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Article ; Online: Virus-Encoded Circular RNAs: Role and Significance in Viral Infections.

Sberna, Giuseppe / Maggi, Fabrizio / Amendola, Alessandra

International journal of molecular sciences

2023 Volume 24, Issue 22

Abstract: Circular RNAs (circRNAs) have been the focus of intense scientific research to understand their biogenesis, mechanisms of action and regulatory functions. CircRNAs are single stranded, covalently closed RNA molecules lacking the 5'-terminal cap and the 3' ...

Abstract	Circular RNAs (circRNAs) have been the focus of intense scientific research to understand their biogenesis, mechanisms of action and regulatory functions. CircRNAs are single stranded, covalently closed RNA molecules lacking the 5'-terminal cap and the 3'-terminal polyadenine chain, characteristics that make them very stable and resistant. Synthesised by both cells and viruses, in the past circRNAs were considered to have no precise function. Today, increasing evidence shows that circRNAs are ubiquitous, some of them are tissue- and cell-specific, and critical in multiple regulatory processes (i.e., infections, inflammation, oncogenesis, gene expression). Moreover, circRNAs are emerging as important biomarkers of viral infection and disease progression. In this review, we provided an updated overview of current understanding of virus-encoded and cellular-encoded circRNAs and their involvement in cellular pathways during viral infection.
MeSH term(s)	Humans ; RNA, Circular/genetics ; RNA/genetics ; Virus Diseases/genetics ; Biomarkers/metabolism ; Viruses/genetics
Chemical Substances	RNA, Circular ; RNA (63231-63-0) ; Biomarkers
Language	English
Publishing date	2023-11-20
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms242216547
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Article ; Online: Monitoring of SARS-CoV-2 circulation using saliva testing in school children in Rome, Italy.

Sberna, Giuseppe / Guarini, Rosanna / Vaia, Francesco / Maggi, Fabrizio / Bordi, Licia

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2022 Volume 124, Page(s) 11–13

Abstract: Objectives: To describe the trend of SARS-CoV-2 RNA in saliva samples from children attending nine schools in Rome in the local surveillance unit RM3 during the period of September 2021-March 2022, in parallel with the trend of SARS-CoV-2 RNA observed ... ...

Abstract	Objectives: To describe the trend of SARS-CoV-2 RNA in saliva samples from children attending nine schools in Rome in the local surveillance unit RM3 during the period of September 2021-March 2022, in parallel with the trend of SARS-CoV-2 RNA observed in nasopharyngeal swabs (NPSs) from the population in the same catchment area that was routinely tested at our laboratory in the same period. Methods: Saliva samples were collected using the Copan LolliSponge Results: The percentage of positivity in the two populations was different; of the 2222 saliva samples from students, 0.99% had positive results, whereas the percentage was higher (33.43%) in the 8994 NPSs representing the population from local surveillance unit RM3. Interestingly, the trend of SARS-CoV-2 RNA in saliva samples from students was consistent with that observed in NPSs from the population in same catchment area, although with peaks slightly anticipated. Conclusion: Overall, screening of saliva in the schools represents a good system to monitor SARS-CoV-2 circulation in the population, allowing early detection and quick isolation of students who are asymptomatic with positive test results and thus prevention of virus transmission.
MeSH term(s)	Child ; Humans ; SARS-CoV-2/genetics ; Saliva ; RNA, Viral/genetics ; Rome/epidemiology ; COVID-19/diagnosis ; COVID-19/epidemiology ; Specimen Handling/methods ; Nasopharynx
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-09-08
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2022.09.007
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Article ; Online: Evaluating the Dual-Target Aptima HIV-1 Quant Dx Assay: Comparison between Viral Loads Measured with

Sberna, Giuseppe / Sarti, Silvia / Cicalini, Stefania / Antinori, Andrea / Garbuglia, Anna Rosa / Amendola, Alessandra

Microbiology spectrum

2022 Volume 10, Issue 5, Page(s) e0136122

Abstract: For effective management of HIV-1 patients, accurate measurement of HIV-1-RNA viral load (VL) is fundamental. The latest generation molecular assays for monitoring VL perform simultaneous detection of two regions of the viral genome, but without ... ...

