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Guo Y, Su X, Wu K, Yong KT. Numerical Analysis of Three-dimensional Nanodisk Array-based Surface Plasmon Resonance Biosensors for SARS-CoV-2 Detection. PLASMONICS (NORWELL, MASS.) 2023; 18:769-779. [PMID: 36852386 PMCID: PMC9947906 DOI: 10.1007/s11468-023-01802-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
UNLABELLED With continuous mutations of SARS-CoV-2 virus, new highly contagious and fast-spreading variants have emerged, including Delta and Omicron. The popular label-free immunosensor based on surface plasmon resonance (SPR) technique can be used for real-time monitoring of the ligand-analyte or antibody-antigen interactions occurring on the sensor surface. In this work, an SPR-based biosensor combined with a nanodisk array was presented to enhance the sensitivity toward virus detection. The nanodisk arrays were employed to enhance the adsorption of molecules for better detection by increasing the SPR field. Four optimal sensing configurations of silver or gold nanodisks on gold thin films with different aspect ratios were achieved through systematic optimization of all parameters to yield the best sensor performance. The resonance angle can be modulated simply by the aspect ratio of nanodisk array. The sensitivity of the optimized sensors has been improved, and the detection limit is smaller than that of bare gold-based sensor. The multi-jump resonance angle curves at tiny refractive index can clearly distinguish the difference of trace concentrations, which is very important for the accurate detection of trace substances. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11468-023-01802-3.
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Affiliation(s)
- Yan Guo
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018 China
| | - Xianglong Su
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018 China
| | - Kaihua Wu
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018 China
| | - Ken-Tye Yong
- School of Biomedical Engineering, The University of Sydney, Sydney, Australia
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From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol. Vaccines (Basel) 2022; 10:vaccines10081359. [PMID: 36016246 PMCID: PMC9412868 DOI: 10.3390/vaccines10081359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
(1) Background: Over the last few years, there has been growing interest in the whole genome sequencing (WGS) of rapidly mutating pathogens, such as influenza viruses (IVs), which has led us to carry out in-depth studies on viral evolution in both research and diagnostic settings. We aimed at describing and determining the validity of a WGS protocol that can obtain the complete genome sequence of A(H3N2) IVs directly from clinical specimens. (2) Methods: RNA was extracted from 80 A(H3N2)-positive respiratory specimens. A one-step RT-PCR assay, based on the use of a single set of specific primers, was used to retro-transcribe and amplify the entire IV type A genome in a single reaction, thus avoiding additional enrichment approaches and host genome removal treatments. Purified DNA was quantified; genomic libraries were prepared and sequenced by using Illumina MiSeq platform. The obtained reads were evaluated for sequence quality and read-pair length. (3) Results: All of the study specimens were successfully amplified, and the purified DNA concentration proved to be suitable for NGS (at least 0.2 ng/µL). An acceptable coverage depth for all eight genes of influenza A(H3N2) virus was obtained for 90% (72/80) of the clinical samples with viral loads >105 genome copies/mL. The mean depth of sequencing ranged from 105 to 200 reads per position, with the majority of the mean depth values being above 103 reads per position. The total turnaround time per set of 20 samples was four working days, including sequence analysis. (4) Conclusions: This fast and reliable high-throughput sequencing protocol should be used for influenza surveillance and outbreak investigation.
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Schmit T, Guo K, Tripathi JK, Wang Z, McGregor B, Klomp M, Ambigapathy G, Mathur R, Hur J, Pichichero M, Kolls J, Khan MN. Interferon-γ promotes monocyte-mediated lung injury during influenza infection. Cell Rep 2022; 38:110456. [PMID: 35235782 DOI: 10.1016/j.celrep.2022.110456] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/20/2021] [Accepted: 02/08/2022] [Indexed: 12/17/2022] Open
Abstract
Influenza A virus (IAV) infection triggers an exuberant host response that promotes acute lung injury. However, the host response factors that promote the development of a pathologic inflammatory response to IAV remain incompletely understood. In this study, we identify an interferon-γ (IFN-γ)-regulated subset of monocytes, CCR2+ monocytes, as a driver of lung damage during IAV infection. IFN-γ regulates the recruitment and inflammatory phenotype of CCR2+ monocytes, and mice deficient in CCR2 (CCR2-/-) or IFN-γ (IFN-γ-/-) exhibit reduced lung inflammation, pathology, and disease severity. Adoptive transfer of wild-type (WT) (IFN-γR1+/+) but not IFN-γR1-/- CCR2+ monocytes restore the WT-like pathological phenotype of lung damage in IAV-infected CCR2-/- mice. CD8+ T cells are the main source of IFN-γ in IAV-infected lungs. Collectively, our data highlight the requirement of IFN-γ signaling in the regulation of CCR2+ monocyte-mediated lung pathology during IAV infection.
