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Florence Nicot
Virology Laboratory, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, 31300 Toulouse, France

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Journal article
Published: 12 May 2021 in Viruses
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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.

ACS Style

Chloé Dimeglio; Marine Milhes; Jean-Michel Loubes; Noémie Ranger; Jean-Michel Mansuy; Pauline Trémeaux; Nicolas Jeanne; Justine Latour; Florence Nicot; Cécile Donnadieu; Jacques Izopet. Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2. Viruses 2021, 13, 898 .

AMA Style

Chloé Dimeglio, Marine Milhes, Jean-Michel Loubes, Noémie Ranger, Jean-Michel Mansuy, Pauline Trémeaux, Nicolas Jeanne, Justine Latour, Florence Nicot, Cécile Donnadieu, Jacques Izopet. Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2. Viruses. 2021; 13 (5):898.

Chicago/Turabian Style

Chloé Dimeglio; Marine Milhes; Jean-Michel Loubes; Noémie Ranger; Jean-Michel Mansuy; Pauline Trémeaux; Nicolas Jeanne; Justine Latour; Florence Nicot; Cécile Donnadieu; Jacques Izopet. 2021. "Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2." Viruses 13, no. 5: 898.

Microbiology
Published: 28 January 2021 in Frontiers in Microbiology
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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.

ACS Style

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; Jacques Izopet. Classification of the Zoonotic Hepatitis E Virus Genotype 3 Into Distinct Subgenotypes. Frontiers in Microbiology 2021, 11, 1 .

AMA Style

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, Jacques Izopet. Classification of the Zoonotic Hepatitis E Virus Genotype 3 Into Distinct Subgenotypes. Frontiers in Microbiology. 2021; 11 ():1.

Chicago/Turabian Style

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; Jacques Izopet. 2021. "Classification of the Zoonotic Hepatitis E Virus Genotype 3 Into Distinct Subgenotypes." Frontiers in Microbiology 11, no. : 1.

Journal article
Published: 01 July 2020 in Journal of General Virology
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In this recommendation, we update our 2016 table of reference sequences of subtypes of hepatitis E virus (HEV; species Orthohepevirus A, family Hepeviridae) for which complete genome sequences are available (Smith et al., 2016). This takes into account subsequent publications describing novel viruses and additional proposals for subtype names; there are now eight genotypes and 36 subtypes. Although it remains difficult to define strict criteria for distinguishing between virus subtypes, and is not within the remit of the International Committee on Taxonomy of Viruses (ICTV), the use of agreed reference sequences will bring clarity and stability to researchers, epidemiologists and clinicians working with HEV.

ACS Style

Donald B. Smith; Jacques Izopet; Florence Nicot; Peter Simmonds; Shahid Jameel; Xiang-Jin Meng; Heléne Norder; Hiroaki Okamoto; Wim H.M. Van Der Poel; Gábor Reuter; Michael A. Purdy. Update: proposed reference sequences for subtypes of hepatitis E virus (species Orthohepevirus A). Journal of General Virology 2020, 101, 692 -698.

AMA Style

Donald B. Smith, Jacques Izopet, Florence Nicot, Peter Simmonds, Shahid Jameel, Xiang-Jin Meng, Heléne Norder, Hiroaki Okamoto, Wim H.M. Van Der Poel, Gábor Reuter, Michael A. Purdy. Update: proposed reference sequences for subtypes of hepatitis E virus (species Orthohepevirus A). Journal of General Virology. 2020; 101 (7):692-698.

Chicago/Turabian Style

Donald B. Smith; Jacques Izopet; Florence Nicot; Peter Simmonds; Shahid Jameel; Xiang-Jin Meng; Heléne Norder; Hiroaki Okamoto; Wim H.M. Van Der Poel; Gábor Reuter; Michael A. Purdy. 2020. "Update: proposed reference sequences for subtypes of hepatitis E virus (species Orthohepevirus A)." Journal of General Virology 101, no. 7: 692-698.

Journal article
Published: 23 October 2018 in AIDS
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Next-generation sequencing is a sensitive method for determining HIV-1 tropism but there is a lack of data on the quantification of X4 variants. We evaluated MiSeq and 454 GS-Junior platforms for determining HIV-1 tropism and for quantifying X4 variants. Both platforms were 93% concordant for determining HIV-1 tropism and correlated well for determining the proportion of X4 variants (Spearman correlation, ρ = 0.748; p

ACS Style

Stephanie Raymond; Constance Delaugerre; Florence Nicot; Lambert Assoumou; Rémi Lancar; Lydie Beniguel; Jacques Izopet. Accurate quantification of CXCR4-using HIV-1 variants by Illumina deep-sequencing. AIDS 2018, 32, 2429 -2431.

AMA Style

Stephanie Raymond, Constance Delaugerre, Florence Nicot, Lambert Assoumou, Rémi Lancar, Lydie Beniguel, Jacques Izopet. Accurate quantification of CXCR4-using HIV-1 variants by Illumina deep-sequencing. AIDS. 2018; 32 (16):2429-2431.

Chicago/Turabian Style

Stephanie Raymond; Constance Delaugerre; Florence Nicot; Lambert Assoumou; Rémi Lancar; Lydie Beniguel; Jacques Izopet. 2018. "Accurate quantification of CXCR4-using HIV-1 variants by Illumina deep-sequencing." AIDS 32, no. 16: 2429-2431.

