoon Kang
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
- Major of Nanobiotechnology and Bioinformatics
| | - Pankee Bae
- BioNano Health Guard Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon
- Republic of Korea
| | - Juyeon Jung
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
- Major of Nanobiotechnology and Bioinformatics
| | - Eun-Kyung Lim
- Hazards Monitoring BioNano Research Center
- Korea Research Institute of Bioscience and Biotechnology
- Daejeon
- Republic of Korea
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12
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Cebey-López M, Herberg J, Pardo-Seco J, Gómez-Carballa A, Martinón-Torres N, Salas A, Martinón-Sánchez JM, Gormley S, Sumner E, Fink C, Martinón-Torres F. Viral Co-Infections in Pediatric Patients Hospitalized with Lower Tract Acute Respiratory Infections. PLoS One 2015; 10:e0136526. [PMID: 26332375 PMCID: PMC4558027 DOI: 10.1371/journal.pone.0136526] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/04/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Molecular techniques can often reveal a broader range of pathogens in respiratory infections. We aim to investigate the prevalence and age pattern of viral co-infection in children hospitalized with lower tract acute respiratory infection (LT-ARI), using molecular techniques. METHODS A nested polymerase chain reaction approach was used to detect Influenza (A, B), metapneumovirus, respiratory syncytial virus (RSV), parainfluenza (1-4), rhinovirus, adenovirus (A-F), bocavirus and coronaviruses (NL63, 229E, OC43) in respiratory samples of children with acute respiratory infection prospectively admitted to any of the GENDRES network hospitals between 2011-2013. The results were corroborated in an independent cohort collected in the UK. RESULTS A total of 204 and 97 nasopharyngeal samples were collected in the GENDRES and UK cohorts, respectively. In both cohorts, RSV was the most frequent pathogen (52.9% and 36.1% of the cohorts, respectively). Co-infection with multiple viruses was found in 92 samples (45.1%) and 29 samples (29.9%), respectively; this was most frequent in the 12-24 months age group. The most frequently observed co-infection patterns were RSV-Rhinovirus (23 patients, 11.3%, GENDRES cohort) and RSV-bocavirus / bocavirus-influenza (5 patients, 5.2%, UK cohort). CONCLUSION The presence of more than one virus in pediatric patients admitted to hospital with LT-ARI is very frequent and seems to peak at 12-24 months of age. The clinical significance of these findings is unclear but should warrant further analysis.
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Affiliation(s)
- Miriam Cebey-López
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Jethro Herberg
- Section of Paediatrics, Division of Infectious Disease, Imperial College of London, South Kensington Campus, London, United Kingdom
| | - Jacobo Pardo-Seco
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Alberto Gómez-Carballa
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Nazareth Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - José María Martinón-Sánchez
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Stuart Gormley
- Section of Paediatrics, Division of Infectious Disease, Imperial College of London, South Kensington Campus, London, United Kingdom
| | - Edward Sumner
- Micropathology Ltd., University of Warwick Science Park, Coventry, United Kingdom
| | - Colin Fink
- Micropathology Ltd., University of Warwick Science Park, Coventry, United Kingdom
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
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13
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Development of high yield reassortants for influenza type B viruses and analysis of their gene compositions. Vaccine 2015; 33:879-84. [DOI: 10.1016/j.vaccine.2014.12.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/01/2014] [Accepted: 12/15/2014] [Indexed: 01/24/2023]
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14
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Goldenberg SD, Edgeworth JD. The Enigma ML FluAB-RSV assay: a fully automated molecular test for the rapid detection of influenza A, B and respiratory syncytial viruses in respiratory specimens. Expert Rev Mol Diagn 2015; 15:23-32. [PMID: 25399865 DOI: 10.1586/14737159.2015.983477] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Enigma(®) ML FluAB-RSV assay (Enigma Diagnostics, Porton Down, Salisbury, UK) is a CE-IVD marked multiplex molecular panel for the detection of influenza A, B and respiratory syncytial viruses in nasopharyngeal swabs. The assay runs on the fully automated Enigma ML platform without further specimen manipulation and provides a sample-to-answer result within 95 min. The reported sensitivity and specificity for influenza A are 100% (95% CI: 98.2-100) and 98.3% (95% CI: 95.5-99.4), respectively, for influenza B are 100% (95% CI: 98.2-100) and 98.7% (95% CI: 96-99.6), respectively, and for respiratory syncytial virus are 100% (95% CI: 98.2-100) and 99.4% (95% CI: 97.2-99.9), respectively.
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Affiliation(s)
- Simon D Goldenberg
- Centre for Clinical Infection and Diagnostics Research, King's College London and Guy's and St Thomas' NHS Foundation Trust, London SE1 7EH, UK
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15
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Broberg E, Pereyaslov D, Struelens M, Palm D, Meijer A, Ellis J, Zambon M, McCauley J, Daniels R. Laboratory preparedness in EU/EEA countries for detection of novel avian influenza A(H7N9) virus, May 2013. ACTA ACUST UNITED AC 2014; 19. [PMID: 24507469 DOI: 10.2807/1560-7917.es2014.19.4.20682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Following human infections with novel avian influenza A(H7N9) viruses in China, the European Centre for Disease Prevention and Control, the World Health Organization (WHO) Regional Office for Europe and the European Reference Laboratory Network for Human Influenza (ERLI-Net) rapidly posted relevant information, including real-time RT-PCR protocols. An influenza RNA sequence-based computational assessment of detection capabilities for this virus was conducted in 32 national influenza reference laboratories in 29 countries, mostly WHO National Influenza Centres participating in the WHO Global Influenza Surveillance and Response System (GISRS). Twenty-seven countries considered their generic influenza A virus detection assay to be appropriate for the novel A(H7N9) viruses. Twenty-two countries reported having containment facilities suitable for its isolation and propagation. Laboratories in 27 countries had applied specific H7 real-time RT-PCR assays and 20 countries had N9 assays in place. Positive control virus RNA was provided by the WHO Collaborating Centre in London to 34 laboratories in 22 countries to allow evaluation of their assays. Performance of the generic influenza A virus detection and H7 and N9 subtyping assays was good in 24 laboratories in 19 countries. The survey showed that ERLI-Net laboratories had rapidly developed and verified good capability to detect the novel A(H7N9) influenza viruses.
