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Park HJ, Yang SC, Choo J. Early Diagnosis of Influenza Virus A Using Surface-enhanced Raman Scattering-based Lateral Flow Assay. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.11021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hyun Ji Park
- Department of Bionano Technology; Hanyang University; Ansan South Korea
| | - Sung Chul Yang
- School of Architectural Engineering; Hongik University; Sejong South Korea
| | - Jaebum Choo
- Department of Bionano Technology; Hanyang University; Ansan South Korea
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Delangue J, Roca Sanchez Y, Piorkowski G, Bessaud M, Baronti C, Thirion-Perrier L, Mafayle RL, Ardaya CA, Aguilera GA, Guzman JR, Riera JL, de Lamballerie X. Viral aetiology influenza like illnesses in Santa Cruz, Bolivia (2010-2012). Virol J 2014; 11:35. [PMID: 24564892 PMCID: PMC4015617 DOI: 10.1186/1743-422x-11-35] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/10/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Acute respiratory infections represent a serious public health issue worldwide but virological aetiologies of Influenza Like Illnesses (ILIs) remain largely unknown in developing countries. This study represents the first attempt to characterise viral aetiologies of ILIs in Bolivia. METHODS It was performed in Santa Cruz city from January 2010 to September 2012, based on 564 naso-pharyngeal swabs collected in a National Reference Laboratory and real-time PCR techniques, viral cultures and phylogenetic analyses. RESULTS 50.2% of samples were positive for at least one virus with influenza viruses (Flu A: ~15%; Flu B: ~9%), rhinoviruses (~8%), coronaviruses (~5%) and hRSV (~4%) being the most frequently identified. The pattern of viral infections varied according to age groups. The elucidation rate was the highest (>60%) amongst patients under 10 yo and the lowest (<40%) amongst patients ≥60 yo. Nearly 3% of samples showed dual viral infections. Epidemiological peaks were associated with a predominant virus but generally included 30-50% of infections by different viruses. Unexpectedly, the frequency of influenza in the 0-4 yo population was very low and a complete hRSV eclipse occurred in 2011. Genetic analyses indicated that distinct evolutionary lineages of Flu A(H1N1)pdm2009, Flu A/H3N2 and Flu B have co-circulated in Bolivia in the study period, originating from Central and North America, Europe, Asia and Australia. CONCLUSION Our results emphasise the requirement for a reinforced epidemiological and genetic follow-up of influenza and other ILIs in Bolivia to further inform the preparation of vaccines used in the region, guide vaccination campaigns and improve the medical management of patients.
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Affiliation(s)
- Julie Delangue
- IRD French Institute of Research for Development, EHESP French School of Public Health, UMR_D 190 "Emergence des Pathologies Virales", Aix Marseille Univ, 13005 Marseille, France.
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3
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Mycoplasma removal: simple curative methods for viral supernatants. J Virol Methods 2012; 187:234-7. [PMID: 23117065 DOI: 10.1016/j.jviromet.2012.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/11/2012] [Accepted: 09/17/2012] [Indexed: 11/22/2022]
Abstract
As a partner of the European Virus Archive (EVA) FP7 infrastructure, our research group is maintaining and developing a large virus collection. To meet the standards of the quality management system adopted by all European Virus Archive partners, the detection and eradication of mycoplasma in cell culture supernatants (stored at -80°C or freeze-dried) has to be improved. Although the methods for mycoplasma elimination from infected cell lines were largely described, the decontamination procedures of precious cell culture supernatants was poorly documented. In this study, a large panel of mycoplasma-contaminated virus stocks (enveloped and non enveloped, RNA and DNA viruses) was tested successfully for mycoplasma removal using two simple optimized methods. These easy-to-perform protocols, using respectively Plasmocin™ (InvivoGen, Cayla, France) and chloroform, were shown to remove mycoplasma completely from cell supernatant without incidence in viral infectivity.
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Pascalis H, Temmam S, Turpin M, Rollot O, Flahault A, Carrat F, de Lamballerie X, Gérardin P, Dellagi K. Intense co-circulation of non-influenza respiratory viruses during the first wave of pandemic influenza pH1N1/2009: a cohort study in Reunion Island. PLoS One 2012; 7:e44755. [PMID: 22984554 PMCID: PMC3440351 DOI: 10.1371/journal.pone.0044755] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/07/2012] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE The aim of the present study was to weigh up, at the community level, the respective roles played by pandemic Influenza (pH1N1) virus and co-circulating human Non-Influenza Respiratory Viruses (NIRVs) during the first wave of the 2009 pH1N1 pandemic. METHODS A population-based prospective cohort study was conducted in Reunion Island during the austral winter 2009 (weeks 30-44) that allowed identification of 125 households with at least one member who developed symptoms of Influenza-like illness (ILI). Three consecutive nasal swabs were collected from each household member (443 individuals) on day 0, 3 and 8 post-ILI report and tested for pH1N1 and 15 NIRVs by RT-PCR. RESULTS Two successive waves of viral infections were identified: a first wave (W33-37) when pH1N1 was dominant and co-circulated with NIRVs, sharply interrupted by a second wave (W38-44), almost exclusively composed of NIRVs, mainly human Rhinoviruses (hRV) and Coronaviruses (hCoV). Data suggest that some interference may occur between NIRVs and pH1N1 when they co-circulate within the same household, where NIRVs were more likely to infect pH1N1 negative individuals than pH1N1 positive peers (relative risk: 3.13, 95% CI: 1.80-5.46, P<0.001). Viral shedding was significantly shorter (P = 0.035) in patients who were co-infected by pH1N1 and NIRV or by two different NIRVs compared to those who were infected with only one virus, whatever this virus was (pH1N1 or NIRVs). Although intense co-circulation of NIRVs (especially hRV) likely brought pH1N1 under the detection threshold, it did not prevent spread of the pandemic Influenza virus within the susceptible population nor induction of an extensive herd immunity to it. CONCLUSION Our results suggest that NIRV co-infections during Influenza epidemics may act as cofactors that contribute to shape an outbreak and modulate the attack rate. They further warrant broad spectrum studies to fully understand viral epidemics.
