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

Author

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

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

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

Published
2023
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2. In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control

Author

Pauline Trémeaux, Frédéric Lemoine, Adeline Mélard, Marine Gousset, Faroudy Boufassa, Sylvie Orr, Valérie Monceaux, Olivier Gascuel, Olivier Lambotte, Laurent Hocqueloux, Asier Saez-Cirion, Christine Rouzioux, and Véronique Avettand-Fenoel

Subjects
posttreatment HIV controller, HIV reservoirs, provirus, defective proviruses, next-generation sequencing, posttreatment HIV controllers, Microbiology, QR1-502
Abstract

ABSTRACT In the search for control of human immunodeficiency virus type 1 (HIV-1) infection without antiretroviral therapy, posttreatment controllers (PTCs) are models of HIV remission. To better understand their mechanisms of control, we characterized the HIV blood reservoirs of 8 PTCs (median of 9.4 years after treatment interruption) in comparison with those of 13 natural HIV infection controllers (HICs) (median of 18 years of infection) and with those of individuals receiving efficient antiretroviral therapy initiated during either primary HIV infection (PHIs; n = 8) or chronic HIV infection (CHIs; n = 6). This characterization was performed with single-genome amplification and deep sequencing. The proviral diversity, which reflects the history of past viral replication, was lower in the PTCs, PHIs, and aviremic HICs than in the blipper HICs and CHIs. The proportions of intact and defective proviruses among the proviral pool in PTCs were not significantly different from those of other groups. When looking at the quantities of proviruses per million peripheral blood mononuclear cells (PBMCs), they had similar amounts of intact proviruses as other groups but smaller amounts of defective proviruses than CHIs, suggesting a role of these forms in HIV pathogenesis. Two HICs but none of the PTCs harbored only proviruses with deletion in nef; these attenuated strains could contribute to viral control in these participants. We show, for the first time, the presence of intact proviruses and low viral diversity in PTCs long after treatment interruption, as well as the absence of evolution of the proviral quasispecies in subsequent samples. This reflects low residual replication over time. Further data are necessary to confirm these results. IMPORTANCE Most people living with HIV need antiretroviral therapy to control their infection and experience viral relapse in case of treatment interruption, because of viral reservoir (proviruses) persistence. Knowing that proviruses are very diverse and most of them are defective in treated individuals, we aimed to characterize the HIV blood reservoirs of posttreatment controllers (PTCs), rare models of drug-free remission, in comparison with spontaneous controllers and treated individuals. At a median time of 9 years after treatment interruption, which is unprecedented in the literature, we showed that the proportions and quantities of intact proviruses were similar between PTCs and other individuals. Unlike 2/7 spontaneous controllers who harbored only nef-deleted proviruses, which are attenuated strains, which could contribute to their control, no such case was observed in PTCs. Furthermore, PTCs displayed low viral genetic diversity and no evolution of their reservoirs, indicating very low residual replication, despite the presence of intact proviruses.

Published
2023
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3. Omicron Wave SARS-CoV-2 Diagnosis: Evaluation of Saliva, Anterior Nasal, and Nasopharyngeal Swab Samples

Author

Marion Migueres, Jean-Michel Mansuy, Sandrine Vasseur, Nicolas Claverie, Catherine Lougarre, Françoise Soulier, Pauline Trémeaux, and Jacques Izopet

Subjects
SARS-CoV-2, COVID-19, Omicron, saliva, anterior nasal swab, RT-PCR, Microbiology, QR1-502
Abstract

ABSTRACT The Omicron variant differs from earlier strains of SARS-CoV-2 in the way it enters host cells and grows in vitro. We therefore reevaluated its diagnosis using saliva, nasopharyngeal swab (NPs), and anterior nasal swab (ANs) specimens from 202 individuals (64.9% symptomatic) tested at the Toulouse University Hospital SARS-CoV-2 drive-through testing center. All tests were done with the Thermo Fisher TaqPath COVID-19 reverse transcription-PCR (RT-PCR) kit. Overall, 92 subjects (45.5%) had one or more positive specimens. Global sensitivities of saliva, NPs, and ANs were 94.6%, 90.2%, and 82.6%, respectively. Saliva provided significantly greater sensitivity among symptomatic patients tested within 5 days of symptom onset (100%) than did ANs (83.1%) or NPs (89.8%). We obtained follow-up samples for 7/20 individuals with discordant results. Among them, 5 symptomatic patients were diagnosed positive on saliva sample only, soon after symptom onset; NPs and ANs became positive only later. Thus, saliva samples are effective tools for the detection of the Omicron variant. In addition to its many advantages, such as improved patient acceptance and reduced cost, saliva sampling could help limit viral spread through earlier viral detection. IMPORTANCE Diagnostic testing for SARS-CoV-2 is an essential component of the global strategy for the prevention and control of COVID-19. Since the beginning of the pandemic, numerous studies have evaluated the diagnostic sensitivity of different respiratory and oral specimens for SARS-CoV-2 detection. The pandemic has been since dominated by the emergence of new variants, the latest being the Omicron variant characterized by numerous mutations and changes in host tropism in vitro that might affect the diagnostic performance of tests depending on the sampling location. In this prospective study, we evaluated the clinical performance of NPs, ANs, and saliva for SARS-CoV-2 diagnosis during the Omicron wave. Our results highlight the effectiveness of saliva-based RT-PCR for the early detection of the Omicron variant. These findings may help to refine guidelines and support the use of a highly sensitive diagnostic method that allows earlier diagnosis, when transmission is the most critical.

