1
|
Kwasiborski A, Hourdel V, Balière C, Hoinard D, Grassin Q, Feher M, De La Porte Des Vaux C, Cresta M, Vanhomwegen J, Manuguerra JC, Batéjat C, Caro V. Direct metagenomic and amplicon-based Nanopore sequencing of French human monkeypox from clinical specimen. Microbiol Resour Announc 2024; 13:e0081123. [PMID: 38047654 DOI: 10.1128/mra.00811-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023] Open
Abstract
We report the whole-genome sequence of monkeypox virus obtained using MinION technology (Oxford Nanopore Technologies) from a French clinical specimen during the 2022 epidemic. Amplicon-based sequencing and shotgun metagenomic approaches were directly applied to the sample.
Collapse
Affiliation(s)
- Aurelia Kwasiborski
- Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats , Paris, France
| | - Véronique Hourdel
- Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats , Paris, France
| | - Charlotte Balière
- Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats , Paris, France
| | - Damien Hoinard
- Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats , Paris, France
| | - Quentin Grassin
- Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats , Paris, France
| | - Maxence Feher
- Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats , Paris, France
| | | | | | - Jessica Vanhomwegen
- Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats , Paris, France
| | - Jean-Claude Manuguerra
- Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats , Paris, France
| | - Christophe Batéjat
- Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats , Paris, France
| | - Valérie Caro
- Institut Pasteur, Université Paris Cité, Environment and Infectious Risks Unit, Laboratory for Urgent Response to Biological Threats , Paris, France
| |
Collapse
|
2
|
Balière C, Hourdel V, Kwasiborski A, Grassin Q, Feher M, Hoinard D, Vanhomwegen J, Taieb F, Consigny PH, Manuguerra JC, Leclercq I, Batéjat C, Caro V. Complete Genome Sequences of Monkeypox Virus from a French Clinical Sample and the Corresponding Isolated Strain, Obtained Using Nanopore Sequencing. Microbiol Resour Announc 2023; 12:e0000923. [PMID: 36971577 PMCID: PMC10112124 DOI: 10.1128/mra.00009-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
We report the whole-genome sequences of a monkeypox virus from the skin lesion of a French patient and the corresponding isolated viral strain. Both viral genomic sequences were successfully obtained by applying shotgun metagenomics using the Oxford Nanopore Technologies sequencing approach.
Collapse
|
3
|
Batéjat C, Grassin Q, Feher M, Hoinard D, Vanhomwegen J, Manuguerra JC, Leclercq I. Heat inactivation of monkeypox virus. J Biosaf Biosecur 2022; 4:121-123. [PMID: 36245694 PMCID: PMC9534137 DOI: 10.1016/j.jobb.2022.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 01/26/2023] Open
Abstract
Different kinds of media spiked with monkeypox virus (MPXV) were subjected to heat inactivation at different temperatures for various periods of time. The results showed that MPXV was inactivated in less than 5 min at 70 °C and less than 15 min at 60 °C, with no difference between viruses from the West African and Central African clades. The present findings could help laboratory workers to manipulate MPXV in optimal biosafety conditions and improve their protocols.