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Affiliation(s)
- E Broberg
- Surveillance and Response Support, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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16
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Kiyota N, Kobayashi M, Tsukagoshi H, Ryo A, Harada S, Kusaka T, Obuchi M, Shimojo N, Noda M, Kimura H. Genetic analysis of human rhinovirus species A to C detected in patients with acute respiratory infection in Kumamoto prefecture, Japan 2011-2012. INFECTION GENETICS AND EVOLUTION 2013; 21:90-102. [PMID: 24200591 DOI: 10.1016/j.meegid.2013.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/25/2013] [Accepted: 10/26/2013] [Indexed: 10/26/2022]
Abstract
We performed detailed genetic analysis of the VP4/VP2 coding region in human rhinovirus species A to C (HRV-ABC) strains detected in patients with a variety of acute respiratory infections in Kumamoto, Japan in the period 2011-12. The phylogenetic tree and evolutionary timescale were obtained by the Bayesian Markov chain Monte Carlo method. Phylogenetic analyses showed that the present HRV-A, -B, and -C strains belonged to 25, 4, and 18 genotypes, respectively. Some new genotypes were confirmed as prevalent strains of HRV-C. An ancestor of the present HRV-ABCs could be dated back to about 20,000 years ago. The present HRV-A and -C strains have wide genetic divergence (pairwise distance >0.2) with rapid evolutionary rates (around 7 × 10(-4) to 4 × 10(-3)substitutions/site/year). Over 100 sites were found to be under negative selection, while no positively selected sites were found in the analyzed region. No evidence of recombination events was found in this region of the present strains. Our results indicate that the present HRV strains have rapidly evolved and subsequently diverged over a long period into multiple genotypes.
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Affiliation(s)
- Naoko Kiyota
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Uto-shi, Kumamoto 869-0425, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Uto-shi, Kumamoto 869-0425, Japan
| | - Takashi Kusaka
- Maternal Perinatal Center, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Masatsugu Obuchi
- Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-shi, Toyama 939-0363, Japan
| | - Naoki Shimojo
- Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.
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17
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Pabbaraju K, Wong S, Wong A, May‐Hadford J, Tellier R, Fonseca K. Detection of influenza C virus by a real-time RT-PCR assay. Influenza Other Respir Viruses 2013; 7:954-60. [PMID: 23445084 PMCID: PMC4634283 DOI: 10.1111/irv.12099] [Citation(s) in RCA: 28] [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] [Accepted: 01/23/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Influenza C virus can cause both upper and lower respiratory tract infections and has been reported to be prevalent in children. However, these infections have been under-diagnosed, and epidemiological data available are limited due to the lack of convenient detection assays. OBJECTIVE Design and validate a real-time reverse-transcriptase PCR (rt RT-PCR) assay for the detection of influenza C. STUDY DESIGN Respiratory samples from two primary settings, namely, children who were hospitalized or seen in the emergency department, and respiratory outbreaks for which no other viral etiology was found were used for the detection of influenza C. RESULTS AND CONCLUSIONS The assay was sensitive and specific for the detection of influenza C. Eleven of 474 (2·32%) patients, all less than 10 years of age, were positive for influenza C. The strains clustered into two lineages, namely C/Kanagawa and C/Sao Paulo, based upon sequencing of the hemagglutinin-esterase gene. Epidemiological data showed that a higher proportion of influenza C infections occur in younger children and during the winter months. This is the first report of the detection of influenza C in Alberta, Canada, and suggests that the detection of this virus should be included in respiratory virus testing panels.
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Affiliation(s)
| | - Sallene Wong
- Provincial Laboratory for Public HealthCalgaryAlbertaCanada
| | - Anita Wong
- Provincial Laboratory for Public HealthCalgaryAlbertaCanada
| | | | - Raymond Tellier
- Provincial Laboratory for Public HealthCalgaryAlbertaCanada
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryAlbertaCanada
| | - Kevin Fonseca
- Provincial Laboratory for Public HealthCalgaryAlbertaCanada
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryAlbertaCanada
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18
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Boku S, Naito T, Murai K, Tanei M, Inui A, Nisimura H, Isonuma H, Takahashi H, Kikuchi K. Near point-of-care administration by the attending physician of the rapid influenza antigen detection immunochromatography test and the fully automated respiratory virus nucleic acid test: contribution to patient management. Diagn Microbiol Infect Dis 2013; 76:445-9. [PMID: 23743175 DOI: 10.1016/j.diagmicrobio.2013.04.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 04/04/2013] [Accepted: 04/26/2013] [Indexed: 11/13/2022]
Abstract
Rapid influenza antigen detection tests (RIADTs) using immunochromatography are the most readily available tools for the diagnosis and management of influenza. This study was designed to assess whether near point-of-care administration by primary care physicians of the RIADT and a fully automated respiratory virus nucleic acid test (Verigene Respiratory Virus Plus®; RV+) would contribute to improved patient management. When viral culture and RT-PCR/bi-directional sequencing were used as the gold standard, sensitivities and specificities for RIADT and RV+ were 58.3% and 90.9%, and 97.2% and 100%, respectively. Within 12 hours from onset of fever, sensitivities were 44.4% and 94.4%, respectively, for RIADT and RV+. In clinical situations where a higher-sensitivity test is needed, such as during pre-admission evaluations, for testing of hospital employees during the prodromal phase of infection, during the therapeutic decision-making process, and during outbreaks, we suggest that patients testing negative by the RIADT can be reassessed with the RV+ test to achieve maximal diagnostic accuracy.
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Affiliation(s)
- Soushin Boku
- Department of General Medicine, Juntendo University Nerima Hospital, Tokyo, Japan.
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19
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Molecular evolution of attachment glycoprotein (G) gene in human respiratory syncytial virus detected in Japan 2008-2011. INFECTION GENETICS AND EVOLUTION 2013; 18:168-73. [PMID: 23707845 DOI: 10.1016/j.meegid.2013.05.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 05/01/2013] [Accepted: 05/13/2013] [Indexed: 11/23/2022]
Abstract
We investigated the evolution of the C-terminal 3rd hypervariable region of G gene in the prevalent human respiratory syncytial virus (RSV) subgroups A (RSV-A) and B (RSV-B) in Japan in 2008-2011. Phylogenetic analysis and the evolutionary timescale was obtained by the Bayesian Markov Chain Monte Carlo method. All 38 RSV-A strains detected were classified into genotype NA1 and the 17 RSV-B strains detected belonged to genotypes BA and GB2. NA1 subdivided around 1998 in the present phylogenetic tree. Genotype BA subdivided around 1994. The evolutionary rates for RSV-A and RSV-B were estimated at 3.63×10⁻³ and 4.56×10⁻³ substitutions/site/year, respectively. The mean evolutionary rate of RSV-B was significantly faster than that of RSV-A during all seasons. The pairwise distance was relatively short (less than 0.06). In addition, some unique sites under positive selection were found. The results suggested that this region of the RSV strains rapidly evolved with some unique amino acid substitutions due to positive pressure.