Published
2022
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4. Rapid investigation of BA.4/BA.5 cases in France

Author

Alain-Claude Kouamen, Helena Da Cruz, Mohamed Hamidouche, Anais Lamy, Anna Lloyd, Javier Castro Alvarez, Mathilde Roussel, Laurence Josset, Vincent Enouf, Charlotte Felici, Georges Dos Santos, Justine Schaeffer, Anna Maisa, Regional COVID-19 Investigation Group, Laboratory Group, Gwenola Picard, Vikpognon Michée Géraud, Alice Brembilla, Ellen Dahl, Souhaila Chent, Alizé Mercier, Gwladys Nadia Gbaguidi, Carine Grenier, Adeline Riondel, Huchet-Kervella Caroline, Bekheira Leila, Kemeny Stephan, Claire Vignault, Pauline Trémeaux, Pierre-Edouard Fournier, Sophie Vallet, Diane Descamps, Lionel Chollet, Nefert Dossou, Alice Moisan, Anais Soares, Marie Christine Jaffar Bandjee, Alexis de Rougement, Cécile Henquell, and Anne Lavergne

Subjects
SARS-CoV-2, variant, Omicron, hospitalization, symptoms, BA.4, Public aspects of medicine, RA1-1270
Abstract

AimWe aimed to describe the characteristics of individuals infected by BA.4 or BA.5 in France in comparison to BA.1, and analyze the factors associated with hospitalization among BA.4 and BA.5 cases.MethodsA standardized questionnaire was used to collect information on confirmed and probable Omicron cases. Hospitalization risk factors among BA.4/BA.5 cases were analyzed using Poisson regression. Variables with a p-value below 0.2 in the univariate analysis and a priori confounders were included in the multivariable regression model.ResultsThe median age of the 301 cases investigated was 47 years and 97% of cases were symptomatic. The most common clinical signs were asthenia/fatigue (75.7%), cough (58.3%), fever (58.3%), headache (52.1%) and rhinorrhea (50.7%). Twelve cases were hospitalized, and 27.1% reported risk factors. No admissions to intensive care and no deaths were reported. Vaccination status was available for 292 cases, 20.9% were unvaccinated, 1.4% had received one dose, 38.3% two doses and 39.4% three doses. Cases presenting at least one risk factor were almost seventeen times more likely to be hospitalized than those with no risk factors (aRR = 16.72 [95% CI2.59–326.86]).ConclusionDespite the longer duration of and the differences in symptoms and their possible immune escape, BA.4/BA.5 Omicron sub-lineages globally showed no severe clinical presentation. The presence of at least one risk factor for severe disease significantly increased the risk of hospitalization for those infected with BA.4 or BA.5.

Published
2022
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5. Will the latest wave of the COVID‐19 pandemic be an ecological disaster? There is an urgent need to replace plastic by ecologically virtuous materials

Author

Jean‐Michel Mansuy, Marion Migueres, Pauline Trémeaux, and Jacques Izopet

Subjects
antigen, COVID‐19, diagnosis, ecology, PCR, plastic, Medicine
Abstract

Abstract Background and Aims Direct virological diagnosis of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS‐CoV‐2) infectionis based on either viral antigen or viral genome detection. These methods, in addition to the dedicated reagents and transport packaging, require the use of quantities of plastic that may individually appear negligible but which, in the context of a pandemic, are very high. The aim was to estimate the amount of plastic involved in a diagnostic assay whether molecular or antigenic. Methods We weighed the plastics used to obtain a diagnostic assay result for SARS‐CoV‐2 infection in our hospital. Results Each ready‐to‐use antigen assay requires about 20 g of plastic whereas the PCR assay implies the use of 30 g. This unit mass, when compared to our laboratory's SARS‐CoV‐2 genomic screening activity,represents more than 10 tons of plastic for 2021. At our region level (#6.10 inhabitants), more than 350 tons of plastic were used to carry out more than 7 million declared PCR assays and as many antigenic assays. Conclusions The virologic diagnostic activityl inked to the SARS‐CoV‐2 pandemic has highlighted once more our dependance for plastic use. We must already think about a more environmentally virtuous diagnostic activity by integrating a reasonned use of diagnostic tools and a higher use of ecological friendly material. Parallel the notion of waste management must also be addressed in order to limit their environmental impact.