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Affiliation(s)
- Hervé Pascalis
- Centre de Recherche et de Veille sur les maladies émergentes dans l’Océan Indien (CRVOI), Sainte-Clotilde, La Réunion, France
- Institut de Recherche pour le Développement (IRD), Sainte-Clotilde, La Réunion, France
| | - Sarah Temmam
- Centre de Recherche et de Veille sur les maladies émergentes dans l’Océan Indien (CRVOI), Sainte-Clotilde, La Réunion, France
- Ecologie microbienne (UMR 5557) CNRS-Université de Claude Bernard, Lyon, France
| | - Magali Turpin
- Centre de Recherche et de Veille sur les maladies émergentes dans l’Océan Indien (CRVOI), Sainte-Clotilde, La Réunion, France
- Institut de Recherche pour le Développement (IRD), Sainte-Clotilde, La Réunion, France
| | - Olivier Rollot
- Centre d’Investigation Clinique-Epidémiologie Clinique (CIC-EC), (INSERM/CHR/Université/URMLR), Centre Hospitalier Régional, Saint-Pierre, La Réunion, France
| | - Antoine Flahault
- Ecole des Hautes Etudes en Santé Publique, EHESP, Rennes, France
| | - Fabrice Carrat
- Epidémiologie des Maladies Infectieuses et Modélisation (UMR-S 707), INSERM-Université Pierre et Marie Curie, Paris, France
| | - Xavier de Lamballerie
- Unité des Virus Emergents (UMR-S 190), IRD-Université de la Méditerranée, Marseille, France
| | - Patrick Gérardin
- Centre d’Investigation Clinique-Epidémiologie Clinique (CIC-EC), (INSERM/CHR/Université/URMLR), Centre Hospitalier Régional, Saint-Pierre, La Réunion, France
| | - Koussay Dellagi
- Centre de Recherche et de Veille sur les maladies émergentes dans l’Océan Indien (CRVOI), Sainte-Clotilde, La Réunion, France
- Institut de Recherche pour le Développement (IRD), Sainte-Clotilde, La Réunion, France
- * E-mail:
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Thiberville SD, Ninove L, Vu Hai V, Botelho-Nevers E, Gazin C, Thirion L, Salez N, de Lamballerie X, Charrel R, Brouqui P. The viral etiology of an influenza-like illness during the 2009 pandemic. J Med Virol 2012; 84:1071-9. [PMID: 22585724 PMCID: PMC7166619 DOI: 10.1002/jmv.23265] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many viruses are known to cause influenza-like illness (ILI); however, in nearly 50% of patients, the etiologic agent remains unknown. The distribution of viruses in patients with ILI was investigated during the 2009 A/H1N1 influenza pandemic (A/H1N1p). From June 2009 to January 2010, 660 patients with suspected influenza were questioned and examined, and nasal swabs were collected. All patient samples were tested for influenza virus, and 286 negative nasal swabs were tested further for 18 other respiratory viruses using real-time RT-PCR. Two waves of ILI were observed in the epidemic curve (weeks 35-42 and 42-49). At least eight viruses co-circulated during this period: human rhinovirus (HRV) (58), parainfluenza 1-4 viruses (PIV) (9), human Coronavirus (hCoV) OC43 (9), enterovirus (5), adenovirus (AdV) (4), and human metapneumovirus (hMPV) (2); however, 204 samples remained negative for all viruses tested. ILI symptoms, according to the Centers for Disease Control and Prevention criteria for ILI definition, were reported in 75% of cases. These patients had positive swabs for A/H1N1p, HRV, hCoV-OC43, PIV, AdV, and hMPV without significant difference with non-ILI patients. This study found that many respiratory viruses circulated during this period and that the A/H1N1p did not impact on the kinetics of other respiratory viruses. The proportion of non-documented cases remains high. ILI could not distinguish A/H1N1p infection from that due to other respiratory viruses. However, in multivariate anlaysis, cough, chills, hyperemia, and dyspnea were associated significantly with influenza virus versus other respiratory viruses.