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20
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Abstract
In 2009, pandemic influenza A (H1N1) virus (H1N1 09) started to spread quickly in many countries. It causes respiratory infection with signs and symptoms of common infectious agents. Thus, clinicians sometimes may miss the H1N1 patient. Clinical laboratory tests are important for the diagnosis of the H1N1 infection. There are several tests available, however, the rapid test and direct fluorescence antigen test are unable to rule out the influenza virus infection and viral culture test is time consuming. Therefore, nucleic acid amplification techniques based on reverse transcription polymerase chain reaction assays are regarded as a specific diagnosis to confirm the influenza virus infection. Although the nucleic acid-based techniques are highly sensitive and specific, the high mutation rate of the influenza RNA-dependent RNA polymerase could limit the utility of the techniques. In addition, their use depends on the availability, cost and throughput of the diagnostic techniques. To overcome these drawbacks, evaluation and development of the techniques should be continued. This review provides an overview of various techniques for specific diagnosis of influenza infection.
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Affiliation(s)
- Dae-Ki Kim
- Department of Immunology and Institute of Medical Sciences, Chonbuk National University Medical School, Jeonju, Korea
| | - Barun Poudel
- Department of Immunology and Institute of Medical Sciences, Chonbuk National University Medical School, Jeonju, Korea
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21
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Kosasih H, R, N, Klimov A, Xiyan X, Lindstrom S, Mahoney F, Beckett C, Burgess TH, Blair PJ, Uyeki TM, Sedyaningsih ER. Surveillance of influenza in Indonesia, 2003–2007. Influenza Other Respir Viruses 2013; 7:312-20. [PMID: 22804910 PMCID: PMC5779827 DOI: 10.1111/j.1750-2659.2012.00403.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Longitudinal data are limited about the circulating strains of influenza viruses and their public health impact in Indonesia. We conducted influenza surveillance among outpatients and hospitalized patients with influenza-like illness (ILI) across the Indonesian archipelago from 2003 through 2007. METHODOLOGY Demographic, clinical data, and respiratory specimens were collected for 4236 ILI patients tested for influenza virus infection by RT-PCR and viral culture. PRINCIPAL FINDINGS Influenza A and B viruses co-circulated year-round with seasonal peaks in influenza A virus activity during the rainy season (December–January). During 2003–2007, influenza viruses were identified in 20·1% (4236 ⁄ 21 030) of ILI patients, including 20·1% (4015 ⁄ 20 012) of outpatients, and 21·7% (221 ⁄ 1018) of inpatients. One H5N1 case was identified retrospectively in an outpatient with ILI. Antigenic drift in circulating influenza A and B virus strains was detected during the surveillance period in Indonesia. In a few instances, antigenically drifted viruses similar to the World Health Organization (WHO) vaccine strains were detected earlier than the date of their designation by WHO. CONCLUSIONS Influenza A and B virus infections are an important cause of influenza-like illness among outpatients and hospitalized patients in Indonesia. While year-round circulation of influenza viruses occurs, prevention and control strategies should be focused upon the seasonal peak during rainy season months. Ongoing virologic surveillance and influenza disease burden studies in Indonesia are important priorities to better understand the public health impact of influenza in South-East Asia and the implications of influenza viral evolution and global spread.
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Affiliation(s)
- Herman Kosasih
- Ministry of Health, Republic of Indonesia, Jakarta, Indonesia
- U.S. Naval Medical Research Unit (NAMRU), Jakarta, Indonesia
| | - Roselinda
- Ministry of Health, Republic of Indonesia, Jakarta, Indonesia
| | - Nurhayati
- U.S. Naval Medical Research Unit (NAMRU), Jakarta, Indonesia
| | - Alexander Klimov
- U.S. Centers for Disease Control and Prevention, Influenza Division, Atlanta, GA, USA
| | - Xu Xiyan
- U.S. Centers for Disease Control and Prevention, Influenza Division, Atlanta, GA, USA
| | - Stephen Lindstrom
- U.S. Centers for Disease Control and Prevention, Influenza Division, Atlanta, GA, USA
| | - Frank Mahoney
- U.S. Centers for Disease Control and Prevention, Jakarta, Indonesia
| | | | - Timothy H. Burgess
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | - Timothy M. Uyeki
- U.S. Centers for Disease Control and Prevention, Influenza Division, Atlanta, GA, USA
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22
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Kiyota N, Kushibuchi I, Kobayashi M, Tsukagoshi H, Ryo A, Nishimura K, Hirata-Saito A, Harada S, Arakawa M, Kozawa K, Noda M, Kimura H. Genetic analysis of the VP4/VP2 coding region in human rhinovirus species C in patients with acute respiratory infection in Japan. J Med Microbiol 2013; 62:610-617. [DOI: 10.1099/jmm.0.049072-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Naoko Kiyota
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Izumi Kushibuchi
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Koichi Nishimura
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Asumi Hirata-Saito
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Mika Arakawa
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
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23
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Wei X, Zheng L, Luo F, Lin Z, Guo L, Qiu B, Chen G. Fluorescence biosensor for the H5N1 antibody based on a metal–organic framework platform. J Mater Chem B 2013; 1:1812-1817. [DOI: 10.1039/c3tb00501a] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Downard KM. An immunoproteomics approach to screen the antigenicity of the influenza virus. Methods Mol Biol 2013; 1061:141-153. [PMID: 23963935 DOI: 10.1007/978-1-62703-589-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The structure and antigenicity of protein antigens of the influenza virus are screened in a single step employing an immunoproteomics approach. Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) coupled to gel electrophoresis is used both to identify viral antigens and screen their antigenicity. Earlier evidence that antigen-antibody complexes can survive on MALDI targets has allowed both the primary structure and antigenicity of viral strains to be rapidly screened with the specific localization of protein epitopes. The approach is anticipated to have a greater role in the future surveillance of the virus and should also aid in the development of immunogenic peptide constructs as alternatives to whole virus for vaccination.
