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Mazzotta V, Mazzaferri F, Lanini S, Mirandola M, Cozzi Lepri A, Vergori A, Savoldi A, Santoro A, Maccarrone G, Mastrorosa I, Simonetti O, Zottis FD, Nicastri E, Rosini G, Rovigo L, Tavernaro L, Sarmati L, Tascini C, Girardi E, Cattelan AM, Antinori A, Tacconelli E. Pooled analysis of the MANTICO2 and MONET randomized controlled trials comparing drug efficacy for early treatment of COVID-19 during Omicron waves. J Infect 2024; 89:106294. [PMID: 39343244 DOI: 10.1016/j.jinf.2024.106294] [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: 08/08/2024] [Accepted: 09/23/2024] [Indexed: 10/01/2024]
Abstract
BACKGROUND The clinical effectiveness of early therapies for mild-to-moderate COVID-19, comparing antivirals and monoclonal antibodies (mAbs) during the Omicron era, has not been conclusively assessed through a post-approval comparative trial. We present a pooled analysis of two randomized clinical trials conducted during Omicron waves. METHODS The MANTICO2/MONET trial is a pooled analysis of two multicentric, independent, phase-4, three-arm, superiority, randomized, open-label trials. Nonhospitalized patients with early mild-to-moderate COVID-19 (≤5 days after symptoms' onset) and at least one risk factor for disease progression were randomized 1:1:1 to receive 500 mg of intravenous sotrovimab (SOT) or 600 mg of intramuscular tixagevimab/cilgavimab (TGM/CGM) or oral 5-days course of nirmatrelvir/ritonavir (NMV/r) 300/100 mg BID. Primary outcome was COVID-19-related hospitalization or death within 29 days after randomization. Fisher's exact test for pooled data and incidence of failure was reported as overall and by arm with respective 95% CI. Pairwise comparisons across the arms were conducted using unadjusted exact logistic regression. An analysis by means of a doubly robust marginal model using augmented inverse probability weighting (AIPW) was also conducted to estimate the potential outcomes (Pom) in each treatment group and their difference by the average treatment effect (ATE). Analysis of symptom persistence within 30 days after randomization was performed using a 2-level hierarchical mixed-effects logistic model with a random intercept at the patient's level. Point estimates and 95% confidence intervals were adjusted for age and sex and calculated using ANOVA-like methods for the mixed effects logistic model. These trials are registered with the European Clinical Trials Database, EudraCT2021-002612-31 (MANTICO2) and EudraCT2021-004188-28 (MONET) and ClinicalTrials.gov, NCT05321394 (MANTICO2). FINDINGS Between March 2022 and February 2023, 991 patients (SOT = 332, TGM/CGM = 327, NMV/r = 332) were enrolled in 15 Italian centers. The overall mean age was 66 years; 482 participants (48.80%) were male, and 856 were vaccinated with at least a primary course (86%). Among the 8/991 hospitalizations observed, one resulted in death. The overall estimate of failure was 0.81% (95%CI; 0.35-1.58%). The odds ratio (OR) for the primary outcome in the NMV/r arm compared to the TGM/CGM and SOT arms was 8.41 (95% CI 1.21 to infinity; p = 0.015) and 2.42 (95% CI 0.19 to infinity; p = 0.499), respectively. No significant difference was observed between SOT and TGM/CGM (OR 0.32; 95% CI 0.032-1.83; p = 0.174). Results were similar when we applied the marginal weighted model accounting for potential residual confounding bias. There was no evidence for a difference in the prevalence of symptoms between treatment groups, except for cough, which was higher in the SOT group compared to the other two groups at the 21-day follow-up (P = 0.039) and a higher prevalence of nausea at the 7-day follow-up in the NMV/r group compared to the mAbs group (p = 0.036). INTERPRETATION NMV/r was superior to TGM/CGM in reducing hospital admission or death in clinically vulnerable patients with SARS-CoV-2 infection treated within 5 days of symptoms' onset. No significant difference in symptom prevalence over time across the arms was found.