Published
2022
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6. 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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7. Increasing contribution of integrated forms to total HIV DNA in blood during HIV disease progression from primary infectionResearch in context

Author

Pauline Trémeaux, Tiphaine Lenfant, Faroudy Boufassa, Asma Essat, Adeline Mélard, Marine Gousset, Olivier Delelis, Jean-Paul Viard, Marc Bary, Cécile Goujard, Christine Rouzioux, Laurence Meyer, and Véronique Avettand-Fenoel

Subjects
Medicine, Medicine (General), R5-920
Abstract

Background: In the current context of research on HIV reservoirs, offering new insights into the persistence of HIV DNA in infected cells, which prevents viral eradication, may aid in identifying cure strategies. This study aimed to describe the establishment of stable integrated forms among total HIV DNA during primary infection (PHI) and their dynamics during the natural history of infection. Methods: Total and integrated HIV DNA were quantified in blood from 74 PHI patients and 97 recent seroconverters (

Published
2019
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8. 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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9. Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing

Author

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

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

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

Published
2021
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10. 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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11. 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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13. 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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14. 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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15. 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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16. 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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17. Resistance mutations in SARS-CoV-2 omicron variant in patients treated with sotrovimab

Author

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

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

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

Published
2022
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18. False-negative Results of Human Immunodeficiency Virus (HIV) Rapid Testing in HIV Controllers

Author

Mehdi Hage-Sleiman, Olivier Lambotte, Christine Rouzioux, Elise Gardiennet, Véronique Avettand-Fenoel, Alice-Andrée Mariaggi, Marine Fillion, Faroudy Boufassa, Pauline Trémeaux, Jean-Christophe Plantier, Adeline Melard, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Virologie [CHU Cochin], Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris-Sud - Paris 11 (UP11), Université Paris-Saclay, Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Laboratoire de virologie [Rouen], Hôpital Charles Nicolle [Rouen]-CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Département de microbiologie : Bactério, Virologie, Parasito, Hygiène, Laboratoire de Virologie [CHU Necker], Université Paris Descartes - Paris 5 (UPD5), Immunologie des Maladies Virales et Autoimmunes (IMVA - U1184), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Codex ANRS cohort study group, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Université de Caen Normandie (UNICAEN), Hôpital Charles Nicolle [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-CHU Rouen, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Cochin [AP-HP], Epidemiology and Population Health, Epidemiology of HIV and STI Team (U1018 Inserm ), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Normandie Université (NU)-Normandie Université (NU)-Département de microbiologie : Bactério, Virologie, Parasito, Hygiène-Hôpital Charles Nicolle [Rouen]-CHU Rouen, and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Necker - Enfants Malades [AP-HP]

Subjects
0301 basic medicine, Microbiology (medical), HIV rapid screening test, Blotting, Western, HIV diagnosis, Human immunodeficiency virus (HIV), Enzyme-Linked Immunosorbent Assay, HIV Infections, HIV Antibodies, medicine.disease_cause, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, Serology, Immunoenzyme Techniques, 03 medical and health sciences, Rapid screening test, 0302 clinical medicine, Western blot, medicine, Humans, 030212 general & internal medicine, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Rapid testing, medicine.diagnostic_test, business.industry, HIV, HIV controllers, MESH: ELISA, HIV-1 Western blot, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030112 virology, Virology, 3. Good health, Infectious Diseases, Immunoassay, HIV-2, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, ELISA, business, Negative Results
Abstract

Serological assays were performed on 85 human immunodeficiency virus-controller samples . 6% presented a negative rapid screening test 7% presented an indeterminate Western blot. The enzyme immunoassay ratio decreased in controllers who had continual negative ultrasensitive HIV RNA results since inclusion.

Published
2019
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19. 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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20. Evaluation of the Aptima™ transcription-mediated amplification assay (Hologic®) for detecting SARS-CoV-2 in clinical specimens

Author

Jacques Izopet, Jean Michel Mansuy, Florence Abravanel, Stéphanie Raymond, Catherine Mengelle, Pauline Trémeaux, Sébastien Lhomme, CCSD, Accord Elsevier, 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), 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
Male, 0301 basic medicine, Transcription-mediated amplification, medicine.disease_cause, Diagnostic tools, COVID-19 Testing, 0302 clinical medicine, MESH: Aged, 80 and over, MESH: Betacoronavirus / genetics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine, MESH: COVID-19, Prospective Studies, 030212 general & internal medicine, Coronavirus, Aged, 80 and over, MESH: Aged, MESH: Middle Aged, Middle Aged, Infectious Diseases, Molecular Diagnostic Techniques, MESH: COVID-19 Vaccines, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, Coronavirus Infections, Nucleic Acid Amplification Techniques, MESH: Nucleic Acid Amplification Techniques / methods, Adult, MESH: Betacoronavirus / isolation & purification, 2019-20 coronavirus outbreak, MESH: Pandemics, COVID-19 Vaccines, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Pneumonia, Viral, 030106 microbiology, MESH: Pneumonia, Viral / diagnosis, Hologic® Panther System, Article, Virus, Betacoronavirus, 03 medical and health sciences, Virology, Humans, MESH: SARS-CoV-2, Pandemics, Aged, Retrospective Studies, MESH: Humans, Clinical Laboratory Techniques, business.industry, SARS-CoV-2, MESH: COVID-19 Testing, COVID-19, MESH: Adult, MESH: Retrospective Studies, MESH: Prospective Studies, MESH: Male, MESH: Coronavirus Infections / diagnosis, Hologic®Panther System, MESH: Clinical Laboratory Techniques / methods, MESH: Molecular Diagnostic Techniques / methods, business, MESH: Female, Kappa
Abstract

