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Vauloup-Fellous C, Maylin S, Périllaud-Dubois C, Brichler S, Alloui C, Gordien E, Rameix-Welti MA, Gault E, Moreau F, Fourati S, Challine D, Pawlotsky JM, Houhou-Fidouh N, Damond F, Mackiewicz V, Charpentier C, Méritet JF, Rozenberg F, Podglajen I, Marot S, Petit H, Burrel S, Akhavan S, Leruez-Ville M, Avettand-Fenoel V, Fourgeaud J, Guilleminot T, Gardiennet E, Bonacorsi S, Carol A, Carcelain G, Villemonteix J, Boukli N, Gozlan J, Morand-Joubert L, Legoff J, Delaugerre C, Chaix ML, Roque-Afonso AM, Dortet L, Naas T, Ronat JB, Lepape S, Marcelin AG, Descamps D. Performance of 30 commercial SARS-CoV-2 serology assays in testing symptomatic COVID-19 patients. Eur J Clin Microbiol Infect Dis 2021; 40:2235-2241. [PMID: 33782783 PMCID: PMC8007057 DOI: 10.1007/s10096-021-04232-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/17/2021] [Indexed: 01/08/2023]
Abstract
We report evaluation of 30 assays' (17 rapid tests (RDTs) and 13 automated/manual ELISA/CLIA assay (IAs)) clinical performances with 2594 sera collected from symptomatic patients with positive SARS-CoV-2 rRT-PCR on a respiratory sample, and 1996 pre-epidemic serum samples expected to be negative. Only 4 RDT and 3 IAs fitted both specificity (> 98%) and sensitivity (> 90%) criteria according to French recommendations. Serology may offer valuable information during COVID-19 pandemic, but inconsistent performances observed among the 30 commercial assays evaluated, which underlines the importance of independent evaluation before clinical implementation.
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Taouqi M, Veyri M, Brégigeon S, Pibarot M, Solas C, Makinson A, Marcelin AG, Choquet S, Spano JP, Poizot-Martin I. [Survey on HIV, HBV and HCV screening practices in cancerology, France]. Bull Cancer 2021; 108:369-376. [PMID: 33714539 DOI: 10.1016/j.bulcan.2020.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/05/2020] [Accepted: 11/16/2020] [Indexed: 11/29/2022]
Abstract
HIV testing is recommended at time of cancer diagnosis, HBV and HCV screening because of the risk of reactivation with certain anticancer drugs.This is a cross-sectional study. The objectives were to assess the screening practices in cancer patients and the satisfaction of professionals in the event of use of the CancerHIV network. A questionnaire drafted by the CancerHIV expert and the OncoPaca-Corse Regional Cancer Network (RCN) was distributed in the region at the end of 2018 (part 1: V1) before being extended to the national level via the CancerHIV network (part 2: V2). Participation reached 160 and 130 respondents (V1 and V2, respectively). At the initial cancer assessment, 23% of respondents declared that they systematically screened for HIV at V1 (V2: 17%), 25% for HBV (V2: 20%) and 24% for HCV (V2: 19%). Before immunotherapy, the rates were 54% for HIV in V1 (V2: 52%), 57% for HBV (V2: 60%) and 55% for HCV (V2: 57%). Among the respondents, satisfaction when requesting a regional or national remedy was high (almost 100%). Screening for HIV, HBV and HCV allows supervised prescription of immunosuppressive or cytotoxic treatment to a potentially immunosuppressed patient. This study, resulting of an original collaboration between a RCN and a national expert network, underlines the lack of screening at the 2 examined stages of patient care, and the need for raising practitioners' awareness to recommendations.
