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1. Study of the cellular and humoral immune responses to SARS-CoV-2 vaccination

Author

Faustine Montmaneix-Engels, Chloé Dimeglio, Laeticia Staes, Isabelle Da Silva, Marion Porcheron, Isabelle Jougla, Fabrice Hérin, and Jacques Izopet

Subjects
COVID-19 vaccination, SARS-CoV-2, Cellular immunity, Humoral immunity, Interferon gamma release assay, Science (General), Q1-390, Social sciences (General), H1-99
Abstract

Our understanding of cellular immunity in response to COVID-19 infection or vaccination is limited because of less commonly used techniques. We investigated both the cellular and humoral immune responses before and after the administration of a third dose of the SARS-CoV-2 vaccine among a group of healthcare workers. Cellular immunity was evaluated using the VIDAS interferon-gamma (IFNγ) RUO test, which enables automated measurement of IFNγ levels after stimulating peripheral blood lymphocytes.Booster doses significantly enhanced both cellular and humoral immunity. Concerning cellular response, the booster dose increased the percentage of positive IFNγ release assay (IGRA) results but no difference in IFNγ release was found. The cellular response was not associated with protection against SARS-CoV-2 infection. Interestingly, vaccinated and infected healthcare workers exhibited the highest levels of anti-spike and neutralizing antibodies.In conclusion, the IGRA is a simple method for measuring cellular immune responses after vaccination. However, its usefulness as a complement to the study of humoral responses is yet to be demonstrated in future research.

Published
2024
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2. 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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3. Decreased Efficiency of Neutralizing Antibodies from Previously Infected or Vaccinated Individuals against the B.1.617.2 (Delta) SARS-CoV-2 Variant

Author

Chloé Dimeglio, Fabrice Herin, Isabelle Da-Silva, Caroline Gernigon, Marion Porcheron, Sabine Chapuy-Regaud, and Jacques Izopet

Subjects
binding antibodies, neutralizing antibodies, SARS-CoV-2, Delta variant, protection, Microbiology, QR1-502
Abstract

ABSTRACT The neutralizing antibody response is a key component of adaptive immunity and a primary protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The increased transmissibility of the SARS-CoV-2 Delta variant and its capacity to cause more severe disease could be linked to a significant reduction in neutralizing antibodies generated during a previous infection or vaccination. We analyzed blood samples from 162 unvaccinated health care workers (HCWs) collected 1 to 3 months postinfection and from 263 vaccinated health care workers 1 month after the last injection. We have compared the neutralizing antibody titers obtained using two virus strains, B.1.160 and B.1.617.2 (Delta variant). Binding antibody concentrations were measured by an immunoassay. The median neutralizing antibody titer against the B.1.160 strain was 128 (interquartile range [IQR], 16 to 256) and 32 (IQR, 8 to 128) against the Delta variant. To obtain a neutralizing antibody titer of 32 or 64, a binding antibody concentration of 182 binding antibody units (BAU)/mL (IQR, 81 to 974) was required with the strain B.1.160, while a concentration of 2,595 BAU/mL (IQR, 1,176 to 5,353) was required with the Delta variant. Our data indicate that antibodies neutralize the SARS-CoV-2 Delta variant 4 times less efficiently than they neutralize an earlier strain. Half of the HCWs had decreased protection from 94% to 76.8% or less for the same total antibody concentration. But neutralization might be correlated with other immune responses. The contributions of other responses, such as those of the T cell and B cell systems, to protection require further investigation. IMPORTANCE Recent studies showed that the neutralizing antibody titer is an important contributor to protection against SARS-CoV-2. With the emergence of new variants, the question arises of maintaining the neutralizing capacities of vaccines and/or of a past infection. We had protective data associated with total antibody concentrations and neutralizing antibody titers for a B.1.160 strain. We showed that to maintain the same levels of protection and, therefore, the same levels of neutralizing antibodies, a total antibody concentration 8.5 times greater is required with the Delta strain. (This study has been registered at ClinicalTrials.gov under registration no. NCT04385108.)

Published
2022
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4. The real seroprevalence of SARS-CoV-2 in France and its consequences for virus dynamics

Author

Chloé Dimeglio, Jean-Michel Loubes, Marcel Miedougé, Fabrice Herin, Jean-Marc Soulat, and Jacques Izopet

Subjects
Medicine, Science
Abstract

Abstract The SARS-CoV-2 virus has spread world-wide since December 2019, killing more than 2.9 million of people. We have adapted a statistical model from the SIR epidemiological models to predict the spread of SARS-CoV-2 in France. Our model is based on several parameters and assumed a 4.2% seroprevalence in Occitania after the first lockdown. The recent use of serological tests to measure the effective seroprevalence of SARS-CoV-2 in the population of Occitania has led to a seroprevalence around 2.4%. This implies to review the parameters of our model to conclude at a lower than expected virus transmission rate, which may be due to infectivity varying with the patient’s symptoms or to a constraint due to an uneven population geographical distribution.

Published
2021
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5. Weaker Effects of the Fourth Dose of BNT162b2 SARS-CoV-2 Vaccine on the Elderly Human Population

Author

Chloé Dimeglio, Isabelle Da-Silva, Marion Porcheron, Marie-Pierre Panero, Laetitia Staes, Pauline Trémeaux, Hélène Villars, and Jacques Izopet

Subjects
vaccination, vulnerable population, SARS-CoV-2, immune monitoring, Medicine
Abstract

The vaccines presently available are less effective in older people due to senescence of their immune systems. We measured the antibody responses of 42 adults living in nursing homes after the third and the fourth doses of an mRNA vaccine and found that the strain (BA.2 and BA.2.75: from 64 to 128, BA.5: from 16 to 32, BQ.1.1: from 16 to 64 among the uninfected) influenced the effect of the fourth dose of vaccine on neutralizing antibodies. The fourth dose also increased binding antibodies (from 1036 BAU/mL to 5371 BAU/mL among the uninfected, from 3700 BAU/mL to 6773 BAU/mL among the BA.5 infected). This effect was less significant than that of the third dose of vaccine for both neutralizing (BA.2: from 8 to 128, BA.5: from 2 to 16, BA.2.75: from 8 to 64, BQ.1.1: from 2 to 16) and binding antibodies (from 139.8 BAU/mL to 2293 BAU/mL). However, the fourth dose attained the 5000 BAU/mL threshold conferring approximately 80% protection against a SARS-CoV-2 BA.2 infection in most individuals, unlike the third.

Published
2023
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6. Antibody Titers and Protection against Omicron (BA.1 and BA.2) SARS-CoV-2 Infection

Author

Chloé Dimeglio, Marion Migueres, Naémie Bouzid, Sabine Chapuy-Regaud, Caroline Gernigon, Isabelle Da-Silva, Marion Porcheron, Guillaume Martin-Blondel, Fabrice Herin, and Jacques Izopet

Subjects
SARS-CoV-2, Omicron, antibodies, protection, public health, Medicine
Abstract

The emergence of the SARS-CoV-2 variants of concern has greatly influenced the immune correlates of protection, and there are little data about the antibody threshold concentrations to protect against infection with SARS-CoV-2 Omicron BA.1 or BA.2. We analyzed the antibody responses of 259 vaccinated healthcare workers, some of whom had been previously infected by SARS-CoV-2. The median follow-up was 179 days (IQR: 171–182) after blood collection. We detected 88 SARS-CoV-2 Omicron infections during the follow-up period, 55 (62.5%) with SARS-CoV-2 BA.1, and 33 (37.5%) with SARS-CoV-2 BA.2. A neutralizing antibody titer below 8 provided no protection against a BA.1 infection, a titer of 16 or 32 gave 73.2% protection, and a titer of 64 or 128 provided 78.4% protection. Conversely, the BA.2 infection rate did not vary as a function of anti-BA.2 neutralizing antibody titers. Binding antibody concentrations below 6000 BAU/mL provided no protection against Omicron BA.1 infection, 6000–20,000 BAU/mL provided 55.6% protection, and 20,000 or more provided 87.7% protection. There was no difference in BA.2 infection depending on the binding antibody concentration. Further studies are needed to investigate the relationship between antibody concentrations and infection with the Omicron BA.4/5 variants that are becoming predominant worldwide.

