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1. Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis

Author

Veneri, C, Brandtner, D, Mancini, P, Bonanno Ferraro, G, Iaconelli, M, Suffredini, E, Petrillo, M, Leoni, G, Paracchini, V, Gawlik, B, Marchini, A, Torlontano, P, Aprea, G, Scattolini, S, Acciari, V, La Bianca, M, Cifarelli, R, Palma, A, Lauria, G, La Vecchia, G, Giordano, V, Cossentino, L, Pennino, F, Lombardi, A, Gentili, L, Angelini, P, Nasci, D, Alborali, G, Formenti, N, Guarneri, F, Fontani, N, Guercio, M, Mariuz, M, Trani, G, Pariani, A, De Lellis, L, Ancona, C, Barca, A, Serio, F, Giorgi, D, Ferrante, I, Capparuccini, V, Scicluna, M, Cersini, A, Pietrella, G, Nicosia, E, Grasselli, E, Izzotti, A, Tomesani, I, Bellisomi, M, Rosatto, S, Ammoni, E, Cereda, D, Bertasi, B, Losio, M, Oliva, D, Castiglioni, S, Schiarea, S, Binda, S, Primache, V, Pellegrinelli, L, Cocuzza, C, Musumeci, R, Bolognini, L, Filippetti, F, Paniccia', M, Briscolini, S, Magi, S, Grucci, A, Colitti, M, Ciccaglione, A, Montanaro, C, Griglio, B, Costa, A, Decastelli, L, Romano, A, Bianchi, M, Carraro, E, Pignata, C, Macrì, M, Bonetta, S, Albano, N, Di Vittorio, G, Mongelli, O, Apollonio, F, Triggiano, F, De Giglio, O, Montagna, M, Palermo, M, Maida, C, Mazzucco, W, Tramuto, F, De Grazia, S, Giammanco, G, Filizzolo, C, Purpari, G, Gucciardi, F, Ferrante, M, Agodi, A, Barchitta, M, Cala', P, Carducci, A, Verani, M, Federigi, I, Macrì, S, Federici, E, Petricciuolo, M, Carnevali, A, Russo, F, Pitter, G, Groppi, V, Rigoli, F, Zampini, M, Baldovin, T, Amoruso, I, Cadonna, M, Postinghel, M, Foladori, P, Zago, L, Stenico, A, Marco, M, Matteo, D, La Rosa, G, Veneri, C., Brandtner, D., Mancini, P., Bonanno Ferraro, G., Iaconelli, M., Suffredini, E., Petrillo, M., Leoni, G., Paracchini, V., Gawlik, B. M., Marchini, A., Torlontano, Paolo, Aprea, Giuseppe, Scattolini, Silvia, Acciari, Vicdalia Aniela, La Bianca, Michele, Cifarelli, Rosa Anna, Palma, Achille, Lauria, Giuseppe, La Vecchia, Giovanna, Giordano, Vincenzo, Cossentino, Luigi, Pennino, Francesca, Lombardi, Annalisa, Gentili, Lisa, Angelini, Paola, Nasci, Daniele, Alborali, Giovanni, Formenti, Nicoletta, Guarneri, Flavia, Fontani, Nadia, Guercio, Marco, Mariuz, Marika, Trani, Gabriella, Pariani, Anna, De Lellis, Laura, Ancona, Carla, Barca, Alessandra, Serio, Flavia, Giorgi, Doriana Antonella, Ferrante, Irene, Capparuccini, Valeria, Scicluna, Maria Teresa, Cersini, Antonella, Pietrella, Gabriele, Nicosia, Elena, Grasselli, Elena, Izzotti, Alberto, Tomesani, Irene, Bellisomi, Marta, Rosatto, Stefano, Ammoni, Emanuela, Cereda, Danilo, Bertasi, Barbara, Losio, Marina Nadia, Oliva, Desdemona, Castiglioni, Sara, Schiarea, Silvia, Binda, Sandro, Primache, Valeria, Pellegrinelli, Laura, Cocuzza, Clementina, Musumeci, Rosario, Bolognini, Luigi, Filippetti, Fabio, Paniccia', Marta, Briscolini, Sara, Magi, Silvia, Grucci, Annalisa, Colitti, Michele, Ciccaglione, Angela, Montanaro, Carmen, Griglio, Bartolomeo, Costa, Angela, Decastelli, Lucia, Romano, Angelo, Bianchi, Manila, Carraro, Elisabetta, Pignata, Cristina, Macrì, Manuela, Bonetta, Silvia, Albano, Nehludoff, Di Vittorio, Giuseppe, Mongelli, Onofrio, Apollonio, Francesca, Triggiano, Francesco, De Giglio, Osvalda, Montagna, Maria Teresa, Palermo, Mario, Maida, Carmelo Massimo, Mazzucco, Walter, Tramuto, Fabio, De Grazia, Simona, Giammanco, Giovanni Maurizio, Filizzolo, Chiara, Purpari, Giuseppa, Gucciardi, Francesca, Ferrante, Margherita, Agodi, Antonella, Barchitta, Martina, Cala', Piergiuseppe, Carducci, Annalaura, Verani, Marco, Federigi, Ileana, Macrì, Salvatore, Federici, Ermanno, Petricciuolo, Maya, Carnevali, Agnese, Russo, Francesca, Pitter, Gisella, Groppi, Vanessa, Rigoli, Franco, Zampini, Marco, Baldovin, Tatjana, Amoruso, Irene, Cadonna, Maria, Postinghel, Mattia, Foladori, Paola, Zago, Lorella, Stenico, Alberta, Marco, Morelli, Matteo, Dossena, La