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1. Intact proviruses are enriched in the colon and associated with PD-1+TIGIT− mucosal CD4+ T cells of people with HIV-1 on antiretroviral therapyResearch in context

Author

Camille Vellas, Manon Nayrac, Nived Collercandy, Mary Requena, Nicolas Jeanne, Justine Latour, Chloé Dimeglio, Michelle Cazabat, Karl Barange, Laurent Alric, Nicolas Carrere, Guillaume Martin-Blondel, Jacques Izopet, and Pierre Delobel

Subjects
HIV reservoir, Gut, Intact and defective proviruses, CD4+ memory T cells, PD-1, TIGIT, Medicine, Medicine (General), R5-920
Abstract

Summary: Background: The persistence of intact replication-competent HIV-1 proviruses is responsible for the virological rebound off treatment. The gut could be a major reservoir of HIV-1 due to the high number of infected target cells. Methods: We collected blood samples and intestinal biopsies (duodenum, ileum, colon) from 42 people with HIV-1 receiving effective antiretroviral therapy. We used the Intact Proviral DNA Assay to estimate the frequency of intact HIV-1 proviruses in the blood and in the intestinal mucosa of these individuals. We analyzed the genetic complexity of the HIV-1 reservoir by performing single-molecule next-generation sequencing of HIV-1 env DNA. The activation/exhaustion profile of mucosal T lymphocytes was assessed by flow cytometry. Findings: Intact proviruses are particularly enriched in the colon. Residual HIV-1 transcription in the gut is associated with persistent mucosal and systemic immune activation. The HIV-1 intestinal reservoir appears to be shaped by the proliferation of provirus-hosting cells. The genetic complexity of the viral reservoir in the colon is positively associated with TIGIT expression but negatively with PD-1, and inversely related to its intact content. The size of the intact reservoir in the colon is associated with PD-1+TIGIT− mucosal CD4+ T cells, particularly in CD27+ memory cells, whose proliferation and survival could contribute to the enrichment of the viral reservoir by intact proviruses. Interpretation: Enrichment in intact proviruses makes the gut a key compartment for HIV-1 persistence on antiretroviral therapy. Funding: This project was supported by grants from the ANRS-MIE (ANRS EP61 GALT), Sidaction, and the Institut Universitaire de France.

Published
2024
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2. SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing

Author

Pauline Trémeaux, Justine Latour, Noémie Ranger, Vénicia Ferrer, Agnès Harter, Romain Carcenac, Pauline Boyer, Sofia Demmou, Florence Nicot, Stéphanie Raymond, and Jacques Izopet

Subjects
SARS-CoV-2, co-infection, genomic surveillance, long-read sequencing, quasispecies, recombination, Microbiology, QR1-502
Abstract

ABSTRACT Co-infection with at least 2 strains of virus is the prerequisite for recombination, one of the means of genetic diversification. Little is known about the prevalence of these events in SARS-CoV-2, partly because it is difficult to detect them. We used long-read PacBio single-molecule real-time (SMRT) sequencing technology to sequence whole genomes and targeted regions for haplotyping. We identified 17 co-infections with SARS-CoV-2 strains belonging to different clades in 6829 samples sequenced between January and October, 2022 (prevalence 0.25%). There were 3 Delta/Omicron co-infections and 14 Omicron/Omicron co-infections (4 cases of 21K/21L, 1 case of 21L/22A, 2 cases of 21L/22B, 4 cases of 22A/22B, 2 cases of 22B/22C and 1 case of 22B/22E). Four of these patients (24%) also harbored recombinant minor haplotypes, including one with a recombinant virus that was selected in the viral quasispecies over the course of his chronic infection. While co-infections remain rare among SARS-CoV-2-infected individuals, long-read SMRT sequencing is a useful tool for detecting them as well as recombinant events, providing the basis for assessing their clinical impact, and a precise indicator of epidemic evolution. IMPORTANCE SARS-CoV-2 variants have been responsible for the successive waves of infection over the 3 years of pandemic. While co-infection followed by recombination is one driver of virus evolution, there have been few reports of co-infections, mainly between Delta and Omicron variants or between the first 2 Omicron variants 21K_BA.1 and 21L_BA.2. The 17 co-infections we detected during 2022 included cases with the recent clades of Omicron 22A, 22B, 22C, and 22E; 24% harbored recombinant variants. This study shows that long-read SMRT sequencing is well suited to SARS-CoV-2 genomic surveillance.