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Affiliation(s)
- Valentina Mazzotta
- Clinical Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy; PhD Course in Microbiology, Immunology, Infectious Diseases, and Transplants (MIMIT), University of Rome Tor Vergata, Rome, Italy
| | - Fulvia Mazzaferri
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Simone Lanini
- Infectious Diseases Division, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy.
| | - Massimo Mirandola
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Alessandro Cozzi Lepri
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation (CREME), Institute for Global Health, UCL, London, UK
| | - Alessandra Vergori
- Clinical Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Alessia Savoldi
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Andrea Santoro
- Department of Health Sciences, San Paolo University Hospital, Milan, Italy
| | - Gaia Maccarrone
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Ilaria Mastrorosa
- Clinical Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Omar Simonetti
- Infectious Diseases Division, Azienda Sanitaria Universitaria Giuliano Isontina, Trieste, Italy
| | - Federico De Zottis
- Clinical Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Emanuele Nicastri
- Clinical Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giulia Rosini
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Laura Rovigo
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Lorenzo Tavernaro
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Loredana Sarmati
- Infectious Diseases Unit, Tor Vergata University Hospital, Rome, Italy
| | - Carlo Tascini
- Infectious Diseases Division, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Andrea Antinori
- Clinical Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Evelina Tacconelli
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
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Gruber CEM, Tucci FG, Giombini E, Mazzotta V, Spezia PG, Rueca M, Mastrorosa I, Fabeni L, Berno G, Butera O, Rosati S, Specchiarello E, Carletti F, Focosi D, Nicastri E, Girardi E, Antinori A, Maggi F. Molnupiravir increases SARS-CoV-2 genome diversity and complexity: A case-control cohort study. J Med Virol 2024; 96:e29642. [PMID: 38708812 DOI: 10.1002/jmv.29642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
Molnupiravir, an oral direct-acting antiviral effective in vitro against SARS-CoV-2, has been largely employed during the COVID-19 pandemic, since December 2021. After marketing and widespread usage, a progressive increase in SARS-CoV-2 lineages characterized by a higher transition/transversion ratio, a characteristic signature of molnupiravir action, appeared in the Global Initiative on Sharing All Influenza Data (GISAID) and International Nucleotide Sequence Database Collaboration (INSDC) databases. Here, we assessed the drug effects by SARS-CoV-2 whole-genome sequencing on 38 molnupiravir-treated persistently positive COVID-19 outpatients tested before and after treatment. Seventeen tixagevimab/cilgavimab-treated outpatients served as controls. Mutational analyses confirmed that SARS-CoV-2 exhibits an increased transition/transversion ratio seven days after initiation of molnupiravir. Moreover we observed an increased G->A ratio compared to controls, which was not related to apolipoprotein B mRNAediting enzyme, catalytic polypeptide-like (APOBEC) activity. In addition, we demonstrated for the first time an increased diversity and complexity of the viral quasispecies.
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Affiliation(s)
| | | | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Valentina Mazzotta
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Pietro Giorgio Spezia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Ilaria Mastrorosa
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Ornella Butera
- Laboratory of Microbiology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Silvia Rosati
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Eliana Specchiarello
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Fabrizio Carletti
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Emanuele Nicastri
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | - Andrea Antinori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
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3
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Vita S, Giombini E, De Marco P, Rueca M, Gruber CEM, Beccacece A, Scorzolini L, Mazzotta V, Pinnetti C, Caputi P, Focosi D, Girardi E, Antinori A, Maggi F, D'Abramo A, Nicastri E. Antiviral and Monoclonal Antibody Combination Therapy in Haematological Patients in the Omicron Era. Mediterr J Hematol Infect Dis 2024; 16:e2024043. [PMID: 38882452 PMCID: PMC11178048 DOI: 10.4084/mjhid.2024.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/18/2024] [Indexed: 06/18/2024] Open
Abstract
Abstract: Im We describe here a single-center case series of 27 IC COVID-19 inpatients (mostly with haematological disorders) treated with a combined therapy based on tixagevimab/cilgavimab (T/C) plus small-molecule antivirals (AV), between April 1 2022 and November 30 2022.