Journal article
Published: 02 July 2018 in Journal of Infection
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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. 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. 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 < 0.001). 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.

ACS Style

Florence Abravanel; Julie Pique; Elisabeth Couturier; Florence Nicot; Chloé Dimeglio; Sebastien Lhomme; Julie Chiabrando; Karine Sauné; Jean-Marie Péron; Nassim Kamar; Solène Evrard; Henriette de Valk; Pascal Cintas; Jacques Izopet. Acute hepatitis E in French patients and neurological manifestations. Journal of Infection 2018, 77, 220 -226.

AMA Style

Florence Abravanel, Julie Pique, Elisabeth Couturier, Florence Nicot, Chloé Dimeglio, Sebastien Lhomme, Julie Chiabrando, Karine Sauné, Jean-Marie Péron, Nassim Kamar, Solène Evrard, Henriette de Valk, Pascal Cintas, Jacques Izopet. Acute hepatitis E in French patients and neurological manifestations. Journal of Infection. 2018; 77 (3):220-226.

Chicago/Turabian Style

Florence Abravanel; Julie Pique; Elisabeth Couturier; Florence Nicot; Chloé Dimeglio; Sebastien Lhomme; Julie Chiabrando; Karine Sauné; Jean-Marie Péron; Nassim Kamar; Solène Evrard; Henriette de Valk; Pascal Cintas; Jacques Izopet. 2018. "Acute hepatitis E in French patients and neurological manifestations." Journal of Infection 77, no. 3: 220-226.

Review
Published: 25 June 2018 in Reviews in Medical Virology
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Hepatitis E virus genotype 3 (HEV‐3) can lead to chronic infection in immunocompromised patients, and ribavirin is the treatment of choice. Recently, mutations in the polymerase gene have been associated with ribavirin failure but their frequency before treatment according to HEV‐3 subtypes has not been studied on a large data set. We used single‐molecule real‐time sequencing technology to sequence 115 new complete genomes of HEV‐3 infecting French patients. We analyzed phylogenetic relationships, the length of the polyproline region, and mutations in the HEV polymerase gene. Eighty‐five (74%) were in the clade HEV‐3efg, 28 (24%) in HEV‐3chi clade, and 2 (2%) in HEV‐3ra clade. Using automated partitioning of maximum likelihood phylogenetic trees, complete genomes were classified into subtypes. Polyproline region length differs within HEV‐3 clades (from 189 to 315 nt). Investigating mutations in the polymerase gene, distinct polymorphisms between HEV‐3 subtypes were found (G1634R in 95% of HEV‐3e, G1634K in 56% of HEV‐3ra, and V1479I in all HEV‐3efg, clade HEV‐3ra, and HEV‐3k strains). Subtype‐specific polymorphisms in the HEV‐3 polymerase have been identified. Our study provides new complete genome sequences of HEV‐3 that could be useful for comparing strains circulating in humans and the animal reservoir.

ACS Style

Florence Nicot; Nicolas Jeanne; Alain Roulet; Caroline Lefebvre; Romain Carcenac; Maxime Manno; Martine Dubois; Nassim Kamar; Sebastien Lhomme; Florence Abravanel; Jacques Izopet. Diversity of hepatitis E virus genotype 3. Reviews in Medical Virology 2018, 28, e1987 .

AMA Style

Florence Nicot, Nicolas Jeanne, Alain Roulet, Caroline Lefebvre, Romain Carcenac, Maxime Manno, Martine Dubois, Nassim Kamar, Sebastien Lhomme, Florence Abravanel, Jacques Izopet. Diversity of hepatitis E virus genotype 3. Reviews in Medical Virology. 2018; 28 (5):e1987.

Chicago/Turabian Style

Florence Nicot; Nicolas Jeanne; Alain Roulet; Caroline Lefebvre; Romain Carcenac; Maxime Manno; Martine Dubois; Nassim Kamar; Sebastien Lhomme; Florence Abravanel; Jacques Izopet. 2018. "Diversity of hepatitis E virus genotype 3." Reviews in Medical Virology 28, no. 5: e1987.

Comparative study
Published: 11 May 2018 in Journal of Medical Virology
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The present study compares the performances of an in‐house sequencing protocol developed on MiSeq, the Sanger method, and the 454 GS‐FLX for detecting and quantifying drug‐resistant mutations (DRMs) in the human immunodeficiency virus polymerase gene (reverse transcriptase [RT] and protease [PR]). MiSeq sequencing identified all the resistance mutations detected by bulk sequencing (n = 84). Both the MiSeq and 454 GS‐FLX platforms identified 67 DRMs in the RT and PR regions, but a further 25 DRMs were identified by only one or other of them. Pearson’s analysis showed good concordance between the percentage of drug‐resistant variants determined by MiSeq and 454 GS‐FLX sequencing (ρ = .77, P < .0001). The MiSeq platform is as accurate as the 454 GS‐FLX Roche system for determining RT and PR DRMs and could be used for monitoring human immunodeficiency virus type 1 drug resistance.

ACS Style

Florence Nicot; Nicolas Jeanne; Stephanie Raymond; Olivier Delfour; Romain Carcenac; Caroline Lefebvre; Karine Sauné; Pierre Delobel; Jacques Izopet. Performance comparison of deep sequencing platforms for detecting HIV-1 variants in the pol gene. Journal of Medical Virology 2018, 90, 1486 -1492.