Published
2023
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3. Classification of the Zoonotic Hepatitis E Virus Genotype 3 Into Distinct Subgenotypes

Author

Florence Nicot, Chloé Dimeglio, Marion Migueres, Nicolas Jeanne, Justine Latour, Florence Abravanel, Noémie Ranger, Agnès Harter, Martine Dubois, Sonia Lameiras, Sylvain Baulande, Sabine Chapuy-Regaud, Nassim Kamar, Sébastien Lhomme, and Jacques Izopet

Subjects
HEV-3, subtype, classification, diversity, full-length genome, phylogeny, Microbiology, QR1-502
Abstract

Hepatitis E virus (HEV) genotype 3 is the most common genotype linked to HEV infections in Europe and America. Three major clades (HEV-3.1, HEV-3.2, and HEV-3.3) have been identified but the overlaps between intra-subtype and inter-subtype p-distances make subtype classification inconsistent. Reference sequences have been proposed to facilitate communication between researchers and new putative subtypes have been identified recently. We have used the full or near full-length HEV-3 genome sequences available in the Genbank database (April 2020; n = 503) and distance analyses of clades HEV-3.1 and HEV-3.2 to determine a p-distance cut-off (0.093 nt substitutions/site) in order to define subtypes. This could help to harmonize HEV-3 genotyping, facilitate molecular epidemiology studies and investigations of the biological and clinical differences between HEV-3 subtypes.

Published
2021
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4. Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing

Author

Sébastien Lhomme, Justine Latour, Nicolas Jeanne, Pauline Trémeaux, Noémie Ranger, Marion Migueres, Gérald Salin, Cécile Donnadieu, and Jacques Izopet

Subjects
SARS-CoV-2, PacBio SMRT sequencing, Illumina sequencing, S1 domain, clade, lineage, Microbiology, QR1-502
Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of the COVID-19 pandemic that emerged in late 2019. The outbreak of variants with mutations in the region encoding the spike protein S1 sub-unit that can make them more resistant to neutralizing or monoclonal antibodies is the main point of the current monitoring. This study examines the feasibility of predicting the variant lineage and monitoring the appearance of reported mutations by sequencing only the region encoding the S1 domain by Pacific Bioscience Single Molecule Real-Time sequencing (PacBio SMRT). Using the PacBio SMRT system, we successfully sequenced 186 of the 200 samples previously sequenced with the Illumina COVIDSeq (whole genome) system. PacBio SMRT detected mutations in the S1 domain that were missed by the COVIDseq system in 27/186 samples (14.5%), due to amplification failure. These missing positions included mutations that are decisive for lineage assignation, such as G142D (n = 11), N501Y (n = 6), or E484K (n = 2). The lineage of 172/186 (92.5%) samples was accurately determined by analyzing the region encoding the S1 domain with a pipeline that uses key positions in S1. Thus, the PacBio SMRT protocol is appropriate for determining virus lineages and detecting key mutations.

Published
2021
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5. Hepatitis E Virus Quasispecies in Cerebrospinal Fluid with Neurological Manifestations

Author

Florence Abravanel, Florence Nicot, Sébastien Lhomme, Michele Cazabat, Thomas Drumel, Aurélie Velay, Justine Latour, Julie Belliere, Pascal Cintas, Nassim Kamar, and Jacques Izopet

Subjects
hepatitis E virus, quasispecies, chronic infection, cerebrospinal fluid, compartmentalization, Medicine
Abstract