Collapse
|
4
|
ten Bosch Q, Andrianaivoarimanana V, Ramasindrazana B, Mikaty G, Rakotonanahary RJL, Nikolay B, Rahajandraibe S, Feher M, Grassin Q, Paireau J, Rahelinirina S, Randremanana R, Rakotoarimanana F, Melocco M, Rasolofo V, Pizarro-Cerdá J, Le Guern AS, Bertherat E, Ratsitorahina M, Spiegel A, Baril L, Rajerison M, Cauchemez S. Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar. PLoS Biol 2022; 20:e3001736. [PMID: 35969599 PMCID: PMC9410560 DOI: 10.1371/journal.pbio.3001736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 08/25/2022] [Accepted: 06/30/2022] [Indexed: 11/18/2022] Open
Abstract
During outbreaks, the lack of diagnostic “gold standard” can mask the true burden of infection in the population and hamper the allocation of resources required for control. Here, we present an analytical framework to evaluate and optimize the use of diagnostics when multiple yet imperfect diagnostic tests are available. We apply it to laboratory results of 2,136 samples, analyzed with 3 diagnostic tests (based on up to 7 diagnostic outcomes), collected during the 2017 pneumonic (PP) and bubonic plague (BP) outbreak in Madagascar, which was unprecedented both in the number of notified cases, clinical presentation, and spatial distribution. The extent of these outbreaks has however remained unclear due to nonoptimal assays. Using latent class methods, we estimate that 7% to 15% of notified cases were Yersinia pestis-infected. Overreporting was highest during the peak of the outbreak and lowest in the rural settings endemic to Y. pestis. Molecular biology methods offered the best compromise between sensitivity and specificity. The specificity of the rapid diagnostic test was relatively low (PP: 82%, BP: 85%), particularly for use in contexts with large quantities of misclassified cases. Comparison with data from a subsequent seasonal Y. pestis outbreak in 2018 reveal better test performance (BP: specificity 99%, sensitivity: 91%), indicating that factors related to the response to a large, explosive outbreak may well have affected test performance. We used our framework to optimize the case classification and derive consolidated epidemic trends. Our approach may help reduce uncertainties in other outbreaks where diagnostics are imperfect. The response to the 2017 plague outbreak in Madagascar was complicated by the lack of a perfect or "gold standard" diagnostic. This study shows how multiple, imperfect diagnostic tests can be used to improve the response to an outbreak.
Collapse
Affiliation(s)
- Quirine ten Bosch
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, F-75015 Paris, France
- Quantitative Veterinary Epidemiology, Department of Animal Sciences, Wageningen University and Research, Wageningen, the Netherlands
- * E-mail:
| | | | | | - Guillain Mikaty
- Environment and Infectious Risks Research Unit, Laboratory for Urgent Response to Biological Threats (ERI-CIBU), Institut Pasteur, Paris, France
| | | | - Birgit Nikolay
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, F-75015 Paris, France
| | | | - Maxence Feher
- Environment and Infectious Risks Research Unit, Laboratory for Urgent Response to Biological Threats (ERI-CIBU), Institut Pasteur, Paris, France
| | - Quentin Grassin
- Environment and Infectious Risks Research Unit, Laboratory for Urgent Response to Biological Threats (ERI-CIBU), Institut Pasteur, Paris, France
| | - Juliette Paireau
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, F-75015 Paris, France
| | | | - Rindra Randremanana
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo Madagascar
| | - Feno Rakotoarimanana
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo Madagascar
| | - Marie Melocco
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo Madagascar
| | | | - Javier Pizarro-Cerdá
- Yersinia Research Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 6047, F-75015 Paris, France
- National Reference Laboratory for Plague and other Yersiniosis, Institut Pasteur, F-75015 Paris, France
- World Health Organization Collaborating Center for Plague FRA-140, Institut Pasteur, F-75015 Paris, France
| | - Anne-Sophie Le Guern
- Yersinia Research Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 6047, F-75015 Paris, France
- National Reference Laboratory for Plague and other Yersiniosis, Institut Pasteur, F-75015 Paris, France
- World Health Organization Collaborating Center for Plague FRA-140, Institut Pasteur, F-75015 Paris, France
| | - Eric Bertherat
- World Health Organization, Health Emergency Programme, Department of Infectious Hazard Management, Geneva, Switzerland
| | - Maherisoa Ratsitorahina
