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Article: HIV-1 RNA monitoring with a dual-target diagnostic assay: A case report.

Sberna, Giuseppe / Gagliardini, Roberta / Rozera, Gabriella / Forbici, Federica / Cicalini, Stefania / Antinori, Andrea / Maggi, Fabrizio / Amendola, Alessandra

Heliyon

2024 Volume 10, Issue 9, Page(s) e29842

Abstract: In a restricted subset of people living with HIV-1 (PLWH) on antiretroviral therapy (ART) with persistent suppressed viral load (i.e., ...

Abstract	In a restricted subset of people living with HIV-1 (PLWH) on antiretroviral therapy (ART) with persistent suppressed viral load (i.e.,
Language	English
Publishing date	2024-04-19
Publishing country	England
Document type	Case Reports
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e29842
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Article ; Online: Partial N-gene target failure in the Seegene Allplex SARS-CoV-2 Master Assay as a proxy of SARS-CoV-2 BA.2.86.

Valli, Maria Beatrice / Schiavone, Maria Letizia / Rueca, Martina / Berno, Giulia / Spezia, Pietro Giorgio / Gruber, Cesare Ernesto Maria / Forbici, Federica / Fabeni, Lavinia / Focosi, Daniele / Girardi, Enrico / Meledandri, Marcello / Maggi, Fabrizio

Microbiology spectrum

2024 , Page(s) e0017924

Language	English
Publishing date	2024-04-22
Publishing country	United States
Document type	Letter
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.00179-24
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Article ; Online: Evaluation of integrase resistance in individuals who failed a regimen containing dolutegravir in French and Italian clinical settings.

Armenia, Daniele / Santoro, Maria M / Charpentier, Charlotte / Bertoli, Ada / Forbici, Federica / Calvez, Vincent / Descamps, Diane / Ceccherini-Silberstein, Francesca / Marcelin, Anne-Genevieve / Flandre, Philippe

The Journal of antimicrobial chemotherapy

2023 Volume 78, Issue 6, Page(s) 1415–1422

Abstract: Background: This work aims to evaluate integrase resistance and its predictors in HIV-1 infected combined antiretroviral therapy (cART) experienced individuals failing a dolutegravir-based regimen.: Methods: Major resistance mutations (MRM) and ... ...

Abstract	Background: This work aims to evaluate integrase resistance and its predictors in HIV-1 infected combined antiretroviral therapy (cART) experienced individuals failing a dolutegravir-based regimen. Methods: Major resistance mutations (MRM) and genotypic susceptibility score (GSS) of dolutegravir companion drugs were evaluated on plasma genotypic resistance test (GRT) performed at dolutegravir failure. Logistic regression was used to evaluate factors associated to the risk of integrase strand-transfer inhibitors (INSTI)-resistance at dolutegravir failure. Results: We retrospectively analysed 467 individuals. At failure GRT, individuals had been under dolutegravir for a median (IQR) time of 11 (5-20) months; around half of them had never been exposed to INSTI (52%) and 10.7% were at first-line regimen. Fifty-eight (12.4%) individuals showed ≥1 INSTI MRM. Among them, people INSTI-exposed showed significantly higher prevalence of INSTI resistance compared to those who were INSTI naïve [46 (21.2%) versus 9 (3.9%), P < 0.001].N155H was the most prevalent MRM (5.4%), followed by G140S (4.5%) and Q148H (4.3%). These MRM were more probably present in INSTI-experienced individuals compared to those INSTI naïve. Despite failure, 89.5% of individuals harboured viral strains fully susceptible to dolutegravir and bictegravir and 85.0% to all INSTI. No INSTI exposure before receiving dolutegravir [OR: 0.35 (0.16-0.78), P < 0.010] and a GSS for companion drugs ≥2 (OR: 0.09 [0.04-0.23], P < 0.001) were negatively associated with INSTI resistance at failure. Conclusions: In a large set of individuals failing dolutegravir in real-life, INSTI resistance was low and mainly related to previous first-generation INSTI exposure. Surveillance of integrase resistance remains crucial to preserve efficacy of INSTI class in the future.
MeSH term(s)	Humans ; HIV Infections/drug therapy ; HIV Infections/epidemiology ; Retrospective Studies ; Drug Resistance, Viral ; Heterocyclic Compounds, 3-Ring/therapeutic use ; Heterocyclic Compounds, 3-Ring/pharmacology ; Pyridones/therapeutic use ; Mutation ; HIV Integrase/genetics ; Italy ; HIV Integrase Inhibitors/pharmacology ; HIV Integrase Inhibitors/therapeutic use
Chemical Substances	dolutegravir (DKO1W9H7M1) ; Heterocyclic Compounds, 3-Ring ; Pyridones ; HIV Integrase (EC 2.7.7.-) ; HIV Integrase Inhibitors
Language	English
Publishing date	2023-05-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dkad101
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Article ; Online: Analysis of HIV quasispecies and virological outcome of an HIV D+/R+ kidney–liver transplantation

