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Guilbaud R, Franco Yusti AM, Leducq V, Zafilaza K, Bridier-Nahmias A, Todesco E, Soulie C, Fauchois A, Le Hingrat Q, Kramer L, Goulenok T, Salpin M, Daugas E, Dorent R, Ottaviani S, Zalcman G, Ghosn J, Choquet S, Cacoub P, Amoura Z, Barroux B, Pourcher V, Spano JP, Louet M, Marcelin AG, Calvez V, Charpentier C, Descamps D, Marot S, Ferré VM, Coppée R. Higher Levels of SARS-CoV-2 Genetic Variation in Immunocompromised Patients: A Retrospective Case-Control Study. J Infect Dis 2024; 229:1041-1049. [PMID: 37956413 DOI: 10.1093/infdis/jiad499] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection lasts longer in immunocompromised hosts than in immunocompetent patients. Prolonged infection is associated with a higher probability of selection for novel SARS-CoV-2 mutations, particularly in the spike protein, a critical target for vaccines and therapeutics. METHODS From December 2020 to September 2022, respiratory samples from 444 immunocompromised patients and 234 health care workers positive for SARS-CoV-2, diagnosed at 2 hospitals in Paris, France, were analyzed using whole-genome sequencing using Nanopore technology. Custom scripts were developed to assess the SARS-CoV-2 genetic diversity between the 2 groups and within the host. RESULTS Most infections were SARS-CoV-2 Delta or Omicron lineages. Viral genetic diversity was significantly higher in infections of immunocompromised patients than those of controls. Minor mutations were identified in viruses sequenced from immunocompromised individuals, which became signature mutations for newer SARS-CoV-2 variants as the epidemic progressed. Two patients were coinfected with Delta and Omicron variants. The follow-up of immunocompromised patients revealed that the SARS-CoV-2 genome evolution differed in the upper and lower respiratory tracts. CONCLUSIONS This study found that SARS-CoV-2 infection in immunocompromised patients is associated with higher genetic diversity, which could lead to the emergence of new SARS-CoV-2 variants with possible immune evasion or different virulence characteristics.
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Affiliation(s)
- Romane Guilbaud
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Anna-Maria Franco Yusti
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Valentin Leducq
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Karen Zafilaza
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Antoine Bridier-Nahmias
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Eve Todesco
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Cathia Soulie
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Antoine Fauchois
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Quentin Le Hingrat
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Laura Kramer
- Service de Pharmacie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Tiphaine Goulenok
- Service de Médecine Interne, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Mathilde Salpin
- Service de Pneumologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Eric Daugas
- Service de Néphrologie, Université Paris Cité, Inserm U1149, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Richard Dorent
- Service de Cardiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Sébastien Ottaviani
- Service de Rhumatologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Gérard Zalcman
- Service d'Oncologie Thoracique, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
- Service de Maladies Infectieuses, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Sylvain Choquet
- Service d'Hématologie Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Patrice Cacoub
- Service de Médecine Interne et Immunologie Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Zahir Amoura
- Service de Médecine Interne 2, Centre National de Référence des Histiocytoses, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Benoit Barroux
- Service d'Urologie et de Transplantation Rénale, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Valérie Pourcher
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Service de Maladies Infectieuses et Tropicales, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière, Paris, France
| | - Jean-Philippe Spano
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Service d'Oncologie Médicale, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Martine Louet
- Service de Santé au Travail, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Anne-Geneviève Marcelin
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Vincent Calvez
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Charlotte Charpentier
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Diane Descamps
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Stéphane Marot
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Valentine Marie Ferré
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Romain Coppée
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
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Leducq V, Zafilaza K, Fauchois A, Ghidaoui E, Sayon S, Dorival C, Meledje ML, Lusivika-Nzinga C, Yordanov Y, Martin-Blondel G, Carrat F, Marcelin AG, Soulie C. Spike protein genetic evolution in patients at high-risk of severe COVID-19 treated by monoclonal antibodies. J Infect Dis 2023:jiad523. [PMID: 37996072 DOI: 10.1093/infdis/jiad523] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND High-risk patients, often immunocompromised and not responding to vaccine, continue to experience severe COVID-19 and death. Monoclonal antibodies (mAbs) were shown effective to prevent severe COVID-19 for these patients. Nevertheless, concerns about the emergence of resistance mutations were raised. METHODS We conducted a multicentric prospective cohort study, including 264 patients with mild-to moderate COVID-19 at high risk for progression to severe COVID-19 and treated early with Casirivimab/Imdevimab, Sotrovimab or Tixagevimab/Cilgavimab. We sequenced the SARS-CoV-2 genome during follow-up and searched for emerging Spike mutations. RESULTS Immunocompromised patients have a 6-fold increased risk of developing mutations, which are associated with a prolonged duration of viral clearance but no clinical worsening. Emerging P337S/R/L/H, E340D/K/A/Q/V/G and K356T/R substitutions in patients treated with Sotrovimab are associated with higher viral RNA loads for up to 14 days post-treatment initiation. Tixagevimab/Cilgavimab is associated with a 5-fold increased risk of developing mutations. R346K/I/T/S and K444R/N/M substitutions associated with Tixagevimab/Cilgavimab have been identified in multiple SARS-CoV-2 lineages, including BQ.1 and XBB. CONCLUSIONS In conclusion, the probability of emerging mutations arising in response to mAbs is significant, emphasizing the crucial need to investigate these mutations thoroughly and assess their impact on patients and the evolutionary trajectory of the SARS-CoV-2.
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Affiliation(s)
- Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Karen Zafilaza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Antoine Fauchois
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Emna Ghidaoui
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Sophie Sayon
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Céline Dorival
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Marie-Laure Meledje
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Clovis Lusivika-Nzinga
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Youri Yordanov
- Sorbonne Université, Hôpital Saint Antoine, Service d'Accueil des Urgences, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Guillaume Martin-Blondel
- Service des Maladies Infectieuses et Tropicales, CHU de Toulouse, France, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity) INSERM, Université Toulouse III., Toulouse, France
| | - Fabrice Carrat
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Unité de Santé Publique, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Cathia Soulie
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
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Teyssou E, Marot S, Gothland A, Malet I, Zafilaza K, Leducq V, Cocherie T, Todesco E, Soulié C, Marcelin AG, Calvez V. SARS-CoV-2 variant-dependent inflammasome activation. J Infect 2023; 87:62-63. [PMID: 37060923 PMCID: PMC10101480 DOI: 10.1016/j.jinf.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/17/2023]
Affiliation(s)
- Elisa Teyssou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France.
| | - Stéphane Marot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France
| | - Adélie Gothland
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France
| | - Isabelle Malet
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France
| | - Karen Zafilaza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France
| | - Théophile Cocherie
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France
| | - Eve Todesco
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France
| | - Cathia Soulié
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Laboratoire de Virologie, F-75013 Paris, France
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4
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Coppée R, Blanquart F, Jary A, Leducq V, Ferré VM, Franco Yusti AM, Daniel L, Charpentier C, Lebourgeois S, Zafilaza K, Calvez V, Descamps D, Marcelin AG, Visseaux B, Bridier-Nahmias A. Phylodynamics of SARS-CoV-2 in France, Europe and the world in 2020. eLife 2023; 12:82538. [PMID: 37159510 PMCID: PMC10179682 DOI: 10.7554/elife.82538] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/15/2023] [Indexed: 05/11/2023] Open
Abstract
Although France was one of the most affected European countries by the COVID-19 pandemic in 2020, the dynamics of SARS-CoV-2 movement within France, but also involving France in Europe and in the world, remain only partially characterized in this timeframe. Here, we analyzed GISAID deposited sequences from 1st January to 31th December 2020 (n = 638,706 sequences at the time of writing). To tackle the challenging number of sequences without the bias of analyzing a single subsample of sequences, we produced 100 subsamples of sequences and related phylogenetic trees from the whole dataset for different geographic scales (worldwide, European countries and French administrative regions) and time periods (from 1st January to 25th July 2020, and from 26th July to 31th December 2020). We applied a maximum likelihood discrete trait phylogeographic method to date exchange events (i.e., a transition from one location to another one), to estimate the geographic spread of SARS-CoV-2 transmissions and lineages into, from and within France, Europe and the world. The results unraveled two different patterns of exchange events between the first and second half of 2020. Throughout the year, Europe was systematically associated with most of the intercontinental exchanges. SARS-CoV-2 was mainly introduced into France from North America and Europe (mostly by Italy, Spain, United Kingdom, Belgium and Germany) during the first European epidemic wave. During the second wave, exchange events were limited to neighboring countries without strong intercontinental movement, but Russia widely exported the virus into Europe during the summer of 2020. France mostly exported B.1 and B.1.160 lineages, respectively during the first and second European epidemic waves. At the level of French administrative regions, the Paris area was the main exporter during the first wave. But, for the second epidemic wave, it equally contributed to virus spread with Lyon area, the second most populated urban area after Paris in France. The main circulating lineages were similarly distributed among the French regions. To conclude, by enabling the inclusion of tens of thousands of viral sequences, this original phylodynamic method enabled us to robustly describe SARS-CoV-2 geographic spread through France, Europe and worldwide in 2020.