Rosa, G., Veneri, C, Brandtner, D, Mancini, P, Bonanno Ferraro, G, Iaconelli, M, Suffredini, E, Petrillo, M, Leoni, G, Paracchini, V, Gawlik, B, Marchini, A, Torlontano, P, Aprea, G, Scattolini, S, Acciari, V, La Bianca, M, Cifarelli, R, Palma, A, Lauria, G, La Vecchia, G, Giordano, V, Cossentino, L, Pennino, F, Lombardi, A, Gentili, L, Angelini, P, Nasci, D, Alborali, G, Formenti, N, Guarneri, F, Fontani, N, Guercio, M, Mariuz, M, Trani, G, Pariani, A, De Lellis, L, Ancona, C, Barca, A, Serio, F, Giorgi, D, Ferrante, I, Capparuccini, V, Scicluna, M, Cersini, A, Pietrella, G, Nicosia, E, Grasselli, E, Izzotti, A, Tomesani, I, Bellisomi, M, Rosatto, S, Ammoni, E, Cereda, D, Bertasi, B, Losio, M, Oliva, D, Castiglioni, S, Schiarea, S, Binda, S, Primache, V, Pellegrinelli, L, Cocuzza, C, Musumeci, R, Bolognini, L, Filippetti, F, Paniccia', M, Briscolini, S, Magi, S, Grucci, A, Colitti, M, Ciccaglione, A, Montanaro, C, Griglio, B, Costa, A, Decastelli, L, Romano, A, Bianchi, M, Carraro, E, Pignata, C, Macrì, M, Bonetta, S, Albano, N, Di Vittorio, G, Mongelli, O, Apollonio, F, Triggiano, F, De Giglio, O, Montagna, M, Palermo, M, Maida, C, Mazzucco, W, Tramuto, F, De Grazia, S, Giammanco, G, Filizzolo, C, Purpari, G, Gucciardi, F, Ferrante, M, Agodi, A, Barchitta, M, Cala', P, Carducci, A, Verani, M, Federigi, I, Macrì, S, Federici, E, Petricciuolo, M, Carnevali, A, Russo, F, Pitter, G, Groppi, V, Rigoli, F, Zampini, M, Baldovin, T, Amoruso, I, Cadonna, M, Postinghel, M, Foladori, P, Zago, L, Stenico, A, Marco, M, Matteo, D, La Rosa, G, Veneri, C., Brandtner, D., Mancini, P., Bonanno Ferraro, G., Iaconelli, M., Suffredini, E., Petrillo, M., Leoni, G., Paracchini, V., Gawlik, B. M., Marchini, A., Torlontano, Paolo, Aprea, Giuseppe, Scattolini, Silvia, Acciari, Vicdalia Aniela, La Bianca, Michele, Cifarelli, Rosa Anna, Palma, Achille, Lauria, Giuseppe, La Vecchia, Giovanna, Giordano, Vincenzo, Cossentino, Luigi, Pennino, Francesca, Lombardi, Annalisa, Gentili, Lisa, Angelini, Paola, Nasci, Daniele, Alborali, Giovanni, Formenti, Nicoletta, Guarneri, Flavia, Fontani, Nadia, Guercio, Marco, Mariuz, Marika, Trani, Gabriella, Pariani, Anna, De Lellis, Laura, Ancona, Carla, Barca, Alessandra, Serio, Flavia, Giorgi, Doriana Antonella, Ferrante, Irene, Capparuccini, Valeria, Scicluna, Maria Teresa, Cersini, Antonella, Pietrella, Gabriele, Nicosia, Elena, Grasselli, Elena, Izzotti, Alberto, Tomesani, Irene, Bellisomi, Marta, Rosatto, Stefano, Ammoni, Emanuela, Cereda, Danilo, Bertasi, Barbara, Losio, Marina Nadia, Oliva, Desdemona, Castiglioni, Sara, Schiarea, Silvia, Binda, Sandro, Primache, Valeria, Pellegrinelli, Laura, Cocuzza, Clementina, Musumeci, Rosario, Bolognini, Luigi, Filippetti, Fabio, Paniccia', Marta, Briscolini, Sara, Magi, Silvia, Grucci, Annalisa, Colitti, Michele, Ciccaglione, Angela, Montanaro, Carmen, Griglio, Bartolomeo, Costa, Angela, Decastelli, Lucia, Romano, Angelo, Bianchi, Manila, Carraro, Elisabetta, Pignata, Cristina, Macrì, Manuela, Bonetta, Silvia, Albano, Nehludoff, Di Vittorio, Giuseppe, Mongelli, Onofrio, Apollonio, Francesca, Triggiano, Francesco, De Giglio, Osvalda, Montagna, Maria Teresa, Palermo, Mario, Maida, Carmelo Massimo, Mazzucco, Walter, Tramuto, Fabio, De Grazia, Simona, Giammanco, Giovanni Maurizio, Filizzolo, Chiara, Purpari, Giuseppa, Gucciardi, Francesca, Ferrante, Margherita, Agodi, Antonella, Barchitta, Martina, Cala', Piergiuseppe, Carducci, Annalaura, Verani, Marco, Federigi, Ileana, Macrì, Salvatore, Federici, Ermanno, Petricciuolo, Maya, Carnevali, Agnese, Russo, Francesca, Pitter, Gisella, Groppi, Vanessa, Rigoli, Franco, Zampini, Marco, Baldovin, Tatjana, Amoruso, Irene, Cadonna, Maria, Postinghel, Mattia, Foladori, Paola, Zago, Lorella, Stenico, Alberta, Marco, Morelli, Matteo, Dossena, and La Rosa, G.