Hepatitis E virus (HEV) infection can lead to a variety of neurological disorders. While HEV RNA is known to be present in the central nervous system, HEV quasispecies in serum and cerebrospinal fluid (CSF) have rarely been explored. We studied the virus’ quasispecies in the blood and the CSF of five patients at the onset of their neurological symptoms. The samples of three patients suffering from meningitis, neuralgic amyotrophy and acute inflammatory polyradiculoneuropathy were taken at the acute phase of the HEV infection. The samples from the other two patients were taken during the chronic phase (5 years after HEV diagnosis) when they presented with clinical signs of encephalitis. We sequenced at least 20 randomly polyproline regions of the selected virus clones. Phylogenetic analysis of the virus variants in the blood and the CSF revealed no virus compartmentalization for the three acute-phase patients but there was clear evidence of HEV quasispecies compartmentalization in the CSF of the two patients during chronic infection. In conclusion, prolonged infection in the immunocompromised condition can lead to independent virus replication in the liver and the tissues, producing viruses in CSF.

Published
2021
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6. Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2

Author

Chloé Dimeglio, Marine Milhes, Jean-Michel Loubes, Noémie Ranger, Jean-Michel Mansuy, Pauline Trémeaux, Nicolas Jeanne, Justine Latour, Florence Nicot, Cécile Donnadieu, and Jacques Izopet

Subjects
SARS-CoV-2, public health, statistical model, variant B.1.1.7, Microbiology, QR1-502
Abstract

The spread of SARS-CoV-2 and the resulting disease COVID-19 has killed over 2.6 million people as of 18 March 2021. We have used a modified susceptible, infected, recovered (SIR) epidemiological model to predict how the spread of the virus in regions of France will vary depending on the proportions of variants and on the public health strategies adopted, including anti-COVID-19 vaccination. The proportion of SARS-CoV-2 variant B.1.1.7, which was not detected in early January, increased to become 60% of the forms of SARS-CoV-2 circulating in the Toulouse urban area at the beginning of February 2021, but there was no increase in positive nucleic acid tests. Our prediction model indicates that maintaining public health measures and accelerating vaccination are efficient strategies for the sustained control of SARS-CoV-2.

Published
2021
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7. Influence of Nasopharyngeal Viral Load on the Spread of the Omicron BA.2 Variant

Author

Marion Migueres, Chloé Dimeglio, Jean-Michel Mansuy, Florence Abravanel, Stéphanie Raymond, Justine Latour, Nicolas Jeanne, Noémie Ranger, Sébastien Lhomme, Karine Saune, Pauline Tremeaux, and Jacques Izopet

Subjects
Microbiology (medical), Infectious Diseases
Abstract

We used variant typing polymerase chain reaction to describe the evolution of severe acute respiratory syndrome coronavirus 2 Omicron sublineages between December 2021 and mid-March 2022. The selective advantage of the BA.2 variant over BA.1 is not due to greater nasopharyngeal viral loads.

Published
2022
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9. Evidence of co-infections during Delta and Omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing

Author

Patricia, Combes, Maxime, Bisseux, Antonin, Bal, Pierre, Marin, Justine, Latour, Christine, Archimbaud, Amélie, Brebion, Hélène, Chabrolles, Christel, Regagnon, Jérémy, Lafolie, Gregory, Destras, Bruno, Simon, Jacques, Izopet, Laurence Josset, Cécile, Henquell, Audrey, Mirand, Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Thérapie ciblée combinatoire en Onco-Hématologie (EA3846), Université d'Auvergne - Clermont-Ferrand I (UdA), Service de Virologie Médicale et Moléculaire [CHU Clermont-Ferrand], CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand-CHU Estaing [Clermont-Ferrand], CHU Clermont-Ferrand, Université Clermont Auvergne, CNRS, LMGE, 63000 Clermont–Ferrand, France, Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Hôpital de la Croix-Rousse [CHU - HCL], Virology and human respiratory Pathologies - Virology and human respiratory Pathologies (VirPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Virologie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Infection Inflammation et Interaction Hôtes Pathogènes [CHU Clermont-Ferrand] (3IHP ), Direction de la recherche clinique et de l’innovation [CHU Clermont-Ferrand] (DRCI), CHU Clermont-Ferrand-CHU Clermont-Ferrand, Centre Hospitalier de Vichy (CH Vichy), Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR - laboratoire associé), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Terrasol, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, SARS-CoV-2, Coinfection, Single nucleotide polymorphism screening, COVID-19, General Medicine, Recombination, SARS-CoV-2 co-infection, Infectious Diseases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Whole genome sequencing, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, Prospective Studies, Sequence Analysis, Delta and Omicron VOC
Abstract