Rozera, Gabriella / Visco-Comandini, Ubaldo / Giombini, Emanuela / Santini, Francesco / Forbici, Federica / Berno, Giulia / Gruber, Cesare / De Paolis, Paolo / Colonnelli, Roberto / D’Offizi, Gianpiero / Ettorre, Giuseppe Maria / Grossi, Paolo / Capobianchi, Maria Rosaria / Ippolito, Giuseppe / Abbate, Isabella

Virol J. 2022 Dec., v. 19, no. 1 p.4-4

2022

Abstract: INTRODUCTION: Transplantation among HIV positive patients may be a valuable therapeutic intervention. This study involves an HIV D+/R+ kidney–liver transplantation, where PBMC-associated HIV quasispecies were analyzed in donor and transplant recipients ( ... ...

Abstract	INTRODUCTION: Transplantation among HIV positive patients may be a valuable therapeutic intervention. This study involves an HIV D+/R+ kidney–liver transplantation, where PBMC-associated HIV quasispecies were analyzed in donor and transplant recipients (TR) prior to transplantation and thereafter, together with standard viral monitoring. METHODS: The donor was a 54 year of age HIV infected woman: kidney and liver recipients were two HIV infected men, aged 49 and 61. HIV quasispecies in PBMC was analyzed by ultra-deep sequencing of V3 env region. During TR follow-up, plasma HIV-1 RNA, HIV-1 DNA in PBMC, analysis of proviral integration sites and drug-resistance genotyping were performed. Other virological and immunological monitoring included CMV and EBV DNA quantification in blood and CD4 T cell counts. RESULTS: Donor and TR were all ART-HIV suppressed at transplantation. Thereafter, TR maintained a nearly suppressed HIV-1 viremia, but HIV-1 RNA blips and the increase of proviral integration sites in PBMC attested some residual HIV replication. A transient peak in HIV-1 DNA occurred in the liver recipient. No major changes of drug-resistance genotype were detected after transplantation. CMV and EBV transient reactivations were observed only in the kidney recipient, but did not require specific treatment. CD4 counts remained stable. No intermixed quasispecies between donor and TR was observed at transplantation or thereafter. Despite signs of viral evolution in TR, HIV genetic heterogeneity did not increase over the course of the months of follow up. CONCLUSIONS: No evidence of HIV superinfection was observed in the donor nor in the recipients. The immunosuppressive treatment administrated to TR did not result in clinical relevant viral reactivations.
Keywords	CD4-positive T-lymphocytes ; DNA ; RNA ; drug resistance ; evolution ; genetic heterogeneity ; genotype ; genotyping ; immunosuppression ; kidneys ; liver ; superinfection ; therapeutics ; viremia ; women
Language	English
Dates of publication	2022-12
Size	p. 4.
Publishing place	BioMed Central
Document type	Article ; Online
ZDB-ID	2160640-7
ISSN	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-021-01730-w
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Article: Evaluation of HIV-1 integrase variability by combining computational and probabilistic approaches

Vergni, Davide / Santoni, Daniele / Bouba, Yagai / Lemme, Saverio / Fabeni, Lavinia / Carioti, Luca / Bertoli, Ada / Gennari, William / Forbici, Federica / Perno, Carlo Federico / Gagliardini, Roberta / Ceccherini-Silberstein, Francesca / Santoro, Maria Mercedes

Infection, genetics, and evolution. 2022 July, v. 101

2022

Abstract: This study aimed at updating previous data on HIV-1 integrase variability, by using effective bioinformatics methods combining different statistical instruments from simple entropy and mutation rate to more specific approaches such as Hellinger distance. ...