AMA Style

Florence Nicot, Nicolas Jeanne, Stephanie Raymond, Olivier Delfour, Romain Carcenac, Caroline Lefebvre, Karine Sauné, Pierre Delobel, Jacques Izopet. Performance comparison of deep sequencing platforms for detecting HIV-1 variants in the pol gene. Journal of Medical Virology. 2018; 90 (9):1486-1492.

Chicago/Turabian Style

Florence Nicot; Nicolas Jeanne; Stephanie Raymond; Olivier Delfour; Romain Carcenac; Caroline Lefebvre; Karine Sauné; Pierre Delobel; Jacques Izopet. 2018. "Performance comparison of deep sequencing platforms for detecting HIV-1 variants in the pol gene." Journal of Medical Virology 90, no. 9: 1486-1492.

Evaluation study
Published: 12 February 2018 in Journal of Antimicrobial Chemotherapy
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To evaluate the diagnostic performance of the Vela next-generation sequencing (NGS) system in conjunction with the Sentosa SQ HIV Genotyping Assay for genotyping HIV-1. Plasma RNA was extracted and templates prepared with the Sentosa SX instrument before sequencing the HIV-1 polymerase on the Sentosa SQ301 Sequencer (PGM IonTorrent). The Vela NGS System was compared with direct sequencing and the 454 GS-FLX (Roche) and MiSeq (Illumina) systems for genotypic resistance testing on clinical samples. The Vela NGS system detected majority resistance mutations in subtype B and CRF02-AG samples at 500 copies/mL and minority variants with a sensitivity of 5% at 100 000 copies/mL. The Vela NGS system and direct sequencing identified resistance mutations with 97% concordance in 46 clinical samples. Vela identified 1/20 of the 1%-5% mutations identified by 454, 5/12 of the 5%-20% mutations and 60/61 of the >20% mutations. Vela identified 3/14 of the 1%-5% mutations identified by MiSeq, 0/2 of the 5%-20% mutations and 47/47 of the >20% mutations. The resistance mutation quantifications by Vela and 454 were concordant (bias: 2.31%), as were those by Vela and MiSeq (bias: 1.06%). The Vela NGS system provides automated nucleic acid extraction, PCR reagent distribution, library preparation and bioinformatics analysis. The analytical performance was very good when compared with direct sequencing, but was less sensitive than two other NGS platforms for detecting minority variants.

ACS Style

Stéphanie Raymond; Florence Nicot; Romain Carcenac; Caroline Lefebvre; Nicolas Jeanne; Karine Saune; Pierre Delobel; Jacques Izopet. HIV-1 genotypic resistance testing using the Vela automated next-generation sequencing platform. Journal of Antimicrobial Chemotherapy 2018, 73, 1152 -1157.

AMA Style

Stéphanie Raymond, Florence Nicot, Romain Carcenac, Caroline Lefebvre, Nicolas Jeanne, Karine Saune, Pierre Delobel, Jacques Izopet. HIV-1 genotypic resistance testing using the Vela automated next-generation sequencing platform. Journal of Antimicrobial Chemotherapy. 2018; 73 (5):1152-1157.

Chicago/Turabian Style

Stéphanie Raymond; Florence Nicot; Romain Carcenac; Caroline Lefebvre; Nicolas Jeanne; Karine Saune; Pierre Delobel; Jacques Izopet. 2018. "HIV-1 genotypic resistance testing using the Vela automated next-generation sequencing platform." Journal of Antimicrobial Chemotherapy 73, no. 5: 1152-1157.

Validation study
Published: 19 August 2016 in Viruses
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The sensitivity of real-time PCR for hepatitis E virus (HEV) RNA quantification differs greatly among techniques. Standardized tools that measure the real quantity of virus are needed. We assessed the performance of a reverse transcription droplet digital PCR (RT-ddPCR) assay that gives absolute quantities of HEV RNA. Analytical and clinical validation was done on HEV genotypes 1, 3 and 4, and was based on open reading frame (ORF)3 amplification. The within-run and between-run reproducibilities were very good, the analytical sensitivity was 80 HEV RNA international units (IU)/mL and linearities of HEV genotype 1, 3 and 4 were very similar. Clinical validation based on 45 samples of genotype 1, 3 or 4 gave results that correlated well with a validated reverse transcription quantitative PCR (RT-qPCR) assay (Spearman rs = 0.89, p < 0.0001). The RT-ddPCR assay is a sensitive method and could be a promising tool for standardizing HEV RNA quantification in various sample types.

ACS Style

Florence Nicot; Michelle Cazabat; Sébastien Lhomme; Olivier Marion; Karine Sauné; Julie Chiabrando; Martine Dubois; Nassim Kamar; Florence Abravanel; Jacques Izopet. Quantification of HEV RNA by Droplet Digital PCR. Viruses 2016, 8, 233 .

AMA Style

Florence Nicot, Michelle Cazabat, Sébastien Lhomme, Olivier Marion, Karine Sauné, Julie Chiabrando, Martine Dubois, Nassim Kamar, Florence Abravanel, Jacques Izopet. Quantification of HEV RNA by Droplet Digital PCR. Viruses. 2016; 8 (8):233.

Chicago/Turabian Style

Florence Nicot; Michelle Cazabat; Sébastien Lhomme; Olivier Marion; Karine Sauné; Julie Chiabrando; Martine Dubois; Nassim Kamar; Florence Abravanel; Jacques Izopet. 2016. "Quantification of HEV RNA by Droplet Digital PCR." Viruses 8, no. 8: 233.