International audience; Objectives: To describe Delta/Omicron SARS-CoV-2 variants co-infection detection and confirmation during the fifth wave of COVID-19 pandemics in France in 7 immunocompetent and epidemiologically unrelated patients.Methods: Since December 2021, the surveillance of Delta/Omicron SARS-CoV-2 variants of concern (VOC) circulation was performed through prospective screening of positive-samples using single nucleotide polymorphism (SNP) PCR assays targeting SARS-CoV-2 S-gene mutations K417N (Omicron specific) and L452R (Delta specific). Samples showing unexpected mutational profiles were further submitted to whole genome sequencing (WGS) using three different primer sets.Results: Between weeks 49-2021 and 02-2022, SARS-CoV-2 genome was detected in 3831 respiratory samples, of which 3237 (84.5%) were screened for VOC specific SNPs. Unexpected mutation profiles suggesting a dual Delta/Omicron population were observed in 7 nasopharyngeal samples (0.2%). These co-infections were confirmed by WGS. For 2 patients, the sequence analyses of longitudinal samples collected 7 to 11 days apart showed that Delta or Omicron can outcompete the other variant during dual infection. Additionally, for one of these samples, a recombination event between Delta and Omicron was detected.Conclusions: This work demonstrates that SARS-CoV-2 Delta/Omicron co-infections are not rare in high virus co-circulation periods. Moreover, co-infections can further lead to genetic recombination which may generate new chimeric variants with unpredictable epidemic or pathogenic properties that could represent a serious health threat.

Published
2022
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10. Whole‐genome sequencing of SARS‐CoV‐2: Comparison of target capture and amplicon single molecule real‐time sequencing protocols

Author

Florence Nicot, Pauline Trémeaux, Justine Latour, Nicolas Jeanne, Noémie Ranger, Stéphanie Raymond, Chloé Dimeglio, Gérald Salin, Cécile Donnadieu, and Jacques Izopet

Subjects
Infectious Diseases, Virology
Abstract

Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Single-molecule real-time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT PacBio protocol for whole-genome sequencing (WGS) of SARS-CoV-2 to that of an amplicon PacBio SMRT sequencing protocol. The median genome coverage was higher (p 0.05) with the target capture protocol (99.3% [interquartile range, IQR: 96.3-99.5]) than with the amplicon protocol (99.3% [IQR: 69.9-99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for C

Published
2022
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11. Persistence of hepatitis E virus in the cerebrospinal fluid despite apparently successful ribavirin therapy

Author

Sébastien Lhomme, Amandine Fayard, Sonia Mirafzal, Romain Carcenac, Pauline Boyer, Justine Latour, Amélie Brebion, Jacques Olivier Bay, Cécile Henquell, Jacques Izopet, Role of intra-Clonal Heterogeneity and Leukemic environment in ThErapy Resistance of chronic leukemias (CHELTER), and Université Clermont Auvergne (UCA)

Subjects
Pharmacology, Microbiology (medical), Infectious Diseases, Ribavirin, Hepatitis E virus, Humans, RNA, Viral, Pharmacology (medical), Drug Therapy, Combination, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Antiviral Agents, Hepatitis E
Abstract

International audience

Published
2022
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12. Influence of vaccination and prior immunity on the dynamics of Omicron BA.1 and BA.2 sub-variants