Institution	on behalf of the HIV drug-resistance group
Abstract	This study aimed at updating previous data on HIV-1 integrase variability, by using effective bioinformatics methods combining different statistical instruments from simple entropy and mutation rate to more specific approaches such as Hellinger distance. A total of 2133 HIV-1 integrase sequences were analyzed in: i) 1460 samples from drug-naïve [DN] individuals; ii) 386 samples from drug-experienced but INI-naïve [IN] individuals; iii) 287 samples from INI-experienced [IE] individuals. Within the three groups, 76 amino acid positions were highly conserved (≤0.2% variation, Hellinger distance: <0.25%), with 35 fully invariant positions; while, 80 positions were conserved (>0.2% to <1% variation, Hellinger distance: <1%). The H12-H16-C40-C43 and D64-D116-E152 motifs were all well conserved. Some residues were affected by dramatic changes in their mutation distributions, especially between DN and IE samples (Hellinger distance ≥1%). In particular, 15 positions (D6, S24, V31, S39, L74, A91, S119, T122, T124, T125, V126, K160, N222, S230, C280) showed a significant decrease of mutation rate in IN and/or IE samples compared to DN samples. Conversely, 8 positions showed significantly higher mutation rate in samples from treated individuals (IN and/or IE) compared to DN. Some of these positions, such as E92, T97, G140, Y143, Q148 and N155, were already known to be associated with resistance to integrase inhibitors; other positions including S24, M154, V165 and D270 are not yet documented to be associated with resistance. Our study confirms the high conservation of HIV-1 integrase and identified highly invariant positions using robust and innovative methods. The role of novel mutations located in the critical region of HIV-1 integrase deserves further investigation.
Keywords	amino acids ; bioinformatics ; entropy ; infection ; integrases ; mutation ; mutation rate
Language	English
Dates of publication	2022-07
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2022.105294
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Article ; Online: Evaluation of HIV-1 integrase variability by combining computational and probabilistic approaches.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2022 Volume 101, Page(s) 105294

Abstract	This study aimed at updating previous data on HIV-1 integrase variability, by using effective bioinformatics methods combining different statistical instruments from simple entropy and mutation rate to more specific approaches such as Hellinger distance. A total of 2133 HIV-1 integrase sequences were analyzed in: i) 1460 samples from drug-naïve [DN] individuals; ii) 386 samples from drug-experienced but INI-naïve [IN] individuals; iii) 287 samples from INI-experienced [IE] individuals. Within the three groups, 76 amino acid positions were highly conserved (≤0.2% variation, Hellinger distance: <0.25%), with 35 fully invariant positions; while, 80 positions were conserved (>0.2% to <1% variation, Hellinger distance: <1%). The H12-H16-C40-C43 and D64-D116-E152 motifs were all well conserved. Some residues were affected by dramatic changes in their mutation distributions, especially between DN and IE samples (Hellinger distance ≥1%). In particular, 15 positions (D6, S24, V31, S39, L74, A91, S119, T122, T124, T125, V126, K160, N222, S230, C280) showed a significant decrease of mutation rate in IN and/or IE samples compared to DN samples. Conversely, 8 positions showed significantly higher mutation rate in samples from treated individuals (IN and/or IE) compared to DN. Some of these positions, such as E92, T97, G140, Y143, Q148 and N155, were already known to be associated with resistance to integrase inhibitors; other positions including S24, M154, V165 and D270 are not yet documented to be associated with resistance. Our study confirms the high conservation of HIV-1 integrase and identified highly invariant positions using robust and innovative methods. The role of novel mutations located in the critical region of HIV-1 integrase deserves further investigation.
MeSH term(s)	Drug Resistance, Viral/genetics ; HIV Infections/drug therapy ; HIV Integrase/chemistry ; HIV Integrase Inhibitors/pharmacology ; HIV-1/genetics ; Humans ; Mutation
Chemical Substances	HIV Integrase Inhibitors ; HIV Integrase (EC 2.7.7.-) ; p31 integrase protein, Human immunodeficiency virus 1 (YY6481J2FF)
Language	English
Publishing date	2022-05-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2022.105294
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Article ; Online: Correction: The dual-target approach in viral HIV-1 viremia testing: An added value to virological monitoring?