Published
2022
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7. Analyses of Clinical and Biological Data for French and Belgian Immunocompetent Patients Infected With Hepatitis E Virus Genotypes 4 and 3

Author

Florence Micas, Vanessa Suin, Jean-Marie Péron, Caroline Scholtes, Edouard Tuaillon, Thomas Vanwolleghem, Laurence Bocket, Sébastien Lhomme, Chloé Dimeglio, Jacques Izopet, and Florence Abravanel

Subjects
hepatitis E virus, genotype 4, pathogenicity, immunocompetent, Europe, acute hepatitis, Microbiology, QR1-502
Abstract

Hepatitis E virus (HEV) genotypes 3 and 4 are the major causes of acute hepatitis in industrialized countries. Genotype 3 is mainly found in Europe and America, while genotype 4 is predominant in Asia. Several Japanese studies have suggested that genotype 4 is more virulent than genotype 3. We investigated this aspect by analyzing the clinical and biological data for 27 French and Belgian immunocompetent patients infected with HEV genotype 4. Their infections were probably acquired locally, since none of these patients reported traveling outside France or Belgium during the 2–8 weeks before symptoms onset. Each patient was matched for age (±5 years) and gender with two patients infected with HEV genotype 3. Bivariate analysis indicated that the HEV genotype 4-infected patients had significantly higher alanine aminotransferase (ALT) (2067 IU/L) and aspartate aminotransferase (AST) (1581 IU/L) activities and total bilirubin concentrations (92.4 μmol/L) than did those infected with HEV genotype 3 (1566 IU/L, p = 0.016; 657 IU/L, p = 0.003 and 47 μmol/L, p = 0.046) at diagnosis. In contrast, more patients infected with HEV genotype 3 reported dark urine (71% vs. 39%, p = 0.02) and experienced asthenia (89% vs. 58%, p < 0.01) than did those infected with HEV genotype 4. Two HEV genotype 4-infected patients died of multi-organ failure, while none of the genotype 3-infected patients died (p = 0.035). Finally, stepwise regression analysis retained only a greater increase in ALT (odds-ratio: 1.0005, 95% confidence interval: 1.00012–1.00084) and less frequent fever (odds-ratio = 0.1244; 95% confidence interval: 0.01887–0.82020) for patients infected with HEV genotype 4. We conclude that HEV-4 infections are likely to be associated with higher ALT activity than HEV-3 infections. Additional immunological and virological studies are required to confirm these findings and better understand the influence, if any, of genotype on HEV pathophysiology.

Published
2021
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8. 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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9. Posttraumatic Stress Disorder Symptoms in Lymphoma Patients: A Prospective Study

Author

Claire Camille, Chloé Dimeglio, Antoine Yrondi, Gisèle Compaci, Emmanuelle Delmas, Mélanie Gauché, Guy Laurent, and Philippe Birmes

Subjects
cancer, lymphoma, peritraumatic distress, peritraumatic dissociation, posttraumatic stress disorder, stressor, Psychiatry, RC435-571
Abstract

The cancer experience may be marked by repeat stressors and/or traumas. The aim of our study was to assess traumatic events in a group of patients diagnosed with lymphoma and to determine which of these contribute to the development of Post-Traumatic Stress Disorder/PTSD. Two weeks after receiving a diagnosis of lymphoma, patients were referred for an assessment of peritraumatic distress (using the Peritraumatic Distress Inventory/PDI) and peritraumatic dissociation (using the Peritraumatic Dissociative Experiences Questionnaire/PDEQ). Three months after the diagnosis, we recorded the following parameters: the patients' worst experiences, the presence of PTSD symptoms, using the PTSD CheckList/PCL, as it related to the diagnosis, and symptoms of anxiety using the Hospital Anxiety and Depression/HAD scale and of depression using the Beck Depression Inventory/BDI-II. The study recruited 129 patients, with a mean age of 46 years (SD = 17.3); 70 (54%) men, 87 (67.5%) with Non-Hodgkin's lymphoma, and 42 with Hodgkin's lymphoma. Two weeks after the diagnosis, 49% of patients reported peritraumatic distress, and 20% peritraumatic dissociation, during or immediately after being informed of the lymphoma diagnosis. Three months after the diagnosis, the severity of PTSD symptoms was evaluated. At this stage none of the patients suffered PTSD, but 29 (23%) individuals exhibited partial PTSD: 13.4% correlated it to receiving the lymphoma diagnosis, 8% to telling family members, and 1.6% to adverse effects. Peritraumatic distress and dissociation as a result of receiving a lymphoma diagnosis, as well as anxiety and a mucositis within the first 3 months post-diagnosis, were factors that were significantly associated with PTSD symptoms, accounting for 35.8% in PTSD symptom load. Our study reveals that clinicians should assess the impact of a number of stressors, which are risk factors for PTSD symptoms, starting from the time point of the initial lymphoma diagnosis.

Published
2020
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10. Insertions and Duplications in the Polyproline Region of the Hepatitis E Virus

Author

Sébastien Lhomme, Florence Nicot, Nicolas Jeanne, Chloé Dimeglio, Alain Roulet, Caroline Lefebvre, Romain Carcenac, Maxime Manno, Martine Dubois, Jean-Marie Peron, Laurent Alric, Nassim Kamar, Florence Abravanel, and Jacques Izopet

Subjects
hepatitis E virus, polyproline region, genomic rearrangement, virus-host recombinant variants, virus-virus recombinant variants, Microbiology, QR1-502
Abstract

Recombinant strains of hepatitis E virus (HEV) with insertions of human genomic fragments or HEV sequence duplications in the sequence encoding the polyproline region (PPR) were previously described in chronically infected patients. Such genomic rearrangements confer a replicative advantage in vitro but little is known about their frequency, location, or origin. As the sequences of only a few virus genomes are available, we analyzed the complete genomes of 114 HEV genotype 3 strains from immunocompromised (n = 85) and immunocompetent (n = 29) patients using the single molecular real-time sequencing method to determine the frequency, location, and origin of inserted genomic fragments, plus the proportions of variants with genomic rearrangements in each virus quasispecies. We also examined the amino acid compositions and post-translational modifications conferred by these rearrangements by comparing them to sequences without human gene insertions or HEV gene duplications. We found genomic rearrangements in 7/114 (6.1%) complete genome sequences (4 HEV-3f, 1 HEV-3e, 1 HEV-3 h, and 1 HEV-3chi-new), all from immunocompromised patients, and 3/7 were found at the acute phase of infection. Six of the seven patients harbored virus-host recombinant variants, including one patient with two different recombinant variants. We also detected three recombinant variants with genome duplications of the PPR or PPR + X domains in a single patient. All the genomic rearrangements (seven human fragment insertions of varying origins and three HEV genome duplications) occurred in the PPR. The sequences with genomic rearrangements had specific characteristics: increased net load (p < 0.001) and more ubiquitination (p < 0.001), phosphorylation (p < 0.001), and acetylation (p < 0.001) sites. The human fragment insertions and HEV genome duplications had slightly different characteristics. We believe this is the first description of HEV strains with genomic rearrangements in patients at the acute phase of infection; perhaps these strains are directly transmitted. Clearly, genomic rearrangements produce a greater net load with duplications and insertions having different features. Further studies are needed to clarify the mechanisms by which such modifications influence HEV replication.