Keywords: immunocompromised; SARS-CoV-2 infection; monoclonal antibodies; antivirals; persistent infection; viral evolution
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Affiliation(s)
- Serena Vita
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Emanuela Giombini
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Patrizia De Marco
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | | | - Alessia Beccacece
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Laura Scorzolini
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Valentina Mazzotta
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Carmen Pinnetti
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Priscilla Caputi
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Enrico Girardi
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Andrea Antinori
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Fabrizio Maggi
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Alessandra D'Abramo
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
| | - Emanuele Nicastri
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS-Rome Italy
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Rueca M, Berno G, Agresta A, Spaziante M, Gruber CEM, Fabeni L, Giombini E, Butera O, Barca A, Scognamiglio P, Girardi E, Maggi F, Valli MB, Vairo F. Genomic and Epidemiologic Surveillance of SARS-CoV-2 in the Pandemic Period: Sequencing Network of the Lazio Region, Italy. Viruses 2023; 15:2192. [PMID: 38005872 PMCID: PMC10674723 DOI: 10.3390/v15112192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Since the beginning of the COVID-19 pandemic, large-scale genomic sequencing has immediately pointed out that SARS-CoV-2 has rapidly mutated during the course of the pandemic, resulting in the emergence of variants with a public health impact. In this context, strictly monitoring the circulating strains via NGS has proven to be crucial for the early identification of new emerging variants and the study of the genomic evolution and transmission of SARS-CoV-2. Following national and international guidelines, the Lazio region has created a sequencing laboratory network (WGSnet-Lazio) that works in synergy with the reference center for epidemiological surveillance (SERESMI) to monitor the circulation of SARS-CoV-2. Sequencing was carried out with the aims of characterizing outbreak transmission dynamics, performing the genomic analysis of viruses infecting specific categories of patients (i.e., immune-depressed, travelers, and people with severe symptoms) and randomly monitoring variant circulation. Here we report data emerging from sequencing activities carried out by WGSnet-Lazio (from February 2020 to October 2022) linked with epidemiological data to correlate the circulation of variants with the clinical and demographic characteristics of patients. The model of the sequencing network developed in the Lazio region proved to be a useful tool for SARS-CoV-2 surveillance and to support public health measures for epidemic containment.
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Affiliation(s)
- Martina Rueca
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Giulia Berno
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Alessandro Agresta
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Martina Spaziante
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Cesare Ernesto Maria Gruber
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Lavinia Fabeni
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Emanuela Giombini
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Ornella Butera
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Alessandra Barca
- Direzione Regionale Salute E Integrazione Sociosanitaria, Area Promozione Della Salute E Prevenzione—Regione Lazio, 00145 Rome, Italy;
| | - Paola Scognamiglio
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
- Direzione Regionale Salute E Integrazione Sociosanitaria, Area Promozione Della Salute E Prevenzione—Regione Lazio, 00145 Rome, Italy;
| | - Enrico Girardi
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Fabrizio Maggi
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Maria Beatrice Valli
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
| | - Francesco Vairo
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, IRCCS, 00149 Rome, Italy; (M.R.); (G.B.); (A.A.); (M.S.); (L.F.); (E.G.); (O.B.); (P.S.); (E.G.); (F.M.); (M.B.V.); (F.V.)
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5
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Gruber CEM, Tucci FG, Rueca M, Mazzotta V, Gramigna G, Vergori A, Fabeni L, Berno G, Giombini E, Butera O, Focosi D, Prandi IG, Chillemi G, Nicastri E, Vaia F, Girardi E, Antinori A, Maggi F. Treatment-Emergent Cilgavimab Resistance Was Uncommon in Vaccinated Omicron BA.4/5 Outpatients. Biomolecules 2023; 13:1538. [PMID: 37892220 PMCID: PMC10605390 DOI: 10.3390/biom13101538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/03/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Mutations in the SARS-CoV-2 Spike glycoprotein can affect monoclonal antibody efficacy. Recent findings report the occurrence of resistant mutations in immunocompromised patients after tixagevimab/cilgavimab treatment. More recently, the Food and Drug Agency revoked the authorization for tixagevimab/cilgavimab, while this monoclonal antibody cocktail is currently recommended by the European Medical Agency. We retrospectively reviewed 22 immunocompetent patients at high risk for disease progression who received intramuscular tixagevimab/cilgavimab as early COVID-19 treatment and presented a prolonged high viral load. Complete SARS-CoV-2 genome sequences were obtained for a deep investigation of mutation frequencies in Spike protein before and during treatment. At seven days, only one patient showed evidence of treatment-emergent cilgavimab resistance. Quasispecies analysis revealed two different deletions on the Spike protein (S:del138-144 or S:del141-145) in combination with the resistance S:K444N mutation. The structural and dynamic impact of the two quasispecies was characterized by using molecular dynamics simulations, showing the conservation of the principal functional movements in the mutated systems and their capabilities to alter the structure and dynamics of the RBD, responsible for the interaction with the ACE2 human receptor. Our study underlines the importance of prompting an early virological investigation to prevent drug resistance or clinical failures in immunocompetent patients.