Amendola, Alessandra / Sberna, Giuseppe / Forbici, Federica / Abbate, Isabella / Lorenzini, Patrizia / Pinnetti, Carmela / Antinori, Andrea / Capobianchi, Maria Rosaria

PloS one

2020 Volume 15, Issue 2, Page(s) e0230018

Abstract: This corrects the article DOI: 10.1371/journal.pone.0228192.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.pone.0228192.].
Language	English
Publishing date	2020-02-27
Publishing country	United States
Document type	Published Erratum
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0230018
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Article ; Online: The dual-target approach in viral HIV-1 viremia testing: An added value to virological monitoring?

Amendola, Alessandra / Sberna, Giuseppe / Forbici, Federica / Abbate, Isabella / Lorenzini, Patrizia / Pinnetti, Carmela / Antinori, Andrea / Capobianchi, Maria Rosaria

PloS one

2020 Volume 15, Issue 2, Page(s) e0228192

Abstract: New methods of HIV-1 RNA quantification based on dual-target detection are increasingly used in HIV viral load monitoring, but clinical implications and impact of dual-target detection on HIV-1 infection management are not established. Aptima HIV-1 Quant ...

Abstract	New methods of HIV-1 RNA quantification based on dual-target detection are increasingly used in HIV viral load monitoring, but clinical implications and impact of dual-target detection on HIV-1 infection management are not established. Aptima HIV-1 Quant Dx assay is a last generation HIV viral load method, that uses pol and LTR as simultaneous target, providing quantitative results based mainly on pol target, while LTR target is used to report the results when pol signal is absent. In our laboratory, about 6% of results of all HIV-1 viral load tests performed with this platform in one year period resulted from LTR signal. Interestingly, LTR-based viremia (sometimes exceeding 1,000 copies/mL) was observed in a small proportion (up to 1%) of patients under ART, considered for long time virologically suppressed on the basis of a single target (pol-based) assay. Male gender, >700 vs <200 CD4 cell/mL and dual therapy including NRTI plus either NNRTI, or PI/b or INSTI were independently associated with increased risk of LTR-based HIV-1 viral load detection by multivariable logistic regression. A significant linear correlation was observed between LTR-based HIV-1 RNA levels and PBMC-associated proviral DNA. Moreover, in a small group of patients with HIV-1 RNA levels >200 copies/mL, longitudinal assessments showed parallel kinetics between plasma viremia and proviral DNA. Sequencing of pol region for drug resistance assessment in patients with LTR-based viremia failed on plasma HIV-1 RNA, while it was successful on proviral DNA. The detection/quantification of HIV-1 viremia based only on LTR signal with a dual target assay in samples resulting undetectable with the more conventional target pol needs accurate evaluation; unravelling the biological basis of this phenomenon, here described for the first time, is mandatory to establish relevance and implication by both pathogenetic (i.e. infectivity of LTR-detected viruses, reservoir turnover, immune activation, etc.) and clinical standpoint.
MeSH term(s)	Adult ; Anti-Retroviral Agents/therapeutic use ; CD4 Lymphocyte Count ; DNA, Viral/blood ; Drug Resistance, Viral ; Female ; Gene Products, pol/genetics ; Genotype ; HIV Infections/drug therapy ; HIV Infections/pathology ; HIV Infections/virology ; HIV Long Terminal Repeat/genetics ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; Leukocytes, Mononuclear/cytology ; Leukocytes, Mononuclear/virology ; Logistic Models ; Male ; Middle Aged ; Proviruses/genetics ; Proviruses/isolation & purification ; RNA, Viral/blood ; Viral Load ; Viremia/pathology ; Viremia/virology
Chemical Substances	Anti-Retroviral Agents ; DNA, Viral ; Gene Products, pol ; RNA, Viral
Language	English
Publishing date	2020-02-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0228192
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Article ; Online: Analysis of HIV quasispecies and virological outcome of an HIV D+/R+ kidney-liver transplantation.

Rozera, Gabriella / Visco-Comandini, Ubaldo / Giombini, Emanuela / Santini, Francesco / Forbici, Federica / Berno, Giulia / Gruber, Cesare / De Paolis, Paolo / Colonnelli, Roberto / D'Offizi, Gianpiero / Ettorre, Giuseppe Maria / Grossi, Paolo / Capobianchi, Maria Rosaria / Ippolito, Giuseppe / Abbate, Isabella

Virology journal

2022 Volume 19, Issue 1, Page(s) 4

Abstract: Introduction: Transplantation among HIV positive patients may be a valuable therapeutic intervention. This study involves an HIV D+/R+ kidney-liver transplantation, where PBMC-associated HIV quasispecies were analyzed in donor and transplant recipients ( ...