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Affiliation(s)
- S D Thiberville
- UMR 190 (Aix-Marseille Univ IRD EHESP), Emergence des Pathologies Virales, Marseille, France
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6
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Pascalis H, Temmam S, Wilkinson DA, Dsouli N, Turpin M, de Lamballerie X, Dellagi K. Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. PLoS One 2012; 7:e43742. [PMID: 22952752 PMCID: PMC3428279 DOI: 10.1371/journal.pone.0043742] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/23/2012] [Indexed: 01/08/2023] Open
Abstract
Background/Objectives Molecular epidemiology is a powerful tool to decipher the dynamics of viral transmission, quasispecies temporal evolution and origins. Little is known about the pH1N1 molecular dynamics in general population. A prospective study (CoPanFlu-RUN) was carried out in Reunion Island to characterize pH1N1 genetic variability and molecular evolution occurring in population during the pH1N1 Influenza pandemic in 2009. Methodology We directly amplified pH1N1 genomes from 28 different nasal swabs (26 individuals from 21 households). Fifteen strains were fully sequenced and 13 partially. This includes pairs of sequences from different members of 5 separate households; and two pairs from individuals, collected at different times. We assessed the molecular evolution of pH1N1 by genetic variability and phylogenetic analyses. Principal Findings We found that i) Reunion pH1N1 sequences stemmed from global “clade 7” but shaped two phylogenetic sub-clades; ii) D239E mutation was identified in the hemagglutinin protein of all Reunion sequences, a mutation which has been associated elsewhere with mild-, upper-respiratory tract pH1N1 infecting strains; iii) Date estimates from molecular phylogenies predicted clade emergence some time before the first detection of pH1N1 by the epidemiological surveillance system; iv) Phylogenetic relatedness was observed between Reunion pH1N1 viruses and those from other countries in South-western Indian Ocean area; v) Quasispecies populations were observed within households and individuals of the cohort-study. Conclusions Surveillance and/or prevention systems presently based on Influenza virus sequence variation should take into account that the majority of studies of pH1N1 Influenza generate genetic data for the HA/NA viral segments obtained from hospitalized-patients, which is potentially non-representative of the overall viral diversity within whole populations. Our observations highlight the importance of collecting unbiased data at the community level and conducting whole genome analysis to accurately understand viral dynamics.
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Affiliation(s)
- Hervé Pascalis
- GIS CRVOI, Centre de Recherche et de Veille sur maladies émergentes dans l'Océan Indien, Plateforme technologique CYROI, Saint-Denis, La Réunion, France.
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7
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Motte A, Roquelaure B, Galambrun C, Bernard F, Zandotti C, Colson P. Hepatitis E in three immunocompromized children in southeastern France. J Clin Virol 2011; 53:162-6. [PMID: 22177988 DOI: 10.1016/j.jcv.2011.11.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/09/2011] [Accepted: 11/16/2011] [Indexed: 12/17/2022]
Abstract
Hepatitis E virus (HEV) causes an emerging autochthonous disease in developed countries where links with a viral porcine reservoir have been evidenced. Moreover, chronic HEV infection and associated-cirrhosis have been described in severely immunocompromized patients. Nonetheless, only few studies have focused on pediatric HEV infections worldwide and only four autochthonous cases have been reported in children in developed countries. We describe here acute hepatitis E in three immunocompromized children. Case no. 1 was a 9-year-old liver transplant recipient girl in whom H1N1 2009 flu infection was diagnosed concurrently with hepatitis E. Case no. 2 was a 12-year-old boy presenting early medullar relapse of lymphoblastic leukemia of type B and in whom HEV RNA was detected over a 29-week period. Case no. 3 was a 9-year-old boy with a rare primary immunodeficiency due to XIAP deficiency. HEV infections were all autochthonously acquired and involved different viruses classified as subtype f, c, and e of genotype 3, which are those described in autochthonous cases in Europe. These three observations prompt to consider HEV as a causative agent of hepatitis in children in developed countries, and to perform particularly HEV testing in those severely immunocompromized who may develop chronic hepatitis E.