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Affiliation(s)
- Romain Coppée
- Université Paris Cité and Sorbonne Paris Nord, Inserm, IAME, Paris, France
| | - François Blanquart
- Centre for Interdisciplinary Research in Biology, Collège de France, Paris, France
| | - Aude Jary
- Sorbonne Université, Inserm, iPLESP, Paris, France
| | | | | | | | - Léna Daniel
- Université Paris Cité and Sorbonne Paris Nord, Inserm, IAME, Paris, France
| | | | - Samuel Lebourgeois
- Université Paris Cité and Sorbonne Paris Nord, Inserm, IAME, Paris, France
| | | | | | - Diane Descamps
- Service de Virologie, Hôpital Bichat-Claude-Bernard, Paris, France
| | | | - Benoit Visseaux
- Service de Virologie, Hôpital Bichat-Claude-Bernard, Paris, France
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5
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Salle R, Mayslich C, Grange PA, Leducq V, Ollagnier G, Heller U, Saule J, Martinet P, Robert JL, Benhaddou N, Fouere S, Dupin N. Specific detection of Treponema pallidum in clinical samples: validation of a qPCR assay combining two genomic targets. Sex Transm Infect 2023; 99:91-96. [PMID: 35459752 DOI: 10.1136/sextrans-2021-055364] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/01/2022] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES We evaluated a real-time quantitative PCR (qPCR) for detection of the Treponema pallidum (TP) genome in clinical samples through simultaneous detection of two genomic targets. METHODS We performed qPCR with TaqMan technology using two TP genes, polA and tpp47, as targets, with an internal positive control. The qPCR assay was compared with syphilis diagnosis based on a combination of clinical examination, serological results and inhouse nested PCR (nPCR). Samples were analysed at the National Reference Center for STIs at Cochin Hospital in Paris. RESULTS In total, from October 2010 to December 2016, 320 documented clinical samples (mucosal and cutaneous swabs) were collected from patients with or without syphilis attending STI centres in France. The qPCR had an overall sensitivity of 89% (95% CI 85.1% to 92.1%), a specificity of 100%, a positive predictive value of 100% and a negative predictive value of 88% (95% CI 84.3% to 91.5%). The agreement between qPCR and nPCR results was 94% (κ=0.88, 95% CI 0.83 to 0.93). Calibration of the qPCR assay, by cloning both the polA and tpp47 genes, defined the detection threshold as 1 copy/µL of DNA elution. CONCLUSIONS We validated a new qPCR for detecting the TP genome in clinical samples with excellent sensitivity and specificity. The cloning of polA and tpp47 genes for calibration would be interesting in the evaluation of bacterial loads in samples.
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Affiliation(s)
- Romain Salle
- INSERM, Institut Cochin U1016-CNRS UMR8104, Équipe Biologie Cutané, Université de Paris, Paris, France.,Service de Dermatologie-Vénéréologie et CeGIDD, Hôpital Cochin, APHP, CNR IST Bactériennes - Expertise Syphilis, Paris, France
| | - Constance Mayslich
- INSERM, Institut Cochin U1016-CNRS UMR8104, Équipe Biologie Cutané, Université de Paris, Paris, France
| | - Philippe Alain Grange
- INSERM, Institut Cochin U1016-CNRS UMR8104, Équipe Biologie Cutané, Université de Paris, Paris, France.,Service de Dermatologie-Vénéréologie et CeGIDD, Hôpital Cochin, APHP, CNR IST Bactériennes - Expertise Syphilis, Paris, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Department of Virology, F-75013, Paris, France
| | - Guillaume Ollagnier
- INSERM, Institut Cochin U1016-CNRS UMR8104, Équipe Biologie Cutané, Université de Paris, Paris, France.,Service de Dermatologie-Vénéréologie et CeGIDD, Hôpital Cochin, APHP, CNR IST Bactériennes - Expertise Syphilis, Paris, France
| | - Ugo Heller
- Service de Chirurgie Maxillo-Faciale, Hôpital Beaujon, APHP, Clichy, France
| | - Julie Saule
- CeGIDD-Conseil Départemental 13 Joliette, Marseille, France
| | - Pervenche Martinet
- CeGIDD-Conseil Départemental 13 Joliette; CeGIDD-Conseil Départemental 13 Saint Adrien, Marseille, France
| | - Jean-Luc Robert
- CeGIDD-Conseil Départemental 13 d'Aix, Aix-en-Provence, France
| | - Nadjet Benhaddou
- Service de Bactériologie, APHP, CNR Streptocoques, Paris, France
| | - Sebastien Fouere
- Groupe Hospitalier Saint-Louis, Lariboisière, Fernand-Widal, CeGIDD, APHP, Paris, France
| | - Nicolas Dupin
- INSERM, Institut Cochin U1016-CNRS UMR8104, Équipe Biologie Cutané, Université de Paris, Paris, France .,Service de Dermatologie-Vénéréologie et CeGIDD, Hôpital Cochin, APHP, CNR IST Bactériennes - Expertise Syphilis, Paris, France
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6
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Palich R, Burrel S, Monsel G, Nouchi A, Bleibtreu A, Seang S, Bérot V, Brin C, Gavaud A, Wakim Y, Godefroy N, Fayçal A, Tamzali Y, Grunemwald T, Ohayon M, Todesco E, Leducq V, Marot S, Calvez V, Marcelin AG, Pourcher V. Viral loads in clinical samples of men with monkeypox virus infection: a French case series. Lancet Infect Dis 2023; 23:74-80. [PMID: 36183707 PMCID: PMC9534074 DOI: 10.1016/s1473-3099(22)00586-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Monkeypox virus (MPXV) is currently spreading among men who have sex with men, outside of sub-Saharan Africa, and close contact during sex seems to be one of the key pathways of viral transmission in the current outbreak. Our aim was to describe the distribution of MPXV in the human body, as it might play a role in its dissemination through sexual contact. METHODS The study population in this case series consisted of patients with confirmed MPXV infection attending the Pitié-Salpêtrière Hospital (Paris, France), who had been sampled from multiple anatomical sites, including skin, anus, throat, blood, urine, and semen, at diagnosis and 2 weeks later. We compared the proportion of positive samples and MPXV viral loads (given as PCR cycle thresholds [Ct]) between anatomical sites, and between day 0 (D0) and D14. FINDINGS Overall, 356 samples were collected between May 20 and June 13, 2022, from 50 men with a median age of 34 years (IQR 29-40). 22 (44%) of the 50 men were classified as HIV-negative on day (D)0, and 22 (44%) were living with HIV. At D0, MPXV detection was more frequent from skin (44 [88%] of 50), anus (30 [71%] of 42), and throat (36 [77%] of 47) than from blood (13 [29%] of 45), urine (nine [22%] of 41), or semen (13 [54%] of 24). Viral loads were significantly higher from skin lesions (Ct 19·8) and anal samples (Ct 20·9) than from throat (Ct 27·2), blood (Ct 32·8), urine (31·1), or semen samples (Ct 27·8). When analysing the 107 samples taken from 24 patients at D14, the proportion of positive samples strongly decreased between D0 and D14 at all sites: skin (four [22%] of 18), anus (two [9%] of 22), throat (none of 21), blood (one [5%] of 21), urine (none of 14), and semen (two [9%] of 11). INTERPRETATION These data contribute to a better understanding of how the virus might spread between sexual partners over a relatively short period of time. High MPXV viral loads from skin and mucosa, including genital and anal sites, suggest that transmission most likely occurs through direct body contact rather than through the respiratory route or contact with body fluids, which should help to refine the prevention messages delivered to individuals most exposed to the virus. FUNDING None.
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Affiliation(s)
- Romain Palich
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France,Correspondence to: Dr Romain Palich, Department of Infectious Diseases, Pierre Louis Epidemiological and Public Health Institute, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, 75013 Paris, France
| | - Sonia Burrel
- Department of Virology, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Gentiane Monsel
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Agathe Nouchi
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Alexandre Bleibtreu
- Pierre Louis Epidemiological and Public Health Institute, and Department of Infectious Diseases, Infectious Diseases Immunology Center (Cimi-Paris), INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Sophie Seang
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Vincent Bérot
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Cécile Brin
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Ariane Gavaud
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Yara Wakim
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Nagisa Godefroy
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Antoine Fayçal
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Yanis Tamzali
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | | | | | - Eve Todesco
- Department of Virology, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Valentin Leducq
- Department of Virology, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Stéphane Marot
- Department of Virology, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Vincent Calvez
- Department of Virology, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Anne-Geneviève Marcelin
- Department of Virology, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Valérie Pourcher
- Department of Infectious Diseases, INSERM, Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
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7
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Boluda S, Mokhtari K, Mégarbane B, Annane D, Mathon B, Cao A, Adam C, Androuin A, Bielle F, Brochier G, Charlotte F, Chougar L, El Hachimi KH, Eloit M, Haïk S, Hervé D, Kasri A, Leducq V, Lehéricy S, Levavasseur E, Lobsiger C, Lorin de La Grandmaison G, Malet I, Malissin I, Marot S, Marty S, Pérot P, Plu I, Prigent A, Stimmer L, Potier MC, Marcelin AG, Delatour B, Duyckaerts C, Seilhean D. Golgi localization of SARS-CoV-2 spike protein and interaction with furin in cerebral COVID-19 microangiopathy: a clue to the central nervous system involvement? Free Neuropathol 2023; 4:4-1. [PMID: 37283933 PMCID: PMC10240951 DOI: 10.17879/freeneuropathology-2023-4584] [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] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/06/2023] [Indexed: 06/08/2023]
Abstract
In a neuropathological series of 20 COVID-19 cases, we analyzed six cases (three biopsies and three autopsies) with multiple foci predominantly affecting the white matter as shown by MRI. The cases presented with microhemorrhages evocative of small artery diseases. This COVID-19 associated cerebral microangiopathy (CCM) was characterized by perivascular changes: arterioles were surrounded by vacuolized tissue, clustered macrophages, large axonal swellings and a crown arrangement of aquaporin-4 immunoreactivity. There was evidence of blood-brain-barrier leakage. Fibrinoid necrosis, vascular occlusion, perivascular cuffing and demyelination were absent. While no viral particle or viral RNA was found in the brain, the SARS-CoV-2 spike protein was detected in the Golgi apparatus of brain endothelial cells where it closely associated with furin, a host protease known to play a key role in virus replication. Endothelial cells in culture were not permissive to SARS-CoV-2 replication. The distribution of the spike protein in brain endothelial cells differed from that observed in pneumocytes. In the latter, the diffuse cytoplasmic labeling suggested a complete replication cycle with viral release, notably through the lysosomal pathway. In contrast, in cerebral endothelial cells the excretion cycle was blocked in the Golgi apparatus. Interruption of the excretion cycle could explain the difficulty of SARS-CoV-2 to infect endothelial cells in vitro and to produce viral RNA in the brain. Specific metabolism of the virus in brain endothelial cells could weaken the cell walls and eventually lead to the characteristic lesions of COVID-19 associated cerebral microangiopathy. Furin as a modulator of vascular permeability could provide some clues for the control of late effects of microangiopathy.