Published
2020
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11. Influence of the Delta Variant and Vaccination on the SARS-CoV-2 Viral Load

Author

Marion Migueres, Chloé Dimeglio, Pauline Trémeaux, Stéphanie Raymond, Sébastien Lhomme, Isabelle Da Silva, Kévin Oliveira Mendes, Florence Abravanel, Marie-Pierre Félicé, Jean-Michel Mansuy, and Jacques Izopet

Subjects
SARS-CoV-2, COVID-19, viral load, delta variant, vaccination, Microbiology, QR1-502
Abstract

Studies comparing SARS-CoV-2 nasopharyngeal (NP) viral load (VL) according to virus variant and host vaccination status have yielded inconsistent results. We conducted a single center prospective study between July and September 2021 at the drive-through testing center of the Toulouse University Hospital. We compared the NP VL of 3775 patients infected by the Delta (n = 3637) and Alpha (n = 138) variants, respectively. Patient’s symptoms and vaccination status (2619 unvaccinated, 636 one dose and 520 two doses) were recorded. SARS-CoV-2 RNA testing and variant screening were assessed by using Thermo Fisher® TaqPath™ COVID-19 and ID solutions® ID™ SARS-CoV-2/VOC evolution Pentaplex assays. Delta SARS-CoV-2 infections were associated with higher VL than Alpha (coef = 0.68; p ≤ 0.01) independently of patient’s vaccination status, symptoms, age and sex. This difference was higher for patients diagnosed late after symptom onset (coef = 0.88; p = 0.01) than for those diagnosed early (coef = 0.43; p = 0.03). Infections in vaccinated patients were associated with lower VL (coef = −0.18; p ≤ 0.01) independently of virus variant, symptom, age and sex. Our results suggest that Delta infections could lead to higher VL and for a longer period compared to Alpha infections. By effectively reducing the NP VL, vaccination could allow for limiting viral spread, even with the Delta variant.

Published
2022
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12. The Prevalence of Hepatitis E in a Patient Cohort Presenting With Addictive Injection Behavior

Author

Antoine Yrondi, Juliette Salles, Jean Marie Péron, Marie Sporer, Simon Taib, Adeline Gallini, Chloé Noilhan, Chloé Dimeglio, Flora Entajan, Marie Crequy, Jacques Izopet, and Laurent Schmitt

Subjects
addiction, hepatitis E, injection, intravenous, seroprevalence, Psychiatry, RC435-571
Abstract

Introduction: Hepatitis E is the most common cause of acute viral hepatitis worldwide. Seroprevalence is approximately 15% in developed countries, and 22% in France. hepatitis E virus (HEV) can be transmitted via transfusions and therefore possibly intravenous (IV) drug use. Hepatitis E serology is routinely tested in patients who seek medical advice for addictive injection behavior at the addiction treatment, support and prevention unit of Toulouse University Hospital. We assume that hepatitis E is more prevalent in patients presenting with addictive injection behavior than in the general French population.Methods: Hepatitis E serological assays [immunoglobulin M (IgM) and IgG] were carried out for all patients presenting with addictive injection behavior during an initial evaluation. The controls were taken from a cohort of 3,353 blood donors living in southern France and who donated blood during the first 2 weeks of October 2011.Results: We included 52 patients presenting with addictive injection behavior and 103 healthy controls matched for age, sex, and area of residence. We found no difference between patients and controls for the prevalence of hepatitis E: patients vs. healthy controls: positive IgGs: 42.31%, 95% confidence interval (CI) (28.73–56.80%) vs. 43.43%, 95% CI (33.50–53.77%) (p = 0.89) and positive IgMs: 3.85%, 95% CI (0.47–13.22%) vs. 4.85%, 95% CI (0.16–10.97%) (p = 0.57).Conclusion: There was no difference in HEV seroprevalence between IV drug users and the general population, suggesting that the IV route of HEV infection is not significant in this population.

Published
2019
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13. 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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14. Hepatitis E prevalence in French Polynesian blood donors.

Author

Chloé Dimeglio, Frédéric Beau, Julien Broult, Patrice Gouy, Jacques Izopet, Stéphane Lastère, and Florence Abravanel

Subjects
Medicine, Science
Abstract

The HEV seroprevalence in mainland France is elevated (22.4%). In contrast, anti-HEV seroprevalence appears to be lower in Oceania. However, none is available for French Polynesia. We assessed the anti-HEV IgG and IgM prevalence on samples from 300 consecutive blood donors living on Tahiti and Moorea islands. Epidemiological information was collected using a specific questionnaire. Overall IgM seroprevalence was 0.6% and overall IgG seroprevalence was 7.7%. The presence of anti-HEV IgG was associated with increasing age (p = 0.01), eating chicken offal (p = 0.01) and cooked rabbit (p = 0.02). Conversely, eating fafaru-traditional Polynesian condiment-was associated with a lower rate of anti-HEV IgG (p

Published
2018
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15. Plasma Hepatitis E Virus Kinetics in Solid Organ Transplant Patients Receiving Ribavirin

Author

Sebastien Lhomme, Swati DebRoy, Nassim Kamar, Florence Abravanel, David Metsu, Olivier Marion, Chloé Dimeglio, Scott J. Cotler, Jacques Izopet, and Harel Dahari

Subjects
hepatitis E virus, viral kinetics, ribavirin, chronic infection, Microbiology, QR1-502
Abstract

Hepatitis E virus (HEV) infection causes chronic hepatitis in solid organ transplant (SOT) recipients. Antiviral therapy consists of three months of ribavirin, although response rates are not optimal. We characterized plasma HEV kinetic patterns in 41 SOT patients during ribavirin therapy. After a median pharmacological delay of three (range: 0−21) days, plasma HEV declined from a median baseline level of 6.12 (3.53−7.45) log copies/mL in four viral kinetic patterns: (i) monophasic (n = 18), (ii) biphasic (n = 13), (iii) triphasic (n = 8), and (iv) flat-partial response (n = 2). The mean plasma HEV half-life was estimated to be 2.0 ± 0.96 days. Twenty-five patients (61%) had a sustained virological response (SVR) 24 weeks after completion of therapy. Viral kinetic patterns (i)−(iii) were not associated with baseline characteristics or outcome of therapy. A flat-partial response was associated with treatment failure. All patients with a log concentration decrease of plasma HEV at day seven of >15% from baseline achieved SVR. In conclusion, viral kinetic modeling of plasma HEV under ribavirin therapy showed, for the first time, four distinct kinetic profiles, a median pharmacologic delay of three days, and an estimated HEV half-life of two days. Viral kinetic patterns were not associated with response to therapy, with the exception of a flat-partial response.

Published
2019
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16. Hepatitis E Virus Infections among Patients with Acute Febrile Jaundice in Burkina Faso

Author

Chloé Dimeglio, Dramane Kania, Judith Mbombi Mantono, Thérèse Kagoné, Sylvie Zida, Souleymane Tassembedo, Amadou Dicko, Bachirou Tinto, Seydou Yaro, Hervé Hien, Jérémi Rouamba, Brice Bicaba, Isaïe Medah, Nicolas Meda, Oumar Traoré, Edouard Tuaillon, Florence Abravanel, and Jacques Izopet

Subjects
Burkina Faso, hepatitis E virus, epidemiology, risk factors, Microbiology, QR1-502
Abstract

Hepatitis E virus infection is a significant public health problem in many parts of the world including Africa. We tested serum samples from 900 patients in Burkina Faso presenting with febrile icterus. They all tested negative for yellow fever, but those from 23/900 (2.6%) patients contained markers of acute HEV infection (anti-HEV IgM and HEV RNA positive). Genotyping indicated that 14 of the strains were HEV genotype 2b. There was an overall HEV IgG seroprevalence of 18.2% (164/900). In a bivariate analysis, the factors linked to HEV exposure were climate and patient age. Older patients and those living in arid regions were more likely to have HEV infection. HEV genotype 2b circulating only in humans can be involved in some acute febrile icterus cases in Burkina Faso. Better access to safe water, sanitation, and improved personal hygiene should improve control of HEV infection in this country.

Published
2019
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18. Post-vaccination SARS-CoV-2 antibody kinetics and protection duration against Omicron in elderly population

Author

Chloé Dimeglio, Pauline Trémeaux, Fabrice Herin, Isabelle Da-Silva, Marion Porcheron, Guillaume Martin-Blondel, Caroline Gernigon, Sabine Chapuy-Regaud, Hélène Villars, 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), Centre d'Epidémiologie et de Recherche en santé des POPulations (CERPOP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Service Maladies Professionnelles et Environnementales [CHU Toulouse], Pôle Santé publique et médecine publique [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Service Maladies infectieuses et tropicales [CHU Toulouse], Pôle Inflammation, infection, immunologie et loco-moteur [CHU Toulouse] (Pôle I3LM Toulouse), Pôle Gériatrie [CHU Toulouse], and Benson-Rumiz, Alicia

Subjects
MESH: Aged, Microbiology (medical), [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, MESH: COVID-19* / prevention & control, MESH: Kinetics, SARS-CoV-2, Vaccination, COVID-19, MESH: Vaccination, Antibodies, Viral, Kinetics, Infectious Diseases, MESH: SARS-CoV-2, Humans, MESH: Antibodies, Viral, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Aged
Abstract

International audience; Coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 is particularly severe in older individuals because of an impaired immune response.1 The vaccines presently available are less efficacious in older individuals, because of the senescence of their immune systems.2 A recent letter in Journal of Infection showed the need of a third vaccine dose due to a waning antibody response against new SARS-CoV-2 variants in healthy and immunocompromised individuals.3 In this study, we analysed the protection against Omicron provided by the immune responses of nursing home residents (NHRs) and a population of healthcare workers (HCWs).