Abstract

The emergence of new SARS-CoV-2 variants poses challenges to global surveillance efforts, necessitating swift actions in their detection, evaluation, and management. Among the most recent variants, Omicron BA.2.86 and its sub-lineages have gained attention due to their potential immune evasion properties. This study describes the development of a digital PCR assay for the rapid detection of BA.2.86 and its descendant lineages, in wastewater samples. By using this assay, we analyzed wastewater samples collected in Italy from September 2023 to January 2024. Our analysis revealed the presence of BA.2.86 lineages already in October 2023 with a minimal detection rate of 2% which then rapidly increased, becoming dominant by January 2024, accounting for a prevalence of 62%. The findings emphasize the significance of wastewater-based surveillance in tracking emerging variants and underscore the efficacy of targeted digital PCR assays for environmental monitoring.

Published
2024

3. Recombinant GII.P16 genotype challenges RT-PCR-based typing in region A of norovirus genome

Author

Chiara Filizzolo, Simona De Grazia, Noemi Urone, Leonardo Mangiaracina, Vito Martella, Floriana Bonura, Giovanni M. Giammanco, Celestino Bonura, Giuseppa Sciortino, Giuseppa L. Sanfilippo, Bonura F., Urone N., Bonura C., Mangiaracina L., Filizzolo C., Sciortino G., Sanfilippo G.L., Martella V., Giammanco G.M., and De Grazia S.

Subjects
0301 basic medicine, Microbiology (medical), Settore MED/07 - Microbiologia E Microbiologia Clinica, Genotype, 030106 microbiology, medicine.disease_cause, 03 medical and health sciences, chemistry.chemical_compound, fluids and secretions, 0302 clinical medicine, RNA polymerase, medicine, Humans, 030212 general & internal medicine, Typing, Child, Polymerase Gene, Phylogeny, Polymerase, Caliciviridae Infections, biology, Reverse Transcriptase Polymerase Chain Reaction, Norovirus, virus diseases, Virology, Infectious Diseases, Real-time polymerase chain reaction, Italy, chemistry, Degenerate primers, GII.P16, Norovirus, Polymerase,Typing, biology.protein, Primer (molecular biology)
Abstract