Abstract	Introduction: Transplantation among HIV positive patients may be a valuable therapeutic intervention. This study involves an HIV D+/R+ kidney-liver transplantation, where PBMC-associated HIV quasispecies were analyzed in donor and transplant recipients (TR) prior to transplantation and thereafter, together with standard viral monitoring. Methods: The donor was a 54 year of age HIV infected woman: kidney and liver recipients were two HIV infected men, aged 49 and 61. HIV quasispecies in PBMC was analyzed by ultra-deep sequencing of V3 env region. During TR follow-up, plasma HIV-1 RNA, HIV-1 DNA in PBMC, analysis of proviral integration sites and drug-resistance genotyping were performed. Other virological and immunological monitoring included CMV and EBV DNA quantification in blood and CD4 T cell counts. Results: Donor and TR were all ART-HIV suppressed at transplantation. Thereafter, TR maintained a nearly suppressed HIV-1 viremia, but HIV-1 RNA blips and the increase of proviral integration sites in PBMC attested some residual HIV replication. A transient peak in HIV-1 DNA occurred in the liver recipient. No major changes of drug-resistance genotype were detected after transplantation. CMV and EBV transient reactivations were observed only in the kidney recipient, but did not require specific treatment. CD4 counts remained stable. No intermixed quasispecies between donor and TR was observed at transplantation or thereafter. Despite signs of viral evolution in TR, HIV genetic heterogeneity did not increase over the course of the months of follow up. Conclusions: No evidence of HIV superinfection was observed in the donor nor in the recipients. The immunosuppressive treatment administrated to TR did not result in clinical relevant viral reactivations.
MeSH term(s)	HIV Infections ; Humans ; Kidney ; Leukocytes, Mononuclear ; Liver ; Liver Transplantation ; Quasispecies
Language	English
Publishing date	2022-01-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-021-01730-w
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Article ; Online: Use of Pembrolizumab for Treatment of Progressive Multifocal Leukoencephalopathy in People Living with HIV.

Pinnetti, Carmela / Cimini, Eleonora / Vergori, Alessandra / Mazzotta, Valentina / Grassi, Germana / Mondi, Annalisa / Forbici, Federica / Amendola, Alessandra / Grisetti, Susanna / Baldini, Francesco / Candela, Caterina / Casetti, Rita / Campioni, Paolo / Capobianchi, Maria Rosaria / Agrati, Chiara / Antinori, Andrea

Viruses

2022 Volume 14, Issue 5

Abstract: Progressive Multifocal Leukoencephalopathy (PML) is a demyelinating disease occurring in advanced HIV infection, caused by the reactivation of poliomavirus JC (JCV). The use of pembrolizumab for treatment is based on the inhibition of programmed cell ... ...

Abstract	Progressive Multifocal Leukoencephalopathy (PML) is a demyelinating disease occurring in advanced HIV infection, caused by the reactivation of poliomavirus JC (JCV). The use of pembrolizumab for treatment is based on the inhibition of programmed cell death protein 1 (PD-1), potentially improving the anti JCV-specific response. We used pembrolizumab with combined antiretroviral treatment (cART) on a compassionate-use basis. At each administration, clinical evaluation, MRI and laboratory testing, including CD3, CD4, CD8, PD-1 markers, HIV-RNA and JCV-DNA in cerebrospinal fluid (CSF)/plasma pairs, were performed. The JCV-specific T cell response was analysed by Elispot assay. This study included five HIV patients: four male, median age 43 years (29-52), median CD4 and CD8 count 150 (15-158) and 973 (354-1250) cell/mm
MeSH term(s)	Adult ; Antibodies, Monoclonal, Humanized/therapeutic use ; DNA, Viral/genetics ; HIV Infections/complications ; HIV Infections/drug therapy ; Humans ; JC Virus ; Leukoencephalopathy, Progressive Multifocal/drug therapy ; Leukoencephalopathy, Progressive Multifocal/virology ; Male ; Middle Aged ; Polyomavirus Infections/complications ; Polyomavirus Infections/drug therapy ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; RNA, Viral ; Virus Activation
Chemical Substances	Antibodies, Monoclonal, Humanized ; DNA, Viral ; Programmed Cell Death 1 Receptor ; RNA, Viral ; pembrolizumab (DPT0O3T46P)
Language	English
Publishing date	2022-05-05
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14050970
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