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Affiliation(s)
- Taylor Schmit
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Kai Guo
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jitendra Kumar Tripathi
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Zhihan Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Brett McGregor
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Mitch Klomp
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Ganesh Ambigapathy
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Ramkumar Mathur
- Department of Geriatrics, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Junguk Hur
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Michael Pichichero
- Rochester General Hospital Research Institute, 1425 Portland Avenue, Rochester, NY 14621, USA
| | - Jay Kolls
- Center for Translational Research in Infection and Inflammation, Department of Pediatrics and Department of Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - M Nadeem Khan
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32603, USA.
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Suderman M, Moniwa M, Alkie TN, Ojkic D, Broes A, Pople N, Berhane Y. Comparative Susceptibility of Madin–Darby Canine Kidney (MDCK) Derived Cell Lines for Isolation of Swine Origin Influenza A Viruses from Different Clinical Specimens. Viruses 2021; 13:v13122346. [PMID: 34960614 PMCID: PMC8704103 DOI: 10.3390/v13122346] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 12/19/2022] Open
Abstract
Madin–Darby canine kidney (MDCK) cells are commonly used for the isolation of mammalian influenza A viruses. The goal of this study was to compare the sensitivity and suitability of the original MDCK cell line in comparison with MDCK-derived cell lines, MDCK.2, MDCK SIAT-1 and MDCK-London for isolation of swine-origin influenza A viruses (IAV-S) from clinical specimens. One-hundred thirty clinical specimens collected from pigs in the form of nasal swabs, lung tissue and oral fluids that were positive by PCR for the presence of IAV-S RNA were inoculated in the cell cultures listed above. MDCK-SIAT1 cells yielded the highest proportion of positive IAV-S isolations from all specimen types. For nasal swabs, 58.62% of the specimens were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (36.21%), and conventional MDCK and MDCK.2 cells (27.5%). For lung specimens, 59.38% were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (40.63%), and conventional MDCK and MDCK.2 cells (18.75–31.25%). Oral fluids yielded the lowest number of positive virus isolation results, but MDCK-SIAT1 cells were still had the highest rate (35%) of IAV-S isolation, whereas the isolation rate in other cells ranged from 5–7.5%. Samples with lower IAV-S PCR cycle threshold (Ct) values were more suitable for culturing and isolation. The isolated IAV-S represented H1N1-β, H1N2-α, H1N1pdm and H3N2 cluster IV and cluster IVB viruses. The result of the current study demonstrated the importance of using the most appropriate MDCK cells when isolating IAV-S from clinical samples.
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Affiliation(s)
- Matthew Suderman
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (M.S.); (M.M.); (T.N.A.)
| | - Mariko Moniwa
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (M.S.); (M.M.); (T.N.A.)
| | - Tamiru N. Alkie
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (M.S.); (M.M.); (T.N.A.)
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Andre Broes
- Biovet Inc., Saint-Hyacinthe, QC J2S 8W2, Canada;
| | - Neil Pople
- Veterinary Diagnostic Services, Manitoba Agriculture and Resource Development, 545 University Crescent, Winnipeg, MB R3T 5S6, Canada;
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (M.S.); (M.M.); (T.N.A.)
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Correspondence:
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Xie J, Pang XL, Tarr GAM, Mu Y, Zhuo R, Chui L, Lee BE, Vanderkooi OG, Tarr PI, Ali S, MacDonald SE, Freedman SB. Influenza virus detection in the stool of children with acute gastroenteritis. J Clin Virol 2020; 131:104565. [PMID: 32810839 DOI: 10.1016/j.jcv.2020.104565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/18/2020] [Accepted: 07/28/2020] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To determine if the clinical characteristics of children with gastroenteritis and influenza identified in their stool differ from those whose stool was influenza-negative. METHODS Children <18-years with gastroenteritis whose stool tested negative for enteropathogen were tested for influenza in stool. The clinical features between influenza-positive and influenza-negative gastroenteritis cases were compared. Stools from controls without infection were also tested for influenza. RESULTS Among the 440 gastroenteritis cases, those who were influenza test-positive were older [median age 4.0 (IQR: 2.3, 5.5) vs. 1.5 (IQR: 0.5, 4.0) years; P = 0.008], more likely to present in fall or winter (92.3 % vs. 48.0 %; P = 0.001), be febrile (84.6 % vs. 30.6 %; P < 0.001), have respiratory symptoms (91.7 % vs. 44.8 %; P = 0.002), have dehydration [median Clinical Dehydration Scale score: 4 (IQR: 1.5, 4.5) vs. 2 (IQR: 0, 3); P = 0.034], and have higher Modified Vesikari Scale scores [median: 13 (IQR: 10.5, 14.0) vs. 10 (IQR: 9.0, 13.0); P = 0.044], than those who tested negative. Thirteen gastroenteritis cases (13/440; 3.0 %) including one child without respiratory symptoms vs. one control (1/250; 0.4 %) were influenza stool positive. CONCLUSIONS Fever, respiratory symptoms, more severe illness, and older age were more common in children with gastroenteritis with influenza detected in stool, compared to those tested negative.