Abstract	For effective management of HIV-1 patients, accurate measurement of HIV-1-RNA viral load (VL) is fundamental. The latest generation molecular assays for monitoring VL perform simultaneous detection of two regions of the viral genome, but without specifying the target used for VL quantitation. By using the "open" software (research use only [RUO]) of Aptima HIV-1 Quant Dx Assay (Aptima) which provides both results obtained with the
MeSH term(s)	Humans ; Viral Load/methods ; HIV-1/genetics ; RNA, Viral/genetics ; RNA, Viral/analysis ; Reagent Kits, Diagnostic ; Molecular Diagnostic Techniques/methods ; Sensitivity and Specificity ; HIV Infections/diagnosis ; HIV Infections/drug therapy
Chemical Substances	RNA, Viral ; Reagent Kits, Diagnostic
Language	English
Publishing date	2022-09-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01361-22
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Article ; Online: Changes in the Circulation of Common Respiratory Pathogens among Hospitalized Patients with Influenza-like Illnesses in the Lazio Region (Italy) during Fall Season of the Past Three Years.

Sberna, Giuseppe / Lalle, Eleonora / Valli, Maria Beatrice / Bordi, Licia / Garbuglia, Anna Rosa / Amendola, Alessandra

International journal of environmental research and public health

2022 Volume 19, Issue 10

Abstract: A descriptive analysis of common respiratory pathogens (CRPs) detected in nasopharyngeal swabs (NPSs) from hospitalized patients with influenza-like illness during the fall seasons of the past three years, 2019-2021, in the Lazio region, Italy, was ... ...

Abstract	A descriptive analysis of common respiratory pathogens (CRPs) detected in nasopharyngeal swabs (NPSs) from hospitalized patients with influenza-like illness during the fall seasons of the past three years, 2019-2021, in the Lazio region, Italy, was conducted to assess whether or not CRP circulation changed because of COVID-19 during the fall season. The results observed in a total of 633 NPSs subjected to molecular diagnosis for CRPs by multiplex PCR assay during the autumn seasons (exactly from week 41 to week 50) were compared with each other. In 2019, in 144 NPSs, the more represented CRPs were rhinovirus/enterovirus (7.6%) and influenza A/B (4.2%). In 2020, 55 (21.6%) out of 255 NPSs resulted positive for SARS-CoV-2 and, except for one case of
MeSH term(s)	Adult ; COVID-19/epidemiology ; Humans ; Influenza, Human/epidemiology ; Italy/epidemiology ; Pandemics ; Respiratory Syncytial Viruses ; SARS-CoV-2 ; Seasons ; Virus Diseases/epidemiology ; Viruses
Language	English
Publishing date	2022-05-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2175195-X
ISSN	1660-4601 ; 1661-7827
ISSN (online)	1660-4601
ISSN	1661-7827
DOI	10.3390/ijerph19105962
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Article: Co-Circulation of SARS-CoV-2 and Other Respiratory Pathogens in Upper and Lower Respiratory Tracts during Influenza Season 2022-2023 in Lazio Region.

Bordi, Licia / Vulcano, Antonella / Sberna, Giuseppe / Nonis, Marino / Giacomini, Paolo / Maggi, Fabrizio / Fontana, Carla / Lalle, Eleonora

Microorganisms

2023 Volume 11, Issue 9

Abstract: Lower respiratory tract infections (LRTIs) occur when there is a lower airway tract infection. They are well-known for increasing the susceptibility of patients to bacterial/fungal co-infections and super-infections. In this study, we present the results ...

Abstract	Lower respiratory tract infections (LRTIs) occur when there is a lower airway tract infection. They are well-known for increasing the susceptibility of patients to bacterial/fungal co-infections and super-infections. In this study, we present the results of our investigation, which involved 381 consecutive patients admitted to our hospital during the Influenza season from October 2022 to April 2023. Among the 381 specimens, 75 were bronchoalveolar (BAL), and 306 were nasopharyngeal swabs (NPSs). Notably, 34.4% of the examined samples tested positive for SARS-CoV-2. Of these, we observed that 7.96% of NPSs showed positivity only for other respiratory viruses, while a substantial percentage (77%) of BAL specimens exhibited positive results only for bacterial co-infections. The results of our study not only confirm the importance of co-infections in COVID-19 but also emphasize the significance of utilizing rapid diagnostic tests (RDTs) for the timely diagnosis of LRTIs. In fact, RDTs allow for the identification of multiple pathogens, providing clinicians with useful and timely information to establish effective therapy.
Language	English
Publishing date	2023-09-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms11092239
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Article ; Online: HIV-1-Host Interaction in Gut-Associated Lymphoid Tissue (GALT): Effects on Local Environment and Comorbidities.