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Affiliation(s)
- Anne Motte
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, 264 rue Saint-Pierre, 13385 Marseille CEDEX 05, France
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Murray M, Grant J, Bryce E, Chilton P, Forrester L. Facial protective equipment, personnel, and pandemics: impact of the pandemic (H1N1) 2009 virus on personnel and use of facial protective equipment. Infect Control Hosp Epidemiol 2011; 31:1011-6. [PMID: 20731598 DOI: 10.1086/656564] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Before the emergence of the pandemic (H1N1) 2009 virus, estimates of the stockpiles of facial protective equipment (FPE) and the impact that information had on personnel during a pandemic varied. OBJECTIVE To describe the impact of H1N1 on FPE use and hospital employee absenteeism. Setting. One tertiary care hospital and 2 community hospitals in the Vancouver Coastal Health (VCH) region, Vancouver, Canada. Patients. All persons with influenza-like illness admitted to the 3 VCH facilities during the period from June 28 through December 19, 2009. METHODS Data on patients and on FPE use were recorded prospectively. Data on salaried employee absenteeism were recorded during the period from August 1 through December 19, 2009. RESULTS During the study period, 865 patients with influenza-like illness were admitted to the 3 VCH facilities. Of these patients, 149 (17.2%) had laboratory-confirmed H1N1 influenza infection. The mean duration of hospital stay for these patients was 8.9 days, and the mean duration of intensive care unit stay was 9.2 days. A total of 134,281 masks and 173,145 N95 respirators (hereafter referred to as respirators) were used during the 24-week epidemic, double the weekly use of both items, compared with the previous influenza season. A ratio of 3 masks to 4 respirators was observed. Use of disposable eyewear doubled. Absenteeism mirrored the community epidemiologic curve, with a 260% increase in sick calls at the epidemic peak, compared with the nadir. CONCLUSION Overall, FPE use more than doubled, compared with the previous influenza season, with respirator use exceeding literature estimates. A significant proportion of FPE resources were used while managing suspected cases. Planners should prepare for at least a doubling in mask and respirator use, and a 3.6-fold increase in staff sick calls.
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Affiliation(s)
- Melanie Murray
- Department of Internal Medicine, Division of Infectious Disease, University of British Columbia, Vancouver, British Columbia, Canada
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9
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Ninove L, Nougairede A, Gazin C, Thirion L, Delogu I, Zandotti C, Charrel RN, De Lamballerie X. RNA and DNA bacteriophages as molecular diagnosis controls in clinical virology: a comprehensive study of more than 45,000 routine PCR tests. PLoS One 2011; 6:e16142. [PMID: 21347398 PMCID: PMC3036576 DOI: 10.1371/journal.pone.0016142] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 12/06/2010] [Indexed: 01/09/2023] Open
Abstract
Real-time PCR techniques are now commonly used for the detection of viral genomes in various human specimens and require for validation both external and internal controls (ECs and ICs). In particular, ICs added to clinical samples are necessary to monitor the extraction, reverse transcription, and amplification steps in order to detect false-negative results resulting from PCR-inhibition or errors in the technical procedure. Here, we performed a large scale evaluation of the use of bacteriophages as ICs in routine molecular diagnosis. This allowed to propose simple standardized procedures (i) to design specific ECs for both DNA and RNA viruses and (ii) to use T4 (DNA) or MS2 (RNA) phages as ICs in routine diagnosis. Various technical formats for using phages as ICs were optimised and validated. Subsequently, T4 and MS2 ICs were evaluated in routine real-time PCR or RT-PCR virological diagnostic tests, using a series of 8,950 clinical samples (representing 36 distinct specimen types) sent to our laboratory for the detection of a variety of DNA and RNA viruses. The frequency of inefficient detection of ICs was analyzed according to the nature of the sample. Inhibitors of enzymatic reactions were detected at high frequency in specific sample types such as heparinized blood and bone marrow (>70%), broncho-alveolar liquid (41%) and stools (36%). The use of T4 and MS2 phages as ICs proved to be cost-effective, flexible and adaptable to various technical procedures of real-time PCR detection in virology. It represents a valuable strategy for enhancing the quality of routine molecular diagnosis in laboratories that use in-house designed diagnostic systems, which can conveniently be associated to the use of specific synthetic ECs. The high rate of inhibitors observed in a variety of specimen types should stimulate the elaboration of improved technical protocols for the extraction and amplification of nucleic acids.
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Affiliation(s)
- Laetitia Ninove
- UMR190, Université de la Méditerranée and Institut de Recherche pour le Développement, Marseille, France.
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Evaluation of twelve real-time reverse transcriptase PCR primer-probe sets for detection of pandemic influenza A/H1N1 2009 virus. J Clin Microbiol 2011; 49:1434-40. [PMID: 21289144 DOI: 10.1128/jcm.01914-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time reverse transcriptase PCR (rRT-PCR) assays have greatly contributed to the detection, control, and prevention of the pandemic influenza A/H1N1 2009 virus. To improve the rRT-PCR assays for detection of pandemic influenza A/H1N1 2009 virus, we evaluated the sensitivity, specificity, and performance of 12 rRT-PCR primer-probe sets [SW (a) to SW (l)] using a panel of virus strains and clinical specimens. These primer-probe sets were derived from published work and designed for detecting the hemagglutinin (HA) or the neuraminidase (NA) gene of the pandemic influenza A/H1N1 2009 virus. A primer-probe set, SW (CDC), developed by the Centers for Disease Control and Prevention (U.S. CDC) to target the HA gene of pandemic influenza A/H1N1 2009 virus, was used as a referee method. Our results demonstrated that although all primer-probe sets in this study had as high as 98.4 to 100% in silico coverage, some of the primer-probe sets had better specificity, sensitivity, and amplification efficiency than others. Two primer-probe sets, SW (h) and SW (l), which target the NA gene of pandemic influenza A/H1N1 2009 virus, were highly sensitive (10(4) copies/reaction), had high detection rates (56/60, P = 0.134, and 59/60, P = 1.000), and showed ideal specificity compared with SW (CDC). In addition, a cocktail of primer-probe sets targeted to the HA and NA genes displayed higher detection sensitivity than primer-probe sets targeting HA or NA alone, indicating that for practical applications, a combination of primer-probes targeting HA and NA genes is the best option for the detection of pandemic influenza A/H1N1 2009 virus.
