María Francesca Cortese

Vall d'Hebron Hospital Universitari

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Co-Authors

David Tabernero

Vall d'Hebron Institut de Recerca

Ariadna Rando‐Segura

Instituto de Salud Carlos III

Marı́a Buti

Vall d'Hebron Hospital Universitari

Francisco Rodríguez‐Frias

Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas

Josep Quer

Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas

Josep Gregori

Vall d'Hebron Institut de Recerca

Mar Riveiro‐Barciela

Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas

Rafael Esteban

Vall d'Hebron Institut de Recerca

Rosario Casillas

Vall d'Hebron Hospital Universitari

Beatriz Pacín Ruiz

Vall d'Hebron Institut de Recerca

Cooperative Institutions

Instituto de Salud Carlos III

106

Vall d'Hebron Hospital Universitari

101

Universitat Autònoma de Barcelona

101

Vall d'Hebron Institut de Recerca

100

Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas

Universitat de Barcelona

Centro de Investigación Biomédica en Red

University of Rome Tor Vergata

Hospital Clínic de Barcelona

Bellvitge University Hospital

Author Statistics

Papers

Citation

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Specific mutations in the C-terminus domain of HBV surface antigen significantly correlate with low level of serum HBV-DNA in patients with chronic HBV infection

Journal of Infection (2014)

Carmen Mirabelli Matteo Surdo Formijn J. van Hemert Zhichao Lian Romina Salpini

Liver disease

10.1016/j.jinf.2014.10.015

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Citations (15)

The novel HBx mutation F30V correlates with hepatocellular carcinoma in vivo, reduces hepatitis B virus replicative efficiency and enhances anti-apoptotic activity of HBx N terminus in vitro

Clinical Microbiology and Infection (2018)

Romina Salpini Matteo Surdo María Francesca Cortese G.A. Palumbo Luca Carioti

HBx

cccDNA

10.1016/j.cmi.2018.11.017

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Citations (15)

Hepatitis B Virus Variants with Multiple Insertions and/or Deletions in the X Open Reading Frame 3′ End: Common Members of Viral Quasispecies in Chronic Hepatitis B Patients

Biomedicines (2022)

Selene García-García Andrea Caballero-Garralda David Tabernero María Francesca Cortese Josep Gregori

Deletions in the 3' end region of the hepatitis B virus (HBV) X open reading frame (HBX) may affect the core promoter (Cp) and have been frequently associated with hepatocellular carcinoma (HCC). The aim of this study was to investigate the presence of variants with deletions and/or insertions (Indels) in this region in the quasispecies of 50 chronic hepatitis B (CHB) patients without HCC. We identified 103 different Indels in 47 (94%) patients, in a median of 3.4% of their reads (IQR, 1.3-8.4%), and 25% (IQR, 13.1-40.7%) of unique sequences identified in each quasispecies (haplotypes). Of those Indels, 101 (98.1%) caused 44 different altered stop codons, the most commonly observed were at positions 128, 129, 135, and 362 (putative position). Moreover, 39 (37.9%) Indels altered the TATA-like box (TA) sequences of Cp; the most commonly observed caused TA2 + TA3 fusion, creating a new putative canonical TATA box. Four (8%) patients developed negative clinical outcomes after a median follow-up of 9.4 (8.7-12) years. In conclusion, we observed variants with Indels in the HBX 3' end in the vast majority of our CHB patients, some of them encoding alternative versions of HBx with potential functional roles, and/or alterations in the regulation of transcription.

Viral quasispecies

HBx

Indel

ORFS

10.3390/biomedicines10051194

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Citations (3)

Next-Generation Sequencing for Confronting Virus Pandemics

Viruses (2022)

Josep Quer Sergi Colomer-Castell Carolina Campos Cristina Andrés María Piñana

Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission.

Pandemic

Identification

Human virome

10.3390/v14030600

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Citations (44)

Host-dependent editing of SARS-CoV-2 in COVID-19 patients

Figshare (2021)

Josep Gregori María Francesca Cortese María Piñana Carolina Campos Damir García‐Cehic

A common trait among RNA viruses is their high capability to acquire genetic variability due to viral and host mechanisms. Next-generation sequencing (NGS) analysis enables the deep study of the viral quasispecies in samples from infected individuals. In this study, the viral quasispecies complexity and single nucleotide polymorphisms of the SARS-CoV-2 spike gene of coronavirus disease 2019 (COVID-19) patients with mild or severe disease were investigated using next-generation sequencing (Illumina platform). SARS-CoV-2 spike variability was higher in patients with long-lasting infection. Most substitutions found were present at frequencies lower than 1%, and had an A → G or T → C pattern, consistent with variants caused by adenosine deaminase acting on RNA-1 (ADAR1). ADAR1 affected a small fraction of replicating genomes, but produced multiple, mainly non-synonymous mutations. ADAR1 editing during replication rather than the RNA-dependent RNA polymerase (nsp12) was the predominant mechanism generating SARS-CoV-2 genetic variability. However, the mutations produced are not fixed in the infected human population, suggesting that ADAR1 may have an antiviral role, whereas nsp12-induced mutations occurring in patients with high viremia and persistent infection are the main source of new SARS-CoV-2 variants.