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Affiliation(s)
- Jianling Xie
- Section of Pediatric Emergency Medicine, Department of Pediatric, Alberta Children Hospital, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Xiao-Li Pang
- Alberta Precision Laboratories-Provincial Laboratory for Public Health, Edmonton, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Gillian A M Tarr
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Yuan Mu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ran Zhuo
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Linda Chui
- Alberta Precision Laboratories-Provincial Laboratory for Public Health, Edmonton, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Bonita E Lee
- Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada; Women & Children's Health Research Institute (WCHRI), University of Alberta, Edmonton, Alberta, Canada
| | - Otto G Vanderkooi
- Department of Pediatrics, Microbiology, Immunology and Infectious Diseases, Pathology & Laboratory Medicine and Community Health Sciences and the Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Phillip I Tarr
- Department of Pediatrics, Division of Gastroenterology, Hepatology & Nutrition, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Samina Ali
- Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada; Women & Children's Health Research Institute (WCHRI), University of Alberta, Edmonton, Alberta, Canada
| | - Shannon E MacDonald
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Faculty of Nursing, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen B Freedman
- Section of Pediatric Emergency Medicine, Department of Pediatrics, Alberta Children's Hospital, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Section of Pediatric Gastroenterology, Department of Pediatrics, Alberta Children's Hospital, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
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Sargel CL, Aboud M, Forster A, Langman LJ, Tansmore J, Mueller BA, Smoyer WE, Auletta JJ. Intravenous Ribavirin for Parainfluenza and Respiratory Syncytial Virus in an Infant Receiving Extracorporeal Membrane Oxygenation and Continuous Renal Replacement Therapy. J Pediatr Pharmacol Ther 2018; 23:337-342. [DOI: 10.5863/1551-6776-23.4.337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Viral bronchiolitis remains a significant cause of hospitalization as well as morbidity and mortality during the first year of life, with treatment options beyond supportive care being limited. In cases of severe illness, ribavirin may offer therapeutic benefit.
OBJECTIVE We report the use of intravenous (IV) ribavirin in an infant requiring concomitant venovenous extracorporeal membrane oxygenation (VV-ECMO) and continuous venovenous hemofiltration (CVVH) for respiratory syncytial virus (RSV) and parainfluenza virus (PIV) coinfection.
PATIENTS AND METHODS A 5-week-old male former 33-week preterm infant was admitted with respiratory failure and subsequently tested positive for RSV and PIV-type 1 infection. Progressive clinical deterioration subsequently required the initiation of both VV-ECMO and CVVH. Although the patient received combined VV-ECMO and CVVH, IV ribavirin was administered, and serial plasma and ultrafiltrate samples were obtained for pharmacokinetic analyses after the first dose (collection period 1) and again after an estimated 5 half-lives (collection period 2).
RESULTS Pharmacokinetics for collection period 1 demonstrated a calculated Cmax of 11.99 mg/L, an AUC0–24 of 43.32 mg·hr/L, ke 0.26 hr−1, t½ 2.69 hr, Vd 10.04 L (2.92 L/kg, using patient's dosing weight 3.43 kg), CLT 43.47 mL/min, and CLCVVH 6.75 mL/min. Pharmacokinetics for collection period 2 demonstrated a calculated Cmax of 10.31 mg/L, AUC0–6 of 52.55 mg· hr/L, ke 0.06 hr−1, t½ 10.69 hr, Vd 17.5 L (5.1 L/kg), and CLT 17.44 mL/min. The sieving coefficient during collection period 1 was 1.17 (range, 1.07–1.37). The percent decline between prefilter and postfilter oxygenator was 19.1%.
CONCLUSION Our patient demonstrated therapeutic concentrations of ribavirin, despite drug removal via CVVH and the ECMO oxygenator. Standard ribavirin dosing used and resultant concentrations achieved were associated with viral clearance and clinical improvement.
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Abstract
Influenza viruses are constantly circulating among humans, in which they cause seasonal epidemics of severe respiratory disease. Additionally, these zoonotic viruses infect different mammals and birds, from which new antigenic variants are occasionally transmitted to humans leading to devastating global pandemics. Surveillance programs, in which viruses from the main reservoir (waterfowl), intermediate hosts (like pigs and other farm animals), and other affected species are isolated and characterized, are crucial for the global influenza prevention strategy. This chapter gives an overview of the most commonly used methods for the propagation and titration of influenza viruses, which are key steps in surveillance procedures, as well as in vaccine development and basic research. Depending on the host and the viral strain, primary isolates are obtained from biological samples of different origin and subsequently amplified in embryonated chicken eggs or cell cultures. These propagation procedures are the focus of the first part of this chapter. Once the initial isolates have been amplified, virus titration methods based on particular characteristics of influenza viruses, such as their ability to agglutinate red blood cells (RBCs) or to induce cytopathic effects (CPE) in cell monolayers, are used to estimate the amount of viral particles. Such approaches, like the hemagglutination assay (HA assay), 50% tissue culture infectious dose (TCID50), or plaque assay, are included in the second part of this chapter. Although they are simple and cost-effective, some of these techniques have been partially replaced by faster and more sensitive methods based on the quantification of viral genomes, such as the quantitative real-time reverse transcription PCR (RT-qPCR), which is presented at the end of this section. The different protocols are explained in detail in order to facilitate the preparation and quantification of infectious virus stocks.