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Affiliation(s)
- Susana Boluda
- Department of Neuropathology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Karima Mokhtari
- Department of Neuropathology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Bruno Mégarbane
- Department of Medical and Toxicological Critical Care, Lariboisière Hospital, AP-HP, Paris University, INSERM UMRS-1144, Paris, France
| | - Djillali Annane
- Department of Critical Care, Raymond Poincaré Hospital, Boulevard Raymond Poincaré, APHP, Paris-Saclay University, INSERM U1173, Garches, France
| | - Bertrand Mathon
- Department of Neurosurgery, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
| | - Albert Cao
- Department of Neurology, Neuro-ICU, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
| | - Clovis Adam
- Department of Pathology, Bicêtre Hospital, AP-HP, Paris Saclay University, Le Kremlin-Bicêtre, France
| | - Alexandre Androuin
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Franck Bielle
- Department of Neuropathology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Guy Brochier
- Department of Neuropathology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
- Institut de Myologie, Pitié-Salpêtrière Hospital, Paris, France
| | - Frédéric Charlotte
- Department of Pathology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
| | - Lydia Chougar
- Department of Neuroimaging, Pitié-Salpètrière Hospital, AP-HP Sorbonne University, Paris, France
| | - Khalid Hamid El Hachimi
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences et Lettres (PSL) University, Paris, France
| | - Marc Eloit
- Institut Pasteur, Pathogen Discovery Laboratory, Paris, France
| | - Stéphane Haïk
- Department of Neuropathology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Dominique Hervé
- Department of Neurology, Lariboisière Hospital, AP-HP Nord- Paris University, Paris, France
| | - Amal Kasri
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Valentin Leducq
- Department of Virology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, INSERM 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), Paris, France
| | - Stéphane Lehéricy
- Department of Neuroimaging, Pitié-Salpètrière Hospital, AP-HP Sorbonne University, Paris, France
| | - Etienne Levavasseur
- Department of Neuropathology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Christian Lobsiger
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | | | - Isabelle Malet
- Department of Virology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, INSERM 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), Paris, France
| | - Isabelle Malissin
- Department of Medical and Toxicological Critical Care, Lariboisière Hospital, AP-HP, Paris University, INSERM UMRS-1144, Paris, France
| | - Stéphane Marot
- Department of Virology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, INSERM 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), Paris, France
| | - Serge Marty
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Philippe Pérot
- Institut Pasteur, Pathogen Discovery Laboratory, Paris, France
| | - Isabelle Plu
- Department of Neuropathology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Annick Prigent
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Lev Stimmer
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Marie-Claude Potier
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Anne-Geneviève Marcelin
- Department of Virology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, INSERM 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), Paris, France
| | - Benoît Delatour
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Charles Duyckaerts
- Department of Neuropathology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Danielle Seilhean
- Department of Neuropathology, Pitié-Salpêtrière Hospital, AP-HP Sorbonne University, Paris, France
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm U1127, CNRS UMR7225, APHP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
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8
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Gothland A, Jary A, Grange P, Leducq V, Beauvais-Remigereau L, Dupin N, Marcelin AG, Calvez V. Harnessing Redox Disruption to Treat Human Herpesvirus 8 (HHV-8) Related Malignancies. Antioxidants (Basel) 2022; 12:antiox12010084. [PMID: 36670946 PMCID: PMC9854560 DOI: 10.3390/antiox12010084] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Reprogrammed metabolism is regarded as a hallmark of cancer and offers a selective advantage to tumor cells during carcinogenesis. The redox equilibrium is necessary for growth, spread and the antioxidant pathways are boosted following Reactive Oxygen Species (ROS) production to prevent cell damage in tumor cells. Human herpesvirus 8 (HHV-8), the etiologic agent of Kaposi sarcoma KS and primary effusion lymphoma (PEL), is an oncogenic virus that disrupts cell survival-related molecular signaling pathways leading to immune host evasion, cells growths, angiogenesis and inflammatory tumor-environment. We recently reported that primaquine diphosphate causes cell death by apoptosis in HHV-8 infected PEL cell lines in vivo and exhibits therapeutic anti-tumor activity in mice models and advanced KS. Our findings also suggest that the primaquine-induced apoptosis in PEL cells is mostly influenced by ROS production and targeting the redox balance could be a new approach to treat HHV-8 related diseases. In this review, we summarized the knowledge about the influence of ROS in cancer development; more specifically, the proof of evidence from our work and from the literature that redox pathways are important for the development of HHV-8 pathologies.
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Affiliation(s)
- Adélie Gothland
- INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Department of Virology, Hôpital Pitié-Salpêtrière, Sorbonne Université, 75013 Paris, France
| | - Aude Jary
- INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Department of Virology, Hôpital Pitié-Salpêtrière, Sorbonne Université, 75013 Paris, France
- Correspondence: (A.J.); (V.C.); Tel.: +33-1-42-17-74-01 (A.J.)
| | - Philippe Grange
- Cutaneous Biology Lab, INSERM U1016, UMR8104, Institut Cochin, Université de Paris, 24 Rue du Faubourg St Jacques, 75014 Paris, France
- Department of Dermatology, CeGGID et CNR IST Bactériennes, Hôpital Cochin Site Port Royale, AP-HP, Groupe Hospitalier Paris Centre Cochin-Hôtel Dieu-Broca, 123 Boulevard de Port Royal, 75014 Paris, France
| | - Valentin Leducq
- INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Department of Virology, Hôpital Pitié-Salpêtrière, Sorbonne Université, 75013 Paris, France
| | | | - Nicolas Dupin
- Cutaneous Biology Lab, INSERM U1016, UMR8104, Institut Cochin, Université de Paris, 24 Rue du Faubourg St Jacques, 75014 Paris, France
- Department of Dermatology, CeGGID et CNR IST Bactériennes, Hôpital Cochin Site Port Royale, AP-HP, Groupe Hospitalier Paris Centre Cochin-Hôtel Dieu-Broca, 123 Boulevard de Port Royal, 75014 Paris, France
| | - Anne-Geneviève Marcelin
- INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Department of Virology, Hôpital Pitié-Salpêtrière, Sorbonne Université, 75013 Paris, France
| | - Vincent Calvez
- INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Department of Virology, Hôpital Pitié-Salpêtrière, Sorbonne Université, 75013 Paris, France
- Correspondence: (A.J.); (V.C.); Tel.: +33-1-42-17-74-01 (A.J.)
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9
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Cocherie T, Zafilaza K, Leducq V, Marot S, Calvez V, Marcelin AG, Todesco E. Epidemiology and Characteristics of SARS-CoV-2 Variants of Concern: The Impacts of the Spike Mutations. Microorganisms 2022; 11:30. [PMID: 36677322 PMCID: PMC9866527 DOI: 10.3390/microorganisms11010030] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 expresses on its surface the Spike protein responsible for binding with the ACE2 receptor and which carries the majority of immunodominant epitopes. Mutations mainly affect this protein and can modify characteristics of the virus, giving each variant a unique profile concerning its transmissibility, virulence, and immune escape. The first lineage selected is the B.1 lineage characterized by the D614G substitution and from which all SARS-CoV-2 variants of concern have emerged. The first three variants of concern Alpha, Beta, and Gamma spread in early 2021: all shared the N501Y substitution. These variants were replaced by the Delta variant in summer 2021, carrying unique mutations like the L452R substitution and associated with higher virulence. It was in turn quickly replaced by the Omicron variant at the end of 2021, which has predominated since then, characterized by its large number of mutations. The successive appearance of variants of concern showed a dynamic evolution of SARS-CoV-2 through the selection and accumulation of mutations. This has not only allowed progressive improvement of the transmissibility of SARS-CoV-2, but has also participated in a better immune escape of the virus. This review brings together acquired knowledge about SARS-CoV-2 variants of concern and the impacts of the Spike mutations.
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Affiliation(s)
| | | | | | | | | | | | - Eve Todesco
- Institut Pierre Louis d’Épidémiologie et de Santé Publique (iPLESP), INSERM, Sorbonne Université, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Virologie, 75013 Paris, France
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10
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Leducq V, Couturier J, Granger B, Jolivet S, Morand-Joubert L, Robert J, Denis M, Salauze B, Goldstein V, Zafilaza K, Rufat P, Marcelin AG, Jary A, Barbut F. Investigation of healthcare-associated COVID-19 in a large French hospital group by whole-genome sequencing. Microbiol Res 2022; 263:127133. [PMID: 35901580 PMCID: PMC9306220 DOI: 10.1016/j.micres.2022.127133] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 04/29/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 12/01/2022]
Abstract
OBJECTIVES Despite the quick implementation of infection prevention and control procedures and the use of personal protective equipment within healthcare facilities, many cases of nosocomial COVID-19 transmission have been reported. We aimed to estimate the frequency and impact of healthcare-associated COVID-19 (HA-COVID-19) and evaluate the contribution of whole-genome sequencing (WGS) in cluster investigation. METHODS We estimated the frequency and mortality of HA-COVID-19 infections from September 1 to November 30, 2020, with a focus on the evolution of hospitalized community-associated COVID-19 (CA-COVID-19) cases and cases detected among healthcare workers (HCWs) within the Sorbonne University Hospital Group (Paris, France). We thoroughly examined 12 clusters through epidemiological investigations and WGS. RESULTS Overall, 209 cases of HA-COVID-19 were reported. Evolution of HA-COVID-19 incidence closely correlated with the incidence of CA-COVID-19 and COVID-19 among HCWs. During the study period, 13.9 % of hospitalized patients with COVID-19 were infected in the hospital and the 30-day mortality rate of HA-COVID-19 was 31.5 %. Nosocomial transmission of SARS-CoV-2 led to clusters involving both patients and HCWs. WGS allowed the exclusion of one-third of cases initially assigned to a cluster. CONCLUSIONS WGS analysis combined with comprehensive epidemiological investigations is essential to understand transmission routes and adapt the IPC response to protect both patients and HCWs.