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Affiliation(s)
- Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Fabio Giovanni Tucci
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Valentina Mazzotta
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Giulia Gramigna
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Alessandra Vergori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Ornella Butera
- Laboratory of Microbiology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy;
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy;
| | - Ingrid Guarnetti Prandi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c, 01100 Viterbo, Italy; (I.G.P.); (G.C.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c, 01100 Viterbo, Italy; (I.G.P.); (G.C.)
| | - Emanuele Nicastri
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Francesco Vaia
- General Direction, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy;
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy;
| | - Andrea Antinori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
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6
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Berno G, Fabeni L, Matusali G, Gruber CEM, Rueca M, Giombini E, Garbuglia AR. SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods. Pathogens 2022; 11:1058. [PMID: 36145490 PMCID: PMC9504725 DOI: 10.3390/pathogens11091058] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Since the beginning of COVID-19 pandemic the Real Time sharing of genome sequences of circulating virus supported the diagnostics and surveillance of SARS-CoV-2 and its transmission dynamics. SARS-CoV-2 straightaway showed its tendency to mutate and adapt to the host, culminating in the emergence of variants; so it immediately became of crucial importance to be able to detect them quickly but also to be able to monitor in depth the changes on the whole genome to early identify the new possibly emerging variants. In this scenario, this manuscript aims to provide an overview of the existing methods for the identification of SARS-CoV-2 variants (from rapid method based on identification of one or more specific mutations to Whole Genome sequencing approach-WGS), taking into account limitations, advantages and applications of them in the field of diagnosis and surveillance of SARS-CoV-2.
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Affiliation(s)
| | | | | | | | | | | | - Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy
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7
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Molecular Characterization of Whole-Genome SARS-CoV-2 from the First Suspected Cases of the XE Variant in the Lazio Region, Italy. Diagnostics (Basel) 2022; 12:diagnostics12092219. [PMID: 36140622 PMCID: PMC9497488 DOI: 10.3390/diagnostics12092219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/02/2022] [Accepted: 09/10/2022] [Indexed: 11/30/2022] Open
Abstract
We report two cases of SARS-CoV-2 recombinant variant XE detected in nasopharyngeal swabs (NPS) of hospitalized patients with no evident epidemiological link in Lazio, Central Italy. Whole-Genome Sequencing (WGS) performed on an Ion Torrent GSS5 platform according to Italian flash surveys showed genomes corresponding to the PANGOLIN unclassified lineage and the Nextclade XE clade. Further analyses were then carried out to investigate more deeply the genetic characteristics of these XE-like sequences. When phylogenetic trees, by using IQ-TREE, were built splitting the genome into two regions according to the putative XE recombination site, the upstream and downstream regions were seen to be clustered near BA.1 and BA.2 sequences, respectively. However, our XE-like sequences clustered separately, with a significant bootstrap, from the classified European and Italian XE strains, although the recombination site between BA.1 and BA.2 was identified at the nucleotide site 11556 by RDP4 software, consistent with the putative XE breakpoint. These findings show the risk of the introduction of novel recombinant variants of SARS-CoV-2 and the existence of XE-like strains, phylogenetically separated, that could make their exact taxonomy difficult. It follows the need for continued SARS-CoV-2 surveillance by WGS.