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Jary A, Leducq V, Desire N, Petit H, Palich R, Joly V, Canestri A, Gothland A, Lambert-Niclot S, Surgers L, Amiel C, Descamps D, Spano JP, Katlama C, Calvez V, Marcelin AG. New Kaposi's sarcoma-associated herpesvirus variant in men who have sex with men associated with severe pathologies. J Infect Dis 2021; 222:1320-1328. [PMID: 32282911 DOI: 10.1093/infdis/jiaa180] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/09/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Kaposi sarcoma (KS)-associated herpesvirus (KSHV) subtype depends mostly on patient origin. The current study aimed to assess KSHV diversity in a population of men who have sex with men (MSM) living in France. METHODS The study included 264 patients. In 65 MSM, including 57 human immunodeficiency virus (HIV)-infected men with KS, multicentric Castleman disease, or primary effusion lymphoma and 8 HIV-uninfected men receiving HIV preexposure prophylaxis (PrEP), we performed KSHV typing with K1 open reading frame Sanger and KSHV whole-genome sequencing. In 199 other patients, we performed real-time polymerase chain reaction screening for the new variant. RESULTS We found that 51% of KSHV-strains were subtype C (85% C3), and 33% were subtype A. Four patients with severe KSHV disease (2 with visceral KS, 1 with multicentric Castleman disease, and 1 with primary effusion lymphoma) and 1 asymptomatic PrEP user had a new variant resembling the Ugandan subtype F, but with different K1 open reading frame and KSHV whole-genome sequences and a different epidemiological context (MSM vs African population). Its prevalence was 4.5% in Caucasian MSM, and it was absent in other epidemiological groups. CONCLUSIONS Subtype C predominated among MSM living in France. The new F variant was identified in Caucasian MSM and associated with severe KSHV disease, suggesting that subtype F could be split into F1 and F2 variants. Careful screening for this variant may be required in MSM, given the severe clinical presentation of associated diseases.
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Spano JP, Barre-Sinoussi F, Kieny MP, Marcelin AG, Blay JY. [COVID-19 vaccination for cancer patients: Medical and ethical need]. Bull Cancer 2021; 108:225-227. [PMID: 33674059 PMCID: PMC7885674 DOI: 10.1016/j.bulcan.2021.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Fekkar A, Lampros A, Mayaux J, Poignon C, Demeret S, Constantin JM, Marcelin AG, Monsel A, Luyt CE, Blaize M. Occurrence of Invasive Pulmonary Fungal Infections in Patients with Severe COVID-19 Admitted to the ICU. Am J Respir Crit Care Med 2021; 203:307-317. [PMID: 33480831 PMCID: PMC7874326 DOI: 10.1164/rccm.202009-3400oc] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rationale: Whether severe coronavirus disease (COVID-19) is a significant risk factor for the development of invasive fungal superinfections is of great medical interest and remains, for now, an open question.Objectives: We aim to assess the occurrence of invasive fungal respiratory superinfections in patients with severe COVID-19.Methods: We conducted the study on patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related pneumonia admitted to five ICUs in France who had respiratory and serum sampling performed for specific screening of fungal complications.Measurements and Main Results: The study population included a total of 145 patients; the median age was 55 years old. Most of them were male (n = 104; 72%), were overweight (n = 99; 68%), and had hypertension (n = 83; 57%) and diabetes (n = 46; 32%). Few patients presented preexisting host risk factors for invasive fungal infection (n = 20; 14%). Their global severity was high; all patients were on invasive mechanical ventilation, and half (n = 73, 54%) were on extracorporeal membrane oxygenation support. Mycological analysis included 2,815 mycological tests (culture, galactomannan, β-glucan, and PCR) performed on 475 respiratory samples and 532 sera. A probable/putative invasive pulmonary mold infection was diagnosed in 7 (4.8%) patients and linked to high mortality. Multivariate analysis indicates a significantly higher risk for solid organ transplant recipients (odds ratio, = 4.66; interquartile range, 1.98-7.34; P = 0.004). False-positive fungal test and clinically irrelevant colonization, which did not require the initiation of antifungal treatment, was observed in 25 patients (17.2%).Conclusions: In patients with no underlying immunosuppression, severe SARS-CoV-2-related pneumonia seems at low risk of invasive fungal secondary infection, especially aspergillosis.