Multicenter study
Published: 03 January 2015 in Journal of Antimicrobial Chemotherapy
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The objectives of this study were to determine the prevalence and patterns of resistance to integrase strand transfer inhibitors (INSTIs) in patients experiencing virological failure on raltegravir-based ART and the impact on susceptibility to INSTIs (raltegravir, elvitegravir and dolutegravir). Data were collected from 502 treatment-experienced patients failing a raltegravir-containing regimen in a multicentre study. Reverse transcriptase, protease and integrase were sequenced at failure for each patient. INSTI resistance-associated mutations investigated were those included in the last ANRS genotypic algorithm (v23). Among the 502 patients, at failure, median baseline HIV-1 RNA (viral load) was 2.9 log10 copies/mL. Patients had been previously exposed to a median of five NRTIs, one NNRTI and three PIs. Seventy-one percent harboured HIV-1 subtype B and the most frequent non-B subtype was CRF02_AG (13.3%). The most frequent mutations observed were N155H/S (19.1%), Q148G/H/K/R (15.4%) and Y143C/G/H/R/S (6.7%). At failure, viruses were considered as fully susceptible to all INSTIs in 61.0% of cases, whilst 38.6% were considered as resistant to raltegravir, 34.9% to elvitegravir and 13.9% to dolutegravir. In the case of resistance to raltegravir, viruses were considered as susceptible to elvitegravir in 11% and to dolutegravir in 64% of cases. High HIV-1 viral load at failure (P < 0.001) and low genotypic sensitivity score of the associated treatment with raltegravir (P < 0.001) were associated with the presence of raltegravir-associated mutations at failure. Q148 mutations were selected more frequently in B subtypes versus non-B subtypes (P = 0.004). This study shows that a high proportion of viruses remain susceptible to dolutegravir in the case of failure on a raltegravir-containing regimen.

ACS Style

Slim Fourati; Charlotte Charpentier; Corinne Amiel; Laurence Morand-Joubert; Sandrine Reigadas; Mary-Anne Trabaud; Constance Delaugerre; Florence Nicot; Audrey Rodallec; Anne Maillard; Audrey Mirand; Hélène Jeulin; Brigitte Montès; Francis Barin; Dominique Bettinger; Hélène Le Guillou-Guillemette; Sophie Vallet; Anne Signori-Schmuck; Diane Descamps; Vincent Calvez; Philippe Flandre; Anne-Genevieve Marcelin; E. Lagier; C. Roussel; H. Le Guillou; C. Alloui; C. Pallier; H. Fleury; P. Bellecave; Patricia Recordon-Pinson; C. Payan; A. Vabret; C. Henquell; M. Bouvier-Alias; Alexis De Rougemont; G. Dos Santos; P. Morand; L. Bocket; Sylvie Rogez; P. Andre; J. C. Tardy; C. Tamalet; C. Delamare; E. Schvoerer; V. Ferre; E. André-Garnier; J. Cottalorda; J. Guinard; A. Guiguon; F. Brun-Vézinet; B. Visseaux; G. Peytavin; A. Krivine; A. Si-Mohamed; V. Avettand-Fenoel; S. Lambert-Niclot; C. Soulié; M. Wirden; M. L. Chaix; V. Schneider; G. Giraudeau; V. Brodard; Jean-Christophe Plantier; C. Chaplain; T. Bourlet; S. Fafi-Kremer; F. Stoll-Keller; M. P. Schmitt; H. Barth; S. Yerly; C. Poggi; J. Izopet; S. Raymond; A. Chaillon; S. Marque-Juillet; A. M. Roque-Afonso; S. Haïm-Boukobza; M. Grudé; L. Assoumou; D. Costagliola; T. Allegre; J. L. Schmit; J. M. Chennebault; O. Bouchaud; N. Magy-Bertrand; J. F. Delfraissy; M. Dupon; P. Morlat; D. Neau; S. Ansart; Sylvain Jaffuel; R. Verdon; C. Jacomet; Y. Lévy; S. Dominguez; P. Chavanet; L. Piroth; André Cabié; P. Leclercq; F. Ajana; A. Cheret; P. Weinbreck; L. Cotte; I. Poizot-Martin; I. Ravaud; B. Christian; F. Truchetet; M. Grandidier; J. Reynes; T. May; F. Goehringer; F. Raffi; P. Dellamonica; T. Prazuck; L. Hocqueloux; P. Yéni; R. Landman; O. Launay; L. Weiss; J. P. Viard; C. Katlama; A. Simon; P.M. Girard; J. L. Meynard; J. M. Molina; G. Pialoux; B. Hoen; M. T. Goeger-Sow; I. Lamaury; G. Beaucaire; R. Jaussaud; C. Rouger; C. Michelet; F. Borsa-Lebas; F. Caron; M. A. Khuong; F. Lucht; D. Rey; A. Calmy; Bruno Marchou; G. Gras; A. Greder-Belan; D. Vittecoq; E. Teicher. Cross-resistance to elvitegravir and dolutegravir in 502 patients failing on raltegravir: a French national study of raltegravir-experienced HIV-1-infected patients. Journal of Antimicrobial Chemotherapy 2015, 70, 1507 -1512.