Published
2022
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19. 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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21. Comparative effects of mRNA vaccine booster and natural Omicron infection on the neutralizing antibody response

Author

Chloé Dimeglio, Marion Migueres, Sabine Chapuy-Regaud, Isabelle Da-Silva, Isabelle Jougla, Claire Pradere, Marion Porcheron, Guillaume Martin-Blondel, Catherine Lougarre, Fabrice Herin, and Jacques Izopet

Subjects
Microbiology (medical), Vaccines, Synthetic, Infectious Diseases, Antibody Formation, Humans, mRNA Vaccines, Antibodies, Viral, Antibodies, Neutralizing
Published
2022
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23. One year later: SARS-CoV-2 immune response and vaccination of healthcare workers post-infection

Author

Jacques Izopet, Guillaume Martin-Blondel, Chloé Dimeglio, Marion Porcheron, Fabrice Herin, Jean-Marc Soulat, Isabelle Da-Silva, and Marcel Miedougé

Subjects
Microbiology (medical), Vaccination, 2019-20 coronavirus outbreak, Infectious Diseases, Immune system, Coronavirus disease 2019 (COVID-19), business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Medicine, business, Virology, Post infection
Published
2021
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24. 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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25. HIV-1 resistance genotyping by ultra-deep sequencing and 6-month virological response to first-line treatment

Author

Stéphanie Raymond, Nicolas Jeanne, Florence Nicot, Chloé Dimeglio, Romain Carcenac, Agnès Harter, Noémie Ranger, Guillaume Martin-Blondel, Pierre Delobel, and Jacques Izopet

Subjects
Pharmacology, Microbiology (medical), Infectious Diseases, Pharmacology (medical)
Abstract

Objectives To evaluate the routine use of the Sentosa ultra-deep sequencing (UDS) system for HIV-1 polymerase resistance genotyping in treatment-naïve individuals and to analyse the virological response (VR) to first-line antiretroviral treatment. Methods HIV drug resistance was determined on 237 consecutive samples from treatment-naïve individuals using the Sentosa UDS platform with two mutation detection thresholds (3% and 20%). VR was defined as a plasma HIV-1 virus load Results Resistance to at least one antiretroviral drug with a mutation threshold of 3% was identified in 29% and 16% of samples according to ANRS and Stanford algorithms, respectively. The ANRS algorithm also revealed reduced susceptibility to at least one protease inhibitor (PI) in 14.3% of samples, to one reverse transcriptase inhibitor in 12.7%, and to one integrase inhibitor (INSTI) in 5.1%. For a mutation threshold of 20%, resistance was identified in 24% and 13% of samples according to ANRS and Stanford algorithms, respectively. The 6 months VR was 87% and was similar in the 58% of patients given INSTI-based treatment, in the 16% given PI-based treatment and in the 9% given NNRTI-based treatment. Multivariate analysis indicated that the VR was correlated with the baseline HIV virus load and resistance to at least one PI at both 3% and 20% mutation detection thresholds (ANRS algorithm). Conclusions The Vela UDS platform is appropriate for determining antiretroviral resistance in patients on a first-line antiretroviral treatment. Further studies are needed on the use of UDS for therapeutic management.

Published
2022

26. Influence of immune escape and nasopharyngeal virus load on the spread of SARS-CoV-2 Omicron variant

Author

Marion Migueres, Chloé Dimeglio, Pauline Trémeaux, Florence Abravanel, Stéphanie Raymond, Sébastien Lhomme, 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), and Benson-Rumiz, Alicia

Subjects
Microbiology (medical), Infectious Diseases, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, SARS-CoV-2, Immune escape, Spike Glycoprotein, Coronavirus, Vaccination, Humans, COVID-19, Serologic Tests, Viral load, Omicron variant, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; We read with interest the letter published recently by Costa et al. in the journal of Infection. They analyzed the difference between the viral loads of the SARS-CoV-2 Alpha and Delta variants using the parameters of clinical presentation, time to testing from symptoms onset, age and vaccination status.1 A new variant of concern (VOC), the Omicron variant (B.1.1.529), emerged in South Africa in November 2021, and rapidly spread throughout the world.2 Recent data suggest that this variant is more transmissible,3 less sensitive to vaccination,4 and causes less severe outcomes than the Delta variant.5 In vitro studies have demonstrated changes in cell entry and cellular tropism with the Omicron variant that might explain its greater transmissibility and reduced severity.6,7 However, clinical data comparing Delta and Omicron infections remain scarce, especially for ambulatory patients. We therefore examined the virological features of these two variants found in patients attending testing center.

Published
2022
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27. COVID-19 pandemic period, where are the seasonal viruses?

Author

Jacques Izopet, Jean-Michel Mansuy, Chloé Dimeglio, Pauline Trémeaux, Maximin Bourcier, 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), and 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)

Subjects
2019-20 coronavirus outbreak, SARS coronavirus, Coronavirus disease 2019 (COVID-19), respiratory syncytial virus, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Period (gene), Respiratory Syncytial Virus Infections, influenza virus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Influenza, Human, Pandemic, Prevalence, Humans, Medicine, human rhinovirus 1A, Epidemics, Letters to the Editor, virus classification, Pandemics, Letter to the Editor, Virus classification, Picornaviridae Infections, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, business.industry, COVID-19, Infectious Diseases, Communicable Disease Control, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Seasons, Severe acute respiratory syndrome coronavirus, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; The whole world has been struggling to cope with the SARS-CoV-2 pandemic since the beginning of 2020.The measures initially used to combat the epidemic were nonpharmaceutical, such as physical distancing, mask wearing, tightened basic hygiene, quarantine, and even curfews. These measures were applied, accepted, and effective to varying degrees, depending on the country.Their application did reduce the transmission of SARS-CoV-2 and decreased the virus reproductive number R0. However, the epidemic flared up from time to time and new waves of epidemic appeared, undoubtedly due to noncompliance and/or the partial lifting of containment measures such as curfews and movement restriction.

Published
2022
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28. Casirivimab-imdevimab to Prevent SARS-CoV-2 Infections in Solid Organ Transplant Recipients

Author

Chloé Dimeglio, Arnaud Del Bello, Sabine Chapuy-Regaud, Laure Esposito, Chloé Danet, Chloé Couat, Jacques Izopet, and Nassim Kamar

Subjects
Transplantation, SARS-CoV-2, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, COVID-19, Humans, Organ Transplantation, Antibodies, Monoclonal, Humanized, Letters to the Editor, ComputingMilieux_MISCELLANEOUS, Transplant Recipients
Abstract

[Image: see text]

Published
2022

29. 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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30. Antibody titers and breakthrough infections with Omicron SARS-CoV-2

Author

Chloé Dimeglio, Marion Migueres, Jean-Michel Mansuy, Sylvie Saivin, Marcel Miedougé, Sabine Chapuy-Regaud, and Jacques Izopet

Subjects
Microbiology (medical), Infectious Diseases, SARS-CoV-2, COVID-19, Humans, Immunologic Tests, Antibodies, Viral, Letter to the Editor, Antibodies, Neutralizing
Published
2022

31. Estimating the impact of public health strategies on the spread of SARS‐CoV‐2: Epidemiological modelling for Toulouse, France

Author

Jacques Izopet, Chloé Dimeglio, Marcel Miedougé, Jean-Michel Loubes, Jean-Michel Mansuy, 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 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), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), 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
Adult, Male, 0301 basic medicine, medicine.medical_specialty, 2019-20 coronavirus outbreak, COVID-19 Vaccines, Adolescent, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, Review, Disease, SARS‐CoV‐2, Young Adult, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Environmental health, Epidemiology, medicine, Humans, Child, Aged, Aged, 80 and over, business.industry, SARS-CoV-2, Health Policy, Public health, public health, statistical model, COVID-19, Middle Aged, Vaccination, 030104 developmental biology, Infectious Diseases, Child, Preschool, Communicable Disease Control, Female, France, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting disease COVID-19 has killed over 2 million people as of 22 January 2021. We have used a modified susceptible, infected, recovered epidemiological model to predict how the spread of the virus in France will vary depending on the public health strategies adopted, including anti-COVID-19 vaccination. Our prediction model indicates that the French authorities' adoption of a gradual release from lockdown could lead in March 2021 to a virus prevalence similar to that before lockdown. However, a massive vaccination campaign initiated in January 2021 and the continuation of public health measures over several months could curb the spread of virus and thus relieve the load on hospitals.