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Marot S, Malet I, Leducq V, Zafilaza K, Sterlin D, Planas D, Gothland A, Jary A, Dorgham K, Bruel T, Burrel S, Boutolleau D, Schwartz O, Gorochov G, Calvez V, Marcelin AG. Rapid decline of neutralizing antibodies against SARS-CoV-2 among infected healthcare workers. Nat Commun 2021; 12:844. [PMID: 33558507 PMCID: PMC7870823 DOI: 10.1038/s41467-021-21111-9] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/13/2021] [Indexed: 12/16/2022] Open
Abstract
There are only few data concerning persistence of neutralizing antibodies (NAbs) among SARS-CoV-2-infected healthcare workers (HCW). These individuals are particularly exposed to SARS-CoV-2 infection and at potential risk of reinfection. We followed 26 HCW with mild COVID-19 three weeks (D21), two months (M2) and three months (M3) after the onset of symptoms. All the HCW had anti-receptor binding domain (RBD) IgA at D21, decreasing to 38.5% at M3 (p < 0.0001). Concomitantly a significant decrease in NAb titers was observed between D21 and M2 (p = 0.03) and between D21 and M3 (p < 0.0001). Here, we report that SARS-CoV-2 can elicit a NAb response correlated with anti-RBD antibody levels. However, this neutralizing activity declines, and may even be lost, in association with a decrease in systemic IgA antibody levels, from two months after disease onset. This short-lasting humoral protection supports strong recommendations to maintain infection prevention and control measures in HCW, and suggests that periodic boosts of SARS-CoV-2 vaccination may be required. The humoral immune response to SARS-CoV-2 infection is not yet fully understood. Here, Marot et al. monitor the longitudinal profile and neutralizing activity of IgG, IgA, and IgM among 26 healthcare workers and provide evidence for a short-lasting humoral immune protection due to a decrease of neutralizing antibody titers within 3 months.
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Villoutreix BO, Calvez V, Marcelin AG, Khatib AM. In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Int J Mol Sci 2021; 22:1695. [PMID: 33567580 PMCID: PMC7915722 DOI: 10.3390/ijms22041695] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 exploits angiotensin-converting enzyme 2 (ACE2) as a receptor to invade cells. It has been reported that the UK and South African strains may have higher transmission capabilities, eventually in part due to amino acid substitutions on the SARS-CoV-2 Spike protein. The pathogenicity seems modified but is still under investigation. Here we used the experimental structure of the Spike RBD domain co-crystallized with part of the ACE2 receptor, several in silico methods and numerous experimental data reported recently to analyze the possible impacts of three amino acid replacements (Spike K417N, E484K, N501Y) with regard to ACE2 binding. We found that the N501Y replacement in this region of the interface (present in both the UK and South African strains) should be favorable for the interaction with ACE2, while the K417N and E484K substitutions (South African strain) would seem neutral or even unfavorable. It is unclear if the N501Y substitution in the South African strain could counterbalance the K417N and E484K Spike replacements with regard to ACE2 binding. Our finding suggests that the UK strain should have higher affinity toward ACE2 and therefore likely increased transmissibility and possibly pathogenicity. If indeed the South African strain has a high transmission level, this could be due to the N501Y replacement and/or to substitutions in regions located outside the direct Spike-ACE2 interface but not so much to the K417N and E484K replacements. Yet, it should be noted that amino acid changes at Spike position 484 can lead to viral escape from neutralizing antibodies. Further, these amino acid substitutions do not seem to induce major structural changes in this region of the Spike protein. This structure-function study allows us to rationalize some observations made for the UK strain but raises questions for the South African strain.