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Affiliation(s)
- Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France.
| | - Jeanne Couturier
- Unité de Prévention du Risque Infectieux, Hôpital Saint-Antoine, GH Sorbonne Université, AP-HP, Paris, France
| | - Benjamin Granger
- Département de Santé Publique, Hôpital de la Pitié-Salpêtrière, GH Sorbonne Université, AP-HP, Paris, France
| | - Sarah Jolivet
- Unité de Prévention du Risque Infectieux, Hôpital Saint-Antoine, GH Sorbonne Université, AP-HP, Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, APHP, Hôpital Saint-Antoine, Département de Virologie, Paris, France
| | - Jérôme Robert
- Equipe Opérationnelle d'Hygiène, Hôpital de la Pitié-Salpêtrière, GH Sorbonne Université, AP-HP, Paris, France
| | - Michel Denis
- Equipe Opérationnelle d'Hygiène, Hôpital Tenon, GH Sorbonne Université, AP-HP, Paris, France
| | - Beatrice Salauze
- Equipe Opérationnelle d'Hygiène, Hôpitaux Trousseau et Rothschild, GH Sorbonne Université, AP-HP, Paris, France
| | - Valérie Goldstein
- Equipe Opérationnelle d'Hygiène Hôpital Charles Foix, GH Sorbonne Université, AP-HP, Ivry, France
| | - Karen Zafilaza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - Pierre Rufat
- Département d'Information Médicale, Hôpital de la Pitié-Salpêtrière, GH Sorbonne Université, AP-HP, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - Frédéric Barbut
- Unité de Prévention du Risque Infectieux, Hôpital Saint-Antoine, GH Sorbonne Université, AP-HP, Paris, France
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11
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Seang S, Burrel S, Todesco E, Leducq V, Monsel G, Le Pluart D, Cordevant C, Pourcher V, Palich R. Evidence of human-to-dog transmission of monkeypox virus. Lancet 2022; 400:658-659. [PMID: 35963267 PMCID: PMC9536767 DOI: 10.1016/s0140-6736(22)01487-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 12/29/2022]
Affiliation(s)
- Sophie Seang
- Infectious Diseases Department, Sorbonne University, Pitié-Salpêtrière Hospital, AP-HP, Pierre Louis Epidemiology and Public Health institute, INSERM 1136, Paris 75013, France.
| | - Sonia Burrel
- Virology Department, Sorbonne University, Pitié-Salpêtrière Hospital, AP-HP, Pierre Louis Epidemiology and Public Health institute, INSERM 1136, Paris 75013, France
| | - Eve Todesco
- Virology Department, Sorbonne University, Pitié-Salpêtrière Hospital, AP-HP, Pierre Louis Epidemiology and Public Health institute, INSERM 1136, Paris 75013, France
| | - Valentin Leducq
- Virology Department, Sorbonne University, Pitié-Salpêtrière Hospital, AP-HP, Pierre Louis Epidemiology and Public Health institute, INSERM 1136, Paris 75013, France
| | - Gentiane Monsel
- Infectious Diseases Department, Sorbonne University, Pitié-Salpêtrière Hospital, AP-HP, Pierre Louis Epidemiology and Public Health institute, INSERM 1136, Paris 75013, France
| | - Diane Le Pluart
- Infectious Diseases Department, Bichat-Claude Bernard University Hospital, AP-HP, Paris, France
| | - Christophe Cordevant
- Strategy and Programmes Department, Research and Reference Division, Anses, Maisons-Alfort, France
| | - Valérie Pourcher
- Infectious Diseases Department, Sorbonne University, Pitié-Salpêtrière Hospital, AP-HP, Pierre Louis Epidemiology and Public Health institute, INSERM 1136, Paris 75013, France
| | - Romain Palich
- Infectious Diseases Department, Sorbonne University, Pitié-Salpêtrière Hospital, AP-HP, Pierre Louis Epidemiology and Public Health institute, INSERM 1136, Paris 75013, France
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12
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Jary A, Veyri M, Gothland A, Leducq V, Calvez V, Marcelin AG. Kaposi's Sarcoma-Associated Herpesvirus, the Etiological Agent of All Epidemiological Forms of Kaposi's Sarcoma. Cancers (Basel) 2021; 13:cancers13246208. [PMID: 34944828 PMCID: PMC8699694 DOI: 10.3390/cancers13246208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/27/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 01/08/2023] Open
Abstract
Simple Summary Kaposi’s sarcoma-associated herpesvirus (KSHV) is one of the seven oncogenic viruses currently recognized by the International Agency for Research on Cancer. Its presence for Kaposi’s sarcoma development is essential and knowledge on the oncogenic process has increased since its discovery in 1994. However, some uncertainties remain to be clarified, in particular on the exact routes of transmission and disparities in KSHV seroprevalence and the prevalence of Kaposi’s sarcoma worldwide. Here, we summarized the current data on the KSHV viral particle’s structure, its genome, the replication, its seroprevalence, the viral diversity and the lytic and latent oncogenesis proteins involved in Kaposi’s sarcoma. Lastly, we reported the environmental, immunological and viral factors possibly associated with KSHV transmission that could also play a role in the development of Kaposi’s sarcoma. Abstract Kaposi’s sarcoma-associated herpesvirus (KSHV), also called human herpesvirus 8 (HHV-8), is an oncogenic virus belonging to the Herpesviridae family. The viral particle is composed of a double-stranded DNA harboring 90 open reading frames, incorporated in an icosahedral capsid and enveloped. The viral cycle is divided in the following two states: a short lytic phase, and a latency phase that leads to a persistent infection in target cells and the expression of a small number of genes, including LANA-1, v-FLIP and v-cyclin. The seroprevalence and risk factors of infection differ around the world, and saliva seems to play a major role in viral transmission. KSHV is found in all epidemiological forms of Kaposi’s sarcoma including classic, endemic, iatrogenic, epidemic and non-epidemic forms. In a Kaposi’s sarcoma lesion, KSHV is mainly in a latent state; however, a small proportion of viral particles (<5%) are in a replicative state and are reported to be potentially involved in the proliferation of neighboring cells, suggesting they have crucial roles in the process of tumorigenesis. KSHV encodes oncogenic proteins (LANA-1, v-FLIP, v-cyclin, v-GPCR, v-IL6, v-CCL, v-MIP, v-IRF, etc.) that can modulate cellular pathways in order to induce the characteristics found in all cancer, including the inhibition of apoptosis, cells’ proliferation stimulation, angiogenesis, inflammation and immune escape, and, therefore, are involved in the development of Kaposi’s sarcoma.
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Affiliation(s)
- Aude Jary
- Service de Virologie, Hôpital Pitié-Salpêtrière, AP-HP, Institut Pierre Louis d’Épidémiologie et de Santé Publique (iPLESP), INSERM, Sorbonne Université, 75013 Paris, France; (A.G.); (V.L.); (V.C.); (A.-G.M.)
- Correspondence: ; Tel.: +33-1-4217-7401
| | - Marianne Veyri
- Service d’Oncologie Médicale, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, AP-HP, Institut Pierre Louis d’Épidémiologie et de Santé Publique (iPLESP), INSERM, Sorbonne Université, 75013 Paris, France;
| | - Adélie Gothland
- Service de Virologie, Hôpital Pitié-Salpêtrière, AP-HP, Institut Pierre Louis d’Épidémiologie et de Santé Publique (iPLESP), INSERM, Sorbonne Université, 75013 Paris, France; (A.G.); (V.L.); (V.C.); (A.-G.M.)
| | - Valentin Leducq
- Service de Virologie, Hôpital Pitié-Salpêtrière, AP-HP, Institut Pierre Louis d’Épidémiologie et de Santé Publique (iPLESP), INSERM, Sorbonne Université, 75013 Paris, France; (A.G.); (V.L.); (V.C.); (A.-G.M.)
| | - Vincent Calvez
- Service de Virologie, Hôpital Pitié-Salpêtrière, AP-HP, Institut Pierre Louis d’Épidémiologie et de Santé Publique (iPLESP), INSERM, Sorbonne Université, 75013 Paris, France; (A.G.); (V.L.); (V.C.); (A.-G.M.)
| | - Anne-Geneviève Marcelin
- Service de Virologie, Hôpital Pitié-Salpêtrière, AP-HP, Institut Pierre Louis d’Épidémiologie et de Santé Publique (iPLESP), INSERM, Sorbonne Université, 75013 Paris, France; (A.G.); (V.L.); (V.C.); (A.-G.M.)
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13
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Malonga GA, Jary A, Leducq V, Moudiongui Mboungou Malanda D, Boumba ALM, Chicaud E, Malet I, Calvez V, Peko JF, Marcelin AG. Seroprevalence and molecular diversity of Human Herpesvirus 8 among people living with HIV in Brazzaville, Congo. Sci Rep 2021; 11:17442. [PMID: 34465868 PMCID: PMC8408137 DOI: 10.1038/s41598-021-97070-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/19/2021] [Indexed: 12/30/2022] Open
Abstract
Human herpesvirus 8 (HHV8) is endemic in Africa, although studies of this infection are rare in Congo. We evaluated seroprevalence and HHV-8 diversity among people living with HIV. We included 353 patients receiving highly active antiretroviral therapy. Antibodies against HHV-8 latency-associated nuclear antigen were detected by indirect immunofluorescence. In HHV-8 positive patients, we performed HHV-8 quantification in blood and saliva by real-time PCR and typing by Sanger sequencing of K1 open reading frame. HHV-8 seroprevalence was 19%, being male (odd ratio [OR] = 1.741, [95% Confidence interval {CI}, 0.97-3.07]; p = 0.0581) and having multiple sex partners before HIV diagnosis (OR = 1.682, [CI 95%, 0.97-2.92]; p = 0.0629) tended to be associated with HHV-8 seropositivity. Of the 64 HHV-8 seropositive patients, HHV-8 DNA was detected in 10 (16%) in saliva, 6 (9%) in whole-blood and in 2 (3%) in both whole-blood and saliva. Three out of 6 HHV-8 strains were subtypes A5, 2 subtype B1 and 1 subtype C. HHV-8 seroprevalence was relatively low with more frequent carriage in men, associated with asymptomatic oral excretion and a predominance of subtype A5. These data tend to support the hypothesis of horizontal transmission in people living with HIV in Brazzaville.
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Affiliation(s)
- Gervillien Arnold Malonga
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Department of Virology - CERVI, Pitié-Salpêtrière Hospital, 83 boulevard de l'Hôpital, 75013, Paris, France.