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Affiliation(s)
- Kevin M Downard
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
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25
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Chauhan N, Narang J, Pundir S, Singh S, Pundir CS. Laboratory diagnosis of swine flu: a review. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2012; 41:189-95. [PMID: 23140089 DOI: 10.3109/10731199.2012.716063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Human swine influenza A [H1N1], also referred to as "swine flu," is highly transmissible. The emergence of new strains will continue to pose challenges to public health and the scientific communities will have to prepare to detect them for appropriate treatment. Most sophisticated methods include immunofluorescence staining and antigen subtyping based on hemagglutination inhibition (HI). Another standard method is RT-PCR targeting hemagglutinin and neuraminidase genes. The recent availability of rapid, reliable, and easy-to-perform tests for detecting influenza virus infections has introduced rapid viral diagnosis. This review thus summarizes the current information on the present diagnostic methods for influenza virus H1N1.
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Affiliation(s)
- Nidhi Chauhan
- Department of Biochemistry, M. D. University, Rohtak, Haryana, India
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26
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Influenza viral load and rapid influenza diagnostic tests in children and adults. Diagn Microbiol Infect Dis 2012; 73:99-100. [PMID: 22578943 DOI: 10.1016/j.diagmicrobio.2012.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 01/31/2012] [Accepted: 01/31/2012] [Indexed: 11/21/2022]
Abstract
We compared children and adults with regard to rapid influenza test sensitivity and viral load. Specimen volumes were measured, rapid tests were conducted, and viral load was determined. There was no difference between children and adults in test sensitivity or viral load, but children had higher specimen volumes.
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27
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Update on influenza diagnostics: lessons from the novel H1N1 influenza A pandemic. Clin Microbiol Rev 2012; 25:344-61. [PMID: 22491775 DOI: 10.1128/cmr.05016-11] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The menu of diagnostic tools that can be utilized to establish a diagnosis of influenza is extensive and includes classic virology techniques as well as new and emerging methods. This review of how the various existing diagnostic methods have been utilized, first in the context of a rapidly evolving outbreak of novel influenza virus and then during the different subsequent phases and waves of the pandemic, demonstrates the unique roles, advantages, and limitations of each of these methods. Rapid antigen tests were used extensively throughout the pandemic. Recognition of the low negative predictive values of these tests is important. Private laboratories with preexisting expertise, infrastructure, and resources for rapid development, validation, and implementation of laboratory-developed assays played an unprecedented role in helping to meet the diagnostic demands during the pandemic. FDA-cleared assays remain an important element of the diagnostic armamentarium during a pandemic, and a process must be developed with the FDA to allow manufacturers to modify these assays for detection of novel strains in a timely fashion. The need and role for subtyping of influenza viruses and antiviral susceptibility testing will likely depend on qualitative (circulating subtypes and their resistance patterns) and quantitative (relative prevalence) characterization of influenza viruses circulating during future epidemics and pandemics.
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28
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Mahony JB, Petrich A, Smieja M. Molecular diagnosis of respiratory virus infections. Crit Rev Clin Lab Sci 2012; 48:217-49. [PMID: 22185616 DOI: 10.3109/10408363.2011.640976] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The appearance of eight new respiratory viruses, including the SARS coronavirus in 2003 and swine-origin influenza A/H1N1 in 2009, in the human population in the past nine years has tested the ability of virology laboratories to develop diagnostic tests to identify these viruses. Nucleic acid based amplification tests (NATs) for respiratory viruses were first introduced two decades ago and today are utilized for the detection of both conventional and emerging viruses. These tests are more sensitive than other diagnostic approaches, including virus isolation in cell culture, shell vial culture (SVC), antigen detection by direct fluorescent antibody (DFA) staining, and rapid enzyme immunoassay (EIA), and now form the backbone of clinical virology laboratory testing around the world. NATs not only provide fast, accurate and sensitive detection of respiratory viruses in clinical specimens but also have increased our understanding of the epidemiology of both new emerging viruses such as the pandemic H1N1 influenza virus of 2009, and conventional viruses such as the common cold viruses, including rhinovirus and coronavirus. Multiplex polymerase chain reaction (PCR) assays introduced in the last five years detect up to 19 different viruses in a single test. Several multiplex PCR tests are now commercially available and tests are working their way into clinical laboratories. The final chapter in the evolution of respiratory virus diagnostics has been the addition of allelic discrimination and detection of single nucleotide polymorphisms associated with antiviral resistance. These assays are now being multiplexed with primary detection and subtyping assays, especially in the case of influenza virus. These resistance assays, together with viral load assays, will enable clinical laboratories to provide physicians with new and important information for optimal treatment of respiratory virus infections.
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Affiliation(s)
- James B Mahony
- M.G. DeGroote Institute for Infectious Disease Research, St. Joseph’s Healthcare, Hamilton, Canada.
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Tian J, Zhao H, Liu M, Chen Y, Quan X. Detection of influenza A virus based on fluorescence resonance energy transfer from quantum dots to carbon nanotubes. Anal Chim Acta 2012; 723:83-7. [DOI: 10.1016/j.aca.2012.02.030] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/11/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
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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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31
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Yoshida A, Kiyota N, Kobayashi M, Nishimura K, Tsutsui R, Tsukagoshi H, Hirano E, Yamamoto N, Ryo A, Saitoh M, Harada S, Inoue O, Kozawa K, Tanaka R, Noda M, Okabe N, Tashiro M, Mizuta K, Kimura H. Molecular epidemiology of the attachment glycoprotein (G) gene in respiratory syncytial virus in children with acute respiratory infection in Japan in 2009/2010. J Med Microbiol 2012; 61:820-829. [PMID: 22383445 DOI: 10.1099/jmm.0.041137-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study performed a detailed genetic analysis of the glycoprotein (G) gene of respiratory syncytial virus (RSV) detected in 50 Japanese children with acute respiratory infection (ARI) in the 2009/2010 season. A phylogenetic tree constructed by the neighbour-joining method showed that 34 and 16 of the RSV strains could be classified into subgroups A and B, respectively. Strains belonging to subgroups A and B were further subdivided into GA2 and BA, respectively. The nucleotide and deduced amino acid sequence identities were relatively high among these strains (>90%). The deduced amino acid sequences implied that a relatively high frequency of amino acid substitutions occurred in the C-terminal 3rd hypervariable region of the G protein in these strains. In addition, some positively selected sites were estimated. The results suggest that RSV with genotypes GA2 and BA was associated with ARI in Japanese children in 2009/2010.