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Marot S, Calvez V, Louet M, Marcelin AG, Burrel S. Interpretation of SARS-CoV-2 replication according to RT-PCR crossing threshold value. Clin Microbiol Infect 2021; 27:1056-1057. [PMID: 33524586 PMCID: PMC7845522 DOI: 10.1016/j.cmi.2021.01.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/05/2021] [Accepted: 01/19/2021] [Indexed: 12/18/2022]
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Nguyen T, Valantin MA, Delaugerre C, Amiel C, Netzer E, L'Yavanc T, Ohayon M, Valin N, Day N, Kreplak G, Pialoux G, Calvez V, Molina JM, Marcelin AG, Todesco E. Low level of baseline resistance in recently HCV-infected men who have sex with men with high-risk behaviours. J Glob Antimicrob Resist 2021; 24:311-315. [PMID: 33540082 DOI: 10.1016/j.jgar.2021.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/11/2020] [Accepted: 01/23/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Presence of baseline hepatitis C virus (HCV) resistance-associated substitutions (RASs) can impair treatment outcome of direct-acting antivirals. We investigated the prevalence of pre-treatment HCV resistance among recently HCV-infected men who have sex with men (MSM) with high risk behaviours, either human immunodeficiency virus (HIV) co-infected or at high risk of HIV acquisition and under pre-exposure prophylaxis (PrEP). METHODS NS5A and NS3 fragments were deep sequenced on pre-treatment samples of 72 subjects using Illumina MiSeq paired-end sequencing technology. Ultra-deep sequencing data were analysed by SmartGene® platform. RASs mentioned in the literature were analysed and interpreted depending on genotype (GT) at 10% cut-off. RESULTS HCV genotyping showed 36 (50.0%) GT1a, 31 (43.1%) GT4d and 5 (6.9%) GT3a infections. Fifty-five patients (76.4%) were co-infected with HIV and 15 (20.8%) received PrEP. In GT1a viruses, NS3 RASs were found in 4/30 viruses (13.3%; S122 G/N, R155 K and I170 V) and Q80 K polymorphism was present in 14/30 viruses (46.7%). No NS3 RASs were detected in GT4d and GT3a viruses. NS5A RASs were detected in 3/36 GT1a viruses (8.3%; Q30E/R, L31 M and H58 L). NS5A subtype-specific polymorphisms L30R and T58 P were found at high frequencies in 31/31 (100%) and 16/31 (51.6%) GT4d viruses, respectively. One RAS M31 L was also observed along with the polymorphisms L30R and T58 P. No NS5A RASs were detected in GT3a viruses. CONCLUSION A low level of RASs to NS3 and NS5A inhibitors in pre-treatment samples was detected in the study population. Our findings reassure the clinical management of HCV infection in this high-risk population.
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Palich R, Veyri M, Valantin MA, Marcelin AG, Guihot A, Pourcher V, Jary A, Solas C, Makinson A, Poizot-Martin I, Costagliola D, Spano JP, Katlama C. Recurrence and Occurrence of Kaposi's Sarcoma in Patients Living With Human Immunodeficiency Virus (HIV) and on Antiretroviral Therapy, Despite Suppressed HIV Viremia. Clin Infect Dis 2021; 70:2435-2438. [PMID: 31626689 DOI: 10.1093/cid/ciz762] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/18/2019] [Indexed: 11/14/2022] Open
Abstract
In 21 cutaneous and/or visceral Kaposi's sarcoma cases, occurring in patients living with human immunodeficiency virus (HIV) who were on antiretroviral therapy with suppressed HIV viremia and high CD4 T cell counts, the efficacy of conventional chemotherapies was limited due to cumulative toxicities, comedications, and a lack of immune improvement.
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Klement E, Godefroy N, Burrel S, Kornblum D, Monsel G, Bleibtreu A, Marcelin AG, Calvez V, Caumes E, Boutolleau D, Pourcher V. The First Locally Acquired Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in a Healthcare Worker in the Paris Area. Clin Infect Dis 2020; 71:e530-e531. [PMID: 32211789 PMCID: PMC7184333 DOI: 10.1093/cid/ciaa171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Le Joncour A, Frere C, Martin-Toutain I, Gougis P, Ghillani-Dalbin P, Maalouf G, Vieira M, Marcelin AG, Salem JE, Allenbach Y, Saadoun D, Benveniste O, Cacoub P. Antiphospholipid antibodies and thrombotic events in COVID-19 patients hospitalized in medicine ward. Autoimmun Rev 2020; 20:102729. [PMID: 33321245 PMCID: PMC7834187 DOI: 10.1016/j.autrev.2020.102729] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 01/23/2023]
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Katlama C, Assoumou L, Valantin MA, Soulié C, Martinez E, Béniguel L, Bouchaud O, Raffi F, Molina JM, Fellahi S, Peytavin G, Marcelin AG, Kolta S, Capeau J, Gibowski S, Cardon F, Reynes J, Costagliola D. Dual therapy combining raltegravir with etravirine maintains a high level of viral suppression over 96 weeks in long-term experienced HIV-infected individuals over 45 years on a PI-based regimen: results from the Phase II ANRS 163 ETRAL study—authors’ response. J Antimicrob Chemother 2020; 75:3699-3700. [DOI: 10.1093/jac/dkaa341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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89