Objectives In latest years GII.4[P16] and GII.2[P16] noroviruses have become predominant in some temporal/geographical settings. In parallel with the emergence of the GII.P16 polymerase type, norovirus surveillance activity in Italy experienced increasing difficulties in generating sequence data on the RNA polymerase genomic region A, using the widely adopted JV12A/JV13B primer set. Two sets of modified primers (Deg1 and Deg2) were tested in order to improve amplification and typing of the polymerase gene. Methods Amplification and typing performance of region A primers was assessed in RT-PCR on 452 GII norovirus positive samples obtained from 2194 stool samples collected in 2016–2019 from children hospitalized with acute gastroenteritis. Results The use of Deg1 increased the rate of samples types in region A from 49.5% to 81.4% and from 21.9% to 69.7% in 2016 and 2017, respectively. The rate of Deg1 typed samples remained high in 2018 (90.1%), but sharply decreased to 11.8% in 2019. The second primers set, Deg2, was able to increase to 64.9% the rate of 2019 samples typed in region A, while typing efficiently 73.2%, 69%, and 86.4% of samples collected in 2016, 2017 and 2018, respectively. Conclusions The plasticity of norovirus genomes requires continuous updates of the primers used for strain characterization.

Published
2021

4. Evaluation of the diagnostic performances of two commercially available assays for the detection of enteric adenovirus antigens

Author

Chiara Filizzolo, Donatella Ferraro, Francesca Di Bernardo, Floriana Bonura, Antonella Collura, Vito Martella, Simona De Grazia, Giovanni M. Giammanco, Chiara Mascarella, Celestino Bonura, Bonura F., Mascarella C., Filizzolo C., Bonura C., Ferraro D., Di Bernardo F., Collura A., Martella V., Giammanco G.M., and De Grazia S.

Subjects
Microbiology (medical), medicine.medical_specialty, Settore MED/07 - Microbiologia E Microbiologia Clinica, Adolescent, Adenoviridae Infections, Concordance, Sensitivity and Specificity, Gastroenterology, Adenoviridae, Feces, Antigen, Chemiluminescent immunoassay, Internal medicine, Fecal antigens detection, medicine, Humans, Child, Antigens, Viral, Immuno chromatography, Acute gastroenteriti, business.industry, Significant difference, Infant, Newborn, Enteric adenoviruse, Infant, General Medicine, Acute gastroenteritis, Gastroenteritis, Hospitalization, Infectious Diseases, Italy, Child, Preschool, Luminescent Measurements, Reagent Kits, Diagnostic, Diagnostic performance, business, Viral load
Abstract

The performance of 2 antigenic commercial assays for enteric adenovirus (AdV) infection, bioNexia Rota-Adeno ImmunoChromatographic Tests (ICT) and LIAISON® Adenovirus ChemiLuminescence Immuno Assays (CLIA), was evaluated on 321 stools from children hospitalized for acute gastroenteritis in Palermo, Italy, using a Real time-PCR (Rt-PCR) as reference method. The CLIA showed higher sensitivity (77% vs 60%), accuracy (94.4 vs 90.9) and concordance (k: 0.81 vs 0.67) with respect to ICT, despite equivalent specificity (98.8%). Using the Ct values of the Rt-PCR as a proxy of the fecal viral load, similar Ct values (mean 9.32 vs 9.89) were observed among the true positive samples, whilst a significant difference (P < 0.05) was observed in false negative samples of CLIA (mean Ct 25.68) and ICT (mean Ct 19.87). Cross-reactivity with other enteric viruses was not observed. These results indicate that both the assays tested are suitable for diagnosis of AdV gastroenteritis.

Published
2021

5. Assessing the burden of viral co-infections in acute gastroenteritis in children: An eleven-year-long investigation

Author

Floriana Bonura, Leonardo Mangiaracina, Celestino Bonura, Vito Martella, Chiara Filizzolo, Giovanni M. Giammanco, Simona De Grazia, De Grazia S., Bonura F., Bonura C., Mangiaracina L., Filizzolo C., Martella V., and Giammanco G.M.