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Affiliation(s)
- Ayako Yoshida
- Aomori Prefectural Institute of Public Health and Environment, 1-1-1 Higashitsukurimichi, Aomori-shi, Aomori 030-8566, Japan
| | - Naoko Kiyota
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Kurisaki-machi, Uto-shi, Kumamoto 869-0425, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Koichi Nishimura
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Kurisaki-machi, Uto-shi, Kumamoto 869-0425, Japan
| | - Rika Tsutsui
- Aomori Prefectural Institute of Public Health and Environment, 1-1-1 Higashitsukurimichi, Aomori-shi, Aomori 030-8566, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Eiko Hirano
- Fukui Prefectural Institute of Public Health and Environmental Science, 39-4 Harame-cho, Fukui-shi, Fukui 910-8551, Japan
| | - Norio Yamamoto
- Influenza Virus Research Center and Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Mika Saitoh
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Kurisaki-machi, Uto-shi, Kumamoto 869-0425, Japan
| | - Osamu Inoue
- Aomori Prefectural Institute of Public Health and Environment, 1-1-1 Higashitsukurimichi, Aomori-shi, Aomori 030-8566, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Ryota Tanaka
- Department of Surgery, Institute of Medical Sciences, Kyorin University, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Nobuhiko Okabe
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Masato Tashiro
- Influenza Virus Research Center and Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.,Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
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Comar M, Zanotta N, Rossi T, Pelos G, D'Agaro P. Secondary lymphoid tissue as an important site for WU polyomavirus infection in immunocompetent children. J Med Virol 2011; 83:1446-50. [PMID: 21678449 DOI: 10.1002/jmv.22124] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The polyomaviruses KI and WU (KIPyV and WUPyV) have been identified in respiratory specimens from children with acute respiratory infections, which suggests the respiratory tract as a possible site of infection. However, the persistence of infection in the lymphoid system is unknown. Fresh samples (n = 211) of tonsils, adenoids, and peripheral blood mononuclear cells (PBMCs) from 83 immunocompetent children (mean age 4.8 years) were tested for amplification of the KIPyV VP1 and WUPyV VP2 genes. The known BK and JC polyomaviruses and the lymphotropic human herpesvirus (HHV)-6 were also investigated by quantitative real-time PCR and direct sequencing. In addition, 98 nasopharyngeal swabs collected from children (mean age 6.2 years) affected by seasonal influenza-like illness were tested. Of the lymphoid tissues, 34.9% were positive for WUPyV, 4.8% for BK virus, and 33.8% for HHV-6. KIPyV and JC virus were not detected in these specimens. None of the polyomaviruses were detected in PBMCs. Among the nasopharyngeal samples, the prevalence of WUPyV was 27.5%, although 70% of the positive samples were co-infected with at least one of the following respiratory viruses: influenza virus, adenovirus, and respiratory syncytial virus. Phylogenetic analysis revealed high sequence homology (99%) between lymphoid- and nasopharynx-derived WUPyV strains. These results suggest that the tonsils and adenoids of immunocompetent children are a reservoir for WUPyV infection; probably due to the respiratory route of transmission. In addition, the prevalence of WUPyV was high among the children, and the virus was identified more frequently in older children than during the first years of life.
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Affiliation(s)
- Manola Comar
- Department of Reproductive, Developmental and Public Health Sciences, University of Trieste, Trieste, Italy.
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Takao S, Hara M, Okazaki T, Suzuki K. [Simultaneous multiple assay (Luminex xTAG respiratory viral panel FAST assay) efficacy in human respiratory virus detection]. ACTA ACUST UNITED AC 2011; 85:31-6. [PMID: 21404604 DOI: 10.11150/kansenshogakuzasshi.85.31] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Luminex xTAG respiratory viral panel FAST (RVP FAST) assay detects 17 human respiratory virus strains per measurement. Studying RVP FAST efficacy in detecting respiratory viruses in 67 aspirate samples from the nasal cavities of children with acute respiratory infection, we compared RVP FAST results to those of conventional nucleic acid amplification tests (NAT), e.g., real-time PCR, targeting 8 strains. RVP FAST assay detected 13 strains (98 isolates) in 59 of 67 samples. Of these, 8--influenza virus (Inf.V)-AH1, Inf. V-AH3, novel Inf.V-AH1, and Inf.V-B, and adenovirus, RS virus, metapneumovirus, and bocavirus--were compared to NAT results. RVP FAST showed higher sensitivity (83.3-100%) and specificity (98.2-100%) than NAT. RVP FAST also detected coronavirus (CoV) 229E, OC43, NL63, and HKU1 from 10 virus strain samples and enterovirus and/or rhinovirus from 35. RVP FAST assay thus comprehensively detects clinically important viruses in a single measurement, making RVP FAST assay useful in detecting causative respiratory tract viruses.
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Affiliation(s)
- Shinichi Takao
- Center for Public Health and Environment, Hiroshima Prefectural Technology Research Institute
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Mahony JB. Nucleic acid amplification-based diagnosis of respiratory virus infections. Expert Rev Anti Infect Ther 2011; 8:1273-92. [PMID: 21073292 DOI: 10.1586/eri.10.121] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The appearance of eight new respiratory viruses in the human population in the past 9 years, including two new pandemics (SARS coronavirus in 2003 and swine-origin influenza A/H1N1 in 2009), has tested the ability of virology laboratories to develop diagnostic tests to identify these viruses. Nucleic acid amplification tests (NATs) that first appeared two decades ago have been developed for both conventional and emerging viruses and now form the backbone of the clinical laboratory. NATs provide fast, accurate and sensitive detection of respiratory viruses and have significantly increased our understanding of the epidemiology of these viruses. Multiplex PCR assays have been introduced recently and several commercial tests are now available. The final chapter in the evolution of respiratory virus diagnostics will be the addition of allelic discrimination and detection of single nucleotide polymorphisms associated with antiviral resistance to multiplex assays. These resistance assays together with new viral load tests will enable clinical laboratories to provide physicians with important information for optimal treatment of patients.