Author

Chloé Dimeglio, Jean-Michel Loubes, Marion Migueres, Karine Sauné, Pauline Trémeaux, Sébastien Lhomme, Noémie Ranger, Justine Latour, Jean-Michel Mansuy, Jacques Izopet, Laboratoire Virologie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Benson-Rumiz, Alicia, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), Public health, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Infectious Diseases, Omicron, SARS-CoV-2, Vaccination, COVID-19, Humans, Statistical model, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; The B.1.1.529 SARS-CoV-2 lineage, named Omicron, was recently divided into three lineages (BA.1, BA.2 and BA.3). BA.1 and BA.2 are much more dominant than BA.3. BA.1 could cause breakthrough infections in highly immune populations [1]. Preliminary studies indicate that BA.2 can readily overcome the immunity provided by vaccination and/or infection with an earlier variant. We used data for the French city of Toulouse to evaluate the impact of the proportions of the BA.1 and BA.2 variants in positive-testing samples and the impact of vaccination on SARS-CoV-2 proliferation.

Published
2022
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13. Resistance mutations in SARS-CoV-2 omicron variant in patients treated with sotrovimab

Author

Camille Vellas, Pauline Trémeaux, Arnaud Del Bello, Justine Latour, Nicolas Jeanne, Noémie Ranger, Chloé Danet, Guillaume Martin-Blondel, Pierre Delobel, Nassim Kamar, Jacques Izopet, Benson-Rumiz, Alicia, Laboratoire Virologie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Néphrologie et Transplantation d'organes [CHU Toulouse], Pôle Urologie - Néphrologie - Dialyse - Transplantations - Brûlés - Chirurgie plastique - Explorations fonctionnelles et physiologiques [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Institut de recherche juridique interdisciplinaire (IRJI), Université de Tours (UT), Pôle pharmacie [CHU Toulouse], Service Maladies infectieuses et tropicales [CHU Toulouse], and Pôle Inflammation, infection, immunologie et loco-moteur [CHU Toulouse] (Pôle I3LM Toulouse)

Subjects
Microbiology (medical), Infectious Diseases, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, SARS-CoV-2, Mutation, Humans, General Medicine, Antibodies, Monoclonal, Humanized, Antibodies, Neutralizing, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, COVID-19 Drug Treatment
Abstract

International audience; The SARS-CoV-2 B.1.1.529 (Omicron) variant, divided in five lineages (BA.1/BA.2/BA.3/BA.4/BA.5), harbors numerous spike protein mutations particularly in the receptor-binding domain (RBD). Recent studies showed that the Omicron variant resists the majority of RBD-targeting monoclonal antibodies (mAb). Sotrovimab, a pan-sarbecovirus neutralizing mAb recently authorized, seems to remain efficient to neutralize the omicron variant. However, as it targets a single epitope, the risk of developing resistance mutations is not negligible. We determined the evolution of the virus load, the development of spike mutations, and the evolution of the virus complexity in nasopharyngeal (NP) swabs from sotrovimab-treated ambulatory Omicron-infected patients.

Published
2022
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14. Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2

Author

Jean-Michel Loubes, Nicolas Jeanne, Chloé Dimeglio, Florence Nicot, Cécile Donnadieu, Justine Latour, Jean-Michel Mansuy, Pauline Trémeaux, Marine Milhes, Noémie Ranger, Jacques Izopet, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Virologie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), KALK, MURIELLE, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
2019-20 coronavirus outbreak, medicine.medical_specialty, COVID-19 Vaccines, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV]Life Sciences [q-bio], Disease, 030204 cardiovascular system & hematology, Microbiology, Virus, Article, 03 medical and health sciences, 0302 clinical medicine, SARS-CoV-2, public health, statistical model, variant B.1.1.7, Virology, Epidemiology, medicine, Humans, 030212 general & internal medicine, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Public health, business.industry, Vaccination, COVID-19, QR1-502, [SDV] Life Sciences [q-bio], Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Variant B117, France, Statistical model, business, Epidemiologic Methods
Abstract