Subjects
0301 basic medicine, Rotavirus, Settore MED/07 - Microbiologia E Microbiologia Clinica, medicine.medical_specialty, viruses, 030106 microbiology, medicine.disease_cause, Virus, Astrovirus, 03 medical and health sciences, Feces, fluids and secretions, 0302 clinical medicine, Virology, Epidemiology, Genotype, Medicine, Humans, 030212 general & internal medicine, Child, biology, business.industry, Coinfection, Norovirus, virus diseases, Infant, biology.organism_classification, Gastroenteritis, Co-infection, Ct values, Enteric viruses, Genotypes, Real-time PCR, Infectious Diseases, Italy, business, Viral load
Abstract

Background Acute gastroenteritis is an important cause of childhood morbidity and mortality worldwide. A number of pathogens are responsible for human acute gastroenteritis. The recent introduction of syndromic assays for the diagnosis of enteric infections, including a wide panel of enteric pathogens, has unveiled the frequency of mixed infections. This study was carried out to assess the burden of viral co-infections and the genetic diversity of the viruses detected in children hospitalized with acute gastroenteritis in Italy. Methods A total of 4161 stool samples collected from diarrheic children over 11 years, from January 2008 to December 2018, were investigated for the presence of four enteric viruses, i.e. group A rotavirus, norovirus, astrovirus and adenovirus. The samples were initially screened by either molecular or immunochromatographic assays and subsequently confirmed by Real-time PCR and sequence analyses. Results At least one viral agent was detected in 48.6 %of specimens. Rotavirus was the most prevalent virus (24.7 %) followed by norovirus (19.6 %), adenovirus (5.3 %) and astrovirus (3%). Co-infections were detected in 8.3 % of virus-positive patients, with common viral combination being rotavirus with norovirus (70.6 % of co-infections) or with astrovirus (9.6 %). A variety of viral genotypes was detected in co-infections and in single infections. Using Real-time PCR cycle thresholds as a proxy measure of fecal viral load, rotavirus was generally detected at higher levels in co-infected patients. Conclusions Combining and deciphering measurable indicators of viral load and epidemiological information could be useful for an accurate interpretation of viral co-infections.

Published
2020

6. Detection of Echovirus 11 lineage 1 in wastewater samples in Sicily.

Author

Giammanco GM, Filizzolo C, Pizzo M, Sanfilippo GL, Cacioppo F, Bonura F, Fontana S, Buttinelli G, Stefanelli P, and De Grazia S

Subjects
Humans, Infant, Newborn, Sewage, Sicily, Phylogeny, Enterovirus B, Human genetics, Wastewater, Enterovirus
Abstract

We report the presence of Echovirus 11 (E11) in wastewater in Sicily (Southern Italy), since August 2022. Overall, the 5.4 % of sewage samples (7/130) collected in 2022 were positives for E11 and then the percentage of E11-positive sewage samples reached the value of 27.27(18/66) in the first semester of 2023. Phylogenetic analysis of VP1 sequences showed for most E11-positive samples (16/25: 64 %) close genetic correlation (98.4-99.4 % nucleotide identity) to E11 lineage 1 strains involved in recently reported severe neonatal infections., Competing Interests: Declaration of competing interest Giovanni Maurizio Giammanco reports financial support was provided by AOUP Paolo Giaccone University Hospital Palermo. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Published
2024
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7. Identification of a novel intra-genotype reassortant G1P[8] rotavirus in Italy, 2021.

Author

De Grazia S, Filizzolo C, Bonura F, Pizzo M, Di Bernardo F, Collura A, Pellegrini F, Martella V, and Giammanco GM

Subjects
Humans, Phylogeny, Genome, Viral, Genotype, Sicily, Capsid Proteins genetics, Antigens, Viral genetics, Rotavirus genetics, Rotavirus Infections epidemiology, Rotavirus Infections prevention & control, Rotavirus Vaccines
Abstract

Objectives: Rotaviruses G1P[8] are epidemiologically relevant and are targeted by vaccines. The introduction of vaccines has altered rotavirus epidemiology. Hospital-based surveillance conducted in Sicily, Italy, showed a progressive decline in rotavirus prevalence since 2014, along with an increasing vaccine coverage (63.8% in 2020), and a marked decrease in circulation of G1P[8] strains. Surprisingly in 2021, G1P[8] viruses accounted for 90.5% (19/21) of rotavirus infections. This study aimed to understand if the increased activity of G1P[8]'s was related to virus-related peculiarities., Design: In 2021, 266 patients <15 years of age were hospitalized with acute gastroenteritis (AGE) and included in rotavirus surveillance. Viral proteins (VP7 and VP4) genotyping and sequence data were generated from all rotavirus-positive samples. The genetic makeup of G1P[8] rotaviruses was investigated by full-genome sequencing., Results: Peculiar G1P[8] rotaviruses, with VP7 and VP4 belonging to novel sub-lineages, circulated in 2021, accounting for 76.2% (16/21) of all rotavirus infections. On full-genome analysis, the novel G1P[8] variant displayed an intra-genotype (Wa-like) reassortant constellation, involving G12 and G1 strains, into a unique arrangement never observed before. The novel G1P[8] variant showed peculiar amino acid substitutions in 8-1 and 8-3 epitopes of the VP4 with respect to the Rotarix strain., Conclusions: Prompt identification of virus variants circulating in the human population is pivotal to understanding epidemiological trends and assessing vaccine efficacy., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Published
2024
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8. Biological Specimen Banking as a Time Capsule to Explore the Temporal Dynamics of Norovirus Epidemiology.