Moretti, Sonia / Schietroma, Ivan / Sberna, Giuseppe / Maggiorella, Maria Teresa / Sernicola, Leonardo / Farcomeni, Stefania / Giovanetti, Marta / Ciccozzi, Massimo / Borsetti, Alessandra

International journal of molecular sciences

2023 Volume 24, Issue 15

Abstract: HIV-1 replication in the gastrointestinal (GI) tract causes severe CD4+ T-cell depletion and disruption of the protective epithelial barrier in the intestinal mucosa, causing microbial translocation, the main driver of inflammation and immune activation, ...

Abstract	HIV-1 replication in the gastrointestinal (GI) tract causes severe CD4+ T-cell depletion and disruption of the protective epithelial barrier in the intestinal mucosa, causing microbial translocation, the main driver of inflammation and immune activation, even in people living with HIV (PLWH) taking antiretroviral drug therapy. The higher levels of HIV DNA in the gut compared to the blood highlight the importance of the gut as a viral reservoir. CD4+ T-cell subsets in the gut differ in phenotypic characteristics and differentiation status from the ones in other tissues or in peripheral blood, and little is still known about the mechanisms by which the persistence of HIV is maintained at this anatomical site. This review aims to describe the interaction with key subsets of CD4+ T cells in the intestinal mucosa targeted by HIV-1 and the role of gut microbiome and its metabolites in HIV-associated systemic inflammation and immune activation that are crucial in the pathogenesis of HIV infection and related comorbidities.
MeSH term(s)	Humans ; HIV Infections/drug therapy ; HIV-1 ; Intestinal Mucosa/pathology ; CD4-Positive T-Lymphocytes ; Inflammation ; Lymphoid Tissue
Language	English
Publishing date	2023-07-30
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241512193
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Article ; Online: Virological characterization of HIV-1 RNA elements detected exclusively through the LTR region by the dual-target Aptima HIV-1 Quant Dx assay in a subset of positive patients.

Sberna, Giuseppe / Nardacci, Roberta / Berno, Giulia / Rozera, Gabriella / Giombini, Emanuela / Fabeni, Lavinia / Specchiarello, Eliana / Maggi, Fabrizio / Amendola, Alessandra

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2023 Volume 167, Page(s) 105575

Abstract: Background: In a restricted subset of HIV patients with suppressed viral load (i.e., pol-undetected HIV-RNA), the Aptima HIV-1 Quant Dx Assay (Aptima), a dual-target (pol and LTR) and dual-probe test for viral load (VL) monitoring, can detect HIV-RNA ... ...

Abstract	Background: In a restricted subset of HIV patients with suppressed viral load (i.e., pol-undetected HIV-RNA), the Aptima HIV-1 Quant Dx Assay (Aptima), a dual-target (pol and LTR) and dual-probe test for viral load (VL) monitoring, can detect HIV-RNA exclusively through amplification of the LTR region. Objectives: To analyze the virological characteristics of the HIV-RNA elements detected only through LTR amplification (LTR-e). Study design: LTR-e isolated from plasma and peripheral blood mononuclear cells (PBMC) were evaluated for their ability to trigger productive infections. Viral pellets morphology and ultrastructural characteristics of PBMC from LTR-e patients were examined by electron microscopy. Plasma LTR-e underwent Sanger sequencing. Exosomes were examined with Aptima for LTR-e content. Results: In-vitro, LTR-e could not infect PBMC, induce cytopathic effects, or cause syncytia, even at high VL (e.g., >10,000 copies/mL). Under the electron microscope, plasma pellets and PBMC from patients with LTR-e showed atypical vesicles. Sanger sequencing of LTR-e yielded no results. Moreover, in plasma samples, LTR-e were associated with cell debris, never with exosomes. Conclusions: Differently from other dual-target but single-probe assays, Aptima unveils VL based only on LTR amplification in some HIV patients. Here, we show that LTR-e represent partial/incomplete/non-canonical transcripts unable to trigger productive infection or transmit HIV-1 infection. The recognition of VL based only on LTR-e in infected individuals is crucial as it allows to avoid inappropriate decisions in the clinical management of HIV patients, such as retesting of VL and switching of ART. Physicians and HIV-RNA dual-target assay manufacturers should consider the important implications of not recognizing this singular type of VL.
MeSH term(s)	Humans ; HIV Infections/diagnosis ; HIV-1/genetics ; Leukocytes, Mononuclear ; RNA, Viral/genetics ; Sensitivity and Specificity ; HIV Seropositivity ; Viral Load/methods
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-08-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2023.105575
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Article ; Online: Letter of concern re: "Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan. J. Clin. Virol. 2020; 129: 104543. doi:10.1016/j.jcv.2020.104543".