2019-20 coronavirus outbreak

Sars virus

10.6084/m9.figshare.16571453

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Citations (0)

SAT-381 Low diversity of the TCRbeta repertoire in patients with chronic hepatitis D

Journal of Hepatology (2024)

María Francesca Cortese Adriana Palom Beatriz Pacín Ruiz Francesc Rudilla Emma Enrich Randé

10.1016/s0168-8278(24)02085-3

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Citations (0)

Characterization of hepatitis B virus X gene quasispecies complexity in mono-infection and hepatitis delta virus superinfection

World Journal of Gastroenterology (2019)

Cristina Godoy David Tabernero Sara Sopena Josep Gregori María Francesca Cortese

The WJG is dedicated to become an influential and prestigious journal in gastroenterology and hepatology, to promote the development of above disciplines, and to improve the diagnostic and therapeutic skill and expertise of clinicians.

Viral quasispecies

HBx

Hepatitis D virus

Superinfection

HBeAg

Hepatitis B

10.3748/wjg.v25.i13.1566

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Citations (8)

Cross-sectional evaluation of circulating hepatitis B virus RNA and DNA: Different quasispecies?

World Journal of Gastroenterology (2021)

Selene García-García María Francesca Cortese David Tabernero Josep Gregori Marta Vila

Different forms of pregenomic and other hepatitis B virus (HBV) RNA have been detected in patients' sera. These circulating HBV-RNAs may be useful for monitoring covalently closed circular DNA activity, and predicting hepatitis B e-antigen seroconversion or viral rebound after nucleos(t)ide analog cessation. Data on serum HBV-RNA quasispecies, however, is scarce. It is therefore important to develop methodologies to thoroughly analyze this quasispecies, ensuring the elimination of any residual HBV-DNA. Studying circulating HBV-RNA quasispecies may facilitate achieving functional cure of HBV infection.To establish a next-generation sequencing (NGS) methodology for analyzing serum HBV-RNA and comparing it with DNA quasispecies.Thirteen untreated chronic hepatitis B patients, showing different HBV-genotypes and degrees of severity of liver disease were enrolled in the study and a serum sample with HBV-DNA > 5 Log10 IU/mL and HBV-RNA > 4 Log10 copies/mL was taken from each patient. HBV-RNA was treated with DNAse I to remove any residual DNA, and the region between nucleotides (nt) 1255-1611 was amplified using a 3-nested polymerase chain reaction protocol, and analyzed with NGS. Variability/conservation and complexity was compared between HBV-DNA and RNA quasispecies.No HBV-DNA contamination was detected in cDNA samples from HBV-RNA quasispecies. HBV quasispecies complexity showed heterogeneous behavior among patients. The Rare Haplotype Load at 1% was greater in DNA than in RNA quasispecies, with no statistically significant differences (P = 0.1641). Regarding conservation, information content was equal in RNA and DNA quasispecies in most nt positions [218/357 (61.06%)]. In 102 of the remaining 139 (73.38%), HBV-RNA showed slightly higher variability. Sliding window analysis identified 4 hyper-conserved sequence fragments in each quasispecies, 3 of them coincided between the 2 quasispecies: nts 1258-1286, 1545-1573 and 1575-1604. The 2 hyper-variable sequence fragments also coincided: nts 1311-1344 and 1461-1485. Sequences between nts 1519-1543 and 1559-1587 were only hyper-conserved in HBV-DNA and RNA, respectively.Our methodology allowed analyzing HBV-RNA quasispecies complexity and conservation without interference from HBV-DNA. Thanks to this, we have been able to compare both quasispecies in the present study.

Viral quasispecies

Hepatitis B

10.3748/wjg.v27.i41.7144

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Citations (2)

Comparative replication capacity of raltegravir-resistant strains and antiviral activity of the new-generation integrase inhibitor dolutegravir in human primary macrophages and lymphocytes

Journal of Antimicrobial Chemotherapy (2014)

Michela Pollicita Matteo Surdo F. Di Santo María Francesca Cortese Lavinia Fabeni

ObjectivesTo evaluate the replication capacity and phenotypic susceptibility to dolutegravir and raltegravir of wild-type and raltegravir-resistant HIV-1 strains in several cellular systems.

Dolutegravir

Raltegravir

Integrase inhibitor

10.1093/jac/dku144

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Citations (24)

Silencing HBV expression using LNA gapmers: preliminary data of a new promising strategy

Journal of Hepatology (2020)

María Francesca Cortese Rosario Casillas Ester García-Pras Mireia García‐López Rosa López-Martínez

10.1016/s0168-8278(20)32190-5

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Citations (0)