Author

Bonura F, Filizzolo C, Pizzo M, Sanfilippo GL, Cacioppo F, Palazzotto E, Di Bernardo F, Collura A, Martella V, De Grazia S, and Giammanco GM

Subjects
Child, Humans, Genetic Variation, Molecular Epidemiology, Genotype, Capsid Proteins genetics, Phylogeny, Feces, Norovirus genetics, Caliciviridae Infections epidemiology, Gastroenteritis epidemiology, Epidemics
Abstract

Norovirus is recognised as a major cause of epidemic and sporadic acute gastroenteritis (AGE) in all age groups. Information on the genetic diversity of the noroviruses circulating in the 1980s and 1990s, before the development and adoption of dedicated molecular assays, is limited compared with the last decades. Between 1986 and 2020, uninterrupted viral surveillance was conducted in symptomatic children hospitalized with AGE in Palermo, Italy, providing a unique time capsule for exploring the epidemiological and evolutionary dynamics of enteric viruses. A total of 8433 stool samples were tested using real-time RT-PCR. All samples were stored at -20 or -80 °C until processing. In this 35-year long time span, noroviruses of genogroup II (GII) were detected in 15.6% of AGE requiring hospitalization, whilst GI noroviruses were detected in 1.4% of AGE. Overall, the predominant norovirus capsid (Cap) genotype was GII.4 (60.8%), followed by GII.3 (13.3%) and GII.2 (12.4%). Temporal replacement of the GII.4 Cap variants associated with different polymerase (Pol) types were observed over the study period. The chronology of emergence and circulation of the different GII.4 variants were consistent with data available in the literature. Also, for GII.3 and GII.2 NoVs, the circulation of different lineages/strains, differing in either the Cap or Pol genes or in both, was observed. This long-term study revealed the ability of noroviruses to continuously and rapidly modify their genomic makeup and highlights the importance of surveillance activities in vaccine design.

Published
2023
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9. Clinical and Epidemiologic Features of Viral Gastroenteritis in Hospitalized Children: An 11-Year Surveillance in Palermo (Sicily).

Author

Amodio E, De Grazia S, Genovese D, Bonura F, Filizzolo C, Collura A, Di Bernardo F, and Giammanco GM

Subjects
Child, Humans, Infant, Adenoviridae, Child, Hospitalized, Feces, Sicily, Adenoviridae Infections epidemiology, Adenovirus Infections, Human epidemiology, Astroviridae, Caliciviridae Infections epidemiology, Enteritis, Enterovirus Infections, Gastroenteritis virology, Rotavirus, Rotavirus Infections epidemiology, Virus Diseases epidemiology
Abstract

In order to acquire information regarding viral agents and epidemiologic features of severe paediatric Viral Acute Gastroenteritis (VAGE) across multiple seasons in the pre-rotavirus-vaccine era, the epidemiologic characteristics of VAGE were investigated among paediatric patients hospitalized in a major Sicilian paediatric hospital from 2003 to 2013. Overall, 4725 children were observed and 2355 (49.8%) were diagnosed with a viral infection: 1448 (30.6%) were found positive to rotavirus, 645 (13.7%) to norovirus, 216 (4.6%) to adenovirus, and 46 (0.97%) to astrovirus. Viral infections showed different patterns of hospitalization in terms of age at risk (younger for rotavirus and adenovirus infections), seasonality (increased risk in winter for rotavirus and norovirus), trend over time (reduced risk in 2011-2013 for norovirus and rotavirus) and major diagnostic categories (digestive diseases more frequent in adenovirus and astrovirus but not in norovirus). This study increases general knowledge of VAGE epidemiology and contributes to suggest some a priori diagnostic criteria that could help clinicians to identify and treat viral agents responsible for gastroenteritis in hospital settings.