Background The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which appeared in late 2019, has been limited by isolating infected individuals. However, identifying such individuals requires accurate diagnostic tools. Objective This study evaluates the capacity of the Aptima™ Transcription-Mediated Amplification (TMA) assay (Hologic® Panther System) to detect the virus in clinical samples. Study design We compared the Aptima™ assay to two in-house real-time RT-PCR techniques, one running on the Panther Fusion™ module and the other on the MagNA Pure 96 and Light-Cycler 480 instruments. We included a total of 200 respiratory specimens: 100 tested prospectively and 100 retrospectively (25 -ve/75 +ve). Results The final Cohen’s kappa coefficients were: κ = 0.978 between the Aptima™ and Panther Fusion™ assays, κ = 0.945 between the Aptima™ and MagNA/LC480 assays and κ = 0.956 between the MagNA/LC480 and Panther Fusion™ assays. Conclusion These findings indicate that the Aptima™ SARS-CoV-2 TMA assay data agree well with those obtained with our routine methods and that this assay can be used to diagnose coronavirus disease 2019 (COVID-19).

Published
2020
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21. HIV DNA

Author

Véronique Avettand-Fenoel, Christine Rouzioux, and Pauline Trémeaux

Subjects
0301 basic medicine, Immunology, Human immunodeficiency virus (HIV), Clinical marker, HIV Infections, Clinical settings, medicine.disease_cause, Bioinformatics, 03 medical and health sciences, Virology, Virus latency, medicine, Animals, Humans, Disease Reservoirs, Oncology (nursing), business.industry, virus diseases, Hematology, medicine.disease, Predictive value, Virus Latency, Clinical trial, 030104 developmental biology, Infectious Diseases, Oncology, DNA, Viral, T cell subset, HIV-1, Hiv patients, business, Biomarkers
Abstract

Purpose of review A number studies are currently underway to develop new drugs aimed at reducing the HIV reservoir or achieving ART-free control of HIV infection. Many markers of HIV reservoirs have been proposed, each one having a different meaning. Total HIV DNA dynamics during the course of HIV infection and its predictive value are now well known. This marker allowed to estimate the size of HIV reservoir at different stages of HIV infection in blood, cell subsets and tissues. Therefore, the purpose of this review is timely and relevant, with the objective to discuss how total HIV DNA might be helpful in the clinical settings. Recent findings Among the markers, it appears that HIV DNA is the most well studied, and recent articles confirmed that this marker is easy to use and is precise, specific, practical, robust and reproducible. All these characteristics correspond to what is expected from a helpful clinical marker. Summary HIV DNA level could be considered as a global marker, and it is usually included in current clinical studies to describe the persistence and dynamics of the HIV reservoir, mainly in treated patients. HIV DNA might be helpful in designing clinical trials and personalized medication for HIV patients in the future.

Published
2018
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22. Evaluation of two RT-PCR screening assays for identifying SARS-CoV-2 variants

Author

Jacques Izopet, Sébastien Lhomme, Marion Migueres, Chloé Dimeglio, N. Ranger, Jean-Michel Mansuy, Florence Nicot, J. Latour, Marcel Miedougé, Martine Dubois, and Pauline Trémeaux

Subjects
Variants of concern (VOC), TaqPath, Lineage (genetic), Coronavirus disease 2019 (COVID-19), SARS-CoV-2, Reverse Transcriptase Polymerase Chain Reaction, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), RT-PCR, COVID-19, ID triplex, Biology, Genome sequencing, Virology, DNA sequencing, Virus, Article, Infectious Diseases, Real-time polymerase chain reaction, Multiplex polymerase chain reaction, Humans, Gene, Multiplex Polymerase Chain Reaction
Abstract

Background The recent emergence of new SARS CoV-2 variants (variants of concern, VOC) that spread rapidly and may lead to immune escape has emphasized the urgent need to monitor and control their spread. Methods We analyzed 2018 SARS-CoV-2 positive specimens collected between February 9 and March 22, 2021 using the Thermofisher® TaqPath™ COVID-19 CE-IVD RT-PCR kit (TaqPath) and the ID solutions® ID™ SARS-CoV-2/UK/SA Variant Triplex RT-PCR (ID triplex) assay to screen for VOCs. Results The ID triplex assay identified 62.8% of them as VOCs: 61.8% B.1.1.7 and 0.9% B.1.351/P.1. The agreement between the ID triplex results for B.1.1.7 and the TaqPath S gene target failure (SGTF)/ S gene target late detection (SGTL) profile for this variant agreed very well (k = 0.86). A low virus load was the main cause of discrepancies. Sequencing discordant results with both assays indicated that the TaqPath assay detected the B.1.1.7 lineage slightly better. Both assays suggested that the virus loads of B.1.1.7 variants were significantly higher than those of non-B.1.1.7 strains. Only 10/20 B1.351/P.1 strains detected with the ID triplex assay were confirmed by sequencing. Conclusions We conclude that the SGTF/SGTL profiles identified using the TaqPath assay and ID triplex results are suitable for detecting the B.1.1.7 lineage. The ID triplex assay, which rapidly determines all three current VOCs simultaneously, could be a valuable tool for limiting virus spread by supporting contact-tracing and isolation.