- Faculté des Sciences de la Santé, Université Marien Ngouabi, Brazzaville, Republic of Congo.
| | - Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Department of Virology - CERVI, Pitié-Salpêtrière Hospital, 83 boulevard de l'Hôpital, 75013, Paris, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Department of Virology - CERVI, Pitié-Salpêtrière Hospital, 83 boulevard de l'Hôpital, 75013, Paris, France
| | - Dimitry Moudiongui Mboungou Malanda
- Faculté des Sciences de la Santé, Université Marien Ngouabi, Brazzaville, Republic of Congo
- Service d'Anatomie et Cytologie Pathologiques, Centre Hospitalier Universitaire de Brazzaville, Brazzaville, Republic of Congo
| | - Anicet Luc Magloire Boumba
- Faculté des Sciences de la Santé, Université Marien Ngouabi, Brazzaville, Republic of Congo
- Laboratoire d'Analyses Médicales, Hôpital Général de Loandjili, Pointe-Noire, Republic of Congo
| | - Elodie Chicaud
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Department of Virology - CERVI, Pitié-Salpêtrière Hospital, 83 boulevard de l'Hôpital, 75013, Paris, France
| | - Isabelle Malet
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Department of Virology - CERVI, Pitié-Salpêtrière Hospital, 83 boulevard de l'Hôpital, 75013, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Department of Virology - CERVI, Pitié-Salpêtrière Hospital, 83 boulevard de l'Hôpital, 75013, Paris, France
| | - Jean Felix Peko
- Faculté des Sciences de la Santé, Université Marien Ngouabi, Brazzaville, Republic of Congo
- Service d'Anatomie et Cytologie Pathologiques, Centre Hospitalier Universitaire de Brazzaville, Brazzaville, Republic of Congo
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Department of Virology - CERVI, Pitié-Salpêtrière Hospital, 83 boulevard de l'Hôpital, 75013, Paris, France
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14
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Marot S, Malet I, Leducq V, Abdi B, Teyssou E, Soulie C, Wirden M, Rodriguez C, Fourati S, Pawlotsky JM, Boutolleau D, Burrel S, Calvez V, Marcelin AG, Jary A. Neutralization heterogeneity of United Kingdom and South-African SARS-CoV-2 variants in BNT162b2-vaccinated or convalescent COVID-19 healthcare workers. Clin Infect Dis 2021; 74:707-710. [PMID: 34050731 PMCID: PMC8244299 DOI: 10.1093/cid/ciab492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 03/03/2021] [Indexed: 12/21/2022] Open
Abstract
There are concerns about neutralizing antibodies (NAbs) potency against SARS-CoV-2 variants. Despite decreased NAb titers elicited by BNT162b2-vaccine against VOC202012/01 and 501Y.V2 strains, 28/29 healthcare workers (HCW) had a NAb titer ≥1:10. In contrast, six months after COVID-19 mild-forms, only 9/15 (60%) of HCW displayed detectable NAbs against 501Y.V2 strain.
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Affiliation(s)
- Stéphane Marot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Isabelle Malet
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Basma Abdi
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Elisa Teyssou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Cathia Soulie
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Marc Wirden
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Christophe Rodriguez
- Department of Virology, Hôpitaux Universitaires Henri Mondor, AP-HP, Créteil, France.,Team "Viruses, Hepatology, Cancer", Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris-Est, Créteil, France
| | - Slim Fourati
- Department of Virology, Hôpitaux Universitaires Henri Mondor, AP-HP, Créteil, France.,Team "Viruses, Hepatology, Cancer", Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- Department of Virology, Hôpitaux Universitaires Henri Mondor, AP-HP, Créteil, France.,Team "Viruses, Hepatology, Cancer", Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris-Est, Créteil, France
| | - David Boutolleau
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Sonia Burrel
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
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15
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Marot S, Malet I, Leducq V, Zafilaza K, Sterlin D, Planas D, Gothland A, Jary A, Dorgham K, Bruel T, Burrel S, Boutolleau D, Schwartz O, Gorochov G, Calvez V, Marcelin AG. Author Correction: Rapid decline of neutralizing antibodies against SARS-CoV-2 among infected healthcare workers. Nat Commun 2021; 12:2824. [PMID: 33972561 PMCID: PMC8108407 DOI: 10.1038/s41467-021-23128-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Stéphane Marot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France.
| | - Isabelle Malet
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Karen Zafilaza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Delphine Sterlin
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), AP-HP, Pitié Salpêtrière Hospital, Department of Immunology, Paris, France
| | - Delphine Planas
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - Adélie Gothland
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Karim Dorgham
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), AP-HP, Pitié Salpêtrière Hospital, Department of Immunology, Paris, France
| | - Timothée Bruel
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | | | - Sonia Burrel
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - David Boutolleau
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - Guy Gorochov
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), AP-HP, Pitié Salpêtrière Hospital, Department of Immunology, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
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16
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Teyssou E, Soulie C, Visseaux B, Lambert-Niclot S, Ferre V, Marot S, Jary A, Sayon S, Zafilaza K, Leducq V, Schnuriger A, Abdi B, Wirden M, Houhou-Fidouh N, Charpentier C, Morand-Joubert L, Burrel S, Descamps D, Calvez V, Marcelin AG. The 501Y.V2 SARS-CoV-2 variant has an intermediate viral load between the 501Y.V1 and the historical variants in nasopharyngeal samples from newly diagnosed COVID-19 patients. J Infect 2021; 83:119-145. [PMID: 33932451 PMCID: PMC8080495 DOI: 10.1016/j.jinf.2021.04.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022]
Affiliation(s)
- Elisa Teyssou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France.
| | - Cathia Soulie
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Benoit Visseaux
- Service de Virologie, Université de Paris INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Sidonie Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Universitaire Saint Antoine, laboratoire de virologie, F-75012 Paris, France
| | - Valentine Ferre
- Service de Virologie, Université de Paris INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Stéphane Marot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Sophie Sayon
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Karen Zafilaza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Aurélie Schnuriger
- AP-HP, Hôpital Universitaire Armand-Trousseau, laboratoire de virologie, F-75012, Paris, France
| | - Basma Abdi
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Marc Wirden
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Nadhira Houhou-Fidouh
- Service de Virologie, Université de Paris INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Charlotte Charpentier
- Service de Virologie, Université de Paris INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Universitaire Saint Antoine, laboratoire de virologie, F-75012 Paris, France
| | - Sonia Burrel
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Diane Descamps
- Service de Virologie, Université de Paris INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
| | - Anne Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
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17
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Jary A, Gothland A, Palich R, Leducq V, Monsel G, Imbert S, Schneider L, Simon A, Spano JP, Katlama C, Larabi IA, Alvarez JC, Calvez V, Marcelin AG. Poppers, by Inducing HHV-8 Virion Production, Can Act as a Promoter for HHV-8 Transmission in Men Who Have Sex With Men. Open Forum Infect Dis 2021; 8:ofab166. [PMID: 34250187 PMCID: PMC8266588 DOI: 10.1093/ofid/ofab166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/03/2020] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Environmental factors were reported to increase the risk of human herpesvirus 8 (HHV-8) transmission. In a population of men who have sex with men (MSM), we found evidence that chemsex was associated with human herpesvirus 8 seropositivity in vivo and that poppers induced HHV-8 virion production in vitro. Our finding may explain the higher HHV-8 transmission in MSM.
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Affiliation(s)
- Aude Jary
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Adélie Gothland
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Romain Palich
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Infectious Diseases, Paris, France
| | - Valentin Leducq
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Gentiane Monsel
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Infectious Diseases, Paris, France
| | - Sébastien Imbert
- Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Parasitology-Mycology, Paris, France
| | - Luminita Schneider
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Infectious Diseases, Paris, France
| | - Anne Simon
- Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Internal Medicine, Paris, France
| | - Jean-Philippe Spano
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Oncology, Paris, France
| | - Christine Katlama
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Infectious Diseases, Paris, France
| | - Islam Amine Larabi
- Paris-Saclay University, Institut National de la Santé et de la Recherche Médicale U-1173, Department of Pharmacology Toxicology, Assistance Publique - Hôpitaux de Paris, Raymond Poincaré Hospital, Garches, France
| | - Jean-Claude Alvarez
- Paris-Saclay University, Institut National de la Santé et de la Recherche Médicale U-1173, Department of Pharmacology Toxicology, Assistance Publique - Hôpitaux de Paris, Raymond Poincaré Hospital, Garches, France
| | - Vincent Calvez
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris, Pitié Salpêtrière Hospital, Department of Virology, Paris, France
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18
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Jary A, Leducq V, Desire N, Petit H, Palich R, Joly V, Canestri A, Gothland A, Lambert-Niclot S, Surgers L, Amiel C, Descamps D, Spano JP, Katlama C, Calvez V, Marcelin AG. New Kaposi's sarcoma-associated herpesvirus variant in men who have sex with men associated with severe pathologies. J Infect Dis 2021; 222:1320-1328. [PMID: 32282911 DOI: 10.1093/infdis/jiaa180] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 11/28/2019] [Accepted: 04/09/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Kaposi sarcoma (KS)-associated herpesvirus (KSHV) subtype depends mostly on patient origin. The current study aimed to assess KSHV diversity in a population of men who have sex with men (MSM) living in France. METHODS The study included 264 patients. In 65 MSM, including 57 human immunodeficiency virus (HIV)-infected men with KS, multicentric Castleman disease, or primary effusion lymphoma and 8 HIV-uninfected men receiving HIV preexposure prophylaxis (PrEP), we performed KSHV typing with K1 open reading frame Sanger and KSHV whole-genome sequencing. In 199 other patients, we performed real-time polymerase chain reaction screening for the new variant. RESULTS We found that 51% of KSHV-strains were subtype C (85% C3), and 33% were subtype A. Four patients with severe KSHV disease (2 with visceral KS, 1 with multicentric Castleman disease, and 1 with primary effusion lymphoma) and 1 asymptomatic PrEP user had a new variant resembling the Ugandan subtype F, but with different K1 open reading frame and KSHV whole-genome sequences and a different epidemiological context (MSM vs African population). Its prevalence was 4.5% in Caucasian MSM, and it was absent in other epidemiological groups. CONCLUSIONS Subtype C predominated among MSM living in France. The new F variant was identified in Caucasian MSM and associated with severe KSHV disease, suggesting that subtype F could be split into F1 and F2 variants. Careful screening for this variant may be required in MSM, given the severe clinical presentation of associated diseases.