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Le Joncour A, Biard L, Vautier M, Bugaut H, Mekinian A, Maalouf G, Vieira M, Marcelin AG, Rosenzwajg M, Klatzmann D, Corvol JC, Paccoud O, Carillion A, Salem JE, Cacoub P, Boulaftali Y, Saadoun D. Neutrophil-Platelet and Monocyte-Platelet Aggregates in COVID-19 Patients. Thromb Haemost 2020; 120:1733-1735. [PMID: 33124027 PMCID: PMC7869059 DOI: 10.1055/s-0040-1718732] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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90
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Burrel S, Hausfater P, Dres M, Pourcher V, Luyt CE, Teyssou E, Soulié C, Calvez V, Marcelin AG, Boutolleau D. Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19. Int J Infect Dis 2020; 102:10-13. [PMID: 33115679 PMCID: PMC7585729 DOI: 10.1016/j.ijid.2020.10.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 02/04/2023] Open
Abstract
Objectives This study was performed during the early outbreak period of coronavirus disease 2019 (COVID-19) and the seasonal epidemics of other respiratory viral infections, in order to describe the extent of co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with other respiratory viruses. It also compared the diagnostic performances of upper respiratory tract (URT) and lower respiratory tract (LRT) samples for SARS-CoV-2 infection. Methods From 25 January to 29 March 2020, all URT and LRT samples collected from patients with suspected COVID-19 received in the virology laboratory of Pitié-Salpêtrière University Hospital (Paris, France) were simultaneously tested for SARS-CoV-2 and other respiratory viruses. Results A total of 1423 consecutive patients were tested: 677 (47.6%) males, 746 (52.4%) females, median age 50 (range, 1–103) years. Twenty-one (1.5%) patients were positive for both SARS-CoV-2 and other respiratory viruses. The detection rate of SARS-CoV-2 was significantly higher in LRT than in URT (53.6% vs. 13.4%; p < 0.0001). The analysis of paired samples from 117 (8.2%) patients showed that SARS-CoV-2 load was lower in URT than in LRT samples in 65% of cases. Conclusion The detection of other respiratory viruses in patients during this epidemic period could not rule out SARS-CoV-2 co-infection. Furthermore, LRT samples increased the accuracy of diagnosis of COVID-19.
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Martinot M, Jary A, Fafi-Kremer S, Leducq V, Delagreverie H, Garnier M, Pacanowski J, Mékinian A, Pirenne F, Tiberghien P, Calvez V, Humbrecht C, Marcelin AG, Lacombe K. Remdesivir failure with SARS-CoV-2 RNA-dependent RNA-polymerase mutation in a B-cell immunodeficient patient with protracted Covid-19. Clin Infect Dis 2020; 73:e1762-e1765. [PMID: 32986807 PMCID: PMC7543308 DOI: 10.1093/cid/ciaa1474] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Indexed: 12/31/2022] Open
Abstract
SARS-CoV-2 is a new pandemic virus for which Remdesivir is the only antiviral available. We report the occurrence of a mutation in the RdRP (D484Y) following failure of remdesivir in a 76-year-old woman with a post-rituximab B-cell immunodeficiency and persistent SARS-CoV-2 viremia. Cure was reached after supplementation with convalescent plasma.
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Malet I, Delelis O, Nguyen T, Leducq V, Abdi B, Morand-Joubert L, Calvez V, Marcelin AG. Variability of the HIV-1 3' polypurine tract (3'PPT) region and implication in integrase inhibitor resistance. J Antimicrob Chemother 2020; 74:3440-3444. [PMID: 31730161 DOI: 10.1093/jac/dkz377] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/16/2019] [Accepted: 08/01/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Integrase strand-transfer inhibitors (INSTIs) are efficient at impairing retroviral integration, which is a critical step in HIV-1 replication. To date, resistance to these compounds has been explained by mutations in the viral protein integrase, which catalyses the integration step. Recently, it has been shown that selected mutations in the 3' polypurine tract (3'PPT), a sequence involved in the reverse transcription mechanism, result in high-level resistance to these compounds. This observation was reinforced by the description of a patient who failed INSTI treatment by selecting mutations in the 3'PPT sequence. METHODS Sequences of the 3'PPT region were analysed in 30706 treatment-naive patients from the public Los Alamos database belonging to six different subtypes and, in parallel, in 107 patients failing INSTI treatment. RESULTS The analysis showed that the sequences of patients failing INSTI treatment, in the same way as those of treatment-naive patients, are very well conserved regardless of the presence or absence of resistance mutations in the integrase gene. CONCLUSIONS This study confirms that the selection of a mutation in the 3'PPT region conferring high-level resistance to INSTIs is a rare event. It would require a particular in vivo context and especially a long enough time to be selected, this exposure time being generally reduced by the rapid change of treatment in the case of virological failure. Larger-scale studies in patients with INSTI treatment failure are needed to determine whether the 3'PPT region can play an important role in vivo in INSTI resistance.