Published
2021

23. Hepatitis E virus infections in Europe

Author

Jacques Izopet, Nicolas Capelli, Florence Abravanel, Sébastien Lhomme, Olivier Marion, Jean-Michel Mansuy, Sabine Chapuy-Regaud, Marion Migueres, Pauline Trémeaux, Nassim Kamar, 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), Service de Virologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Département de Néphrologie et Transplantation d'organes [CHU Toulouse], Pôle Urologie - Néphrologie - Dialyse - Transplantations - Brûlés - Chirurgie plastique - Explorations fonctionnelles et physiologiques [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), and CCSD, Accord Elsevier

Subjects
0301 basic medicine, viruses, [SDV]Life Sciences [q-bio], Iatrogenic Disease, medicine.disease_cause, MESH: Genotype, Zoonosis, 0302 clinical medicine, Hepatitis E virus, Zoonoses, Epidemiology, MESH: Animals, 030212 general & internal medicine, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Incidence (epidemiology), MESH: Hepatitis E virus / genetics, virus diseases, Hepatitis E, 3. Good health, Hospitalization, Europe, [SDV] Life Sciences [q-bio], Infectious Diseases, One Health, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Viral, MESH: Hospitalization / statistics & numerical data, MESH: Hepatitis E virus / pathogenicity, Viral hepatitis, Water Microbiology, medicine.medical_specialty, Genotype, 030106 microbiology, MESH: Iatrogenic Disease / epidemiology, MESH: Zoonoses / virology, MESH: Hepatitis E / diagnosis, 03 medical and health sciences, Virology, medicine, Seroprevalence, Animals, Humans, MESH: Food Microbiology, MESH: Hepatitis E / epidemiology, MESH: Humans, business.industry, medicine.disease, MESH: Europe / epidemiology, digestive system diseases, MESH: Water Microbiology, MESH: Zoonoses / epidemiology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Food Microbiology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: RNA, Viral / genetics, business
Abstract

International audience; Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide. The systematic use of improved tools for diagnosing and genotyping has completely changed our understanding of the epidemiology and clinical consequences of HEV infection. Most cases of HEV in Europe arise from infected animals such as pigs, wild boar, deer and rabbits. Zoonotic HEV genotypes (HEV genotypes 3-8) are mainly food-borne or transmitted by direct contact, but recent data suggest that infection can also be water-borne or even iatrogenic throught contamined blood products. HEV-3 is the most prevalent genotype in Europe but the geographic distributions of the 3 major clades and subgenotypes (HEV-3abjkchi, HEV-3efg, and HEV-3ra) differ. Most HEV-3 infections are asymptomatic but they can result in severe acute hepatitis in patients with chronic liver disease, chronic hepatitis in immunocompromised patients, and to extra-hepatic manifestations. Despite more frequent reports of symptomatic hepatitis E cases across Europe, systems for monitoring HEV infections vary greatly. Severe HEV-associated illnesses, hospitalizations and deaths are probably underestimated. The seroprevalence and incidence of locally acquired hepatitis E varies between and within European countries and over time. The precise origin of these variations is uncertain but may be linked to environmental factors or the degree to which HEV contaminates the human food chain. Collaborative initiatives such as the establishment of the One Health platform for HEV sequences (HEVnet database) will be very useful for a better understanding of the epidemiology of HEV in Europe and the development of effective prevention strategies.

Published
2019
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24. [Cell and tissue reservoirs of HIV-1: dynamics during infection]

Author

Pauline, Trémeaux, Christine, Rouzioux, and Véronique, Avettand-Fènoël

Subjects
Transcription, Genetic, Anti-HIV Agents, Lymphoid Tissue, Macrophages, Virus Integration, HIV Infections, Dendritic Cells, Virus Replication, Monocytes, Virus Latency, Viral Tropism, Drug Delivery Systems, Proviruses, DNA, Viral, Disease Progression, HIV-1, Humans, Lymphocytes, Biomarkers, Cells, Cultured, Disease Reservoirs
Abstract

Current antiretroviral therapy allows the control of HIV replication but a relapse occurs most of the time in case of treatment interruption. The viral genome integration explains this persistence of HIV in all body tissues, at very variable levels depending on their density of CD4

Published
2019

25. Increasing contribution of integrated forms to total HIV DNA in blood during HIV disease progression from primary infection