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Affiliation(s)
- Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Nathalie Desire
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Héloïse Petit
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Romain Palich
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Service de Maladies Infectieuses et Tropicales, Paris, France
| | - Véronique Joly
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat, AP-HP, Paris, France
| | - Ana Canestri
- Service de Maladies Infectieuses et Tropicale, AP-HP Hôpital Tenon, Paris, France
| | - Adélie Gothland
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Sidonie Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Saint Antoine, Service de Virologie, Paris, France
| | - Laure Surgers
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses, AP-HP, Hôpital Saint Antoine, Service de Maladies Infectieuses et Tropicales, Paris, France
| | - Corinne Amiel
- Service de Virologie, AP-HP Hôpital Tenon, Paris, France
| | - Diane Descamps
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Jean-Philippe Spano
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Service d'Oncologie Médicale, Paris, France
| | - Christine Katlama
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Service de Maladies Infectieuses et Tropicales, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, Laboratoire de Virologie, Paris, France
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19
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Marot S, Malet I, Leducq V, Zafilaza K, Sterlin D, Planas D, Gothland A, Jary A, Dorgham K, Bruel T, Burrel S, Boutolleau D, Schwartz O, Gorochov G, Calvez V, Marcelin AG. Rapid decline of neutralizing antibodies against SARS-CoV-2 among infected healthcare workers. Nat Commun 2021; 12:844. [PMID: 33558507 PMCID: PMC7870823 DOI: 10.1038/s41467-021-21111-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/13/2021] [Indexed: 12/16/2022] Open
Abstract
There are only few data concerning persistence of neutralizing antibodies (NAbs) among SARS-CoV-2-infected healthcare workers (HCW). These individuals are particularly exposed to SARS-CoV-2 infection and at potential risk of reinfection. We followed 26 HCW with mild COVID-19 three weeks (D21), two months (M2) and three months (M3) after the onset of symptoms. All the HCW had anti-receptor binding domain (RBD) IgA at D21, decreasing to 38.5% at M3 (p < 0.0001). Concomitantly a significant decrease in NAb titers was observed between D21 and M2 (p = 0.03) and between D21 and M3 (p < 0.0001). Here, we report that SARS-CoV-2 can elicit a NAb response correlated with anti-RBD antibody levels. However, this neutralizing activity declines, and may even be lost, in association with a decrease in systemic IgA antibody levels, from two months after disease onset. This short-lasting humoral protection supports strong recommendations to maintain infection prevention and control measures in HCW, and suggests that periodic boosts of SARS-CoV-2 vaccination may be required. The humoral immune response to SARS-CoV-2 infection is not yet fully understood. Here, Marot et al. monitor the longitudinal profile and neutralizing activity of IgG, IgA, and IgM among 26 healthcare workers and provide evidence for a short-lasting humoral immune protection due to a decrease of neutralizing antibody titers within 3 months.
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Affiliation(s)
- Stéphane Marot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France.
| | - Isabelle Malet
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Karen Zafilaza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Delphine Sterlin
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), AP-HP, Pitié Salpêtrière Hospital, Department of Immunology, Paris, France
| | - Delphine Planas
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - Adélie Gothland
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Karim Dorgham
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), AP-HP, Pitié Salpêtrière Hospital, Department of Immunology, Paris, France
| | - Timothée Bruel
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | | | - Sonia Burrel
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - David Boutolleau
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - Guy Gorochov
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), AP-HP, Pitié Salpêtrière Hospital, Department of Immunology, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
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20
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Martinot M, Jary A, Fafi-Kremer S, Leducq V, Delagreverie H, Garnier M, Pacanowski J, Mékinian A, Pirenne F, Tiberghien P, Calvez V, Humbrecht C, Marcelin AG, Lacombe K. Remdesivir failure with SARS-CoV-2 RNA-dependent RNA-polymerase mutation in a B-cell immunodeficient patient with protracted Covid-19. Clin Infect Dis 2020; 73:e1762-e1765. [PMID: 32986807 PMCID: PMC7543308 DOI: 10.1093/cid/ciaa1474] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [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: 08/26/2020] [Indexed: 12/31/2022] Open
Abstract
SARS-CoV-2 is a new pandemic virus for which Remdesivir is the only antiviral available. We report the occurrence of a mutation in the RdRP (D484Y) following failure of remdesivir in a 76-year-old woman with a post-rituximab B-cell immunodeficiency and persistent SARS-CoV-2 viremia. Cure was reached after supplementation with convalescent plasma.
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Affiliation(s)
- Martin Martinot
- Infectious diseases Department, Hôpitaux Civils de Colmar, Colmar, France
| | - Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié-Salpêtrière Hospital, Department of Virology, Paris, France
| | - Samira Fafi-Kremer
- Virology Laboratory, Strasbourg University Hospital, Strasbourg, France Strasbourg University, INSERM, IRM UMR-S, Strasbourg, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié-Salpêtrière Hospital, Department of Virology, Paris, France
| | - Heloise Delagreverie
- Virology Laboratory, Strasbourg University Hospital, Strasbourg, France Strasbourg University, INSERM, IRM UMR-S, Strasbourg, France
| | - Marc Garnier
- Sorbonne Université, GRC, APHP, DMU DREAM, Anesthesiology and Intensive Care Department, Saint-Antoine Hospital - Paris, France
| | - Jérôme Pacanowski
- Infectious diseases Department, Saint-Antoine Hospital, APHP - Sorbonne Université, Paris - France
| | - Arsène Mékinian
- Sorbonne Université, Internal Medicine Department, Inflammation-Immunopathology-Biotherapy Department (DMU i3D), Saint-Antoine Hospital, AP-HP,Paris - France
| | - France Pirenne
- Etablissement Français du Sang, La Plaine St-Denis - France.,Institut Mondor de Recherche Biomédicale, Unité, Equipe: Transfusion et Maladies du Globule Rouge, INSERM, EFS, Université Paris-Est Créteil, Créteil - France
| | - Pierre Tiberghien
- Etablissement Français du Sang, La Plaine St-Denis - France.,UMR 1098 RIGHT Inserm Université de Franche-Comté Etablissement Français du Sang, Besançon
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié-Salpêtrière Hospital, Department of Virology, Paris, France
| | | | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié-Salpêtrière Hospital, Department of Virology, Paris, France
| | - Karine Lacombe
- Sorbonne Université, Inserm IPLESP, Infectious Diseases Department, Saint-Antoine Hospital, APHP, Paris - France
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21
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Malet I, Delelis O, Nguyen T, Leducq V, Abdi B, Morand-Joubert L, Calvez V, Marcelin AG. Variability of the HIV-1 3' polypurine tract (3'PPT) region and implication in integrase inhibitor resistance. J Antimicrob Chemother 2020; 74:3440-3444. [PMID: 31730161 DOI: 10.1093/jac/dkz377] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/16/2019] [Accepted: 08/01/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Integrase strand-transfer inhibitors (INSTIs) are efficient at impairing retroviral integration, which is a critical step in HIV-1 replication. To date, resistance to these compounds has been explained by mutations in the viral protein integrase, which catalyses the integration step. Recently, it has been shown that selected mutations in the 3' polypurine tract (3'PPT), a sequence involved in the reverse transcription mechanism, result in high-level resistance to these compounds. This observation was reinforced by the description of a patient who failed INSTI treatment by selecting mutations in the 3'PPT sequence. METHODS Sequences of the 3'PPT region were analysed in 30706 treatment-naive patients from the public Los Alamos database belonging to six different subtypes and, in parallel, in 107 patients failing INSTI treatment. RESULTS The analysis showed that the sequences of patients failing INSTI treatment, in the same way as those of treatment-naive patients, are very well conserved regardless of the presence or absence of resistance mutations in the integrase gene. CONCLUSIONS This study confirms that the selection of a mutation in the 3'PPT region conferring high-level resistance to INSTIs is a rare event. It would require a particular in vivo context and especially a long enough time to be selected, this exposure time being generally reduced by the rapid change of treatment in the case of virological failure. Larger-scale studies in patients with INSTI treatment failure are needed to determine whether the 3'PPT region can play an important role in vivo in INSTI resistance.
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Affiliation(s)
- Isabelle Malet
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Olivier Delelis
- LBPA, ENS Paris-Saclay, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, F-94235 Cachan, France
| | - Thuy Nguyen
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Besma Abdi
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), APHP, Hôpital Saint-Antoine, laboratoire de virologie, F-75012 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
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22
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Hacein-Bey-Abina S, Estienne M, Bessoles S, Echchakir H, Pederzoli-Ribeil M, Chiron A, Aldaz-Carroll L, Leducq V, Zhang Y, Souyri M, Louache F, Abina AM. Erythropoietin is a major regulator of thrombopoiesis in thrombopoietin-dependent and -independent contexts. Exp Hematol 2020; 88:15-27. [PMID: 32721504 DOI: 10.1016/j.exphem.2020.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/18/2020] [Accepted: 07/22/2020] [Indexed: 01/09/2023]
Abstract
Thrombopoietin (TPO), through activation of its cognate receptor Mpl, is the major regulator of platelet production. However, residual platelets observed in TPO- and Mpl-loss-of-function (LOF) mice suggest the existence of an additional factor to TPO in platelet production. As erythropoietin (EPO) exhibited both in vitro megakaryocytic potential, in association with other early-acting cytokines, and in vivo platelet activation activity, we sought to investigate its role in this setting. Here, we used multiple LOF models to decipher the reciprocal role of EPO and TPO in the regulation of platelet production in TPO-LOF and Mpl-LOF mice and of platelet size heterogeneity in wild-type mice. We first identified EPO as the major thrombopoietic factor in the absence of the TPO-Mpl pathway. Based on the study of several mouse models we found that the EPO-EPO receptor pathway acts on late-stage megakaryopoiesis and is responsible for large-sized platelet production, while the TPO-Mpl pathway promotes small-sized platelet production. On the basis of our data, EPO might be used for thrombocytopenia supportive therapy in congenital amegakaryocytopoiesis. Furthermore, as a distribution skewed toward large platelets is an independent risk factor and a poor prognosis indicator in atherothrombosis, the characterization of EPO's role in the production of large-sized platelets, if confirmed in humans, may open new perspectives in the understanding of the role of EPO-induced platelets in atherothrombosis.