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Botelho-Nevers E, Gautret P, Benarous L, Charrel R, Felkai P, Parola P. Travel-related influenza A/H1N1 infection at a rock festival in Hungary: one virus may hide another one. J Travel Med 2010; 17:197-8. [PMID: 20536890 DOI: 10.1111/j.1708-8305.2010.00410.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mass gathering is well known to concentrate and amplify the transmission of infectious respiratory diseases. Here we report a possible case of coinfection with influenza A/H1N1 and varicella in a young French traveler returning from a rock festival in Hungary. We report a cluster of influenza A/H1N1 cases at this festival.
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Abstract
Molecular-based techniques for detecting influenza viruses have become an integral component of human and animal surveillance programs in the last two decades. The recent pandemic of the swine-origin influenza A virus (H1N1) and the continuing circulation of highly pathogenic avian influenza A virus (H5N1) further stress the need for rapid and accurate identification and subtyping of influenza viruses for surveillance, outbreak management, diagnosis and treatment. There has been remarkable progress on the detection and molecular characterization of influenza virus infections in clinical, mammalian, domestic poultry and wild bird samples in recent years. The application of these techniques, including reverse transcriptase-PCR, real-time PCR, microarrays and other nucleic acid sequencing-based amplifications, have greatly enhanced the capability for surveillance and characterization of influenza viruses.
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Affiliation(s)
- Ruixue Wang
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Development and preliminary evaluation of a rapid oligochromatographic assay for specific detection of new human influenza A H1N1 virus. J Clin Microbiol 2010; 48:1801-5. [PMID: 20220170 DOI: 10.1128/jcm.01487-09] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new oligochromatographic assay, Speed-Oligo Novel Influenza A H1N1, was designed and optimized for the specific detection of the 2009 influenza A H1N1 virus. The assay is based on a PCR method coupled to detection of PCR products by means of a dipstick device. The target sequence is a 103-bp fragment within the hemagglutinin gene. The analytical sensitivity of the new assay was measured with serial dilutions of a plasmid that contained the target sequence, and we determined that down to one copy per reaction of the plasmid was reliably detected. Diagnostic performance was assessed with 103 RNAs from suspected cases (40 positive and 63 negative results) previously analyzed with a reference real-time PCR technique. All positive cases were confirmed, and no false-positive results were detected with the new assay. No cross-reactions were observed when other viral strains or clinical samples with other respiratory viruses were tested. According to these results, this new assay has 100% sensitivity and specificity. The turnaround time for the whole procedure was 140 min. The assay may be especially useful for the specific detection of 2009 H1N1 virus in laboratories not equipped with real-time PCR instruments.
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Nougairède A, Ninove L, Zandotti C, Salez N, Mantey K, Resseguier N, Gazin C, Raoult D, Charrel RN, de Lamballerie X. Novel virus influenza A (H1N1sw) in South-Eastern France, April-August 2009. PLoS One 2010; 5:e9214. [PMID: 20174643 PMCID: PMC2822845 DOI: 10.1371/journal.pone.0009214] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 01/25/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In April 2009, the first cases of pandemic (H1N1)-2009 influenza [H1N1sw] virus were detected in France. Virological surveillance was undertaken in reference laboratories of the seven French Defence Zones. METHODOLOGY/PRINCIPAL FINDINGS We report results of virological analyses performed in the Public Hospitals of Marseille during the first months of the outbreak. (i) Nasal swabs were tested using rapid influenza diagnostic test (RIDT) and two RT-PCR assays. Epidemiological characteristics of the 99 first suspected cases were analyzed, including detection of influenza virus and 18 other respiratory viruses. During three months, a total of 1,815 patients were tested (including 236 patients infected H1N1sw virus) and distribution in age groups and results of RIDT were analyzed. (ii) 600 sera received before April 2009 and randomly selected from in-patients were tested by a standard hemagglutination inhibition assay for antibody to the novel H1N1sw virus. (iii) One early (May 2009) and one late (July 2009) viral isolates were characterized by sequencing the complete hemagglutinine and neuraminidase genes. (iiii) Epidemiological characteristics of a cluster of cases that occurred in July 2009 in a summer camp were analyzed. CONCLUSIONS/SIGNIFICANCE This study presents new virological and epidemiological data regarding infection by the pandemic A/H1N1 virus in Europe. Distribution in age groups was found to be similar to that previously reported for seasonal H1N1. The first seroprevalence data made available for a European population suggest a previous exposure of individuals over 40 years old to influenza viruses antigenically related to the pandemic (H1N1)-2009 virus. Genomic analysis indicates that strains harbouring a new amino-acid pattern in the neuraminidase gene appeared secondarily and tended to supplant the first strains. Finally, in contrast with previous reports, our data support the use of RIDT for the detection of infection in children, especially in the context of the investigation of grouped cases.