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8
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Mugnier N, Griffon A, Simon B, Rambaud M, Regue H, Bal A, Destras G, Tournoud M, Jaillard M, Betraoui A, Santiago E, Cheynet V, Vignola A, Ligeon V, Josset L, Brengel-Pesce K. Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches. Viruses 2022; 14:1674. [PMID: 36016297 PMCID: PMC9416160 DOI: 10.3390/v14081674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/26/2022] Open
Abstract
Whole-genome sequencing has become an essential tool for real-time genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide. The handling of raw next-generation sequencing (NGS) data is a major challenge for sequencing laboratories. We developed an easy-to-use web-based application (EPISEQ SARS-CoV-2) to analyse SARS-CoV-2 NGS data generated on common sequencing platforms using a variety of commercially available reagents. This application performs in one click a quality check, a reference-based genome assembly, and the analysis of the generated consensus sequence as to coverage of the reference genome, mutation screening and variant identification according to the up-to-date Nextstrain clade and Pango lineage. In this study, we validated the EPISEQ SARS-CoV-2 pipeline against a reference pipeline and compared the performance of NGS data generated by different sequencing protocols using EPISEQ SARS-CoV-2. We showed a strong agreement in SARS-CoV-2 clade and lineage identification (>99%) and in spike mutation detection (>99%) between EPISEQ SARS-CoV-2 and the reference pipeline. The comparison of several sequencing approaches using EPISEQ SARS-CoV-2 revealed 100% concordance in clade and lineage classification. It also uncovered reagent-related sequencing issues with a potential impact on SARS-CoV-2 mutation reporting. Altogether, EPISEQ SARS-CoV-2 allows an easy, rapid and reliable analysis of raw NGS data to support the sequencing efforts of laboratories with limited bioinformatics capacity and those willing to accelerate genomic surveillance of SARS-CoV-2.
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Affiliation(s)
- Nathalie Mugnier
- BioMérieux SA, 69280 Marcy-l’Étoile, France; (N.M.); (A.G.); (M.R.); (M.T.); (M.J.); (A.B.); (E.S.); (V.C.); (V.L.)
| | - Aurélien Griffon
- BioMérieux SA, 69280 Marcy-l’Étoile, France; (N.M.); (A.G.); (M.R.); (M.T.); (M.J.); (A.B.); (E.S.); (V.C.); (V.L.)
| | - Bruno Simon
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France; (B.S.); (H.R.); (A.B.); (G.D.); (L.J.)
| | - Maxence Rambaud
- BioMérieux SA, 69280 Marcy-l’Étoile, France; (N.M.); (A.G.); (M.R.); (M.T.); (M.J.); (A.B.); (E.S.); (V.C.); (V.L.)
| | - Hadrien Regue
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France; (B.S.); (H.R.); (A.B.); (G.D.); (L.J.)
| | - Antonin Bal
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France; (B.S.); (H.R.); (A.B.); (G.D.); (L.J.)
| | - Gregory Destras
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France; (B.S.); (H.R.); (A.B.); (G.D.); (L.J.)
| | - Maud Tournoud
- BioMérieux SA, 69280 Marcy-l’Étoile, France; (N.M.); (A.G.); (M.R.); (M.T.); (M.J.); (A.B.); (E.S.); (V.C.); (V.L.)
| | - Magali Jaillard
- BioMérieux SA, 69280 Marcy-l’Étoile, France; (N.M.); (A.G.); (M.R.); (M.T.); (M.J.); (A.B.); (E.S.); (V.C.); (V.L.)
| | - Abel Betraoui
- BioMérieux SA, 69280 Marcy-l’Étoile, France; (N.M.); (A.G.); (M.R.); (M.T.); (M.J.); (A.B.); (E.S.); (V.C.); (V.L.)
| | - Emmanuelle Santiago
- BioMérieux SA, 69280 Marcy-l’Étoile, France; (N.M.); (A.G.); (M.R.); (M.T.); (M.J.); (A.B.); (E.S.); (V.C.); (V.L.)
| | - Valérie Cheynet
- BioMérieux SA, 69280 Marcy-l’Étoile, France; (N.M.); (A.G.); (M.R.); (M.T.); (M.J.); (A.B.); (E.S.); (V.C.); (V.L.)
- Joint Research Unit Hospices Civils de Lyon-bioMerieux, Centre Hospitalier Lyon Sud, 69310 Pierre-Benite, France
| | | | - Véronique Ligeon
- BioMérieux SA, 69280 Marcy-l’Étoile, France; (N.M.); (A.G.); (M.R.); (M.T.); (M.J.); (A.B.); (E.S.); (V.C.); (V.L.)
| | - Laurence Josset
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France; (B.S.); (H.R.); (A.B.); (G.D.); (L.J.)
| | - Karen Brengel-Pesce
- BioMérieux SA, 69280 Marcy-l’Étoile, France; (N.M.); (A.G.); (M.R.); (M.T.); (M.J.); (A.B.); (E.S.); (V.C.); (V.L.)
- Joint Research Unit Hospices Civils de Lyon-bioMerieux, Centre Hospitalier Lyon Sud, 69310 Pierre-Benite, France
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