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Affiliation(s)
- Salima Hacein-Bey-Abina
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France; Clinical Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, Hôpital Kremlin-Bicêtre, Assistance Publique-Hôpitaux de Paris, Le-Kremlin-Bicêtre, France.
| | | | - Stéphanie Bessoles
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France
| | | | - Magali Pederzoli-Ribeil
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France
| | - Andrada Chiron
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France; Clinical Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, Hôpital Kremlin-Bicêtre, Assistance Publique-Hôpitaux de Paris, Le-Kremlin-Bicêtre, France
| | - Lydia Aldaz-Carroll
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France
| | | | - Yanyan Zhang
- INSERM U1170, CNRS GDR 3697 MicroNiT, Institut Gustave Roussy, Villejuif, France
| | - Michèle Souyri
- INSERM UMRS 1131, Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint Louis, Paris, France
| | - Fawzia Louache
- INSERM U1170, CNRS GDR 3697 MicroNiT, Institut Gustave Roussy, Villejuif, France; Université Paris-Sud, Orsay, France
| | - Amine M Abina
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France; NOKAD, Evry, France.
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23
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Jary A, Leducq V, Malet I, Marot S, Klement-Frutos E, Teyssou E, Soulié C, Abdi B, Wirden M, Pourcher V, Caumes E, Calvez V, Burrel S, Marcelin AG, Boutolleau D. Evolution of viral quasispecies during SARS-CoV-2 infection. Clin Microbiol Infect 2020; 26:1560.e1-1560.e4. [PMID: 32717416 PMCID: PMC7378485 DOI: 10.1016/j.cmi.2020.07.032] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [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: 06/08/2020] [Revised: 07/09/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022]
Abstract
Objectives Studies are needed to better understand the genomic evolution of the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe genomic diversity of SARS-CoV-2 by next-generation sequencing (NGS) in a patient with longitudinal follow-up for SARS-CoV-2 infection. Methods Sequential samples collected between January 29th and February 4th, 2020, from a patient infected by SARS-CoV-2 were used to perform amplification of two genome fragments—including genes encoding spike, envelope, membrane and nucleocapsid proteins—and NGS was carried out with Illumina® technology. Phylogenetic analysis was performed with PhyML and viral variant identification with VarScan. Results Majority consensus sequences were identical in most of the samples (5/7) and differed in one synonymous mutation from the Wuhan reference sequence. We identified 233 variants; each sample harboured in median 38 different minority variants, and only four were shared by different samples. The frequency of mutation was similar between genes and correlated with the length of the gene (r = 0.93, p = 0.0002). Most of mutations were substitution variations (n = 217, 93.1%) and about 50% had moderate or high impact on gene expression. Viral variants also differed between lower and upper respiratory tract samples collected on the same day, suggesting independent sites of replication of SARS-CoV-2. Conclusions We report for the first time minority viral populations representing up to 1% during the course of SARS-CoV-2 infection. Quasispecies were different from one day to the next, as well as between anatomical sites, suggesting that in vivo this new coronavirus appears as a complex and dynamic distributions of variants.
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Affiliation(s)
- Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France.
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - Isabelle Malet
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - Stéphane Marot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - Elise Klement-Frutos
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Maladie Infectieuses et Tropicales, Paris, France
| | - Elisa Teyssou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - Cathia Soulié
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - Basma Abdi
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - Marc Wirden
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - Valérie Pourcher
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Maladie Infectieuses et Tropicales, Paris, France
| | - Eric Caumes
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Maladie Infectieuses et Tropicales, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - Sonia Burrel
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - David Boutolleau
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
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24
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André-Garnier E, Hingrat QL, Marcelin AG, Reliquet V, Malet I, Leducq V, Rodallec A, Peytavin G, Ferré V, Charpentier C, Raffi F. Previously unreported emergence of A265V substitution in the integrase gene in association with bictegravir virological failure. Int J Antimicrob Agents 2020; 56:106039. [PMID: 32479891 DOI: 10.1016/j.ijantimicag.2020.106039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 11/17/2022]
Affiliation(s)
| | - Quentin Le Hingrat
- Université de Paris, INSERM UMR 1137 IAME, F-75018 Paris, France; Laboratoire de Virologie, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
| | - Véronique Reliquet
- Infectious Diseases Department, CHU Hôtel Dieu and INSERM CIC 1413 Nantes University, Nantes, France
| | - Isabelle Malet
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
| | - Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
| | - Audrey Rodallec
- Virology Laboratory CHU Hôtel Dieu and INSERM CIC 1413 Nantes University, Nantes, France
| | - Gilles Peytavin
- Université de Paris, INSERM UMR 1137 IAME, F-75018 Paris, France; Laboratoire de Pharmaco-toxicologie, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Virginie Ferré
- Virology Laboratory CHU Hôtel Dieu and INSERM CIC 1413 Nantes University, Nantes, France
| | - Charlotte Charpentier
- Université de Paris, INSERM UMR 1137 IAME, F-75018 Paris, France; Laboratoire de Virologie, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France.
| | - François Raffi
- Infectious Diseases Department, CHU Hôtel Dieu and INSERM CIC 1413 Nantes University, Nantes, France
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25
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Jary A, Dienta S, Leducq V, Le Hingrat Q, Cisse M, Diarra AB, Fofana DB, Ba A, Baby M, Achenbach CJ, Murphy R, Calvez V, Marcelin AG, Maiga AI. Seroprevalence and risk factors for HIV, HCV, HBV and syphilis among blood donors in Mali. BMC Infect Dis 2019; 19:1064. [PMID: 31856758 PMCID: PMC6921458 DOI: 10.1186/s12879-019-4699-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 10/17/2019] [Accepted: 12/11/2019] [Indexed: 12/24/2022] Open
Abstract
Background HIV, HBV and HCV remain a global public health concern especially in Africa. Prevalence of these infections is changing and identification of risk factors associated with each infection in Mali is needed to improve medical care. Methods We conducted a cross-sectional study of all individuals donating blood (n = 8207) in 2018 to the blood bank at university hospital in Bamako, Mali, to assess prevalence and risks factors associated with HIV, HBV, HCV and syphilis infections. Results HIV-seroprevalence was 2.16% and significantly increased with age, being married and decreasing education level. In multivariate analysis, after adjustements with age, marital status and geographical setting, only education level was associated with HIV-infection (OR, 1.54 [95% CI, 1.15–2.07], p = 0.016). HBsAg prevalence was 14.78% and significantly increased with to be male gender. In multivariate analysis, adjusting for age, marital status and type of blood donation, education level (OR, 1.17 [95%CI, 1.05–1.31], p = 0.02) and male gender (OR, 1.37 [95%CI, 1.14–1.65], p = 0.005) were associated with HBV-infection. HCV-prevalence was 2.32% and significantly increased with living outside Bamako. In multivariate analysis, adjusting for gender, age and education level, living outside Bamako was associated with HCV-infection (OR, 1.83 [95% CI, 1.41–2.35], p < 0.001). Syphilis seroprevalence was very low (0.04%) with only 3 individuals infected. Contrary to a prior study, blood donation type was not, after adjustments, an independent risk factor for each infection. Conclusions Overall, HIV and HBV infection was higher in individuals with a lower level of education, HBV infection was higher in men, and HCV infection was higher in people living outside of Bamako. Compared to studies performed in 1999, 2002 and 2007 in the same population, we found that HIV and HCV prevalence have decreased in the last two decades whereas HBV prevalence has remained stable. Our finding will help guide infection prevention and treatment programs in Mali.
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Affiliation(s)
- Aude Jary
- Department of Virology, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Paris, France.
| | - Sidi Dienta
- Département de Biologie Médicale, CHU Gabriel Toure, Bamako, Mali
| | - Valentin Leducq
- Department of Virology, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Paris, France
| | - Quentin Le Hingrat
- Department of Virology, IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Bichat Hospital, APHP, Paris, France
| | - Mahamadou Cisse
- Département de Biologie Médicale, CHU Gabriel Toure, Bamako, Mali
| | | | - Djeneba B Fofana
- Department of Virology, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Saint-Antoine Hospital, Paris, France
| | - Alhassane Ba
- Centre National de Transfusion Sanguine, Bamako, Mali
| | - Mounirou Baby
- Centre National de Transfusion Sanguine, Bamako, Mali
| | - Chad J Achenbach
- Northwestern University, Institute for Global Health, Chicago, IL, USA
| | - Robert Murphy
- Northwestern University, Institute for Global Health, Chicago, IL, USA
| | - Vincent Calvez
- Department of Virology, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Paris, France
| | - Anne-Geneviève Marcelin
- Department of Virology, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Paris, France.
| | - Almoustapha I Maiga
- Département de Biologie Médicale, CHU Gabriel Toure, Bamako, Mali.,Université des Sciences Techniques et des Technologies de Bamako, USTTB, Centre de Recherche et de Formation sur le VIH et la Tuberculose SEREFO, Bamako, Mali
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26
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Sokol H, Jegou S, McQuitty C, Straub M, Leducq V, Landman C, Kirchgesner J, Le Gall G, Bourrier A, Nion-Larmurier I, Cosnes J, Seksik P, Richard ML, Beaugerie L. Specificities of the intestinal microbiota in patients with inflammatory bowel disease and Clostridium difficile infection. Gut Microbes 2017; 9:55-60. [PMID: 28786749 PMCID: PMC5914915 DOI: 10.1080/19490976.2017.1361092] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Clostridium difficile infection (CDI) is a common complication in inflammatory bowel disease (IBD) and has been associated with poor IBD outcome. Intestinal microbiota composition in IBD patients with CDI has not been specifically evaluated to date. The fecal microbiota of 56 IBD patients, including 8 in flare with concomitant CDI, 24 in flare without CDI, and 24 in remission, as well as 24 healthy subjects, was studied using 16S sequencing. Analysis was performed using the Qiime pipeline. Compared to IBD patients without CDI, IBD patients with CDI had more pronounced dysbiosis with higher levels of Ruminococcus gnavus and Enterococcus operational taxonomic units (OTUs) and lower levels of Blautia and Dorea OTUs. Correlation network analysis suggested a disrupted ecosystem in IBD patients in flare, particularly in those with CDI. In patients with IBD, CDI is associated with a more pronounced intestinal dysbiosis with specific alterations in intestinal microorganisms.