Author

Christine Rouzioux, Asma Essat, Véronique Avettand-Fenoel, Adeline Melard, Olivier Delelis, Tiphaine Lenfant, Marc Bary, Marine Gousset, Jean-Paul Viard, Laurence Meyer, Faroudy Boufassa, Cécile Goujard, Pauline Trémeaux, CCSD, Accord Elsevier, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de Virologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris Descartes - Faculté de Médecine (UPD5 Médecine), Université Paris Descartes - Paris 5 (UPD5), Université Sorbonne Paris Cité (USPC), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Centre de Diagnostic et de Thérapeutique, Hôpital de l’Hôtel-Dieu [Paris], Laboratoire de Microbiologie Clinique [AP-HP Hôpital Necker-Enfants Malades], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), The ANRS-PRIMO and SEROCO cohorts are sponsored by the ANRS (French National Agency for Research on AIDS and Viral Hepatitis). This work was funded by the ANRS., ANRS-SEROCO and PRIMO cohorts, and Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Adult, Male, 0301 basic medicine, Research paper, Human immunodeficiency virus (HIV), Natural history, HIV Infections, Context (language use), medicine.disease_cause, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Integrated HIV DNA, 0302 clinical medicine, Acquired immunodeficiency syndrome (AIDS), medicine, Humans, Primary HIV infection, Seroconversion, Proportional Hazards Models, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, business.industry, General Medicine, Middle Aged, medicine.disease, Virology, 3. Good health, Acquired immunodeficiency syndrome, Kinetics, 030104 developmental biology, Anti-Retroviral Agents, Reservoirs, 030220 oncology & carcinogenesis, Cohort, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, HIV-1, Leukocytes, Mononuclear, RNA, Viral, Female, business, Viral hepatitis, Total HIV DNA, Hiv disease
Abstract

International audience; BACKGROUND:In the current context of research on HIV reservoirs, offering new insights into the persistence of HIV DNA in infected cells, which prevents viral eradication, may aid in identifying cure strategies. This study aimed to describe the establishment of stable integrated forms among total HIV DNA during primary infection (PHI) and their dynamics during the natural history of infection.METHODS:Total and integrated HIV DNA were quantified in blood from 74 PHI patients and 97 recent seroconverters (

Published
2019
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26. Dynamics in HIV‐DNA levels over time in HIV controllers

Author

Faroudy Boufassa, Pauline Trémeaux, Valérie Monceaux, Tatiana Bayan, Nicolas Noel, Elise Gardiennet, Olivier Lambotte, Pauline Lopez, Véronique Avettand-Fenoel, Camille Lécuroux, Laurence Meyer, Brigitte Autran, Asier Sáez-Cirión, Christine Rouzioux, Université Sorbonne Paris Cité (USPC), Laboratoire de Virologie [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11), Centre de recherche en épidémiologie et santé des populations (CESP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Sud - Paris 11 (UP11)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Immunologie des Maladies Virales et Autoimmunes (IMVA - U1184), Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Infectious Diseases Models for Innovative Therapies (IDMIT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Laboratoire de Neuro-Immuno-Virologie, Service de Neurovirologie EMI E-01 (UMR E01), Service de Virologie [CHU Cochin], Hôpital Cochin [AP-HP], HIV, Inflammation et persistance, Institut Pasteur [Paris], Immunité et Infection, Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR113-Sorbonne Université (SU), Sorbonne Université - Faculté de Médecine (SU FM), Sorbonne Université (SU), This work was supported by the ANRS (Agence Nationale de Recherche sur le VIH et les Hépatites Virales)., CODEX ANRS Cohort Study Group, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], HIV, Inflammation et persistance - HIV, Inflammation and Persistence, Institut Pasteur [Paris] (IP), IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), and Gestionnaire, Hal Sorbonne Université

Subjects
Hepatitis C virus, Inflammation, long-term follow-up, medicine.disease_cause, Peripheral blood mononuclear cell, HIV reservoir, Serology, Pathogenesis, 03 medical and health sciences, 0302 clinical medicine, Interquartile range, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Cytotoxic T cell, 030212 general & internal medicine, 030505 public health, business.industry, Public Health, Environmental and Occupational Health, virus diseases, HIV controllers, total HIV‐DNA, dynamics, 3. Good health, Infectious Diseases, Cohort, Immunology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine.symptom, 0305 other medical science, business
Abstract

International audience; Introduction: HIV controllers (HIC) maintain viraemia at low levels without antiretroviral treatment and have small HIV reservoirs. Nevertheless, they are heterogeneous regarding their risk of infection progression. The study of reservoirs can help elucidate this control. This study aimed to explore the factors implicated in the pathogenesis of HIV infection that are potentially associated with HIV reservoirs and their dynamics in HIC.Methods: Individuals living with HIV included in the ANRS‐CODEX cohort with at least two HIV‐DNA measurements between 2009 and 2016 were selected. The total HIV‐DNA levels had been quantified prospectively from blood samples. Mixed‐effect linear models estimated the HIV‐DNA dynamics over time.Results: The median (interquartile range (IQR)) HIV‐DNA level was 1.5 (1.3 to 1.9) log copies/million peripheral blood mononuclear cells at inclusion (n = 202 individuals). These low levels showed heterogeneity among HIC. Lower levels were then associated with the protective HLA‐B*27/B*57 alleles and/or lower HIV‐RNA level at inclusion, negative hepatitis C virus serology, lower HIV‐suppressive capacity of specific CD8 T cells and lower levels of immune activation and inflammation. Interestingly, mathematical modelling of the dynamics of HIV‐DNA over time (840 measurements) showed that the number of infected cells decreased in 46% of HIC (follow‐up: 47.6 months) and increased in 54% of HIC. A multivariate analysis indicated that HLA‐B*27/B*57 alleles, a low level of HIV‐RNA and a low level of HIV‐DNA at inclusion were markers independently associated with this decrease.Conclusions: These results offer new insights into the mechanisms of long‐term control in HIC. In half of HIC, the decrease in HIV‐DNA level could be linked to tighter viral control and progressive loss of infected cells. These findings allow the identification of HIC with a low risk of progression who may not need treatment.