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Affiliation(s)
- James B Mahony
- Regional Virology Laboratory, St. Joseph's Healthcare Hamilton, 50 Charlton Ave. East, Hamilton, ON, L8N 4A6, Canada.
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35
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Aich U, Beckley N, Shriver Z, Raman R, Viswanathan K, Hobbie S, Sasisekharan R. Glycomics-based analysis of chicken red blood cells provides insight into the selectivity of the viral agglutination assay. FEBS J 2011; 278:1699-712. [PMID: 21410647 DOI: 10.1111/j.1742-4658.2011.08096.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Agglutination of red blood cells (RBCs), including chicken RBCs (cRBCs), has been used extensively to estimate viral titer, to screen glycan-receptor binding preference, and to assess the protective response of vaccines. Although this assay enjoys widespread use, some virus strains do not agglutinate RBCs. To address these underlying issues and to increase the usefulness of cRBCs as tools for studying viruses, such as influenza, we analyzed the cell surface N-glycans of cRBCs. On the basis of the results obtained from complementary analytical strategies, including MS, 1D and 2D-NMR spectroscopy, exoglycosidase digestions, and HPLC profiling, we report the major glycan structures present on cRBCs. By comparing the glycan structures of cBRCs with those of representative human upper respiratory cells, we offer a possible explanation for the fact that certain influenza strains do not agglutinate cRBCs, using specific human-adapted influenza hemagglutinins as examples. Finally, recent understanding of the role of various glycan structures in high affinity binding to influenza hemagglutinins provides context to our findings. These results illustrate that the field of glycomics can provide important information with respect to the experimental systems used to characterize, detect and study viruses.
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Affiliation(s)
- Udayanath Aich
- Harvard-MIT Division of Health Sciences & Technology, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Sakkou Z, Stripeli F, Papadopoulos NG, Critselis E, Georgiou V, Mavrikou M, Drossatou P, Constantopoulos A, Kafetzis D, Tsolia M. Impact of influenza infection on children's hospital admissions during two seasons in Athens, Greece. Vaccine 2010; 29:1167-72. [PMID: 21172380 DOI: 10.1016/j.vaccine.2010.12.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Revised: 12/02/2010] [Accepted: 12/03/2010] [Indexed: 11/16/2022]
Abstract
A prospective epidemiologic surveillance of hospitalizations associated with influenza was conducted in order to calculate population-based hospitalization rates. Eligible children were 6 months to 13 years of age and were admitted to one of the two large children's hospitals in the Athens area during two influenza seasons. Nasopharyngeal aspirates were tested for influenza by a polymerase reaction assay. Influenza accounted for 9.9-11.8% of all admissions during the influenza season and the overall annual rate of hospitalizations was 13.6-16.8 cases per 10,000 children being highest for children under 5 years of age (26-31.2/10,000 children). Febrile seizures and acute otitis media were the two most common complications associated with influenza and antibiotics were administered to 61% of flu positive patients. Influenza is associated with high hospitalization rates among young children and these may be substantially reduced with the introduction of routine immunization.
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Affiliation(s)
- Z Sakkou
- Second Department of Pediatrics of the University of Athens School of Medicine, Athens, Greece
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37
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Buecher C, Mardy S, Wang W, Duong V, Vong S, Naughtin M, Vabret A, Freymuth F, Deubel V, Buchy P. Use of a multiplex PCR/RT-PCR approach to assess the viral causes of influenza-like illnesses in Cambodia during three consecutive dry seasons. J Med Virol 2010; 82:1762-72. [PMID: 20827775 PMCID: PMC7166949 DOI: 10.1002/jmv.21891] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Acute respiratory infections are a major cause of mortality and morbidity worldwide. Using multiplex PCR/RT‐PCR methods for the detection of 18 respiratory viruses, the circulation of those viruses during 3 consecutive dry seasons in Cambodia was described. Among 234 patients who presented with influenza‐like illness, 35.5% were positive for at least one virus. Rhinoviruses (43.4%), parainfluenza (31.3%) viruses and coronaviruses (21.7%) were the most frequently detected viruses. Influenza A virus, parainfluenza virus 4 and SARS‐coronavirus were not detected during the study period. Ninety apparently healthy individuals were included as controls and 10% of these samples tested positive for one or more respiratory viruses. No significant differences were observed in frequency and in virus copy numbers for rhinovirus detection between symptomatic and asymptomatic groups. This study raises questions about the significance of the detection of some respiratory viruses, especially using highly sensitive methods, given their presence in apparently healthy individuals. The link between the presence of the virus and the origin of the illness is therefore unclear. J. Med. Virol. 82:1762–1772, 2010. © 2010 Wiley‐Liss, Inc.
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38
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Performance of rapid influenza testing in hospitalized children. Eur J Clin Microbiol Infect Dis 2010; 29:683-8. [DOI: 10.1007/s10096-010-0914-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 03/08/2010] [Indexed: 01/21/2023]
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Vabret A, Dina J, Cuvillon-Nimal D, Nguyen E, Gouarin S, Petitjean J, Brouard J, Freymuth F. [Seasonal flu]. ACTA ACUST UNITED AC 2010; 58:e51-7. [PMID: 20303676 PMCID: PMC7126553 DOI: 10.1016/j.patbio.2010.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 01/26/2010] [Indexed: 11/25/2022]
Abstract
La grippe saisonnière est due aux virus influenza A et B. Il s’agit de virus enveloppés dont le génome est constitué de sept à huit fragments d’ARN. Les différents sous-types sont déterminés par la nature des deux glycoprotéines de surface HA et NA. La grippe saisonnière est une maladie épidémique et hivernale dans les zones à climat tempéré. Son épidémiologie est liée à la grande variabilité du virus au cours du temps, nécessitant la mise en place d’un système d’alerte détectant chaque année les variants circulants dominant et déterminant la composition vaccinale. Les symptômes cliniques de la grippe ne sont pas suffisamment spécifiques pour permettre le diagnostic sans examen virologique. Cela est particulièrement vrai en période non épidémique, chez les sujets de plus de 65 ans et chez les enfants de moins de cinq ans. L’enfant représente une cible privilégiée des infections à virus influenza. Le recours à l’hospitalisation est d’autant plus élevé que l’enfant est jeune. Chez le nourrisson, l’infection peut être paucisymptomatique et s’accompagner de manifestations non respiratoires (léthargie, convulsions, malaises). Le diagnostic virologique de la grippe est justifié chez tous les sujets hospitalisés pour un syndrome respiratoire compatible avec une infection à virus influenza. Il existe plusieurs outils permettant une recherche directe du virus dans les sécrétions respiratoires : isolement du virus en culture, détection d’antigènes, détection moléculaire de l’ARN. Le choix de la méthode se fait selon les caractéristiques du test : sensibilité, spécificité, rapidité et simplicité de réalisation, coût.