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Affiliation(s)
- Harry Sokol
- Sorbonne University - UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, Paris, France,INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France,Department of Gastroenterology, Saint Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France,CONTACT Harry Sokol , Service de Gastroentérologie et Nutrition, Hôpital Saint-Antoine, 184 rue du faubourg St Antoine, 75571 Paris cedex 12, France
| | - Sarah Jegou
- Sorbonne University - UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Claire McQuitty
- Sorbonne University - UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Marjolene Straub
- Sorbonne University - UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Valentin Leducq
- Sorbonne University - UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Cecilia Landman
- Department of Gastroenterology, Saint Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Julien Kirchgesner
- Department of Gastroenterology, Saint Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Guillaume Le Gall
- Department of Gastroenterology, Saint Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Anne Bourrier
- Department of Gastroenterology, Saint Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Isabelle Nion-Larmurier
- Department of Gastroenterology, Saint Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Jacques Cosnes
- Department of Gastroenterology, Saint Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Philippe Seksik
- Department of Gastroenterology, Saint Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Mathias L. Richard
- INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
| | - Laurent Beaugerie
- Department of Gastroenterology, Saint Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department, DHU i2B, Paris, France
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27
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Sokol H, Leducq V, Aschard H, Pham HP, Jegou S, Landman C, Cohen D, Liguori G, Bourrier A, Nion-Larmurier I, Cosnes J, Seksik P, Langella P, Skurnik D, Richard ML, Beaugerie L. Fungal microbiota dysbiosis in IBD. Gut 2017; 66:1039-1048. [PMID: 26843508 PMCID: PMC5532459 DOI: 10.1136/gutjnl-2015-310746] [Citation(s) in RCA: 741] [Impact Index Per Article: 105.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 12/13/2022]
Abstract
OBJECTIVE The bacterial intestinal microbiota plays major roles in human physiology and IBDs. Although some data suggest a role of the fungal microbiota in IBD pathogenesis, the available data are scarce. The aim of our study was to characterise the faecal fungal microbiota in patients with IBD. DESIGN Bacterial and fungal composition of the faecal microbiota of 235 patients with IBD and 38 healthy subjects (HS) was determined using 16S and ITS2 sequencing, respectively. The obtained sequences were analysed using the Qiime pipeline to assess composition and diversity. Bacterial and fungal taxa associated with clinical parameters were identified using multivariate association with linear models. Correlation between bacterial and fungal microbiota was investigated using Spearman's test and distance correlation. RESULTS We observed that fungal microbiota is skewed in IBD, with an increased Basidiomycota/Ascomycota ratio, a decreased proportion of Saccharomyces cerevisiae and an increased proportion of Candida albicans compared with HS. We also identified disease-specific alterations in diversity, indicating that a Crohn's disease-specific gut environment may favour fungi at the expense of bacteria. The concomitant analysis of bacterial and fungal microbiota showed a dense and homogenous correlation network in HS but a dramatically unbalanced network in IBD, suggesting the existence of disease-specific inter-kingdom alterations. CONCLUSIONS Besides bacterial dysbiosis, our study identifies a distinct fungal microbiota dysbiosis in IBD characterised by alterations in biodiversity and composition. Moreover, we unravel here disease-specific inter-kingdom network alterations in IBD, suggesting that, beyond bacteria, fungi might also play a role in IBD pathogenesis.
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Affiliation(s)
- Harry Sokol
- Sorbonne University—UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France,Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Valentin Leducq
- Sorbonne University—UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Hugues Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Hang-Phuong Pham
- ILTOO Pharma, iPEPS ICM, Hôpital Pitié Salpêtrière, Paris, France
| | - Sarah Jegou
- Sorbonne University—UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Cecilia Landman
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - David Cohen
- Sorbonne University—UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Giuseppina Liguori
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Anne Bourrier
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Isabelle Nion-Larmurier
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Jacques Cosnes
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Philippe Seksik
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Philippe Langella
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - David Skurnik
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA,Massachusetts Technology and Analytics, Brookline, Massachusetts, USA
| | - Mathias L Richard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Laurent Beaugerie
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
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28
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Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM, Brot L, Taleb S, Couturier-Maillard A, Nion-Larmurier I, Merabtene F, Seksik P, Bourrier A, Cosnes J, Ryffel B, Beaugerie L, Launay JM, Langella P, Xavier RJ, Sokol H. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat Med 2016; 22:598-605. [PMID: 27158904 PMCID: PMC5087285 DOI: 10.1038/nm.4102] [Citation(s) in RCA: 897] [Impact Index Per Article: 112.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 04/08/2016] [Indexed: 12/13/2022]
Abstract
Complex interactions between the host and the gut microbiota govern intestinal homeostasis but remain poorly understood. Here we reveal a relationship between gut microbiota and caspase recruitment domain family member 9 (CARD9), a susceptibility gene for inflammatory bowel disease (IBD) that functions in the immune response against microorganisms. CARD9 promotes recovery from colitis by promoting interleukin (IL)-22 production, and Card9(-/-) mice are more susceptible to colitis. The microbiota is altered in Card9(-/-) mice, and transfer of the microbiota from Card9(-/-) to wild-type, germ-free recipients increases their susceptibility to colitis. The microbiota from Card9(-/-) mice fails to metabolize tryptophan into metabolites that act as aryl hydrocarbon receptor (AHR) ligands. Intestinal inflammation is attenuated after inoculation of mice with three Lactobacillus strains capable of metabolizing tryptophan or by treatment with an AHR agonist. Reduced production of AHR ligands is also observed in the microbiota from individuals with IBD, particularly in those with CARD9 risk alleles associated with IBD. Our findings reveal that host genes affect the composition and function of the gut microbiota, altering the production of microbial metabolites and intestinal inflammation.
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Affiliation(s)
- Bruno Lamas
- Sorbonne University-Université Pierre et Marie Curie (UPMC) Paris, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) Equipe de Recherche Labélisée (ERL) 1157, Avenir Team Gut Microbiota and Immunity, Paris, France
- Centre National de Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7203, Paris, France
- Laboratoire de BioMolécules (LBM), Centre Hospitalo-Universitaire (CHU) Saint-Antoine 27 rue de Chaligny, Paris, France
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Mathias L Richard
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Valentin Leducq
- Sorbonne University-Université Pierre et Marie Curie (UPMC) Paris, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) Equipe de Recherche Labélisée (ERL) 1157, Avenir Team Gut Microbiota and Immunity, Paris, France
- Centre National de Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7203, Paris, France
- Laboratoire de BioMolécules (LBM), Centre Hospitalo-Universitaire (CHU) Saint-Antoine 27 rue de Chaligny, Paris, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Hang-Phuong Pham
- ILTOO Pharma, Incubateur et Pépinière d'Entreprises Paris-Salpêtrière, Hôpital Pitié Salpêtrière, Paris, France
| | - Marie-Laure Michel
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Gregory Da Costa
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Chantal Bridonneau
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Sarah Jegou
- Sorbonne University-Université Pierre et Marie Curie (UPMC) Paris, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) Equipe de Recherche Labélisée (ERL) 1157, Avenir Team Gut Microbiota and Immunity, Paris, France
- Centre National de Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7203, Paris, France
- Laboratoire de BioMolécules (LBM), Centre Hospitalo-Universitaire (CHU) Saint-Antoine 27 rue de Chaligny, Paris, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Thomas W Hoffmann
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Jane M Natividad
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Loic Brot
- Sorbonne University-Université Pierre et Marie Curie (UPMC) Paris, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) Equipe de Recherche Labélisée (ERL) 1157, Avenir Team Gut Microbiota and Immunity, Paris, France
- Centre National de Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7203, Paris, France
- Laboratoire de BioMolécules (LBM), Centre Hospitalo-Universitaire (CHU) Saint-Antoine 27 rue de Chaligny, Paris, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Soraya Taleb
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris-Descartes, Paris, France
| | - Aurélie Couturier-Maillard
- Laboratory of Experimental and Molecular Immunology and Neurogenetics, UMR 7355 CNRS-University of Orleans, Orleans, France
| | - Isabelle Nion-Larmurier
- Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique-Hopitaux de Paris, UPMC, Paris, France
| | - Fatiha Merabtene
- INSERM, UMR S938, Centre de Recherche Saint-Antoine, Plateforme Morphologie du Petit Animal, Paris, France
| | - Philippe Seksik
- Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique-Hopitaux de Paris, UPMC, Paris, France
| | - Anne Bourrier
- Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique-Hopitaux de Paris, UPMC, Paris, France
| | - Jacques Cosnes
- Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique-Hopitaux de Paris, UPMC, Paris, France
| | - Bernhard Ryffel
- Laboratory of Experimental and Molecular Immunology and Neurogenetics, UMR 7355 CNRS-University of Orleans, Orleans, France
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, Republic of South Africa
| | - Laurent Beaugerie
- Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique-Hopitaux de Paris, UPMC, Paris, France
| | - Jean-Marie Launay
- INSERM, UMR S942, Department of Biochemistry, Lariboisière Hospital, Paris, France
- Centre for Biological Resources BB-0033-00064, Lariboisière Hospital, Paris, France
| | - Philippe Langella
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Ramnik J Xavier
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, Massachusetts, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, Massachusetts, USA
| | - Harry Sokol
- Sorbonne University-Université Pierre et Marie Curie (UPMC) Paris, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) Equipe de Recherche Labélisée (ERL) 1157, Avenir Team Gut Microbiota and Immunity, Paris, France
- Centre National de Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7203, Paris, France
- Laboratoire de BioMolécules (LBM), Centre Hospitalo-Universitaire (CHU) Saint-Antoine 27 rue de Chaligny, Paris, France
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
- Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique-Hopitaux de Paris, UPMC, Paris, France
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