- Direction, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Directorate of Health and Epidemiological Surveillance, Ministry of Public Health, Antananarivo, Madagascar
| | - André Spiegel
- Direction, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Laurence Baril
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo Madagascar
| | | | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, F-75015 Paris, France
| |
Collapse
|
5
|
Marchio A, Batejat C, Vanhomwegen J, Feher M, Grassin Q, Chazal M, Raulin O, Farges-Berth A, Reibel F, Estève V, Dejean A, Jouvenet N, Manuguerra JC, Pineau P. ddPCR increases detection of SARS-CoV-2 RNA in patients with low viral loads. Arch Virol 2021; 166:2529-2540. [PMID: 34251549 PMCID: PMC8273560 DOI: 10.1007/s00705-021-05149-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/06/2021] [Indexed: 01/16/2023]
Abstract
RT-qPCR detection of SARS-CoV-2 RNA still represents the method of reference to diagnose and monitor COVID-19. From the onset of the pandemic, however, doubts have been expressed concerning the sensitivity of this molecular diagnosis method. Droplet digital PCR (ddPCR) is a third-generation PCR technique that is particularly adapted to detecting low-abundance targets. We developed two-color ddPCR assays for the detection of four different regions of SARS-CoV-2 RNA, including non-structural (IP4-RdRP, helicase) and structural (E, N) protein-encoding sequences. We observed that N or E subgenomic RNAs are generally more abundant than IP4 and helicase RNA sequences in cells infected in vitro, suggesting that detection of the N gene, coding for the most abundant subgenomic RNA of SARS-CoV-2, increases the sensitivity of detection during the highly replicative phase of infection. We investigated 208 nasopharyngeal swabs sampled in March-April 2020 in different hospitals of Greater Paris. We found that 8.6% of informative samples (n = 16/185, P < 0.0001) initially scored as “non-positive” (undetermined or negative) by RT-qPCR were positive for SARS-CoV-2 RNA by ddPCR. Our work confirms that the use of ddPCR modestly, but significantly, increases the proportion of upper airway samples testing positive in the framework of first-line diagnosis of a French population.
Collapse
Affiliation(s)
- Agnès Marchio
- Unité "Organisation nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, 28, rue du Docteur Roux, 75724, Paris, Cedex 15, France.
| | - Christophe Batejat
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | - Jessica Vanhomwegen
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | - Maxence Feher
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | - Quentin Grassin
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | - Maxime Chazal
- Département de Virologie, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3569, Institut Pasteur, Paris, France
| | - Olivia Raulin
- Laboratoire de Biologie Médicale, Centre Hospitalier Compiègne-Noyon, Compiègne, France
| | - Anne Farges-Berth
- Laboratoire de Biologie Médicale, Groupe Hospitalier Nord-Essonne, Site de Longjumeau, Longjumeau, France
| | - Florence Reibel
- Laboratoire de Biologie Médicale, Groupe Hospitalier Nord-Essonne, Site d'Orsay, Orsay, France
| | - Vincent Estève
- Laboratoire de Biologie Médicale, Groupe Hospitalier Nord-Essonne, Site de Longjumeau, Longjumeau, France
- Laboratoire de Biologie Médicale, Groupe Hospitalier Nord-Essonne, Site d'Orsay, Orsay, France
| | - Anne Dejean
- Unité "Organisation nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, 28, rue du Docteur Roux, 75724, Paris, Cedex 15, France
| | - Nolwenn Jouvenet
- Département de Virologie, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3569, Institut Pasteur, Paris, France
| | | | - Pascal Pineau
- Unité "Organisation nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, 28, rue du Docteur Roux, 75724, Paris, Cedex 15, France.
| |
Collapse
|
6
|
Batéjat C, Grassin Q, Manuguerra JC, Leclercq I. Heat inactivation of the severe acute respiratory syndrome coronavirus 2. J Biosaf Biosecur 2021; 3:1-3. [PMID: 33521591 DOI: 10.1101/2020.05.01.067769] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/18/2020] [Accepted: 12/16/2020] [Indexed: 05/29/2023] Open
Abstract
Cell culture medium, nasopharyngeal and sera samples spiked with SARS-CoV-2 were subjected to heat inactivation for various periods of time, ranging from 30 s to 60 min. Our results showed that SARS-CoV-2 could be inactivated in less than 30 min, 15 min, and 3 min at 56 °C, 65 °C, and 95 °C, respectively. These data could help laboratory workers to improve their protocols by handling the virus in biosafety conditions.