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MESH Headings
- Adolescent
- Adult
- Age Distribution
- Age Factors
- Aged
- Antibodies, Viral/immunology
- Child
- Child, Preschool
- Disease Outbreaks
- Female
- France/epidemiology
- Humans
- Infant
- Infant, Newborn
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza, Human/blood
- Influenza, Human/diagnosis
- Influenza, Human/epidemiology
- Male
- Middle Aged
- Phylogeny
- Prevalence
- Reverse Transcriptase Polymerase Chain Reaction
- Seasons
- Sequence Analysis, DNA
- Viral Load
- Young Adult
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Affiliation(s)
- Antoine Nougairède
- Unité Mixte de Recherche 190: Unité des Virus Emergents, Université de la Méditerranée et Institut de Recherche pour le Développement, Marseille, France
- Laboratoire de Virologie, Pôle Hospitalier de Microbiologie et Maladies Infectieuses (Assistance Publique – Hôpitaux de Marseille), Marseille, France
| | - Laetitia Ninove
- Unité Mixte de Recherche 190: Unité des Virus Emergents, Université de la Méditerranée et Institut de Recherche pour le Développement, Marseille, France
- Laboratoire de Virologie, Pôle Hospitalier de Microbiologie et Maladies Infectieuses (Assistance Publique – Hôpitaux de Marseille), Marseille, France
| | - Christine Zandotti
- Laboratoire de Virologie, Pôle Hospitalier de Microbiologie et Maladies Infectieuses (Assistance Publique – Hôpitaux de Marseille), Marseille, France
| | - Nicolas Salez
- Unité Mixte de Recherche 190: Unité des Virus Emergents, Université de la Méditerranée et Institut de Recherche pour le Développement, Marseille, France
| | - Karine Mantey
- South Interregional Epidemiology Unit, French Institute for Public Health Surveillance, Marseille, France
| | - Noémie Resseguier
- South Interregional Epidemiology Unit, French Institute for Public Health Surveillance, Marseille, France
| | - Céline Gazin
- Laboratoire de Virologie, Pôle Hospitalier de Microbiologie et Maladies Infectieuses (Assistance Publique – Hôpitaux de Marseille), Marseille, France
| | - Didier Raoult
- Laboratoire de Virologie, Pôle Hospitalier de Microbiologie et Maladies Infectieuses (Assistance Publique – Hôpitaux de Marseille), Marseille, France
| | - Rémi N. Charrel
- Unité Mixte de Recherche 190: Unité des Virus Emergents, Université de la Méditerranée et Institut de Recherche pour le Développement, Marseille, France
- Laboratoire de Virologie, Pôle Hospitalier de Microbiologie et Maladies Infectieuses (Assistance Publique – Hôpitaux de Marseille), Marseille, France
| | - Xavier de Lamballerie
- Unité Mixte de Recherche 190: Unité des Virus Emergents, Université de la Méditerranée et Institut de Recherche pour le Développement, Marseille, France
- Laboratoire de Virologie, Pôle Hospitalier de Microbiologie et Maladies Infectieuses (Assistance Publique – Hôpitaux de Marseille), Marseille, France
- * E-mail:
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Nougairede A, Ninove L, Zandotti C, de Lamballerie X, Gazin C, Drancourt M, La Scola B, Raoult D, Charrel RN. Point of care strategy for rapid diagnosis of novel A/H1N1 influenza virus. PLoS One 2010; 5:e9215. [PMID: 20174646 PMCID: PMC2822848 DOI: 10.1371/journal.pone.0009215] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Accepted: 01/25/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Within months of the emergence of the novel A/H1N1 pandemic influenza virus (nA/H1N1v), systematic screening for the surveillance of the pandemic was abandoned in France and in some other countries. At the end of June 2009, we implemented, for the public hospitals of Marseille, a Point Of Care (POC) strategy for rapid diagnosis of the novel A/H1N1 influenza virus, in order to maintain local surveillance and to evaluate locally the kinetics of the pandemic. METHODOLOGY/PRINCIPAL FINDINGS Two POC laboratories, located in strategic places, were organized to receive and test samples 24 h/24. POC strategy consisted of receiving and processing naso-pharyngeal specimens in preparation for the rapid influenza diagnostic test (RIDT) and real-time RT-PCR assay (rtRT-PCR). This strategy had the theoretical capacity of processing up to 36 samples per 24 h. When the flow of samples was too high, the rtRT-PCR test was abandoned in the POC laboratories and transferred to the core virology laboratory. Confirmatory diagnosis was performed in the core virology laboratory twice a day using two distinct rtRT-PCR techniques that detect either influenza A virus or nA/N1N1v. Over a period of three months, 1974 samples were received in the POC laboratories, of which 111 were positive for nA/H1N1v. Specificity and sensitivity of RIDT were 100%, and 57.7% respectively. Positive results obtained using RIDT were transmitted to clinical practitioners in less than 2 hours. POC processed rtRT-PCR results were available within 7 hours, and rtRT-PCR confirmation within 24 hours. CONCLUSIONS/SIGNIFICANCE The POC strategy is of benefit, in all cases (with or without rtRT-PCR assay), because it provides continuous reception/processing of samples and reduction of the time to provide consolidated results to the clinical practitioners. We believe that implementation of the POC strategy for the largest number of suspect cases may improve the quality of patient care and our knowledge of the epidemiology of the pandemic.