Published
2021
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32. Diagnosis options in patients suffering from COVID‐19‐like symptoms

Author

Sébastien Lhomme, Samia Collot, Jacques Izopet, Chloé Dimeglio, Nicolas Sans, Marie Faruch, Karine Sauné, Florence Abravanel, 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 de Virologie [Toulouse], and CHU Toulouse [Toulouse]

Subjects
medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Chest ct, Computed tomography, Antibodies, Viral, Serology, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, MESH: COVID-19 / diagnosis, medicine, Humans, In patient, False Positive Reactions, 030212 general & internal medicine, Medical diagnosis, Lung, MESH: Antibodies, Viral / blood, MESH: Humans, medicine.diagnostic_test, MESH: False Positive Reactions, business.industry, SARS-CoV-2, MESH: COVID-19 / diagnostic imaging, fungi, COVID-19, MESH: SARS-CoV-2 / immunology, MESH: Lung / diagnostic imaging, 3. Good health, body regions, MESH: COVID-19 Nucleic Acid Testing, medicine.anatomical_structure, Infectious Diseases, COVID-19 Nucleic Acid Testing, 030211 gastroenterology & hepatology, Radiology, business, Tomography, X-Ray Computed, MESH: Tomography, X-Ray Computed
Abstract

The role and performance of chest CT in the diagnosis of the coronavirus disease 2019 pandemic remains under active investigation. A recent case report in this journal found that a COVID-19 diagnosis has been made from the serological results despite first CT scan and RT-PCR negative results. We have included 311 consecutive patients with COVID-19-like symptoms who underwent a RT-PCR test on nasopharyngeal swab samples and a chest CT scan. Patients with a positive chest scan and a negative RT-PCR were screened for serum total anti-SARS-CoV-2 antibodies 2 months after the onset of symptoms using the Wantai test in order to arbitrate between RT-PCR and CT scans discordant results. Most of the RT-PCR and chest CT results agreed but the serological tests indicate that most CT positive/NAT negative patients are not infected by SARS-CoV-2 and alternative diagnoses should be seriously considered. This article is protected by copyright. All rights reserved.

Published
2021
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33. Does HEV‐3 subtype play a role in the severity of acute hepatitis E?

Author

Jacques Izopet, Jean-Marie Péron, Mathilde Castanier, Florence Abravanel, Sébastien Lhomme, Nassim Kamar, Chloé Dimeglio, PINIER, CHRISTINE, 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], and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)

Subjects
Multivariate analysis, Genotype, viruses, Stepwise regression analysis, hepatitis E virus, medicine.disease_cause, subtype, MESH: Genotype, 03 medical and health sciences, 0302 clinical medicine, Hepatitis E virus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Humans, pathogenicity, Medicine, Prospective Studies, MESH: Hepatitis E* / diagnosis, MESH: Phylogeny, Virus load, Phylogeny, MESH: Hepatitis E virus* / genetics, MESH: Humans, MESH: Hepatitis E* / epidemiology, Hepatology, business.industry, Acute hepatitis E, Hepatitis E virus genotype, Pathogenicity, Virology, MESH: Prospective Studies, Hepatitis E, Europe, MESH: RNA, Viral, 030220 oncology & carcinogenesis, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RNA, Viral, 030211 gastroenterology & hepatology, MESH: Europe, business, hospitalization, Acute hepatitis
Abstract

International audience; Hepatitis E virus genotype 3 (HEV-3) is a major aetiologic agent of acute hepatitis in industrialized countries. Two main HEV-3 subtypes are found in Europe: subtypes 3c and 3f. We have analysed the clinical and biological parameters from 100 French immunocompetent patients with an HEV subtype 3f or subtype 3c infection, included in a prospective multicentre study. Stepwise regression analysis found that infections with HEV subtype 3f were associated with fever (OR: 6.1 95%CI: 1.4-26.1), have a greater virus load (OR: 7.4; 95%CI: 1.3-42.2) and require more frequent hospitalization (OR: 7.6; 95%CI: 1.1-51.4) than those infected with subtype 3c. The directed acyclic graph strengthens the multivariate analyses indicating a direct link between the HEV subtype, HEV RNA concentration, fever and hospitalization. Further studies on patients in other European countries are needed to confirm this relationship and determine the underlying mechanism

Published
2019
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34. THETA

Author

Nicolas Jeanne, Caroline Lefebvre, Pierre Delobel, Romain Carcenac, Florence Nicot, Chloé Dimeglio, Stéphanie Raymond, Christelle Reynes, Michelle Cazabat, Jacques Izopet, Laboratoire de Virologie [Toulouse], CHU Toulouse [Toulouse], 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), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Service des maladies infectieuses et tropicales [Toulouse], and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse]

Subjects
Statistics and Probability, Receptors, CXCR4, Silver, Genotype, Receptors, CCR5, MESH: HIV-1, viruses, Human immunodeficiency virus (HIV), HIV Infections, Computational biology, MESH: HIV Infections, MESH: Receptors, CCR5, HIV Envelope Protein gp120, Biology, Gp41, medicine.disease_cause, Biochemistry, MESH: Receptors, CXCR4, MESH: Genotype, MESH: HIV Envelope Protein gp120, 03 medical and health sciences, Data sequences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Silver, medicine, Molecular Biology, Tropism, 030304 developmental biology, 0303 health sciences, 030306 microbiology, virus diseases, 3. Good health, Computer Science Applications, Europe, Viral Tropism, Computational Mathematics, Computational Theory and Mathematics, GenBank, HIV-1, Tissue tropism, MESH: Europe, MESH: Viral Tropism, Selection operator
Abstract

Motivation The circulating recombinant form of HIV-1 CRF02-AG is the most frequent non-B subtype in Europe. Anti-HIV therapy and pathophysiological studies on the impact of HIV-1 tropism require genotypic determination of HIV-1 tropism for non-B subtypes. But genotypic approaches based on analysis of the V3 envelope region perform poorly when used to determine the tropism of CRF02-AG. We, therefore, designed an algorithm based on information from the gp120 and gp41 ectodomain that better predicts the tropism of HIV-1 subtype CRF02-AG. Results We used a bio-statistical method to identify the genotypic determinants of CRF02-AG coreceptor use. Toulouse HIV Extended Tropism Algorithm (THETA), based on a Least Absolute Shrinkage and Selection Operator method, uses HIV envelope sequence from phenotypically characterized clones. Prediction of R5X4/X4 viruses was 86% sensitive and that of R5 viruses was 89% specific with our model. The overall accuracy of THETA was 88%, making it sufficiently reliable for predicting the tropism of subtype CRF02-AG sequences. Availability and implementation Binaries are freely available for download at https://github.com/viro-tls/THETA. It was implemented in Matlab and supported on MS Windows platform. The sequence data used in this work are available from GenBank under the accession numbers MK618182-MK618417.