Sberna, Giuseppe / Capobianchi, Maria Rosaria / Bordi, Licia / Lalle, Eleonora

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2020 Volume 132, Page(s) 104635

MeSH term(s)	Betacoronavirus ; COVID-19 ; Coronavirus Infections ; Humans ; Japan ; Orthomyxoviridae ; Pandemics ; Pneumonia, Viral ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-09-09
Publishing country	Netherlands
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2020.104635
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Article ; Online: Comparison of Allplex™ SARS-CoV-2 Assay, Easy SARS-CoV-2 WE and Lumipulse quantitative SARS-CoV-2 antigen test performance using automated systems for the diagnosis of COVID-19.

Sberna, Giuseppe / Basile, Flavia / Guarino, Maria Luisa / Capobianchi, Maria Rosaria / Bordi, Licia / Parisi, Gabriella

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2021 Volume 113, Page(s) 113–115

Abstract: Diagnostic methods based on SARS-CoV-2 antigen detection are a promising alternative to SARS-CoV-2 RNA amplification. We evaluated the automated chemiluminescence-based Lumipulse® G SARS-CoV-2 Ag assay as compared to real time assays (combined results ... ...

Abstract	Diagnostic methods based on SARS-CoV-2 antigen detection are a promising alternative to SARS-CoV-2 RNA amplification. We evaluated the automated chemiluminescence-based Lumipulse® G SARS-CoV-2 Ag assay as compared to real time assays (combined results from RT-PCR Allplex™ SARS-CoV-2 assay and Easy SARS-CoV-2 WE kit) on 513 nasopharyngeal swabs (NPS). Among these, 53.6% resulted positive to RT-PCR, considered as the reference test. Compared to the reference test, overall sensitivity and specificity of Lumipulse® G SARS-CoV-2 Ag assay were 84.0%, and 89.1%, respectively, and overall agreement between the antigen and molecular assays was substantial (κ = 0.727). When stratifying samples into groups based on ranges of RT-PCR cycle threshold (Ct), the antigen test sensitivity was >95% for samples with Ct <30. Linear regression analysis showed strong and highly significant correlation between the Lumipulse Ag concentrations and the RT-PCR Ct values (RdRp gene), irrespective of whether the Ct values from molecular test were combined in a unique regression analysis or analysed separately. Overall, chemiluminescence-based antigen assay may be reliably applied to NPS samples to identify individuals with high viral loads, more likely to transmit the virus.
MeSH term(s)	COVID-19 ; Humans ; Nasopharynx ; RNA, Viral/genetics ; SARS-CoV-2 ; Sensitivity and Specificity ; Viral Load
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-09-29
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2021.09.069
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Article ; Online: Letter of concern re: "Immunochromatographic test for the detection of SARS-CoV-2 in saliva. J Infect Chemother. 2021 Feb;27(2):384-386. doi: 10.1016/j.jiac.2020.11.016."

Sberna, Giuseppe / Lalle, Eleonora / Capobianchi, Maria Rosaria / Bordi, Licia / Amendola, Alessandra

Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy

2021 Volume 27, Issue 7, Page(s) 1129–1130

MeSH term(s)	Antibodies, Viral ; COVID-19 ; Humans ; Immunologic Tests ; SARS-CoV-2 ; Saliva
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2021-04-13
Publishing country	Netherlands
Document type	Letter ; Comment
ZDB-ID	1355399-9
ISSN	1437-7780 ; 1341-321X
ISSN (online)	1437-7780
ISSN	1341-321X
DOI	10.1016/j.jiac.2021.04.003
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