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Affiliation(s)
- Umut Karakus
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland
| | - Michel Crameri
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland
| | - Caroline Lanz
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland
| | - Emilio Yángüez
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland.
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Gould VMW, Francis JN, Anderson KJ, Georges B, Cope AV, Tregoning JS. Nasal IgA Provides Protection against Human Influenza Challenge in Volunteers with Low Serum Influenza Antibody Titre. Front Microbiol 2017; 8:900. [PMID: 28567036 PMCID: PMC5434144 DOI: 10.3389/fmicb.2017.00900] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/03/2017] [Indexed: 01/05/2023] Open
Abstract
In spite of there being a number of vaccines, influenza remains a significant global cause of morbidity and mortality. Understanding more about natural and vaccine induced immune protection against influenza infection would help to develop better vaccines. Virus specific IgG is a known correlate of protection, but other factors may help to reduce viral load or disease severity, for example IgA. In the current study we measured influenza specific responses in a controlled human infection model using influenza A/California/2009 (H1N1) as the challenge agent. Volunteers were pre-selected with low haemagglutination inhibition (HAI) titres in order to ensure a higher proportion of infection; this allowed us to explore the role of other immune correlates. In spite of HAI being uniformly low, there were variable levels of H1N1 specific IgG and IgA prior to infection. There was also a range of disease severity in volunteers allowing us to compare whether differences in systemic and local H1N1 specific IgG and IgA prior to infection affected disease outcome. H1N1 specific IgG level before challenge did not correlate with protection, probably due to the pre-screening for individuals with low HAI. However, the length of time infectious virus was recovered from the nose was reduced in patients with higher pre-existing H1N1 influenza specific nasal IgA or serum IgA. Therefore, IgA contributes to protection against influenza and should be targeted in vaccines.
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Affiliation(s)
- Victoria M W Gould
- Mucosal Infection and Immunity, Section of Virology, Imperial College LondonLondon, United Kingdom
| | - James N Francis
- Altimmune, London BioScience Innovation CentreLondon, United Kingdom
| | - Katie J Anderson
- Altimmune, London BioScience Innovation CentreLondon, United Kingdom
| | - Bertrand Georges
- Altimmune, London BioScience Innovation CentreLondon, United Kingdom
| | - Alethea V Cope
- Mucosal Infection and Immunity, Section of Virology, Imperial College LondonLondon, United Kingdom
| | - John S Tregoning
- Mucosal Infection and Immunity, Section of Virology, Imperial College LondonLondon, United Kingdom
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Ramezannia M, Hosseini SM, Fotouhi F, Khansarinejad B, Mazaheri V. Development of a multiplex real-time RT-PCR assay for detection of human parainfluenza viruses in patients with respiratory symptoms. Future Virol 2016. [DOI: 10.2217/fvl-2016-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: The human parainfluenza viruses (HPIVs) are common viral causes of both upper and lower respiratory tract infections in infants and children. The purpose of this study was to develop a real-time reverse transcription PCR assay to detect HPIVs in clinical specimens in a single test. Specimens: Specific primers and probes matched to conserved region of hemagglutinin–neuraminidase genes were designed. Clinical specimens were collected from hospitalized children of ≤5 years old. Results & conclusion: Of 230 specimens, 48 samples contained one of HPIV types 1–4. The most percentage of positive HPIVs belonged to HPIV2. HPIVs were found in fall, winter and spring but not in summer months. In conclusion, our in-house multiplex real-time reverse transcription PCR is a suitable technique for simultaneous detection of HPIVs in clinical samples.
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Affiliation(s)
- Mahboobeh Ramezannia
- Department of Influenza & Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran
| | - Seyed Masoud Hosseini
- Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran
| | - Fatemeh Fotouhi
- Department of Influenza & Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Behzad Khansarinejad
- Department of Microbiology & Immunology, Arak University of Medical Sciences, Arak, Iran
| | - Vahideh Mazaheri
- Department of Influenza & Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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Thompson MG, Gaglani MJ, Naleway AL, Dowell SH, Spencer S, Ball S, Levine M, Fry A. Reduced serologic sensitivity to influenza A virus illness among inactivated influenza vaccinees. Vaccine 2016; 34:3443-6. [PMID: 27195761 DOI: 10.1016/j.vaccine.2016.04.085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/23/2016] [Accepted: 04/26/2016] [Indexed: 01/05/2023]
Abstract
We compared ≥4-fold increases in antibody titers by hemagglutination inhibition assay to RT-PCR results among 42 adults with PCR-confirmed influenza A virus illnesses. Serologic sensitivity was higher among unvaccinated (69%, 95% confidence interval [CI]=48-90%) than vaccinated healthcare personnel (38%, 95% CI=29-46%) in a 2010-11 prospective cohort.