Published
2019
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35. Strong Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Neutralizing Antibody Response of Previously Infected Healthcare Workers Given 1 Dose of mRNA Vaccine

Author

Fabrice Herin, Marcel Miedougé, Isabelle Da-Silva, Marion Porcheron, Jacques Izopet, Guillaume Martin-Blondel, and Chloé Dimeglio

Subjects
Microbiology (medical), Messenger RNA, 2019-20 coronavirus outbreak, Vaccines, Synthetic, biology, Coronavirus disease 2019 (COVID-19), business.industry, SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Health Personnel, COVID-19, Antibodies, Viral, Virology, Antibodies, Neutralizing, Infectious Diseases, biology.protein, Medicine, Humans, mRNA Vaccines, Neutralizing antibody, business
Published
2021

36. The real seroprevalence of SARS-CoV-2 in France and its consequences for virus dynamics

Author

Jacques Izopet, Jean-Michel Loubes, Chloé Dimeglio, Fabrice Herin, Jean-Marc Soulat, Marcel Miedougé, 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 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), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), 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), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Benson-Rumiz, Alicia, 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), 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), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
Adult, Male, 0301 basic medicine, medicine.medical_specialty, Statistical methods, Epidemiology, Virus transmission, viruses, Science, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Population, Article, Virus, COVID-19 Serological Testing, 03 medical and health sciences, 0302 clinical medicine, Seroepidemiologic Studies, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Humans, Seroprevalence, 030212 general & internal medicine, education, Infectivity, education.field_of_study, Models, Statistical, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Multidisciplinary, SARS-CoV-2, fungi, COVID-19, Middle Aged, body regions, 030104 developmental biology, Geography, Communicable Disease Control, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine, Female, France, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Demography
Abstract

The SARS-CoV-2 virus has spread world-wide since December 2019, killing more than 2.9 million of people. We have adapted a statistical model from the SIR epidemiological models to predict the spread of SARS-CoV-2 in France. Our model is based on several parameters and assumed a 4.2% seroprevalence in Occitania after the first lockdown. The recent use of serological tests to measure the effective seroprevalence of SARS-CoV-2 in the population of Occitania has led to a seroprevalence around 2.4%. This implies to review the parameters of our model to conclude at a lower than expected virus transmission rate, which may be due to infectivity varying with the patient’s symptoms or to a constraint due to an uneven population geographical distribution.

Published
2021
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37. Side effect of a 6 p.m curfew for preventing the spread of SARS-CoV-2

Author

Jacques Izopet, Chloé Dimeglio, Jean-Michel Mansuy, Jean-Michel Loubes, Marcel Miedougé, 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 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), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), 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, Coronavirus disease 2019 (COVID-19), Drug-Related Side Effects and Adverse Reactions, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, SARS-COV-2, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Humans, 030212 general & internal medicine, Epidemics, Letter to the Editor, Public health, fungi, COVID-19, Infectious Diseases, Geography, France, Statistical model, Curfew, Protective measures, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Demography
Abstract

International audience; The spread of SARS-CoV-2 and the resulting disease Covid-19 has killed over 2 million people as of January 22, 2021. We have designed a model and used it to quantify the effect of a 6 p.m curfew on the SARS-CoV-2 epidemic in Toulouse, France. The data show that this measure can lead to the opposite effect from that intended due to larger groups of people on the authorized hours.

Published
2021
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38. 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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39. Influence of age on the spread of SARS-CoV-2 variant B.1.1.7

Author

Jacques Izopet, Chloé Dimeglio, Cécile Donnadieu, Jean-Loup Chappert, Marcel Miedougé, and Florence Nicot

Subjects
2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), business.industry, SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), public health, COVID-19, Virology, Article, Infectious Diseases, age, Mutation, Medicine, Humans, business, variant B.1.1.7
Published
2021

40. Post-Vaccination Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibody Kinetics and Protection Duration

Author

Jacques Izopet, Marion Porcheron, Fabrice Herin, Sabine Chapuy-Regaud, Chloé Dimeglio, Guillaume Martin-Blondel, Isabelle Da-Silva, 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), Centre d'Epidémiologie et de Recherche en santé des POPulations (CERPOP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Service Maladies infectieuses et tropicales [CHU Toulouse], Pôle Inflammation, infection, immunologie et loco-moteur [CHU Toulouse] (Pôle I3LM Toulouse), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), and Pistre, Karine

Subjects
Microbiology (medical), [SDV.IMM] Life Sciences [q-bio]/Immunology, biology, business.industry, [SDV]Life Sciences [q-bio], Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV] Life Sciences [q-bio], [SDV.IMM.VAC] Life Sciences [q-bio]/Immunology/Vaccinology, Infectious Diseases, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Immunology, Post vaccination, biology.protein, [SDV.IMM]Life Sciences [q-bio]/Immunology, Medicine, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology, Antibody, Duration (project management), business
Abstract

International audience; Dear Editor,It will be difficult to mount an effective response to the SARS-CoV-2 pandemic without a clear understanding of the kinetics of the immune response to the virus. A recent study looked at the kinetics of antibody avidity maturation in COVID-19 patients and showed that IgG avidity increased form 1-90 days associated with disease severity. In a complementary way, another study in healthcare workers (HCWs) showed that a total antibody concentration greater than 141 BAU/ml provides 89.3% protection against SARS-CoV-2 infection. In this study we determined the duration of protection conferred by the total antibodies taking into account the pre-vaccination infectious status and the waninghumoral immunity.

Published
2021
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41. Testing individual and pooled saliva samples for sars-cov-2 nucleic acid: a prospective study

Author

Jean-Michel Mansuy, Jacques Izopet, Florence Abravanel, Camille Vellas, Marion Migueres, Venicia Ferrer, Isabelle Da Silva, Chloé Dimeglio, Stéphanie Raymond, 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), and 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)

Subjects
Microbiology (medical), Pooling, Saliva, 2019-20 coronavirus outbreak, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), RT-PCR, Sensitivity and Specificity, Nasopharyngeal swabs, Microbiology, Single test, fluids and secretions, stomatognathic system, Saliva testing, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Nasopharynx, Medicine, Humans, TMA, Prospective cohort study, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, business.industry, Reverse Transcriptase Polymerase Chain Reaction, SARS-CoV-2, COVID-19, General Medicine, stomatognathic diseases, Infectious Diseases, Real-time polymerase chain reaction, Nucleic acid, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RNA, Viral, Original Article, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; Control of the rapid spread of the SARS-CoV-2 virus requires efficient testing. We collected paired nasopharyngeal swab (NPs) and saliva samples from 303 subjects (52.8% symptomatic) at a drive-through testing center; 18% of whom tested positive. The NPs, salivas and five saliva pools were tested for SARS-CoV-2 RNA using the Aptima™ assay and a laboratory-developed test (LDT) on the Panther-Fusion™ Hologic® platform. The saliva sensitivity was 80% (LDT) and 87.5% (Aptima™) whereas that of NPs was 96.4% in both assays. The pooled saliva sensitivity of 72.7% (LDT) and 75% (Aptima™) was not significantly different of that of individual saliva testing. Saliva specimens appear to be suitable for sensitive non-invasive assays to detect SARS-CoV-2 nucleic acid; pooling them for a single test will improve laboratory throughput.