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Affiliation(s)
- Antoine Nougairede
- Fédération de Microbiologie, Assistance Publique - Hôpitaux de Marseille, Marseille, France
- Unité des Virus Emergents, UMR 190 “Emergence des pathologies virales”, Université de la Méditerranée & Institut de Recherche pour le Développement, Marseille, France
| | - Laetitia Ninove
- Fédération de Microbiologie, Assistance Publique - Hôpitaux de Marseille, Marseille, France
- Unité des Virus Emergents, UMR 190 “Emergence des pathologies virales”, Université de la Méditerranée & Institut de Recherche pour le Développement, Marseille, France
| | - Christine Zandotti
- Fédération de Microbiologie, Assistance Publique - Hôpitaux de Marseille, Marseille, France
| | - Xavier de Lamballerie
- Fédération de Microbiologie, Assistance Publique - Hôpitaux de Marseille, Marseille, France
- Unité des Virus Emergents, UMR 190 “Emergence des pathologies virales”, Université de la Méditerranée & Institut de Recherche pour le Développement, Marseille, France
| | - Celine Gazin
- Fédération de Microbiologie, Assistance Publique - Hôpitaux de Marseille, Marseille, France
| | - Michel Drancourt
- Fédération de Microbiologie, Assistance Publique - Hôpitaux de Marseille, Marseille, France
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR CNRS 6236 IRD 3R198, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Bernard La Scola
- Fédération de Microbiologie, Assistance Publique - Hôpitaux de Marseille, Marseille, France
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR CNRS 6236 IRD 3R198, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Didier Raoult
- Fédération de Microbiologie, Assistance Publique - Hôpitaux de Marseille, Marseille, France
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR CNRS 6236 IRD 3R198, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Remi N. Charrel
- Fédération de Microbiologie, Assistance Publique - Hôpitaux de Marseille, Marseille, France
- Unité des Virus Emergents, UMR 190 “Emergence des pathologies virales”, Université de la Méditerranée & Institut de Recherche pour le Développement, Marseille, France
- * E-mail:
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16
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Nougairede A, Ninove L, Zandotti C, Thiberville SD, Gazin C, La Scola B, Charrel RN, de Lamballerie X. Interim report on the A/H1N1 influenza virus pandemic in Marseille, France, April-November 2009. Clin Microbiol Infect 2010; 16:322-5. [PMID: 20121828 PMCID: PMC7162242 DOI: 10.1111/j.1469-0691.2010.03168.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here the results of a 7-month survey of the influenza A/H1N1 pandemic in the Virology laboratory of the public hospitals of Marseille (April–November 2009). In total, 8 587 samples were analysed during this period, of which 1 974 (23%) were positive for the novel influenza variant. The analysis of results obtained using rapid influenza diagnostic tests (RIDTs) revealed a global sensitivity of 49.4% (vs. molecular qRT-PCR detection), strongly correlated with age groups (varying from 30% to 58% for patients >40 age and <10, respectively), indicating that RIDTs can be helpful in accelerating the management of suspected cases. Epidemiological analysis showed that the winter influenza wave began in October in Marseille (i.e. 2 to 3 months earlier than usual seasonal influenza outbreaks) and that the majority of autochthonous cases were observed in patients younger than 20 years old, with a low number of cases in patients over 60 years old. In November 2009, 22.2% (167/754) of patients with a laboratory diagnosis of influenza A/H1N1 infection were hospitalized, of which 9% (15/167) were admitted to an intensive care unit (ICU). Patients in the extreme age groups (>40 years old and <1) were significantly more often hospitalized than others, and 2.4% of hospitalized patients died. During the last 3 weeks of the period, the average number of bed-days attributable to H1N1sw-positive patients was 31.4, of which 5.9 were in ICUs.