Published
2022
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10. Impact of Vaccination on Rotavirus Genotype Diversity: A Nearly Two-Decade-Long Epidemiological Study before and after Rotavirus Vaccine Introduction in Sicily, Italy.

Author

Bonura F, Mangiaracina L, Filizzolo C, Bonura C, Martella V, Ciarlet M, Giammanco GM, and De Grazia S

Abstract

Sicily was the first Italian region to introduce rotavirus (RV) vaccination with the monovalent G1P[8] vaccine Rotarix® in May 2012. In this study, the seasonal distribution and molecular characterization of RV strains detected over 19 years were compared to understand the effect of Rotarix® on the evolutionary dynamics of human RVs. A total of 7846 stool samples collected from children < 5 years of age, hospitalized with acute gastroenteritis, were tested for RV detection and genotyping. Since 2013, vaccine coverage has progressively increased, while the RV prevalence decreased from 36.1% to 13.3% with a loss of seasonality. The local distribution of RV genotypes changed over the time possibly due to vaccine introduction, with a drastic reduction in G1P[8] strains replaced by common and novel emerging RV strains, such as equine-like G3P[8] in the 2018−2019 season. Comparison of VP7 and VP4 amino acid (aa) sequences with the cognate genes of Rotarix® and RotaTeq® vaccine strains showed specific aa changes in the antigenic epitopes of VP7 and of the VP8* portion of VP4 of the Italian RV strains. Molecular epidemiological surveillance data are required to monitor the emergence of novel RV strains and ascertain if these strains may affect the efficacy of RV vaccines.

Published
2022
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11. Assessment of SARS-CoV-2 RNA shedding in semen of 36 males with symptomatic, asymptomatic, and convalescent infection during the first and second wave of COVID-19 pandemic in Italy.

Author

Pavone C, Giammanco GM, Cascino AP, Baiamonte D, Pinelli M, Cangelosi E, Filizzolo C, Sciortino G, Grazia S, and Bonura F

Subjects
Humans, Male, Pandemics, RNA, Viral genetics, SARS-CoV-2 genetics, Semen, COVID-19 diagnosis, COVID-19 epidemiology
Abstract

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) receptor, angiotensin-converting enzyme 2 (ACE2), has been identified in the human testis, but the risk of transmission of SARS-CoV-2 through sexual intercourse still needs to be defined. The goal of our study was to determine if SARS-CoV-2 is detectable in the semen of patients suffering or recovering from coronavirus disease-19 (COVID-19), still testing positive at nasopharyngeal swabs but showing mild or no symptoms at the time of sampling. Detection of SARS-CoV-2 RNA in semen was performed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR targeting open reading frame (ORF) 1ab. Medical history of the enrolled patients was taken, including COVID-19-correlated symptoms, both at the time of diagnosis and at the time of interview. Results of real-time RT-PCR and nested PCR in semen showed no evidence of SARS-CoV-2 RNA in the 36 patients suffering or recovering from COVID-19 but still positive in a nasopharyngeal swab, from over 116 patients enrolled in the study. SARS-CoV-2 detection and persistence in semen would have an impact on both clinical practice and public health strategies, but our results would suggest that SARS-CoV-2 is not present in the semen of men recovering from COVID-19., Competing Interests: None

Published
2022
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12. Evaluation of the diagnostic performances of two commercially available assays for the detection of enteric adenovirus antigens.

Author

Bonura F, Mascarella C, Filizzolo C, Bonura C, Ferraro D, Di Bernardo F, Collura A, Martella V, Giammanco GM, and De Grazia S

Subjects
Adenoviridae genetics, Adolescent, Antigens, Viral genetics, Child, Child, Preschool, Feces virology, Hospitalization, Humans, Infant, Infant, Newborn, Italy, Luminescent Measurements methods, Sensitivity and Specificity, Adenoviridae immunology, Adenoviridae Infections diagnosis, Antigens, Viral immunology, Gastroenteritis diagnosis, Gastroenteritis virology, Luminescent Measurements standards, Reagent Kits, Diagnostic standards
Abstract