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Affiliation(s)
- Mark G Thompson
- Influenza Division/NCIRD/CDC, Atlanta, GA 30333, United States.
| | - Manjusha J Gaglani
- Division of Pediatric Infectious Diseases, Baylor Scott & White Health, Texas A&M HSC COM, Temple, TX 76508, United States
| | - Allison L Naleway
- The Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, United States
| | - Samuel H Dowell
- Influenza Division/NCIRD/CDC, Atlanta, GA 30333, United States
| | - Sarah Spencer
- Influenza Division/NCIRD/CDC, Atlanta, GA 30333, United States
| | - Sarah Ball
- Abt Associates, Cambridge, MA 02138, United States
| | - Min Levine
- Influenza Division/NCIRD/CDC, Atlanta, GA 30333, United States
| | - Alicia Fry
- Influenza Division/NCIRD/CDC, Atlanta, GA 30333, United States
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11
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Thompson MG, Ferber JR, Odouli R, David D, Shifflett P, Meece JK, Naleway AL, Bozeman S, Spencer SM, Fry AM, Li DK. Results of a pilot study using self-collected mid-turbinate nasal swabs for detection of influenza virus infection among pregnant women. Influenza Other Respir Viruses 2016; 9:155-60. [PMID: 25711978 PMCID: PMC4415700 DOI: 10.1111/irv.12309] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2015] [Indexed: 11/30/2022] Open
Abstract
Background We evaluated the feasibility of asking pregnant women to self-collect and ship respiratory specimens. Methods In a preliminary laboratory study, we compared the RT-PCR cycle threshold (CT) values of influenza A and B viruses incubated at 4 storage temperatures (from 4 to 35°C) for 6 time periods (8, 24, 48, 72, and 168 hours and 30 days), resulting in 24 conditions that were compared to an aliquot tested after standard freezing (−20°C) (baseline condition). In a subsequent pilot study, during January–February, 2014, we delivered respiratory specimen collection kits to 53 pregnant women with a medically attended acute respiratory illness using three delivery methods. Results CT values were stable after storage at temperatures <27°C for up to 72 hours for influenza A viruses and 48 hours for influenza B viruses. Of 53 women who received kits during the pilot, 89% collected and shipped nasal swabs as requested. However, 30% (14/47) of the women took over 2 days to collect and ship their specimen. The human control gene, ribonuclease P (RNase P), was detected in 100% of nasal swab specimens. However, the mean CT values for RNase P (26·5, 95% confidence interval [CI] = 26·0–27·1) and for the 8 influenza A virus positives in our pilot (32·2, 95% CI = 28·9–35·5) were significantly higher than the CTs observed in our 2010–2012 study using staff-collected nasal pharyngeal swabs (P-values < 0·01). Discussion Self-collection of respiratory specimens is a promising research method, but further research is needed to quantify the sensitivity and specificity of the approach.
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Affiliation(s)
- Mark G Thompson
- Influenza Division, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
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12
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Critical review of current and emerging quantification methods for the development of influenza vaccine candidates. Vaccine 2015; 33:5913-9. [DOI: 10.1016/j.vaccine.2015.07.104] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 07/10/2015] [Accepted: 07/28/2015] [Indexed: 01/08/2023]
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Koul PA, Mir H, Bhat MA, Khan UH, Khan MM, Chadha MS, Lal RB. Performance of rapid influenza diagnostic tests (QuickVue) for influenza A and B Infection in India. Indian J Med Microbiol 2015; 33 Suppl:26-31. [PMID: 25657152 DOI: 10.4103/0255-0857.148831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Rapid point-of-care (POC) tests provide an economical alternative for rapid diagnosis and treatment of influenza, especially in public health emergency situations. OBJECTIVES To test the performance of a rapid influenza diagnostic test, QuickVue (Quidel) as a POC test against a real-time polymerase chain reaction (RT-PCR) assay for detection of influenza A and B in a developing country setting. STUDY DESIGN In a prospective observational design, 600 patients with influenza-like illness (ILI) or with severe acute respiratory illness (SARI) who were referred to the Influenza Clinic of a tertiary care hospital in Srinagar, India from September 2012 to April 2013, were enrolled for diagnostic testing for influenza using QuickVue or RT-PCR. All influenza A-positive patients by RT-PCR were further subtyped using primers and probes for A/H1pdm09 and A/H3. RESULTS Of the 600 patients, 186 tested positive for influenza A or B by RT-PCR (90 A/H1N1pdm09, 7 A/H3 and 89 influenza B), whereas only 43 tested positive for influenza (influenza A=22 and influenza B=21) by QuickVue. Thus, the sensitivity of the QuickVue was only 23% (95% confidence interval, CI: 17.3-29.8) and specificity was 100% (95% CI: 99.1-100) with a positive predictive value (PPV) of 100% (95% CI 91.8-100) and a negative predictive value (NPV) of 74.3% (95% CI: 70.5-77.9) as compared to RT-PCR. CONCLUSIONS The high specificity of QuickVue suggest that this POC test can be a useful tool for patient management or triaging during a public health crisis but a low sensitivity suggests that a negative test result need to be further tested using RT-PCR.