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Affiliation(s)
- A Vabret
- Laboratoire de virologie, CHU de Caen, avenue Georges-Clémenceau, 14033 Caen, France.
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Influenza virus infection among pediatric patients reporting diarrhea and influenza-like illness. BMC Infect Dis 2010; 10:3. [PMID: 20053294 PMCID: PMC2820480 DOI: 10.1186/1471-2334-10-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 01/07/2010] [Indexed: 11/23/2022] Open
Abstract
Background Influenza is a major cause of morbidity and hospitalization among children. While less often reported in adults, gastrointestinal symptoms have been associated with influenza in children, including abdominal pain, nausea, vomiting, and diarrhea. Methods From September 2005 and April 2008, pediatric patients in Indonesia presenting with concurrent diarrhea and influenza-like illness were enrolled in a study to determine the frequency of influenza virus infection in young patients presenting with symptoms less commonly associated with an upper respiratory tract infection (URTI). Stool specimens and upper respiratory swabs were assayed for the presence of influenza virus. Results Seasonal influenza A or influenza B viral RNA was detected in 85 (11.6%) upper respiratory specimens and 21 (2.9%) of stool specimens. Viable influenza B virus was isolated from the stool specimen of one case. During the time of this study, human infections with highly pathogenic avian influenza A (H5N1) virus were common in the survey area. However, among 733 enrolled subjects, none had evidence of H5N1 virus infection. Conclusions The detection of influenza viral RNA and viable influenza virus from stool suggests that influenza virus may be localized in the gastrointestinal tract of children, may be associated with pediatric diarrhea and may serve as a potential mode of transmission during seasonal and epidemic influenza outbreaks.
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Lee JS, Ki SY, Hwang IS, Park SG, Kim L, Chung MH, Cheong HJ, Kim WJ. Effect of Smoking on Influenza Illness and Vaccine-induced Immune Response in Mice. Infect Chemother 2010. [DOI: 10.3947/ic.2010.42.6.391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Jin-Soo Lee
- Department of Internal Medicine, Inha University College of Medicine, Incheon, Korea
| | - Sae-Yun Ki
- Department of Internal Medicine, Konkuk University College of Medicine, Chungju, Korea
| | - In-Sook Hwang
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Shin-Goo Park
- Department of Occupational and Environmental Medicine, Inha University College of Medicine, Incheon, Korea
| | - Lucia Kim
- Department of Pathology, Inha University College of Medicine, Incheon, Korea
| | - Moon-Hyun Chung
- Department of Internal Medicine, Inha University College of Medicine, Incheon, Korea
| | - Hee-Jin Cheong
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Woo-Joo Kim
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
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Influenza epidemiology and characterization of influenza viruses in patients seeking treatment for acute fever in Cambodia. Epidemiol Infect 2009; 138:199-209. [DOI: 10.1017/s095026880999063x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SUMMARYThe epidemiology, symptomology, and viral aetiology of endemic influenza remain largely uncharacterized in Cambodia. In December 2006, we established passive hospital-based surveillance to identify the causes of acute undifferentiated fever in patients seeking healthcare. Fever was defined as tympanic membrane temperature >38°C. From December 2006 to December 2008, 4233 patients were screened for influenza virus by real-time reverse-transcriptase polymerase chain reaction (rRT–PCR). Of these patients, 1151 (27·2%) were positive for influenza. Cough (68·8%vs. 50·5%,P<0·0001) and sore throat (55·0%vs. 41·9%,P<0·0001) were more often associated with laboratory-confirmed influenza-infected patients compared to influenza-negative enrollees. A clear influenza season was evident between July and December with a peak during the rainy season. Influenza A and B viruses were identified in 768 (66·3%) and 388 (33·7%) of the influenza-positive population (n=1153), respectively. In December 2008, passive surveillance identified infection of the avian influenza virus H5N1 in a 19-year-old farmer from Kandal province who subsequently recovered. From a subset of diagnostic samples submitted in 2007, 15 A(H1N1), seven A(H3N2) and seven B viruses were isolated. The predominant subtype tested was influenza A(H1N1), with the majority antigenically related to the A/Solomon Island/03/2006 vaccine strain. The influenza A(H3N2) isolates and influenza B viruses analysed were closely related to A/Brisbane/10/2007 or B/Ohio/01/2005 (B/Victoria/2/87-lineage) vaccine strains, respectively. Phylogenetic analysis of the HA1 region of the HA gene of influenza A(H1N1) viruses demonstrated that the Cambodian isolates belonged to clade 2C along with representative H1N1 viruses circulating in SE Asia at the time. These viruses remained sensitive to oseltamivir. In total, our data suggest that viral influenza infections contribute to nearly one-fifth of acute febrile illnesses and demonstrate the importance of influenza surveillance in Cambodia.
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Schwahn AB, Downard KM. Antigenicity of a Type A Influenza Virus Through Comparison of Hemagglutination Inhibition and Mass Spectrometry Immunoassays. J Immunoassay Immunochem 2009; 30:245-61. [DOI: 10.1080/15321810903084350] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Awofeso N, Fennell M, Waliuzzaman Z, O'Connor C, Pittam D, Boonwaat L, de Kantzow S, Rawlinson WD. Influenza outbreak in a correctional facility. Aust N Z J Public Health 2009. [DOI: 10.1111/j.1467-842x.2001.tb00290.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Daum LT, Canas LC, Arulanandam BP, Niemeyer D, Valdes JJ, Chambers JP. Real-time RT-PCR assays for type and subtype detection of influenza A and B viruses. Influenza Other Respir Viruses 2009; 1:167-75. [PMID: 19432632 PMCID: PMC4634535 DOI: 10.1111/j.1750-2659.2007.00024.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Influenza viruses type A (H3N2 and H1N1 subtypes) and B are the most prevalently circulating human influenza viruses. However, an increase in several confirmed cases of high pathogenic H5N1 in humans has raised concerns of a potential pandemic underscoring the need for rapid, point of contact detection. In this report, we describe development and evaluation of ‘type,’ i.e., influenza virus A and B, and ‘subtype,’ i.e., H1, H3, and H5, specific, single‐step/reaction vessel format, real‐time RT‐PCR assays using total RNA from archived reference strains, shell‐vial cultured and uncultured primary (throat swab/nasal wash) clinical samples. The type A and B specific assays detected all 16 influenza type A viruses and both currently circulating influenza B lineages (Yamagata and Victoria), respectively. ‘Type’ and ‘subtype’ specific assays utilize one common set of thermocycling conditions, are specific and highly sensitive (detection threshold of approximately 100 target template molecules). All clinical specimens and samples were evaluated using both the unconventional portable Ruggedized Advanced Pathogen Identification Device (RAPID) and standard laboratory bench LightCycler instruments. These potentially field‐deployable assays could offer significant utility for rapid, point of care screening needs arising from a pandemic influenza outbreak.