Published
2021
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42. No evidence of sexual transmission of HEV among individuals using HIV pre‐exposure prophylaxis

Author

Pascale Trimoulet, Florence Abravanel, Marion Migueres, Pierre Delobel, Maïlys Ducours, Charles Cazanave, Chloé Dimeglio, Jacques Izopet, Laboratoire de Virologie [Toulouse], CHU Toulouse [Toulouse], 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), Service des Maladies Infectieuses et Tropicales A [Bordeaux], CHU Bordeaux [Bordeaux]-Groupe hospitalier Pellegrin, Service de virologie et d'immunologie biologique, Service des maladies infectieuses et tropicales [Toulouse], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], USC EA 3671, infections humaines à mycoplasmes et chlamydiae, and Institut National de la Recherche Agronomique (INRA)

Subjects
Male, Sexual transmission, viruses, HIV Pre-exposure prophylaxis, men who have sex with men, HIV Infections, hepatitis E virus, medicine.disease_cause, Men who have sex with men, Sexual and Gender Minorities, 03 medical and health sciences, Pre-exposure prophylaxis, 0302 clinical medicine, Hepatitis E virus, Seroepidemiologic Studies, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, medicine, Humans, Seroprevalence, Hepatitis Antibodies, 030212 general & internal medicine, Homosexuality, Male, Risk factor, Retrospective Studies, Hepatology, seroprevalence, business.industry, Incidence (epidemiology), virus diseases, medicine.disease, digestive system diseases, Hepatitis E, 3. Good health, Infectious Diseases, Immunoglobulin M, incidence, Pre-Exposure Prophylaxis, 030211 gastroenterology & hepatology, Viral hepatitis, business
Abstract

International audience; We investigated the seroprevalence and incidence of hepatitis E virus (HEV) infection in men who have sex with men (MSM) who have been exposed to pre-exposure prophylaxis (PrEP) against HIV as sexual transmission of HEV has been suggested. A total of 147 PrEP-using MSM and 147 blood donors matched for sex, age and geographical area were tested for anti-HEV IgG and IgM. Among them, 135 have been followed for 1 year, at the end of which serological tests for HEV were performed retrospectively on stored samples. Laboratory data on sexual transmitted infections (STIs) and viral hepatitis, including hepatitis A virus (HAV), were collected. Baseline seroprevalence rates in PrEP users were 42.2% (anti-HEV IgG) and 3.4% (anti-HEV IgM). Those of the control blood donors were similar (anti-HEV IgG 43.5% and anti-HEV IgM 4.1%). There was no incident of HEV infection despite the rates of bacterial STIs (incidence rate (IR) = 46.6%) and HAV infection (IR = 15.8%). Age was the only risk factor associated with anti-HEV IgG seropositivity at baseline and at the end of follow-up. Sexual transmission does not seem to be a major route of HEV infection in MSM, unlike HAV.

Published
2020
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43. Quantifying the impact of public health protection measures on the spread of SARS-CoV-2

Author

Jacques Izopet, Jean-Michel Mansuy, Chloé Dimeglio, Jean-Michel Loubes, 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), 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), 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), medicine.medical_specialty, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), viruses, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Article, Health services, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Environmental health, medicine, Humans, skin and connective tissue diseases, Epidemics, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, SARS-CoV-2, Public health, fungi, COVID-19, body regions, Geography, Infectious Diseases, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Statistical model, France, Public Health, Protective measures, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; The new virus, SARS-CoV-2, has probably affected millions of people world-wide since December 2019 and killed thousand. We have designed a model and used it to quantify the effect of local protective measures on the SARS-CoV-2 epidemic, assess their effectiveness and adapt health service strategies in Toulouse, France.

Published
2020
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44. 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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45. Saliva sampling for diagnosing SARS-CoV-2 infections in symptomatic patients and asymptomatic carriers

Author

Jacques Izopet, Pierre Delobel, Catherine Mengelle, Jean-Michel Mansuy, Marion Migueres, M. Alvarez, Alain Didier, Chloé Dimeglio, Laboratoire de Virologie [Toulouse], CHU Toulouse [Toulouse], 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), Service de pneumologie et allergologie pédiatrique [CHU Toulouse], Service des maladies infectieuses et tropicales [Toulouse], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], 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), Service Pneumologie et allergologie pédiatrique [CHU Toulouse], Pôle Enfants [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Service Maladies infectieuses et tropicales [CHU Toulouse], Pôle Inflammation, infection, immunologie et loco-moteur [CHU Toulouse] (Pôle I3LM Toulouse), and PINIER, CHRISTINE

Subjects
MESH: Coronavirus, Saliva, medicine.disease_cause, 0302 clinical medicine, COVID-19 Testing, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: COVID-19, Medicine, Sampling (medicine), 030212 general & internal medicine, Coronavirus, 0303 health sciences, biology, 3. Good health, Infectious Diseases, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Betacoronavirus, Coronavirus Infections, MESH: Pneumonia, Viral / epidemiology, medicine.medical_specialty, 2019-20 coronavirus outbreak, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Pneumonia, Viral, Article, 03 medical and health sciences, Betacoronavirus, MESH: Coronavirus Infections / diagnosis, Virology, Internal medicine, Humans, MESH: SARS-CoV-2, MESH: Saliva, MESH: Coronavirus Infections / epidemiology, Pandemics, MESH: Clinical Laboratory Techniques, MESH: Humans, 030306 microbiology, business.industry, Clinical Laboratory Techniques, SARS-CoV-2, MESH: COVID-19 Testing, COVID-19, medicine.disease, biology.organism_classification, Pneumonia, MESH: Pandemics, business, Asymptomatic carrier
Abstract

International audience; In a recent review of laboratory tests for diagnosing SARS-CoV-2 infection, Zheng et al. concluded that the detection rate of real-time quantitative PCR was lower than that of computed tomography [1]. But the authors did not discuss the possibility of using saliva sampling. Nasopharyngeal (NP) swabs are the preferred collection vehicles in France and many other countries and several studies have indicated that this method is more sensitive than sampling other sites [2–4]. Saliva sampling is less invasive for patients, less hazardous for health care workers, requires fewer experimented staff and is less expensive for mass testing. However, little is known about any differences in the sensitivities of saliva and NP sampling or how any differences vary with presence or absence of clinical symptoms

Published
2020
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46. Children are protected against SARS-CoV-2 infection

Author

Jacques Izopet, Jean Michel Mansuy, Isabelle Claudet, Chloé Dimeglio, Sandrine Charpentier, Laboratoire de Virologie [Toulouse], CHU Toulouse [Toulouse], 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), Service des Urgences (TOULOUSE - Urgences), Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Service d'urgence pédiatrique, PINIER, CHRISTINE, 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), Service d’accueil des urgences - Rangueil [CHU Toulouse] (SAU - Rangueil), Pôle Médecine d'urgences [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
MESH: Coronavirus, China, 2019-20 coronavirus outbreak, MESH: Pandemics, Coronavirus disease 2019 (COVID-19), MESH: Coronavirus Infections, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Pneumonia, Viral, medicine.disease_cause, Cohort Studies, Betacoronavirus, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, MESH: Child, Pandemic, Humans, Medicine, MESH: COVID-19, MESH: SARS-CoV-2, 030212 general & internal medicine, Child, Pandemics, MESH: Cohort Studies, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Coronavirus, 0303 health sciences, MESH: Humans, biology, SARS-CoV-2, business.industry, COVID-19, biology.organism_classification, MESH: China, Infectious Diseases, MESH: Pneumonia, Viral, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Betacoronavirus, Coronavirus Infections, business
Abstract

International audience

Published
2020
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47. Posttraumatic Stress Disorder Symptoms in Lymphoma Patients: A Prospective Study

Author

Chloé Dimeglio, Gisèle Compaci, Mélanie Gauché, Claire Camille, Antoine Yrondi, Emmanuelle Delmas, Philippe Birmes, and Guy Laurent

Subjects
medicine.medical_specialty, medicine.drug_class, lcsh:RC435-571, lymphoma, Dissociative, behavioral disciplines and activities, 03 medical and health sciences, 0302 clinical medicine, peritraumatic dissociation, Internal medicine, lcsh:Psychiatry, mental disorders, Mucositis, Medicine, cancer, stressor, Adverse effect, Prospective cohort study, Psychiatry, business.industry, Stressor, Beck Depression Inventory, Brief Research Report, medicine.disease, 030227 psychiatry, Lymphoma, Psychiatry and Mental health, posttraumatic stress disorder, Anxiety, peritraumatic distress, medicine.symptom, business, 030217 neurology & neurosurgery
Abstract

The cancer experience may be marked by repeat stressors and/or traumas. The aim of our study was to assess traumatic events in a group of patients diagnosed with lymphoma and to determine which of these contribute to the development of Post-Traumatic Stress Disorder/PTSD. Two weeks after receiving a diagnosis of lymphoma, patients were referred for an assessment of peritraumatic distress (using the Peritraumatic Distress Inventory/PDI) and peritraumatic dissociation (using the Peritraumatic Dissociative Experiences Questionnaire/PDEQ). Three months after the diagnosis, we recorded the following parameters: the patients' worst experiences, the presence of PTSD symptoms, using the PTSD CheckList/PCL, as it related to the diagnosis, and symptoms of anxiety using the Hospital Anxiety and Depression/HAD scale and of depression using the Beck Depression Inventory/BDI-II. The study recruited 129 patients, with a mean age of 46 years (SD = 17.3); 70 (54%) men, 87 (67.5%) with Non-Hodgkin's lymphoma, and 42 with Hodgkin's lymphoma. Two weeks after the diagnosis, 49% of patients reported peritraumatic distress, and 20% peritraumatic dissociation, during or immediately after being informed of the lymphoma diagnosis. Three months after the diagnosis, the severity of PTSD symptoms was evaluated. At this stage none of the patients suffered PTSD, but 29 (23%) individuals exhibited partial PTSD: 13.4% correlated it to receiving the lymphoma diagnosis, 8% to telling family members, and 1.6% to adverse effects. Peritraumatic distress and dissociation as a result of receiving a lymphoma diagnosis, as well as anxiety and a mucositis within the first 3 months post-diagnosis, were factors that were significantly associated with PTSD symptoms, accounting for 35.8% in PTSD symptom load. Our study reveals that clinicians should assess the impact of a number of stressors, which are risk factors for PTSD symptoms, starting from the time point of the initial lymphoma diagnosis.