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Valantin MA, Durand L, Wirden M, Assoumou L, Caby F, Soulié C, Nguyen TTT, Tubiana R, Kirstetter M, Junot H, Marcelin AG, Peytavin G, Tilleul P, Katlama C. Antiretroviral drug reduction in highly experienced HIV-infected patients receiving a multidrug regimen: the ECOVIR study. J Antimicrob Chemother 2020; 74:2716-2722. [PMID: 31273376 DOI: 10.1093/jac/dkz255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/06/2019] [Accepted: 05/22/2019] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES In a context of life-long therapy, we asked whether it could be possible to reduce the number of antiretroviral drugs without jeopardizing viral suppression. METHODS ECOVIR was a prospective study aiming to assess whether in patients on combination ART with ≥4 antiretrovirals for ≥24 weeks and virally suppressed for ≥48 weeks, a drug-reduced (DR) regimen could be proposed. The intervention consisted of discontinuing genotypically less susceptible drugs to reach a DR regimen with ≤3 antiretrovirals. The primary endpoint was the proportion of patients maintaining viral suppression at week (W) 24. RESULTS From 89 eligible individuals for the study, a DR regimen was proposed in 86 (97%) patients, of whom 71 were switched to a DR regimen. Baseline characteristics [median (IQR)] were: age 58 (53-65) years, duration of treatment 24 (21-26) years and viral suppression 8 (6-11) years. The cumulative resistance profile showed full resistance to lamivudine/emtricitabine (91%), abacavir (74%), efavirenz/nevirapine (70%), rilpivirine (56%), darunavir (q24h/q12h) (42%/29%), lopinavir (69%), atazanavir (71%) and raltegravir (24%). The final DR regimen consisted of a two-drug or three-drug regimen in 54 patients (76%) and in 17 patients (24%), respectively. The success rate of a DR regimen at W24 was 93.9% (95% CI 84.4-97.6, Kaplan-Meier estimate). Four patients experienced virological failure (at W4, W8 and W12), all with plasma viral load (pVL) <600 copies/mL and no emergence of resistance mutations. The DR strategy allowed a monthly cost saving of 36%. CONCLUSIONS In experienced patients with high-level resistance, individualized strategies based on expert advice can offer DR regimen options with fewer drug-drug interactions and a significant economic impact while ensuring virological success.
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Katlama C, Assoumou L, Valantin MA, Soulié C, Martinez E, Béniguel L, Bouchaud O, Raffi F, Molina JM, Fellahi S, Peytavin G, Marcelin AG, Kolta S, Capeau J, Gibowski S, Cardon F, Reynes J, Costagliola D. Dual therapy combining raltegravir with etravirine maintains a high level of viral suppression over 96 weeks in long-term experienced HIV-infected individuals over 45 years on a PI-based regimen: results from the Phase II ANRS 163 ETRAL study. J Antimicrob Chemother 2020; 74:2742-2751. [PMID: 31269208 DOI: 10.1093/jac/dkz224] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Dual therapy combining integrase inhibitors and NNRTIs represents a promising regimen in ageing HIV-infected individuals with long exposure to nucleoside analogues and PIs. METHODS The ANRS 163 ETRAL trial (NCT02212379) was a 96 week, multicentre, single-arm study evaluating the efficacy and safety of raltegravir (400 mg twice daily)/etravirine (200 mg twice daily) in individuals >45 years, on a PI-containing regimen who were integrase inhibitor and etravirine naive. The primary endpoint was the proportion of participants with virological success, defined by the absence of virological failure up to week 48. Main secondary outcomes included evolution of metabolic parameters, CD4/CD8 count, bone mineral density and inflammatory markers. The study was designed to show an efficacy >90%, assuming a success rate ≥95%, with a power of 80% and a 5% type-1 error. RESULTS One hundred and sixty-five participants (median age 52 years, duration of ART 16.9 years, viral suppression 6.9 years and CD4 count 700 cells/mm3) were enrolled. By ITT analysis, viral suppression was maintained in 99.4% of participants (95% CI = 95.6%-99.9%) at week 48 and 98.7% (95% CI = 95.0%-99.7%) at week 96. Two virological failures occurred (week 24 and week 64) without emergence of integrase inhibitor resistance. Eight participants discontinued raltegravir/etravirine for adverse events, leading to a strategy success rate of 95.1% (95% CI = 90.5%-97.5%) at week 48 and 92.7% (95% CI = 87.5%-95.8%) at week 96. Over 96 weeks, lipid fractions improved (P < 0.001), CD4/CD8 ratio increased, IFNγ-induced protein 10 (IP-10) decreased (-8.1%), soluble CD14 decreased (-27%, P < 0.001) bone mineral density improved and BMI increased. CONCLUSIONS Raltegravir plus etravirine dual therapy demonstrated durable efficacy in virologically suppressed ageing patients.