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Affiliation(s)
- P A Koul
- Department of Internal and Pulmonary Medicine and MSM Project for Influenza, Sher I Kashmir Institute of Medical Sciences, Soura, Srinagar, Jammu and Kashmir, India
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Spencer S, Chung J, Thompson M, Piedra PA, Jewell A, Avadhanula V, Mei M, Jackson ML, Meece J, Sundaram M, Belongia EA, Cross R, Johnson E, Bullotta A, Rinaldo C, Gaglani M, Murthy K, Clipper L, Berman L, Flannery B. Factors associated with real-time RT-PCR cycle threshold values among medically attended influenza episodes. J Med Virol 2015; 88:719-23. [PMID: 26334765 DOI: 10.1002/jmv.24373] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2015] [Indexed: 11/07/2022]
Abstract
We evaluated the cycle threshold (CT) values of 1,160 influenza A positive and 806 influenza B positive specimens from two seasons of the US Flu VE Network to identify factors associated with CT values. Low CT values (high genomic load) were associated with shorter intervals between illness onset and specimen collection, young age (ages 3-8 years old), and self-rated illness severity for both influenza A and B. Low CT values were also associated with reported fever/feverishness and age ≥65 years for influenza A.
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Affiliation(s)
- Sarah Spencer
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
| | - Jessie Chung
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
| | - Mark Thompson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Alan Jewell
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Minghua Mei
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | | | - Jennifer Meece
- Marshfield Clinic Research Foundation, Marshfield Wisconsin
| | - Maria Sundaram
- Marshfield Clinic Research Foundation, Marshfield Wisconsin
| | | | - Rachel Cross
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Emileigh Johnson
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Arlene Bullotta
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Charles Rinaldo
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | | | - LaShondra Berman
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Brendan Flannery
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
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15
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Calarota SA, Chiesa A, De Silvestri A, Morosini M, Oggionni T, Marone P, Meloni F, Baldanti F. T-lymphocyte subsets in lung transplant recipients: association between nadir CD4 T-cell count and viral infections after transplantation. J Clin Virol 2015. [PMID: 26209391 PMCID: PMC7106454 DOI: 10.1016/j.jcv.2015.06.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Little is known about the kinetics of T-cell subsets in lung transplant recipients (LTR) and their association with the occurrence of opportunistic infections (OI). OBJECTIVES To analyze the kinetics of T-lymphocyte subsets in LTR and the association between nadir CD4 T-cell count and viral infections after transplantation. STUDY DESIGN Serial measurements of peripheral blood CD4 and CD8 T-cell counts obtained during the first year post-transplantation from 83 consecutive LTR and their correlation with both viral OI and community-acquired infections post-transplantation were retrospectively analyzed. RESULTS LTR with a nadir CD4 T-cell count <200 cells/μl had consistently lower CD4 and CD8 T-cell counts than LTR with a nadir CD4 T-cell count >200 cells/μl (p<0.001). In LTR with a nadir CD4 T-cell count <200 cells/μl, the cumulative incidence of viral infections detected in peripheral blood and in bronchoalveolar lavage (BAL) samples was higher than in LTR with a nadir CD4 T-cell count >200 cells/μl (p=0.0012 and p=0.0058, respectively). A nadir CD4 T-cell count <200 cells/μl within the first three months post-transplantation predicted a higher frequency of viral infectious episodes in BAL samples within the subsequent six month period (p=0.0066). CONCLUSIONS Stratification of patients according to nadir CD4 T-cell count may represent a new and simple approach for early identification of patients at risk for subsequent virus infections.
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Affiliation(s)
- Sandra A Calarota
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Taramelli 5, 27100 Pavia, Italy
| | - Antonella Chiesa
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Taramelli 5, 27100 Pavia, Italy
| | - Annalisa De Silvestri
- Biometry and Clinical Epidemiology Department, Fondazione IRCCS Policlinico San Matteo, Viale Golgi 19, 27100 Pavia, Italy
| | - Monica Morosini
- Division of Respiratory Diseases, Fondazione IRCCS Policlinico San Matteo, Viale Golgi 19, 27100 Pavia, Italy
| | - Tiberio Oggionni
- Division of Respiratory Diseases, Fondazione IRCCS Policlinico San Matteo, Viale Golgi 19, 27100 Pavia, Italy
| | - Piero Marone
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Taramelli 5, 27100 Pavia, Italy
| | - Federica Meloni
- Division of Respiratory Diseases, Fondazione IRCCS Policlinico San Matteo, Viale Golgi 19, 27100 Pavia, Italy; Department of Molecular Medicine, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Viale Golgi 19, 27100 Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Taramelli 5, 27100 Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Viale Brambilla 74, 27100 Pavia, Italy.