Published
2019
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27. 'Empirical' retreatment of patients with chronic hepatitis C who failed a first direct-acting antiviral-based regimen

Author

Pauline Trémeaux, J.-F. Meritet, L. Kramer, Arielle R. Rosenberg, A Laurain, Stanislas Pol, and Philippe Sultanik

Subjects
Male, 0301 basic medicine, medicine.medical_specialty, Time Factors, Treatment outcome, Genome, Viral, Hepacivirus, Drug resistance, Viral Nonstructural Proteins, Antiviral Agents, Treatment failure, 03 medical and health sciences, 0302 clinical medicine, Viral genetics, Chronic hepatitis, Internal medicine, Drug Resistance, Viral, medicine, Humans, Treatment Failure, Hepatology, business.industry, Hepatitis C, Hepatitis C, Chronic, Middle Aged, medicine.disease, Surgery, Regimen, Treatment Outcome, 030104 developmental biology, Retreatment, Female, 030211 gastroenterology & hepatology, Sofosbuvir, business, Direct acting
Published
2017
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28. Performance of the Xpert HBV Viral Load assay versus the Aptima Quant assay for quantifying hepatitis B virus DNA

Author

Catherine Haslé, Florence Abravanel, Jacques Izopet, Agnès Harter, Stéphanie Raymond, Marion Migueres, Sébastien Lhomme, Laurent Alric, Pauline Trémeaux, Patrick Bruel, Sophie Metivier, 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), CCSD, Accord Elsevier, 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
0301 basic medicine, [SDV]Life Sciences [q-bio], MESH: Molecular Diagnostic Techniques, medicine.disease_cause, Workflow, MESH: Genotype, 0302 clinical medicine, Hbv genotype, Medicine, 030212 general & internal medicine, MESH: Viral Load / standards, GeneXpert MTB/RIF, Clinical performance, virus diseases, General Medicine, Viral Load, Hepatitis B, 3. Good health, [SDV] Life Sciences [q-bio], MESH: Reproducibility of Results, Clinical Practice, Infectious Diseases, Molecular Diagnostic Techniques, Molecular diagnosis, Viral load, MESH: Hepatitis B / diagnosis, Microbiology (medical), Hepatitis B virus, Genotype, 030106 microbiology, Hepatitis B virus DNA, Sensitivity and Specificity, MESH: Workflow, 03 medical and health sciences, MESH: Hepatitis B virus / genetics, Humans, MESH: Hepatitis B / virology, Antiviral treatment, MESH: Humans, business.industry, Reproducibility of Results, Virology, MESH: Sensitivity and Specificity, MESH: Viral Load / methods, digestive system diseases, MESH: DNA, Viral, DNA, Viral, business, GeneXpert instrument
Abstract

International audience; Quantification of HBV DNA is used for initiating and monitoring antiviral treatment. We have evaluated the Xpert HBV Viral Load (VL) assay on the GeneXpert instrument. We estimated its limit of detection to be 7.5 IU/mL. Reproducibility was 1.1-12.7% as assessed by the coefficients of variation for 3 different samples. The assay was linear from 2 to 8 log10 IU/mL for HBV genotypes A to F. Its clinical performance was evaluated by testing prospectively 100 HBV DNA-positive samples with the Xpert HBV VL and Aptima Quant HBV assays. The results from the 2 assays were correlated, with a modest bias (-0.10 log10 IU/mL) between them by Bland-Altman analysis. Patient monitoring with 80 samples performed with both assays gave similar patient profiles with trends in the same direction. The Xpert HBV Viral load assay is reliable enough for quantifying HBV DNA in clinical practice.

Published
2020
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29. Absence of triadin, a protein of the calcium release complex, is responsible for cardiac arrhythmia with sudden death in human