Published
2020

48. On the use of optimal transportation theory to recode variables and application to database merging

Author

Grégory Guernec, Chloé Dimeglio, Valérie Garès, Nicolas Savy, Benoit Lepage, Romain Fantin, Michael R. Kosorok, GARES, Valérie, Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), 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), Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), 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), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), IRMAR-STAT, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UPS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-PRES Université de Toulouse-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), 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), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Statistics and Probability, Biomedical Research, [STAT.ME] Statistics [stat]/Methodology [stat.ME], Databases, Factual, Database, Statistical learning, Computer science, General Medicine, Transportation theory, Biostatistics, Models, Theoretical, computer.software_genre, 01 natural sciences, 010104 statistics & probability, 03 medical and health sciences, 0302 clinical medicine, Covariate, Humans, 030212 general & internal medicine, 0101 mathematics, Statistics, Probability and Uncertainty, computer, Merge (version control), [STAT.ME]Statistics [stat]/Methodology [stat.ME], Algorithms
Abstract

Merging databases is a strategy of paramount interest especially in medical research. A common problem in this context comes from a variable which is not coded on the same scale in both databases we aim to merge. This paper considers the problem of finding a relevant way to recode the variable in order to merge these two databases. To address this issue, an algorithm, based on optimal transportation theory, is proposed. Optimal transportation theory gives us an application to map the measure associated with the variable in database A to the measure associated with the same variable in database B. To do so, a cost function has to be introduced and an allocation rule has to be defined. Such a function and such a rule is proposed involving the information contained in the covariates. In this paper, the method is compared to multiple imputation by chained equations and a statistical learning method and has demonstrated a better average accuracy in many situations. Applications on both simulated and real datasets show that the efficiency of the proposed merging algorithm depends on how the covariates are linked with the variable of interest.

Published
2020
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49. Acute hepatitis E in French patients and neurological manifestations

Author

Jean-Marie Péron, Chloé Dimeglio, Florence Abravanel, Sébastien Lhomme, Julie Pique, Karine Sauné, Jacques Izopet, Florence Nicot, Elisabeth Couturier, Solène M. Evrard, Pascal Cintas, Henriette de Valk, Julie Chiabrando, and Nassim Kamar

Subjects
Adult, Male, 0301 basic medicine, Microbiology (medical), Pediatrics, medicine.medical_specialty, 030106 microbiology, medicine.disease_cause, Foodborne Diseases, 03 medical and health sciences, 0302 clinical medicine, Hepatitis E virus, Risk Factors, Occupational Exposure, medicine, Animals, Humans, Prospective Studies, Aged, Diplopia, Transmission (medicine), business.industry, Risk of infection, Environmental Exposure, Middle Aged, medicine.disease, Pathophysiology, Hepatitis E, Infectious Diseases, Case-Control Studies, Neuropathic pain, Female, 030211 gastroenterology & hepatology, France, Nervous System Diseases, medicine.symptom, business, Meningitis, Encephalitis
Abstract

Summary Objectives Hepatitis E virus (HEV) is a major cause of acute hepatitis worldwide. However, our understanding of the source of contamination is incomplete and the frequency of neurological manifestations in still unknown. Methods 200 eligible cases reported to the French National Reference Center from January 2015 to December 2015 were prospectively included in this case-control study (1 case: 1 control, matched for sex, age and area of living) to investigate the risk of infection. We documented the factors associated with their HEV infection and clinical manifestations. Results The 200 HEV-infected patients included 137 who were immunocompetent and 63 immunocompromised. The factors associated with an HEV infection were contact with farm animals, eating pork liver sausage and eating unpeeled fruit. The 33 patients (16.5%) who reported neurological symptoms included 14 with neuropathic pain suggesting small fiber neuropathy, 9 with painless sensory disorders, 6 with Parsonage–Turner syndrome, one Guillain–Barre syndrome, one meningitis, one encephalitis and one diplopia. Neurological manifestations were more frequent in immunocompetent patients (22.6% vs 3.2%, p Conclusions This study highlights the risk of HEV transmission by the environment in industrialized countries. The higher frequency of neurological disorders in immunocompetent patients suggests pathophysiological mechanisms involving the immune system.

Published
2018
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50. Expectations and boundaries for Big Data approaches in social medicine

Author

Chloé Dimeglio, Thierry Lang, Michelle Kelly-Irving, Cyrille Delpierre, Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), 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), Université Fédérale Toulouse Midi-Pyrénées, Institut de Mathématiques de Toulouse UMR5219 ( IMT ), Université Toulouse 1 Capitole ( UT1 ) -Université Toulouse - Jean Jaurès ( UT2J ) -Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-PRES Université de Toulouse-Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps, Université Toulouse III - Paul Sabatier ( UPS ), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale ( INSERM )

Subjects
0301 basic medicine, Sine qua non, [SDV]Life Sciences [q-bio], Social Medicine, Big data, Pathology and Forensic Medicine, 03 medical and health sciences, 0302 clinical medicine, Social medicine, Humans, 030212 general & internal medicine, Social determinants of health, Objectivity (science), ComputingMilieux_MISCELLANEOUS, Curative care, [ SDV ] Life Sciences [q-bio], business.industry, Forensic Sciences, General Medicine, Viewpoints, Data science, 3. Good health, 030104 developmental biology, Databases as Topic, Public Health, Psychology, business, Law, Social psychology, Know-how, Medical Informatics
Abstract

It seems no longer possible to produce knowledge, even biological knowledge regardless of social, cultural and economic environments in which they were observed. Therefore never the term “social medicine” or more generally “social biology” has appeared more appropriate. This way of linking the social and the biological exceeds the sole social medicine by involving also other medical disciplines. As such, forensics, whose an important activity is represented by clinical forensics in charge of types of violence (physical, psychological, sexual, abuse) and persons held in custody could see its practice heavily modified through the use of various data describing both the clinical situation of patients but also their context of life. A better understanding of mechanisms of violence development and potentially a better prevention of these situations allow forensics not to be restricted (or seen as limited to) a “descriptive medicine”, but to be seen also as a preventive and curative medicine. In this evolution, the potential contribution of Big Data appears significant insofar as information on a wide range of characteristics of the environment or context of life (social, economic, cultural) can be collected and be connected with health data, for example to develop models on social determinants of health. In the common thinking, the use of a larger amount of data and consequently a multiplicity of information via a multiplicity of databases would allow to access to a greater objectivity of a reality that we are approaching by fragmented viewpoints otherwise. In this light, the “bigger” and “more varied” would serve the “better” or at least the “more true”. But to be able to consider together or to link different databases it will be necessary to know how to handle this diversity regarding hypotheses made to build databases and regarding their purposes (by whom, for what bases have been made). It will be equally important to question the representativeness of situations that led to the creation of a database and to question the validity of information and data according to the secondary or tertiary uses anticipated from their original purpose. This step of data validity control for the anticipated use is a sine qua non condition, particularly in the field of public health, to guarantee a sufficient level of quality and exploit in the best way the benefits of Big Data approaches.

Published
2018
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