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16
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L'Huillier AG, Abed Y, Petty TJ, Cordey S, Thomas Y, Bouhy X, Schibler M, Simon A, Chalandon Y, van Delden C, Zdobnov E, Boquete-Suter P, Boivin G, Kaiser L. E119D Neuraminidase Mutation Conferring Pan-Resistance to Neuraminidase Inhibitors in an A(H1N1)pdm09 Isolate From a Stem-Cell Transplant Recipient. J Infect Dis 2015; 212:1726-34. [PMID: 25985905 DOI: 10.1093/infdis/jiv288] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/08/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND An influenza A(H1N1)pdm09 infection was diagnosed in a hematopoietic stem cell transplant recipient during conditioning regimen. He was treated with oral oseltamivir, later combined with intravenous zanamivir. The H275Y neuraminidase (NA) mutation was first detected, and an E119D NA mutation was identified during zanamivir therapy. METHODS Recombinant wild-type (WT) E119D and E119D/H275Y A(H1N1)pdm09 NA variants were generated by reverse genetics. Susceptibility to NA inhibitors (NAIs) was evaluated with a fluorometric assay using the 2'-(4-methylumbelliferyl)-α-D-N-acetylneuraminic acid (MUNANA) substrate. Susceptibility to favipiravir (T-705) was assessed using plaque reduction assays. The NA affinity and velocity values were determined with NA enzymatic studies. RESULTS We identified an influenza A(H1N1)pdm09 E119D mutant that exhibited a marked increase in the 50% inhibitory concentrations against all tested NAIs (827-, 25-, 286-, and 702-fold for zanamivir, oseltamivir, peramivir, and laninamivir, respectively). The double E119D/H275Y mutation further increased oseltamivir and peramivir 50% inhibitory concentrations by 790- and >5000-fold, respectively, compared with the WT. The mutant viruses remained susceptible to favipiravir. The NA affinity and velocity values of the E119D variant decreased by 8.1-fold and 4.5-fold, respectively, compared with the WT. CONCLUSIONS The actual emergence of a single NA mutation conferring pan-NAI resistance in the clinical setting reinforces the pressing need to develop new anti-influenza strategies.
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Affiliation(s)
- Arnaud G L'Huillier
- Laboratory of Virology, Divisions of Infectious Diseases and Laboratory Medicine
| | - Yacine Abed
- Centre Hospitalier Universitaire de Québec and Université Laval, Quebec City, Canada
| | - Tom J Petty
- Department of Genetic Medicine and Development, University of Geneva Medical School Swiss Institute of Bioinformatics, University of Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Divisions of Infectious Diseases and Laboratory Medicine
| | - Yves Thomas
- Laboratory of Virology, Divisions of Infectious Diseases and Laboratory Medicine
| | - Xavier Bouhy
- Centre Hospitalier Universitaire de Québec and Université Laval, Quebec City, Canada
| | - Manuel Schibler
- Laboratory of Virology, Divisions of Infectious Diseases and Laboratory Medicine
| | - Audrey Simon
- Division of Hematology, Department of Internal Medicine Specialties, University of Geneva Hospitals
| | - Yves Chalandon
- Division of Hematology, Department of Internal Medicine Specialties, University of Geneva Hospitals
| | - Christian van Delden
- Division of Infectious Diseases, Department of Internal Medicine Specialties, University of Geneva Hospitals
| | - Evgeny Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School Swiss Institute of Bioinformatics, University of Geneva, Switzerland
| | | | - Guy Boivin
- Centre Hospitalier Universitaire de Québec and Université Laval, Quebec City, Canada
| | - Laurent Kaiser
- Laboratory of Virology, Divisions of Infectious Diseases and Laboratory Medicine University of Geneva Medical School, University of Geneva, Switzerland
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17
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Watson JM, Francis JN, Mesens S, Faiman GA, Makin J, Patriarca P, Treanor JJ, Georges B, Bunce CJ. Characterisation of a wild-type influenza (A/H1N1) virus strain as an experimental challenge agent in humans. Virol J 2015; 12:13. [PMID: 25645025 PMCID: PMC4322439 DOI: 10.1186/s12985-015-0240-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 01/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human challenge models using respiratory viruses such as influenza are increasingly utilised in the development of novel vaccines and anti-viral modalities and can provide preliminary evidence of protection before evaluation in field trials. We describe the results of a clinical study characterising an A/H1N1 influenza challenge virus in humans. METHODS The challenge agent, influenza A/California/2009 (H1N1), was manufactured under cGMP conditions and characterised in accordance with regulatory guidelines. A dose-ascending open-label clinical study was conducted in 29 healthy young adults screened sero-negative to the challenge strain. Subjects were intranasally inoculated with three increasing doses of virus and physician-reported signs, subjected-reported symptoms, viral shedding and immunological responses were monitored. RESULTS A dose-dependent increase in clinical signs and symptoms was observed with 75% of subjects developing laboratory-confirmed illness at the highest inoculum (3.5 × 10(6) TCID50). At the highest dose, physician or subject-reported signs of infection were classified as mild (all subjects), moderate (50%) and severe (16%) with peak symptoms recorded four days after infection. Clinical signs were correlated with nasal mucus weight (P < .001) and subject-reported symptoms (P < .001). Geometric mean peak viral shedding was log10 5.16 TCID50 and occurred three days after inoculation with a median duration of five days. The safety profile was such that physiological responses to viral infection were mainly restricted to the upper airways but were not of such severity to be of clinical concern. CONCLUSIONS A highly characterised wild-type Influenza A/California/2009 (H1N1) virus manufactured for clinical use was shown to induce a good infectivity profile in human volunteers. This clinical challenge model can be used for evaluating potential efficacy of vaccines and anti-viral therapeutics. TRIAL REGISTRATION NCT02014870.