The performance of 2 antigenic commercial assays for enteric adenovirus (AdV) infection, bioNexia Rota-Adeno ImmunoChromatographic Tests (ICT) and LIAISON® Adenovirus ChemiLuminescence Immuno Assays (CLIA), was evaluated on 321 stools from children hospitalized for acute gastroenteritis in Palermo, Italy, using a Real time-PCR (Rt-PCR) as reference method. The CLIA showed higher sensitivity (77% vs 60%), accuracy (94.4 vs 90.9) and concordance (k: 0.81 vs 0.67) with respect to ICT, despite equivalent specificity (98.8%). Using the Ct values of the Rt-PCR as a proxy of the fecal viral load, similar Ct values (mean 9.32 vs 9.89) were observed among the true positive samples, whilst a significant difference (P < 0.05) was observed in false negative samples of CLIA (mean Ct 25.68) and ICT (mean Ct 19.87). Cross-reactivity with other enteric viruses was not observed. These results indicate that both the assays tested are suitable for diagnosis of AdV gastroenteritis., Competing Interests: Conflict of interest The authors declare that they have no conflict of interest., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Published
2021
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13. Recombinant GII.P16 genotype challenges RT-PCR-based typing in region A of norovirus genome.

Author

Bonura F, Urone N, Bonura C, Mangiaracina L, Filizzolo C, Sciortino G, Sanfilippo GL, Martella V, Giammanco GM, and De Grazia S

Subjects
Child, Genotype, Humans, Italy, Phylogeny, Reverse Transcriptase Polymerase Chain Reaction, Caliciviridae Infections epidemiology, Norovirus genetics
Abstract

Objectives: In latest years GII.4[P16] and GII.2[P16] noroviruses have become predominant in some temporal/geographical settings. In parallel with the emergence of the GII.P16 polymerase type, norovirus surveillance activity in Italy experienced increasing difficulties in generating sequence data on the RNA polymerase genomic region A, using the widely adopted JV12A/JV13B primer set. Two sets of modified primers (Deg1 and Deg2) were tested in order to improve amplification and typing of the polymerase gene., Methods: Amplification and typing performance of region A primers was assessed in RT-PCR on 452 GII norovirus positive samples obtained from 2194 stool samples collected in 2016-2019 from children hospitalized with acute gastroenteritis., Results: The use of Deg1 increased the rate of samples types in region A from 49.5% to 81.4% and from 21.9% to 69.7% in 2016 and 2017, respectively. The rate of Deg1 typed samples remained high in 2018 (90.1%), but sharply decreased to 11.8% in 2019. The second primers set, Deg2, was able to increase to 64.9% the rate of 2019 samples typed in region A, while typing efficiently 73.2%, 69%, and 86.4% of samples collected in 2016, 2017 and 2018, respectively., Conclusions: The plasticity of norovirus genomes requires continuous updates of the primers used for strain characterization., Competing Interests: Declaration of Competing Interest The authors declare that they have no conflict of interest., (Copyright © 2021. Published by Elsevier Ltd.)

Published
2021
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14. Assessing the burden of viral co-infections in acute gastroenteritis in children: An eleven-year-long investigation.

Author

De Grazia S, Bonura F, Bonura C, Mangiaracina L, Filizzolo C, Martella V, and Giammanco GM

Subjects
Child, Feces, Humans, Infant, Italy, Coinfection, Gastroenteritis, Norovirus, Rotavirus
Abstract

Background: Acute gastroenteritis is an important cause of childhood morbidity and mortality worldwide. A number of pathogens are responsible for human acute gastroenteritis. The recent introduction of syndromic assays for the diagnosis of enteric infections, including a wide panel of enteric pathogens, has unveiled the frequency of mixed infections. This study was carried out to assess the burden of viral co-infections and the genetic diversity of the viruses detected in children hospitalized with acute gastroenteritis in Italy., Methods: A total of 4161 stool samples collected from diarrheic children over 11 years, from January 2008 to December 2018, were investigated for the presence of four enteric viruses, i.e. group A rotavirus, norovirus, astrovirus and adenovirus. The samples were initially screened by either molecular or immunochromatographic assays and subsequently confirmed by Real-time PCR and sequence analyses., Results: At least one viral agent was detected in 48.6 %of specimens. Rotavirus was the most prevalent virus (24.7 %) followed by norovirus (19.6 %), adenovirus (5.3 %) and astrovirus (3%). Co-infections were detected in 8.3 % of virus-positive patients, with common viral combination being rotavirus with norovirus (70.6 % of co-infections) or with astrovirus (9.6 %). A variety of viral genotypes was detected in co-infections and in single infections. Using Real-time PCR cycle thresholds as a proxy measure of fecal viral load, rotavirus was generally detected at higher levels in co-infected patients., Conclusions: Combining and deciphering measurable indicators of viral load and epidemiological information could be useful for an accurate interpretation of viral co-infections., Competing Interests: Declaration of Competing Interest The authors declare that they have no conflict of interest., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Published
2020
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