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95
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Faury H, Courboulès C, Payen M, Jary A, Hausfater P, Luyt C, Dres M, Pourcher V, Abdi B, Wirden M, Calvez V, Marcelin AG, Boutolleau D, Burrel S. Medical features of COVID-19 and influenza infection: A comparative study in Paris, France. J Infect 2020; 82:e36-e39. [PMID: 32798533 PMCID: PMC7426213 DOI: 10.1016/j.jinf.2020.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/27/2022]
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96
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Castain L, Perrier M, Charpentier C, Palich R, Desire N, Wirden M, Descamps D, Sayon S, Landman R, Valantin MA, Joly V, Peytavin G, Yazdanpanah Y, Katlama C, Calvez V, Marcelin AG, Todesco E. New mechanisms of resistance in virological failure to protease inhibitors: selection of non-described protease, Gag and Gp41 mutations. J Antimicrob Chemother 2020; 74:2019-2023. [PMID: 31050739 DOI: 10.1093/jac/dkz151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/12/2019] [Accepted: 03/18/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To further characterize HIV-1 viruses of patients experiencing unexplained virological failure (VF) on PI-containing regimens, ultradeep sequencing was performed on protease, gag and gp41 genes in patients failing a first-line treatment. METHODS All naive patients initiating an antiretroviral treatment based on boosted darunavir, atazanavir or lopinavir and experiencing VF without any transmitted drug resistance mutation detected by Sanger sequencing on protease and reverse transcriptase genes were selected. Ultradeep sequencing (IlluminaTM Nextera®) was performed on protease, gag and gp41 genes in plasma before initiation of treatment and at VF to identify emergent mutations. RESULTS Among the 32 patients included in the study, emergent and previously undescribed mutations in the viral protease gene were identified in five patients at VF: 64M (1 CRF02_AG), 64M/70R with mutation 15V (2 CRF02_AG), 79A (1 CRF06_cpx) and 79A with mutation 15V (1 CRF02_AG). Two patients showed the emergence of R286K in the gag region, outside of cleavage sites (2 CRF02_AG). In the gp41 region, the V321I mutation emerged inside the cytoplasmic tail (1 subtype A and 1 subtype B). All these patients were treated with a darunavir/ritonavir-based regimen. CONCLUSIONS In some cases of VF to PIs, we observed the emergence of protease, Gag or Gp41 mutations that had not previously been associated with VF or PI resistance. These mutations should be further studied, in particular the 15V/64M/70R pattern in the protease gene identified among CRF02_AG viruses.