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Affiliation(s)
- Jeannette M Watson
- Immune Targeting Systems Ltd, London BioScience Innovation Centre, 2 Royal College Street, London, NW1 0NH, UK.
| | - James N Francis
- Immune Targeting Systems Ltd, London BioScience Innovation Centre, 2 Royal College Street, London, NW1 0NH, UK.
| | - Sofie Mesens
- SGS LSS, Clinical Research Unit, Antwerpen, Belgium.
| | - Gabriel A Faiman
- Immune Targeting Systems Ltd, London BioScience Innovation Centre, 2 Royal College Street, London, NW1 0NH, UK.
| | - Jill Makin
- Jill Makin Consulting Ltd, 7 Cholmondeley Road, West Kirby, Wirral, CH48 7HB, UK.
| | - Peter Patriarca
- Biologics Consulting Group, INC, 1317 King Street, Alexandria, VA, 22314, USA.
| | - John J Treanor
- University of Rochester Medical Center, 601 Elmwood Avenue, Box 689, Rochester, NY, 14642, USA.
| | - Bertrand Georges
- Immune Targeting Systems Ltd, London BioScience Innovation Centre, 2 Royal College Street, London, NW1 0NH, UK.
| | - Campbell J Bunce
- Immune Targeting Systems Ltd, London BioScience Innovation Centre, 2 Royal College Street, London, NW1 0NH, UK.
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18
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Standardization of Nucleic Acid Tests for Clinical Measurements of Bacteria and Viruses. J Clin Microbiol 2014; 53:2008-14. [PMID: 25392365 DOI: 10.1128/jcm.02136-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nucleic acid-based tests for infectious diseases currently used in the clinical laboratory and in point-of-care devices are diverse. Measurement challenges associated with standardization of quantitative viral load testing are discussed in relation to human cytomegalovirus, BK virus, and Epstein-Barr virus, while the importance of defining the performance of qualitative methods is illustrated with Mycobacterium tuberculosis and influenza virus. The development of certified reference materials whose values are traceable to higher-order standards and reference measurement procedures, using, for instance, digital PCR, will further contribute to the understanding of analytical performance characteristics and promote clinical data comparability.
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19
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Krejcova L, Nguyen HV, Hynek D, Guran R, Adam V, Kizek R. Paramagnetic Particles and PNA Probe for Automated Separation and Electrochemical Detection of Influenza. Chromatographia 2014. [DOI: 10.1007/s10337-014-2737-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Zumla A, Al-Tawfiq JA, Enne VI, Kidd M, Drosten C, Breuer J, Muller MA, Hui D, Maeurer M, Bates M, Mwaba P, Al-Hakeem R, Gray G, Gautret P, Al-Rabeeah AA, Memish ZA, Gant V. Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections--needs, advances, and future prospects. THE LANCET. INFECTIOUS DISEASES 2014; 14:1123-1135. [PMID: 25189349 PMCID: PMC7106435 DOI: 10.1016/s1473-3099(14)70827-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Respiratory tract infections rank second as causes of adult and paediatric morbidity and mortality worldwide. Respiratory tract infections are caused by many different bacteria (including mycobacteria) and viruses, and rapid detection of pathogens in individual cases is crucial in achieving the best clinical management, public health surveillance, and control outcomes. Further challenges in improving management outcomes for respiratory tract infections exist: rapid identification of drug resistant pathogens; more widespread surveillance of infections, locally and internationally; and global responses to infections with pandemic potential. Developments in genome amplification have led to the discovery of several new respiratory pathogens, and sensitive PCR methods for the diagnostic work-up of these are available. Advances in technology have allowed for development of single and multiplexed PCR techniques that provide rapid detection of respiratory viruses in clinical specimens. Microarray-based multiplexing and nucleic-acid-based deep-sequencing methods allow simultaneous detection of pathogen nucleic acid and multiple antibiotic resistance, providing further hope in revolutionising rapid point of care respiratory tract infection diagnostics.
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Affiliation(s)
- Alimuddin Zumla
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK; Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia.
| | | | - Virve I Enne
- Division of Infection and Immunity, University College London, London, UK
| | - Mike Kidd
- Division of Infection and Immunity, University College London, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Judy Breuer
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Marcel A Muller
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - David Hui
- Division of Respiratory Medicine and Stanley Ho Center for emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong
| | - Markus Maeurer
- Therapeutic Immunology, Departments of Laboratory Medicine and Microbiology, Tumour and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Matthew Bates
- Division of Infection and Immunity, University College London, London, UK; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Peter Mwaba
- UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Rafaat Al-Hakeem
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Gregory Gray
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Philippe Gautret
- Assistance Publique Hôpitaux de Marseille, CHU Nord, Pôle Infectieux, Institut Hospitalo-Universitaire Méditerranée Infection & Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), Marseille, France
| | - Abdullah A Al-Rabeeah
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Ziad A Memish
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; Al-Faisal University, Riyadh, Saudi Arabia
| | - Vanya Gant
- Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
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