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Affiliation(s)
- A Nougairede
- Unité des Virus Emergents, UMR190, Université de la Méditerranée et Institut de Recherche pour le Développement, Marseille
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Brouqui P, Vu Hai V, Nougairede A, Lagier JC, Botelho E, Ninove L, Zandotti C, Charrel RN, De Lamballerie X, Raoult D. Improving the diagnostic efficiency of H1N1 2009 pandemic flu: analysis of predictive clinical signs through a prospective cohort. PLOS CURRENTS 2009; 1:RRN1120. [PMID: 20029658 PMCID: PMC2766591 DOI: 10.1371/currents.rrn1120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/25/2009] [Indexed: 11/23/2022]
Abstract
In late June 2009, we set up a dedicated flu-like illness outpatient consultation in the Infectious Diseases and Tropical Medicine department of Marseille university hospital to detect the new A/H1N1 pandemic influenza and to contain efficiently the A/H1N1 infected patients. For 3 months, we compiled data corresponding to a total of 307 patients who presented with a flu-like syndrome. 31 of them were positive for H1N1 pandemic flu through real-time RT-PCR (rRT-PCR); among them, 19 were positive for a rapid influenza detection test (RIDT). We report here the significant clinical characteristics of A/H1N1 pandemic flu patients compared with other flu-like illnesses, which were used to improve the predictive value of the diagnosis in the current epidemiological situation. We found that regardless of the prevalence of A/H1N1 positive cases in the suspected patients, the absence of cough rejects the diagnosis of A/H1N1 infection in 100% of cases. Among patients referred for flu-like illness, those with cough should be tested for A/H1N1 by RIDT. In the current situation, the PPV and NPV of RIDT for H1N1 reached 90.5% and 95.8 %, respectively. It is important to notice that the 2 RIDT-positive that were negative for H1N1 were seasonal H3N2 influenza indicating that specificity and PPV of RIDT for all influenza was 100%. Therefore, positive RIDT does not require rRT-PCR confirmatory test. Only negative RIDT should be tested with rRT-PCR assay. Respecting this algorithm would have saved up to 70,000 Euros ( 100.000 USD) for the 307 patients and would have resulted in a significant gain of time to transmit the laboratory results to the clinical ward.
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Affiliation(s)
- Philippe Brouqui
- Infectious Diseases and Tropical Medicine at Service des Maladies Infectieuses et Tropicales, CHU Nord AP-HN, URMITE CNRS/RD 6236, Faculté de Médecine, Université de la Méditérranée, Marseille, France
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Switching gears for an influenza pandemic: validation of a duplex reverse transcriptase PCR assay for simultaneous detection and confirmatory identification of pandemic (H1N1) 2009 influenza virus. J Clin Microbiol 2009; 47:3805-13. [PMID: 19794033 DOI: 10.1128/jcm.01344-09] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid methods for the detection and confirmatory identification of pandemic influenza A virus (also known as pandemic [H1N1] 2009) are of utmost importance. In this study, a conventional reverse transcriptase PCR (RT-PCR) assay for the detection of influenza A virus and the hemagglutinin of swine lineage H1 (swH1) was designed, optimized, and validated. Nucleic acids were extracted from 198 consecutive nasopharyngeal, nasal, or throat swab specimens collected early in the outbreak (127 negative specimens, 66 specimens with pandemic [H1N1] 2009 influenza virus, 3 specimens with seasonal [H1N1] influenza A virus, and 2 specimens with seasonal [H3N2] influenza A virus). The performance characteristics of the duplex RT-PCR assay were assessed and compared to those of various detection methods: a monoplex RT-PCR assay at the National Microbiology Laboratory, a real-time RT-PCR assay using a Centers for Disease Control and Prevention protocol, an in-house multiplex RT-PCR assay (targeting influenza A virus, influenza B virus, and respiratory syncytial virus), and a rapid antigen test (the Binax Now Influenza A & B assay). The sensitivity of the duplex RT-PCR assay for influenza A virus detection was 97.2%, whereas the sensitivities were 74.6%, 71.8%, 47.8%, and 12.7% for the other four assays, respectively. The duplex RT-PCR assay was also able to identify swH1 in 94% of the cases, thereby reducing the number of specimens forwarded to reference laboratories for confirmatory identification. Only a limited number of specimens that contained influenza A virus had amounts of virus that fell below the limit of detection of the assay with the swH1 primers. Overall, the duplex RT-PCR assay is a reliable method for the simultaneous detection and confirmatory identification of pandemic (H1N1) 2009 influenza virus and would be particularly attractive to laboratories without real-time RT-PCR capabilities.
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Nougairede A, Ninove L, Zandotti C, De Lamballerie X, Gazin C, Drancourt M, La Scola B, Raoult D, Charrel RN. Point of care strategy for rapid diagnosis of novel A/H1N1 influenza virus. PLOS CURRENTS 2009; 1:RRN1039. [PMID: 20025202 PMCID: PMC2762773 DOI: 10.1371/currents.rrn1039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/22/2009] [Indexed: 11/19/2022]
Abstract
In late June 2009, we implemented for public hospitals of Marseille Point Of Care strategy for rapid diagnosis of novel A/H1N1 influenza virus. During two months, we have tested more than 900 specimens in both Point Of Care laboratories. We believe that implementation of Point of Care strategy for the largest number of suspects cases may improve quality of patients care and our knowledge of the epidemiology of the pandemic.
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Affiliation(s)
- Antoine Nougairede
- Fédération de microbiologie, Assistance publique-hôpitaux de Marseille, Marseille, France ; Unité des virus Emergents, UMR 190 "Emergence des pathologies virales", Université de la Méditerranée & Institut de Recherche pour le Développement, Marseille, France
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