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97
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Cancella de Abreu M, Choquet C, Petit H, Bouzid D, Damond F, Marot S, Ferre VM, Burrel S, Boutolleau D, Houdou-Fidouh N, Marcelin AG, Descamps D, Hausfater P. SARS-CoV-2 IGM and IGG rapid serologic test for the diagnosis of COVID-19 in the emergency department. J Infect 2020; 81:816-846. [PMID: 32739490 PMCID: PMC7392071 DOI: 10.1016/j.jinf.2020.07.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 01/22/2023]
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98
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Jary A, Leducq V, Malet I, Marot S, Klement-Frutos E, Teyssou E, Soulié C, Abdi B, Wirden M, Pourcher V, Caumes E, Calvez V, Burrel S, Marcelin AG, Boutolleau D. Evolution of viral quasispecies during SARS-CoV-2 infection. Clin Microbiol Infect 2020; 26:1560.e1-1560.e4. [PMID: 32717416 PMCID: PMC7378485 DOI: 10.1016/j.cmi.2020.07.032] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/09/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022]
Abstract
Objectives Studies are needed to better understand the genomic evolution of the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe genomic diversity of SARS-CoV-2 by next-generation sequencing (NGS) in a patient with longitudinal follow-up for SARS-CoV-2 infection. Methods Sequential samples collected between January 29th and February 4th, 2020, from a patient infected by SARS-CoV-2 were used to perform amplification of two genome fragments—including genes encoding spike, envelope, membrane and nucleocapsid proteins—and NGS was carried out with Illumina® technology. Phylogenetic analysis was performed with PhyML and viral variant identification with VarScan. Results Majority consensus sequences were identical in most of the samples (5/7) and differed in one synonymous mutation from the Wuhan reference sequence. We identified 233 variants; each sample harboured in median 38 different minority variants, and only four were shared by different samples. The frequency of mutation was similar between genes and correlated with the length of the gene (r = 0.93, p = 0.0002). Most of mutations were substitution variations (n = 217, 93.1%) and about 50% had moderate or high impact on gene expression. Viral variants also differed between lower and upper respiratory tract samples collected on the same day, suggesting independent sites of replication of SARS-CoV-2. Conclusions We report for the first time minority viral populations representing up to 1% during the course of SARS-CoV-2 infection. Quasispecies were different from one day to the next, as well as between anatomical sites, suggesting that in vivo this new coronavirus appears as a complex and dynamic distributions of variants.
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Perrier M, Castain L, Regad L, Todesco E, Landman R, Visseaux B, Yazdanpanah Y, Rodriguez C, Joly V, Calvez V, Marcelin AG, Descamps D, Charpentier C. HIV-1 protease, Gag and gp41 baseline substitutions associated with virological response to a PI-based regimen. J Antimicrob Chemother 2020; 74:1679-1692. [PMID: 30768160 DOI: 10.1093/jac/dkz043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES To assess, at ART initiation, the impact of baseline substitutions in protease, Gag and gp41 regions on the virological response to a first-line PI-based regimen. PATIENTS AND METHODS One hundred and fifty-four HIV-infected ART-naive patients initiating a PI-based regimen including darunavir (n = 129) or atazanavir (n = 25) were assessed, including 36 experiencing virological failure (VF). Whole pol, gag and gp41 genes were sequenced at ART baseline by ultra-deep sequencing (UDS) using Illumina® technology. Supervised data-mining analyses were performed to identify mutations associated with virological response. Structural analyses were performed to assess the impact of mutations on protease conformation. RESULTS UDS was successful in 127, 138 and 134 samples for protease, Gag and gp41, respectively (31% subtype B and 38% CRF02_AG). Overall, T4A and S37T mutations in protease were identified as being associated with VF (P = 0.02 and P = 0.005, respectively). Among CRF02_AG sequences, I72M and E21D mutations were associated with VF (P = 0.03 for both). They all induced some conformational changes of some protease side-chain residues located near mutated residues. In Gag, mutations associated with VF were G62D, N315H and Y441S (P = 0.005, P = 0.007 and P = 0.0003, respectively). All were localized outside Gag cleavage sites (G62D, matrix; N315H, capsid; and Y441S, p1). In gp41, the I270T mutation, localized in the cytoplasmic tail, was associated with VF (P = 0.003), and the I4L mutation, in the fusion peptide, was associated with virological success (P = 0.004). CONCLUSIONS In this study, new baseline substitutions in Gag, protease and g41, potentially impacting PI-based regimen outcome, were evidenced. Phenotypic analyses are required to confirm their role in the PI-resistance mechanism.
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Jary A, Flandre P, Chabouis A, Nguyen S, Marot S, Burrel S, Boutolleau D, Calvez V, Marcelin AG, Louet M. Clinical presentation of Covid-19 in health care workers from a French University Hospital. J Infect 2020; 81:e61-e63. [PMID: 32579992 PMCID: PMC7306211 DOI: 10.1016/j.jinf.2020.06.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 01/11/2023]
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