International audience; The spread of SARS-CoV-2 and the resulting disease COVID-19 has killed over 2.6 million people as of 18 March 2021. We have used a modified susceptible, infected, recovered (SIR) epidemiological model to predict how the spread of the virus in regions of France will vary depending on the proportions of variants and on the public health strategies adopted, including anti-COVID-19 vaccination. The proportion of SARS-CoV-2 variant B.1.1.7, which was not detected in early January, increased to become 60% of the forms of SARS-CoV-2 circulating in the Toulouse urban area at the beginning of February 2021, but there was no increase in positive nucleic acid tests. Our prediction model indicates that maintaining public health measures and accelerating vaccination are efficient strategies for the sustained control of SARS-CoV-2.

Published
2021
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15. The SARS-CoV-2 seroprevalence is the key factor for deconfinement in France

Author

Benjamin Deporte, Jacques Izopet, Chloé Dimeglio, Jean-Michel Loubes, Martine Dubois, Justine Latour, Jean Michel Mansuy, Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Virologie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), PINIER, CHRISTINE, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Microbiology (medical), 2019-20 coronavirus outbreak, deconfinement, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), viruses, MESH: Pneumonia, Viral / prevention & control, 030106 microbiology, Deconfinement, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Seroprevalence, MESH: COVID-19, MESH: SARS-CoV-2, 030212 general & internal medicine, Socioeconomics, MESH: Pandemics / statistics & numerical data, MESH: Pneumonia, Viral / epidemiology, MESH: France / epidemiology, MESH: Humans, MESH: Seroepidemiologic Studies, seroprevalence, MESH: Coronavirus Infections / prevention & control, SARS-CoV-2, MESH: Pandemics / prevention & control, statistical model, MESH: Pneumonia, Viral / transmission, MESH: Infection Control* / methods, Infectious Diseases, Geography, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Betacoronavirus, MESH: Coronavirus Infections / epidemiology, MESH: Models, Statistical, Healthcare system, MESH: Coronavirus Infections / transmission
Abstract

International audience; A new virus, SARS-CoV-2, has spread world-wide since December 2019, probably affecting millions of people and killing thousands. Failure to anticipate the spread of the virus now seriously threatens many health systems. We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy

Published
2020
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16. J-Domain Proteins in Bacteria and Their Viruses

Author

Roland Barriot, Pierre Genevaux, Gwennaele Fichant, Justine Latour, Marie-Pierre Castanié-Cornet, Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université Fédérale Toulouse Midi-Pyrénées

Subjects
[SDV]Life Sciences [q-bio], Bacterial genome size, Genome, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, Protein Domains, Structural Biology, Escherichia coli, Humans, Bacteriophages, HSP70 Heat-Shock Proteins, Molecular Biology, Cellular localization, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Adenosine Triphosphatases, 0303 health sciences, biology, Bacteria, Escherichia coli Proteins, HSP40 Heat-Shock Proteins, biology.organism_classification, Cell biology, Hsp70, Chaperone (protein), Protein Biosynthesis, biology.protein, bacteria, 030217 neurology & neurosurgery, Biogenesis, Metabolic Networks and Pathways, Molecular Chaperones
Abstract

Molecular chaperones maintain cellular protein homeostasis by acting at almost every step in protein biogenesis pathways. The DnaK/HSP70 chaperone has been associated with almost every known essential chaperone functions in bacteria. To act as a bona fide chaperone, DnaK strictly relies on essential co-chaperone partners known as the J-domain proteins (JDPs, DnaJ, Hsp40), which preselect substrate proteins for DnaK, confer its specific cellular localization, and stimulate both its weak ATPase activity and substrate transfer. Remarkably, genome sequencing has revealed the presence of multiple JDP/DnaK chaperone/co-chaperone pairs in a number of bacterial genomes, suggesting that certain pairs have evolved toward more specific functions. In this review, we have used representative sets of bacterial and phage genomes to explore the distribution of JDP/DnaK pairs. Such analysis has revealed an unexpected reservoir of novel bacterial JDPs co-chaperones with very diverse and unexplored function that will be discussed.

Published
2020
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