Author

Alain Lacampagne, Antoine Leenhardt, Julie Brocard, Nicole Monnier, Nathalie Roux-Buisson, Marine Cacheux, Julien Fauré, V. Lucet, Pierre F. Ray, Jérémy Fauconnier, Anne Fourest-Lieuvin, Isabelle Marty, Pauline Trémeaux, Isabelle Denjoy, Joël Lunardi, Philippe Mabo, Pascale Guicheney, Philippe Durand, Florence Kyndt, Vincent Probst, Hervé Le Marec, Elodie Santoni, Roux-Buisson, Nathalie, INSERM U836, équipe 4, Muscles et pathologies, Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AGeing and IMagery (AGIM), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Biochimie et Génétique Moléculaire, CHU Grenoble-Hôpital Michallon-CHU Grenoble-Hôpital Michallon, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Service de Cardiologie, AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité-Centre de Référence Maladies Cardiaques Héréditaires, Service de Réanimation Pédiatrique et Médecine Néonatale, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Génétique, pharmacologie et physiopathologie des maladies cardiovasculaires, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de génétique médicale - Unité de génétique clinique [Nantes], Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes), Institut du thorax, Université de Nantes (UN)-IFR26-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de rythmologie pédiatrique, Château des Côtes, Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de cardiologie et maladies vasculaires [Rennes] = Cardiac, Thoracic, and Vascular Surgery [Rennes], CHU Pontchaillou [Rennes], Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biochimie et Génétique Moléculaire, CHU Grenoble-Hôpital Michallon, AGeing and IMagery (AGIM), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Biochimie et Génétique Moléculaire, INSERM, Association Française contre les myopathies (AFM), CNRS, Fondation Daniel Ducoin, PHRC, DRC du CHU Grenoble, Société Française de Myologie (SFM), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-École Pratique des Hautes Études (EPHE), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)-AGeing and IMagery (AGIM), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS)-Biochimie et Génétique Moléculaire, CHU Grenoble-Hôpital Michallon-Hôpital Michallon, Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA)-Grenoble Institut des Neurosciences (GIN), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble, AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité-Centre de Référence Maladies Cardiaques Héréditaires, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de cardiologie et maladies vasculaires, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)-Biochimie et Génétique Moléculaire, Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Joseph Fourier - Grenoble 1 (UJF)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Biochimie et Génétique Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Grenoble Institut des Neurosciences (GIN), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Joseph Fourier - Grenoble 1 (UJF)-Université Pierre Mendès France - Grenoble 2 (UPMF)

Subjects
Male, Muscle Proteins, MESH: Myocytes, Cardiac, 030204 cardiovascular system & hematology, MESH: Protein Isoforms, Endoplasmic Reticulum, Ryanodine receptor 2, MESH: Mice, Knockout, Mice, 0302 clinical medicine, Mutant protein, MESH: Reverse Transcriptase Polymerase Chain Reaction, Chlorocebus aethiops, Missense mutation, Protein Isoforms, Myocytes, Cardiac, MESH: Animals, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, Genetics, Mice, Knockout, 0303 health sciences, Ryanodine receptor, Reverse Transcriptase Polymerase Chain Reaction, MESH: Genetic Predisposition to Disease, General Medicine, Articles, 3. Good health, Pedigree, MESH: COS Cells, MESH: Arrhythmias, Cardiac, MESH: Calcium, COS Cells, cardiovascular system, Female, MESH: Mutation, MESH: Rats, MESH: Pedigree, Nonsense mutation, Blotting, Western, Genes, Recessive, MESH: Carrier Proteins, Biology, Catecholaminergic polymorphic ventricular tachycardia, Sudden death, 03 medical and health sciences, MESH: Muscle Proteins, MESH: Endoplasmic Reticulum, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, Humans, MESH: Blotting, Western, Genetic Predisposition to Disease, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, MESH: Mice, MESH: Genes, Recessive, 030304 developmental biology, Family Health, MESH: Humans, Cell Membrane, Arrhythmias, Cardiac, MESH: Death, Sudden, Cardiac, medicine.disease, Molecular biology, MESH: Cercopithecus aethiops, MESH: Male, Rats, Death, Sudden, Cardiac, Triadin, Mutation, Tachycardia, Ventricular, MESH: Family Health, Calcium, MESH: Tachycardia, Ventricular, Carrier Proteins, MESH: Female, MESH: Cell Membrane
Abstract

International audience; Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited arrhythmogenic disease so far related to mutations in the cardiac ryanodine receptor (RYR2) or the cardiac calsequestrin (CASQ2) genes. Because mutations in RYR2 or in CASQ2 are not retrieved in all CPVT cases, we searched for mutations in the physiological protein partners of RyR2 and CSQ2 in a large cohort of CPVT patients with no detected mutation in these two genes. Based on a candidate gene approach, we focused our investigations on triadin and junctin, two proteins that link RyR2 and CSQ2. Mutations in the triadin (TRDN) and in the junctin (ASPH) genes were searched in a cohort of 97 CPVT patients. We identified three mutations in triadin which cosegregated with the disease on a recessive mode of transmission in two families, but no mutation was found in junctin. Two TRDN mutations, a 4 bp deletion and a nonsense mutation, resulted in premature stop codons; the third mutation, a p.T59R missense mutation, was further studied. Expression of the p.T59R mutant in COS-7 cells resulted in intracellular retention and degradation of the mutant protein. This was confirmed after in vivo expression of the mutant triadin in triadin knock-out mice by viral transduction. In this work, we identified TRDN as a new gene responsible for an autosomal recessive form of CPVT. The mutations identified in the two families lead to the absence of the protein, thereby demonstrating the importance of triadin for the normal function of the cardiac calcium release complex in humans.

Published
2012
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