AMA Style

Slim Fourati, Charlotte Charpentier, Corinne Amiel, Laurence Morand-Joubert, Sandrine Reigadas, Mary-Anne Trabaud, Constance Delaugerre, Florence Nicot, Audrey Rodallec, Anne Maillard, Audrey Mirand, Hélène Jeulin, Brigitte Montès, Francis Barin, Dominique Bettinger, Hélène Le Guillou-Guillemette, Sophie Vallet, Anne Signori-Schmuck, Diane Descamps, Vincent Calvez, Philippe Flandre, Anne-Genevieve Marcelin, E. Lagier, C. Roussel, H. Le Guillou, C. Alloui, C. Pallier, H. Fleury, P. Bellecave, Patricia Recordon-Pinson, C. Payan, A. Vabret, C. Henquell, M. Bouvier-Alias, Alexis De Rougemont, G. Dos Santos, P. Morand, L. Bocket, Sylvie Rogez, P. Andre, J. C. Tardy, C. Tamalet, C. Delamare, E. Schvoerer, V. Ferre, E. André-Garnier, J. Cottalorda, J. Guinard, A. Guiguon, F. Brun-Vézinet, B. Visseaux, G. Peytavin, A. Krivine, A. Si-Mohamed, V. Avettand-Fenoel, S. Lambert-Niclot, C. Soulié, M. Wirden, M. L. Chaix, V. Schneider, G. Giraudeau, V. Brodard, Jean-Christophe Plantier, C. Chaplain, T. Bourlet, S. Fafi-Kremer, F. Stoll-Keller, M. P. Schmitt, H. Barth, S. Yerly, C. Poggi, J. Izopet, S. Raymond, A. Chaillon, S. Marque-Juillet, A. M. Roque-Afonso, S. Haïm-Boukobza, M. Grudé, L. Assoumou, D. Costagliola, T. Allegre, J. L. Schmit, J. M. Chennebault, O. Bouchaud, N. Magy-Bertrand, J. F. Delfraissy, M. Dupon, P. Morlat, D. Neau, S. Ansart, Sylvain Jaffuel, R. Verdon, C. Jacomet, Y. Lévy, S. Dominguez, P. Chavanet, L. Piroth, André Cabié, P. Leclercq, F. Ajana, A. Cheret, P. Weinbreck, L. Cotte, I. Poizot-Martin, I. Ravaud, B. Christian, F. Truchetet, M. Grandidier, J. Reynes, T. May, F. Goehringer, F. Raffi, P. Dellamonica, T. Prazuck, L. Hocqueloux, P. Yéni, R. Landman, O. Launay, L. Weiss, J. P. Viard, C. Katlama, A. Simon, P.M. Girard, J. L. Meynard, J. M. Molina, G. Pialoux, B. Hoen, M. T. Goeger-Sow, I. Lamaury, G. Beaucaire, R. Jaussaud, C. Rouger, C. Michelet, F. Borsa-Lebas, F. Caron, M. A. Khuong, F. Lucht, D. Rey, A. Calmy, Bruno Marchou, G. Gras, A. Greder-Belan, D. Vittecoq, E. Teicher. Cross-resistance to elvitegravir and dolutegravir in 502 patients failing on raltegravir: a French national study of raltegravir-experienced HIV-1-infected patients. Journal of Antimicrobial Chemotherapy. 2015; 70 (5):1507-1512.

Chicago/Turabian Style

Slim Fourati; Charlotte Charpentier; Corinne Amiel; Laurence Morand-Joubert; Sandrine Reigadas; Mary-Anne Trabaud; Constance Delaugerre; Florence Nicot; Audrey Rodallec; Anne Maillard; Audrey Mirand; Hélène Jeulin; Brigitte Montès; Francis Barin; Dominique Bettinger; Hélène Le Guillou-Guillemette; Sophie Vallet; Anne Signori-Schmuck; Diane Descamps; Vincent Calvez; Philippe Flandre; Anne-Genevieve Marcelin; E. Lagier; C. Roussel; H. Le Guillou; C. Alloui; C. Pallier; H. Fleury; P. Bellecave; Patricia Recordon-Pinson; C. Payan; A. Vabret; C. Henquell; M. Bouvier-Alias; Alexis De Rougemont; G. Dos Santos; P. Morand; L. Bocket; Sylvie Rogez; P. Andre; J. C. Tardy; C. Tamalet; C. Delamare; E. Schvoerer; V. Ferre; E. André-Garnier; J. Cottalorda; J. Guinard; A. Guiguon; F. Brun-Vézinet; B. Visseaux; G. Peytavin; A. Krivine; A. Si-Mohamed; V. Avettand-Fenoel; S. Lambert-Niclot; C. Soulié; M. Wirden; M. L. Chaix; V. Schneider; G. Giraudeau; V. Brodard; Jean-Christophe Plantier; C. Chaplain; T. Bourlet; S. Fafi-Kremer; F. Stoll-Keller; M. P. Schmitt; H. Barth; S. Yerly; C. Poggi; J. Izopet; S. Raymond; A. Chaillon; S. Marque-Juillet; A. M. Roque-Afonso; S. Haïm-Boukobza; M. Grudé; L. Assoumou; D. Costagliola; T. Allegre; J. L. Schmit; J. M. Chennebault; O. Bouchaud; N. Magy-Bertrand; J. F. Delfraissy; M. Dupon; P. Morlat; D. Neau; S. Ansart; Sylvain Jaffuel; R. Verdon; C. Jacomet; Y. Lévy; S. Dominguez; P. Chavanet; L. Piroth; André Cabié; P. Leclercq; F. Ajana; A. Cheret; P. Weinbreck; L. Cotte; I. Poizot-Martin; I. Ravaud; B. Christian; F. Truchetet; M. Grandidier; J. Reynes; T. May; F. Goehringer; F. Raffi; P. Dellamonica; T. Prazuck; L. Hocqueloux; P. Yéni; R. Landman; O. Launay; L. Weiss; J. P. Viard; C. Katlama; A. Simon; P.M. Girard; J. L. Meynard; J. M. Molina; G. Pialoux; B. Hoen; M. T. Goeger-Sow; I. Lamaury; G. Beaucaire; R. Jaussaud; C. Rouger; C. Michelet; F. Borsa-Lebas; F. Caron; M. A. Khuong; F. Lucht; D. Rey; A. Calmy; Bruno Marchou; G. Gras; A. Greder-Belan; D. Vittecoq; E. Teicher. 2015. "Cross-resistance to elvitegravir and dolutegravir in 502 patients failing on raltegravir: a French national study of raltegravir-experienced HIV-1-infected patients." Journal of Antimicrobial Chemotherapy 70, no. 5: 1507-1512.