Collapse
Affiliation(s)
- Christophe Batéjat
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr. Roux, Paris, France
| | - Quentin Grassin
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr. Roux, Paris, France
| | - Jean-Claude Manuguerra
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr. Roux, Paris, France
| | - India Leclercq
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr. Roux, Paris, France
- Université de Paris, Cellule Pasteur, 28 rue du Dr. Roux F-75015 Paris, France
| |
Collapse
|
7
|
Labadie T, Grassin Q, Batéjat C, Manuguerra JC, Leclercq I. Monitoring Influenza Virus Survival Outside the Host Using Real-Time Cell Analysis. J Vis Exp 2021. [PMID: 33682860 DOI: 10.3791/61133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Methods for virus particle quantification represent a critical aspect of many virology studies. Although several reliable techniques exist, they are either time-consuming or unable to detect small variations. Presented here is a protocol for the precise quantification of viral titer by analyzing electrical impedance variations of infected cells in real-time. Cellular impedance is measured through gold microelectrode biosensors located under the cells in microplates, in which magnitude depends on the number of cells as well as their size and shape. This protocol allows real-time analysis of cell proliferation, viability, morphology and migration with enhanced sensitivity. Also provided is an example of a practical application by quantifying the decay of influenza A virus (IAV) submitted to various physicochemical parameters affecting viral infectivity over time (i.e., temperature, salinity, and pH). For such applications, the protocol reduces the workload needed while also generating precise quantification data of infectious virus particles. It allows the comparison of inactivation slopes among different IAV, which reflects their capacity to persist in given environment. This protocol is easy to perform, is highly reproducible, and can be applied to any virus producing cytopathic effects in cell culture.
Collapse
Affiliation(s)
- Thomas Labadie
- Department of Infection Biology, London School of Hygiene and Tropical Medicine
| | - Quentin Grassin
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU)
| | - Christophe Batéjat
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU)
| | - Jean-Claude Manuguerra
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU)
| | - India Leclercq
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU); Cellule Pasteur, Université de Paris;
| |
Collapse
|
8
|
Batéjat C, Grassin Q, Manuguerra JC, Leclercq I. Heat inactivation of the severe acute respiratory syndrome coronavirus 2. J Biosaf Biosecur 2021; 3:1-3. [PMID: 33521591 PMCID: PMC7825878 DOI: 10.1016/j.jobb.2020.12.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/18/2020] [Accepted: 12/16/2020] [Indexed: 01/04/2023] Open
Abstract
Cell culture medium, nasopharyngeal and sera samples spiked with SARS-CoV-2 were subjected to heat inactivation for various periods of time, ranging from 30 s to 60 min. Our results showed that SARS-CoV-2 could be inactivated in less than 30 min, 15 min, and 3 min at 56 °C, 65 °C, and 95 °C, respectively. These data could help laboratory workers to improve their protocols by handling the virus in biosafety conditions.
Collapse
Affiliation(s)
- Christophe Batéjat
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr. Roux, Paris, France
| | - Quentin Grassin
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr. Roux, Paris, France
| | - Jean-Claude Manuguerra
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr. Roux, Paris, France
| | - India Leclercq
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr. Roux, Paris, France.,Université de Paris, Cellule Pasteur, 28 rue du Dr. Roux F-75015 Paris, France
| |
Collapse
|
9
|
Gaidet N, Leclercq I, Batéjat C, Grassin Q, Daufresne T, Manuguerra JC. Avian Influenza Virus Surveillance in High Arctic Breeding Geese, Greenland. Avian Dis 2018; 62:237-240. [DOI: 10.1637/11793-010418-resnote.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Nicolas Gaidet
- CIRAD, UMR ASTRE, Département BIOS, TA C-47/F111, Campus international de Baillarguet, 34398 Montpellier Cedex 5, France
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr Roux, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité (Cellule Pasteur), rue du Dr Roux 75015 Paris, France
| | - India Leclercq
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr Roux, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité (Cellule Pasteur), rue du Dr Roux 75015 Paris, France
| | - Christophe Batéjat
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr Roux, Paris, France
| | - Quentin Grassin
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr Roux, Paris, France
| | - Tanguy Daufresne
- INRA, UMR 210 Eco&Sols, Bat 12, 2 Place Viala, F-34060 Montpellier Cedex 1, France
| | - Jean-Claude Manuguerra
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence (CIBU), 28 rue du Dr Roux, Paris, France
| |
Collapse
|