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Affiliation(s)
- Luke T Daum
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249, USA
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Bulimo WD, Garner JL, Schnabel DC, Bedno SA, Njenga MK, Ochieng WO, Amukoye E, Magana JM, Simwa JM, Ofula VO, Lifumo SM, Wangui J, Breiman RF, Martin SK. Genetic analysis of H3N2 influenza A viruses isolated in 2006-2007 in Nairobi, Kenya. Influenza Other Respir Viruses 2009; 2:107-13. [PMID: 19453470 PMCID: PMC4634699 DOI: 10.1111/j.1750-2659.2008.00044.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Minimal influenza surveillance has been carried out in sub-Saharan Africa to provide information on circulating influenza subtypes for the purpose of vaccine production and monitoring trends in virus spread and mutations. OBJECTIVE The aim of this study was to investigate a surveillance program in Kenya to isolate and characterize influenza viruses. RESULTS In the 2006-2007 influenza season, nine influenza A viruses were isolated. All were of H3N2 subtype with key amino acid (aa) changes indicating that they were more closely related to recent World Health Organization recommended vaccine strains than to older vaccine strains, and mirroring the evolution of circulating influenza A globally. Hemagglutination inhibition data showed that the 2006 Kenya isolates had titers identical to the 2005-2006 H3N2 vaccine strain but two- to threefold lower titers to the 2006-2007 vaccine strain, suggesting that the isolates were antigenic variants of the 2006-2007 vaccine strains. Analysis of aa substitutions of hemagglutinin-1 (HA1) protein of the 2006 Kenyan viruses revealed unique genetic variations with several aa substitutions located at immunodominant epitopes of the HA1 protein. These mutations included the V112I change at site E, the K 173 E substitution at site D and N 278 K change at site C, mutations that may result in conformational change on the HA molecule to expose novel epitopes thus abrogating binding of pre-existing antibodies at these sites. CONCLUSION Characterization of these important genetic variations in influenza A viruses isolated from Kenya highlights the importance of continuing surveillance and characterization of emerging influenza drift variants in sub-Saharan Africa.
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Shankar B, Sreenivas R, Pattnaik B, Manjunatha B, Sreenivas B, Vinuthan M, Ranjith D, Pradhan H. Identification and Subtyping of Avian Influenza Viruses by Reverse Transcription Polymerase Chain Reaction (RT-PCR) and Agarose Gel Electrophoresis. ACTA ACUST UNITED AC 2009. [DOI: 10.3923/ijps.2009.465.469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Abstract
SUMMARY Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease.
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Alvarez AC, Brunck MEG, Boyd V, Lai R, Virtue E, Chen W, Bletchly C, Heine HG, Barnard R. A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus. Virol J 2008; 5:77. [PMID: 18613963 PMCID: PMC2483269 DOI: 10.1186/1743-422x-5-77] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 07/09/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The emergence of high pathogenicity strains of Influenza A virus in a variety of human and animal hosts, with wide geographic distribution, has highlighted the importance of rapid identification and subtyping of the virus for outbreak management and treatment. Type A virus can be classified into subtypes according to the viral envelope glycoproteins, hemagglutinin and neuraminidase. Here we review the existing specificity and amplification of published primers to subtype neuraminidase genes and describe a new broad spectrum primer pair that can detect all 9 neuraminidase subtypes. RESULTS Bioinformatic analysis of 3,337 full-length influenza A neuraminidase segments in the NCBI database revealed semi-conserved regions not previously targeted by primers. Two degenerate primers with M13 tags, NA8F-M13 and NA10R-M13 were designed from these regions and used to generate a 253 bp cDNA product. One-step RT-PCR testing was successful in 31/32 (97%) cases using a touchdown protocol with RNA from over 32 different cultured influenza A virus strains representing the 9 neuraminidase subtypes. Frozen blinded clinical nasopharyngeal aspirates were also assayed and were mostly of subtype N2. The region amplified was direct sequenced and then used in database searches to confirm the identity of the template RNA. The RT-PCR fragment generated includes one of the mutation sites related to oseltamivir resistance, H274Y. CONCLUSION Our one-step RT-PCR assay followed by sequencing is a rapid, accurate, and specific method for detection and subtyping of different neuraminidase subtypes from a range of host species and from different geographical locations.
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Affiliation(s)
| | - Marion EG Brunck
- Biochip Innovations Pty Ltd., 8 Mile Plains, Queensland, Australia
| | - Victoria Boyd
- CSIRO livestock Industries, Australian Animal Health Laboratory (AAHL), Geelong, Vic, Australia
| | - Richard Lai
- Biochip Innovations Pty Ltd., 8 Mile Plains, Queensland, Australia
| | - Elena Virtue
- CSIRO livestock Industries, Australian Animal Health Laboratory (AAHL), Geelong, Vic, Australia
- Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, The University of Queensland, St. Lucia, Queensland, Australia
| | - Wenbin Chen
- Pathology Queensland, Central Laboratory, Herston Hospitals Campus, Herston, Queensland, Australia
| | - Cheryl Bletchly
- Pathology Queensland, Central Laboratory, Herston Hospitals Campus, Herston, Queensland, Australia
| | - Hans G Heine
- CSIRO livestock Industries, Australian Animal Health Laboratory (AAHL), Geelong, Vic, Australia
| | - Ross Barnard
- Biochip Innovations Pty Ltd., 8 Mile Plains, Queensland, Australia
- School of Molecular and Microbial Sciences, The University of Queensland, St. Lucia, Queensland, Australia
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