Journal article
Published: 20 November 2014 in Journal of Clinical Virology
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The presence of low-frequency HIV-1 variants with mutations making them resistant to non-nucleoside reverse-transcriptase inhibitors (NNRTI) could influence the virological response to first-line NNRTI therapy. This study was designed to describe the proportions and quantities of NRTI and NNRTI-resistant variants in patients with successful first-line NNRTI therapy. We evaluated the presence of drug-resistance mutations (DRMs) prior to treatment initiation in 131 naive chronically HIV-1-infected patients initiating NNRTI-based first-line therapy. DRMs were detected by ultradeep pyrosequencing (UDPS) on a GS Junior instrument (Roche). The mean HIV RNA concentration was 4.78 ± 0.74 log copies/mL and the mean CD4 cell count was 368 ± 184 CD4 cells/mm3. Patients were mainly infected with subtype B (68%) and 96% were treated with efavirenz. The sensitivity threshold for each mutation was 0.13–1.05% for 2000 reads. Major NRTI-resistant or NNRTI-resistant mutations were detected in 40 patients (33.6%). The median frequency of major NRTI-resistant mutations was 1.37% [IQR: 0.39–84.1], i.e.: a median of 556 copies/mL [IQR: 123–37,553]. The median frequency of major NNRTI-resistant DRMs was 0.78% [IQR: 0.67–7.06], i.e.: a median of 715 copies/mL [IQR: 391–3452]. The genotypic susceptibility score (GSS) of 9 (7.3%) patients with mutations to given treatment detected by UDPS was 1.5 or 2. First-line NNRTI-based treatment can produce virological success in naïve HIV-1-infected patients harboring low-frequency DRMs representing <1% of the viral quasispecies. Further studies are needed to determine the clinical cut-off of low-frequency resistant variants associated to virological failure.

ACS Style

F. Nicot; K. Sauné; S. Raymond; N. Jeanne; R. Carcenac; C. Lefebvre; Lise Cuzin; Bruno Marchou; P. Delobel; J. Izopet. Minority resistant HIV-1 variants and the response to first-line NNRTI therapy. Journal of Clinical Virology 2014, 62, 20 -24.

AMA Style

F. Nicot, K. Sauné, S. Raymond, N. Jeanne, R. Carcenac, C. Lefebvre, Lise Cuzin, Bruno Marchou, P. Delobel, J. Izopet. Minority resistant HIV-1 variants and the response to first-line NNRTI therapy. Journal of Clinical Virology. 2014; 62 ():20-24.

Chicago/Turabian Style

F. Nicot; K. Sauné; S. Raymond; N. Jeanne; R. Carcenac; C. Lefebvre; Lise Cuzin; Bruno Marchou; P. Delobel; J. Izopet. 2014. "Minority resistant HIV-1 variants and the response to first-line NNRTI therapy." Journal of Clinical Virology 62, no. : 20-24.

Journal article
Published: 18 July 2013 in Journal of Antimicrobial Chemotherapy
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R5 viruses have long been thought to account for almost all strains present in primary HIV-1 infections (PHIs), but recent studies using sensitive phenotypic assays have revealed that 3%–6.4% of subjects also harbour CXCR4-using viruses. Phenotypic assays provide only qualitative results: the presence or absence of CXCR4-using viruses. We have therefore used ultra-deep pyrosequencing (UDS) to determine the frequency of CXCR4-using viruses among HIV-1 quasispecies. We first screened 200 patients for HIV-1 tropism using a sensitive phenotypic assay during PHI and identified 11 infected with an R5X4 dual/mixed (D/M) virus population. We then used UDS of the V3 env region with the geno2pheno algorithm (false positive rate = 5.75) to identify the HIV-1 quasispecies. CXCR4-using viruses were detected in all but 1 of the 11 patients by UDS, and accounted for 0.2%–100% of the virus populations. The frequency of CXCR4-using viruses was <20% in six subjects and 100% in four subjects. Virus populations containing 100% CXCR4-using variants during PHI persisted for at least 1–2 years after the acute phase. The CCR5 Δ32 heterozygous genotype was similarly prevalent in patients infected with D/M (27%) and R5 (15%) viruses. UDS and the phenotype were concordant for determining HIV-1 coreceptor usage. UDS analysis indicated large differences in the percentage of CXCR4-using viruses in the HIV-1 quasispecies during PHI. Further studies should examine the impact of the proportion of CXCR4-using viruses on disease prognosis.

ACS Style

Stéphanie Raymond; Adrien Saliou; Florence Nicot; Pierre Delobel; Martine Dubois; Romain Carcenac; Karine Sauné; Bruno Marchou; Patrice Massip; Jacques Izopet. Characterization of CXCR4-using HIV-1 during primary infection by ultra-deep pyrosequencing. Journal of Antimicrobial Chemotherapy 2013, 68, 2875 -2881.

AMA Style

Stéphanie Raymond, Adrien Saliou, Florence Nicot, Pierre Delobel, Martine Dubois, Romain Carcenac, Karine Sauné, Bruno Marchou, Patrice Massip, Jacques Izopet. Characterization of CXCR4-using HIV-1 during primary infection by ultra-deep pyrosequencing. Journal of Antimicrobial Chemotherapy. 2013; 68 (12):2875-2881.

Chicago/Turabian Style

Stéphanie Raymond; Adrien Saliou; Florence Nicot; Pierre Delobel; Martine Dubois; Romain Carcenac; Karine Sauné; Bruno Marchou; Patrice Massip; Jacques Izopet. 2013. "Characterization of CXCR4-using HIV-1 during primary infection by ultra-deep pyrosequencing." Journal of Antimicrobial Chemotherapy 68, no. 12: 2875-2881.

Book chapter
Published: 10 October 2011 in Liver Biopsy in Modern Medicine
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ACS Style

Florence Nicot; Nassim Kamar; Lionel Rostaing; Jacques Izopet. Occult Hepatitis C Virus Infection: Where are We Now? Liver Biopsy in Modern Medicine 2011, 1 .

AMA Style

Florence Nicot, Nassim Kamar, Lionel Rostaing, Jacques Izopet. Occult Hepatitis C Virus Infection: Where are We Now? Liver Biopsy in Modern Medicine. 2011; ():1.

Chicago/Turabian Style

Florence Nicot; Nassim Kamar; Lionel Rostaing; Jacques Izopet. 2011. "Occult Hepatitis C Virus Infection: Where are We Now?" Liver Biopsy in Modern Medicine , no. : 1.

Journal article
Published: 24 August 2011 in AIDS
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We used ultra-deep pyrosequencing and the Toulouse Tropism Test phenotypic assay to determine the prevalence of CXCR4-using viruses in 21 patients with primary HIV-1 infections. We found X4-containing virus populations in 9% of patients by ultra-deep pyrosequencing using position-specific scoring matrices (PSSM(X4/R5)) or geno2pheno(5.75) and in 14% using the combined 11/25 and net charge rule. The phenotypic assay identified 9% of CXCR4-using viruses. This confirms that R5 viruses are predominant in primary HIV-1 infections.

ACS Style

Stéphanie Raymond; Adrien Saliou; Florence Nicot; Pierre Delobel; Martine Dubois; Michelle Cazabat; Karine Sandres-Sauné; Bruno Marchou; Patrice Massip; Jacques Izopet. Frequency of CXCR4-using viruses in primary HIV-1 infections using ultra-deep pyrosequencing. AIDS 2011, 25, 1668 -1670.

AMA Style

Stéphanie Raymond, Adrien Saliou, Florence Nicot, Pierre Delobel, Martine Dubois, Michelle Cazabat, Karine Sandres-Sauné, Bruno Marchou, Patrice Massip, Jacques Izopet. Frequency of CXCR4-using viruses in primary HIV-1 infections using ultra-deep pyrosequencing. AIDS. 2011; 25 (13):1668-1670.

Chicago/Turabian Style

Stéphanie Raymond; Adrien Saliou; Florence Nicot; Pierre Delobel; Martine Dubois; Michelle Cazabat; Karine Sandres-Sauné; Bruno Marchou; Patrice Massip; Jacques Izopet. 2011. "Frequency of CXCR4-using viruses in primary HIV-1 infections using ultra-deep pyrosequencing." AIDS 25, no. 13: 1668-1670.

Journal article
Published: 01 October 2010 in Arzneimittelforschung
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Ribavirin (CAS 66510-90-5) associated to peginterferon (CAS 99210-65-8) is the current Standard treatment for chronic hepatitis C. Exposure to ribavirin influences the virological response and anemia. Therefore monitoring plasma concentration of ribavirin is a useful tool for individualizing ribavirin dosing regimens. Ribavirin is a substrate of several nucleoside transporters that play a role in its distribution in erythrocytes. After blood sampling, it is essential to limit this mechanism. The aim of this study was to evaluate the influence of temperature and time on ribavirin plasma concentrations. Two blood samples, collected in EDTA tubes, were taken at the same time from 23 patients. One sample was conserved on ice whereas the second one was kept at room temperature during transport to the laboratory. Upon receipt at the laboratory and at different times post-reception (from 1 to 3 h), 1.5 mL of blood from each sample was centrifuged to obtain plasma that was then stored at −20 °C until assay. Samples were maintained in the same conditions as during transport for the 3 h. Plasma ribavirin was analysed using an HPLC-UV system. The results showed that mean loss of ribavirin concentration, for samples kept on ice as well as at room temperature, was less than 3%, 9% and 13% after 1, 2 and 3 h, respectively. These results suggest that blood samples for ribavirin analysis can be sent at room temperature within a period of 2 h between sampling and centrifugation.

ACS Style

Peggy Gandia; Stéphanie Trancart; Florence Nicot; Karl Barange; Laurent Alric; Jacques Izopet; Patrick Séraissol; Michel Lavit; Georges Houin. Influence of pre-analytical conditions on plasma ribavirin concentrations. Arzneimittelforschung 2010, 60, 636 -639.

AMA Style

Peggy Gandia, Stéphanie Trancart, Florence Nicot, Karl Barange, Laurent Alric, Jacques Izopet, Patrick Séraissol, Michel Lavit, Georges Houin. Influence of pre-analytical conditions on plasma ribavirin concentrations. Arzneimittelforschung. 2010; 60 (10):636-639.

Chicago/Turabian Style

Peggy Gandia; Stéphanie Trancart; Florence Nicot; Karl Barange; Laurent Alric; Jacques Izopet; Patrick Séraissol; Michel Lavit; Georges Houin. 2010. "Influence of pre-analytical conditions on plasma ribavirin concentrations." Arzneimittelforschung 60, no. 10: 636-639.

Review
Published: 18 June 2010 in Expert Opinion on Investigational Drugs
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Importance of the field: The current treatment of chronic hepatitis C based on the combination of pegylated interferon and ribavirin is effective in only 50% of patients. Specific targeted antiviral therapies represent a promising approach to eradicate the infection. Areas covered in this review: This review focuses on progress towards the development of the hepatitis C virus (HCV) polymerase inhibitors that have entered clinical development in recent years. What the reader will gain: Nucleos(t)ide analogues target the active site of the HCV polymerase and acts as chain terminators. They have similar activity against all genotypes and the virus has a high genetic barrier to drug resistance. Non-nucleoside inhibitors achieve polymerase inhibition by binding to one of the at least four allosteric enzyme sites. Most of them have a genotype-specific activity and they may select rapidly drug-resistant variants if HCV replication is not completely suppressed. Nonetheless, they provide additional options for addressing the needs of infected patients. Take home message: NS5B polymerase inhibitors will form an integral part of more effective anti-HCV therapy, in combination with interferon or with other directly acting antiviral agents.

ACS Style

Florence Legrand-Abravanel; Florence Nicot; Jacques Izopet. New NS5B polymerase inhibitors for hepatitis C. Expert Opinion on Investigational Drugs 2010, 19, 963 -975.

AMA Style

Florence Legrand-Abravanel, Florence Nicot, Jacques Izopet. New NS5B polymerase inhibitors for hepatitis C. Expert Opinion on Investigational Drugs. 2010; 19 (8):963-975.

Chicago/Turabian Style

Florence Legrand-Abravanel; Florence Nicot; Jacques Izopet. 2010. "New NS5B polymerase inhibitors for hepatitis C." Expert Opinion on Investigational Drugs 19, no. 8: 963-975.

Research article
Published: 28 November 2006 in Journal of Medical Virology
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Hepatitis C virus (HCV) is a major cause of chronic hepatitis and liver disease worldwide. The genetic heterogeneity of HCV and its spread among infected patients can be examined accurately by nucleotide sequencing. The diversity of HCV genotype 2 strains (HCV‐2) was studied in a large cohort of patients in the Midi Pyrénées area of southern France. Phylogenetic analysis was performed on 344 NS5B sequences from patients infected with HCV‐2. These included 145 strains whose E2 region was also analyzed, and epidemiological data were collected for the corresponding patients. HCV‐2 accounts for 11.3% of HCV infections in this area. Phylogenetic analysis of NS5B sequences revealed eight subtypes, while that of the E2 region provided congruent results for 100% of strains. The most frequent subtypes were 2i (24.7%), 2k (22.4%) 2c (17.4%), and 2a (10.8%). The mean age of HCV‐2‐infected patients was 55.5 years. Epidemiological data showed that blood transfusion is the major route of infection, but it was not associated with any particular subtype. By contrast, intravenous drug users were infected predominantly with genotype 2a. HCV‐2a‐infected patients were younger than patients infected with other subtypes (48 vs. 56.5 years, P < 0.01). This study shows substantial genetic diversity of HCV‐2 subtypes in the south of France and the spread of 2a strains via intravenous drug users. J. Med. Virol. 79:26–34, 2007.

ACS Style

Fabienne Thomas; Florence Nicot; Karine Sandres-Sauné; Martine Dubois; Florence Legrand-Abravanel; Laurent Alric; Jean-Marie Peron; Christophe Pasquier; Jacques Izopet. Genetic diversity of HCV genotype 2 strains in South Western France. Journal of Medical Virology 2006, 79, 26 -34.

AMA Style

Fabienne Thomas, Florence Nicot, Karine Sandres-Sauné, Martine Dubois, Florence Legrand-Abravanel, Laurent Alric, Jean-Marie Peron, Christophe Pasquier, Jacques Izopet. Genetic diversity of HCV genotype 2 strains in South Western France. Journal of Medical Virology. 2006; 79 (1):26-34.

Chicago/Turabian Style

Fabienne Thomas; Florence Nicot; Karine Sandres-Sauné; Martine Dubois; Florence Legrand-Abravanel; Laurent Alric; Jean-Marie Peron; Christophe Pasquier; Jacques Izopet. 2006. "Genetic diversity of HCV genotype 2 strains in South Western France." Journal of Medical Virology 79, no. 1: 26-34.