showing 62 related works from this author
Molecular surveillance of norovirus, 2005–16 : an epidemiological analysis of data collected from the NoroNet network
2018
BACKGROUND: The development of a vaccine for norovirus requires a detailed understanding of global genetic diversity of noroviruses. We analysed their epidemiology and diversity using surveillance data from the NoroNet network.METHODS: We included genetic sequences of norovirus specimens obtained from outbreak investigations and sporadic gastroenteritis cases between 2005 and 2016 in Europe, Asia, Oceania, and Africa. We genotyped norovirus sequences and analysed sequences that overlapped at open reading frame (ORF) 1 and ORF2. Additionally, we assessed the sampling date and country of origin of the first reported sequence to assess when and where novel drift variants originated.FINDINGS: W…
Multiple reassortment and interspecies transmission events contribute to the diversity of feline, canine and feline/canine-like human group A rotavir…
2011
Abstract RNA–RNA hybridization assays and complete genome sequence analyses have shown that feline rotavirus (FRV) and canine rotavirus (CRV) strains display at least two distinct genotype constellations (genogroups), represented by the FRV strain RVA/Cat-tc/AUS/Cat97/1984/G3P[3] and the human rotavirus (HRV) strain RVA/Human-tc/JPN/AU-1/1982/G3P3[9], respectively. G3P[3] and G3P[9] strains have been detected sporadically in humans. The complete genomes of two CRV strains (RVA/Dog-tc/ITA/RV198-95/1995/G3P[3] and RVA/Dog-tc/ITA/RV52-96/1996/G3P[3]) and an unusual HRV strain (RVA/Human-tc/ITA/PA260-97/1997/G3P[3]) were determined to further elucidate the complex relationships among FRV, CRV a…
Antibodies for strain 2117-like vesiviruses (caliciviruses) in humans
2015
The vesivirus strain 2117 has been identified as contaminant of bioreactors used for production of human drugs, due to possible contamination of the reagents used for cell cultivation. Using an ELISA assay, antibodies specific for 2117-like viruses were detected in 32/410 (7.8%) human sera, indicating exposure to these viruses.
Emerging GII.4 norovirus variants affect children with diarrhea in Palermo, Italy in 2006
2008
Although the genetic/antigenic heterogeneity of human noroviruses (NoVs) is impressive, a few genogroup II strains of genotype 4 (GII.4) are dominant worldwide. GII.4 NoVs evolve rapidly and in the last 15 years six epidemic variants have been identified. In 2005-2006, surveillance of sporadic viral gastroenteritis in children in Palermo, Italy, resulted in the detection of NoV strains in 20.9% of the patients admitted to hospital. By restriction fragment length polymorphism (RFLP) and sequence analysis of region A in the RNA-dependent RNA-polymerase (RdRp) gene, 59 NoV strains were successfully characterized. Eighty-one percent of the strains were characterized as GII.4, 14% as GIIb/Hilver…
Identification of the novel Kawasaki 2014 GII.17 human norovirus strain in Italy, 2015
2015
Surveillance of noroviruses in Italy identified the novel GII.17 human norovirus strain, Kawasaki 2014, in February 2015. This novel strain emerged as a major cause of gastroenteritis in Asia during 2014/15, replacing the pandemic GII.4 norovirus strain Sydney 2012, but being reported only sporadically elsewhere. This novel strain is undergoing fast diversification and continuous monitoring is important to understand the evolution of noroviruses and to implement the future strategies on norovirus vaccines.
Sequence analysis of the VP7 and VP4 genes identifies a novel VP7 gene allele of porcine rotaviruses, sharing a common evolutionary origin with human…
2005
AbstractDuring an epidemiological survey encompassing several porcine herds in Saragoza, Spain, the VP7 and VP4 of a rotavirus-positive sample, 34461-4, could not be predicted by using multiple sets of G- and P-type-specific primers. Sequence analysis of the VP7 gene revealed a low amino acid (aa) identity with those of well-established G serotypes, ranging between 58.33% and 88.88%, with the highest identity being to human G2 rotaviruses. Analysis of the VP4 gene revealed a P[23] VP4 specificity, as its VP8* aa sequence was 95.9% identical to that of the P14[23],G5 porcine strain A34, while analysis of the VP6 indicated a genogroup I, that is predictive of subgroup I specificity. Analysis …
Genetic heterogeneity in the VP7 of group C rotaviruses.
2007
AbstractEvidence for a possible zoonotic role of group C rotaviruses (GCRVs) has been recently provided. To gain information on the genetic relationships between human and animal GCRVs, we sequenced the VP7 gene of 10 porcine strains detected during a large surveillance study from different outbreaks of gastroenteritis in piglets. Four GCRV strains were genetically related to the prototype GCRV porcine Cowden strain. A completely new VP7 genotype included 4 strains (344/04-7-like) that shared 92.5% to 97.0% aa identity to each other, but <83% to human GCRVs and <79% to other porcine and bovine GCRVs. A unique 4-aa insertion (SSSV or SSTI), within a variable region at the carboxy-terminus of…
A feline rotavirus G3P[9] carries traces of multiple reassortment events and resembles rare human G3P[9] rotaviruses.
2011
The full-length genome sequence of a feline G3P[9] rotavirus (RV) strain, BA222, identified from the intestinal content of an adult cat, was determined. Strain BA222 possessed a G3-P[9]-I2-R2-C2-M2-A3-N1-T3-E2-H3 genomic constellation, differing substantially from other feline RVs. Phylogenetic analyses of each genome segment revealed common origins with selected animal and zoonotic human RVs, notably with rare multi-reassortant human G3P[9] RVs (Ita/PAI58/96 and Ita/PAH136/96). Altogether, the findings suggest that feline RVs are genetically diverse and that human RVs may occasionally originate either directly or indirectly (via reassortment) from feline RVs.
Nucleotide variation in the VP7 gene affects PCR genotyping of G9 rotaviruses identified in Italy
2003
A modified (aFT9m) and a degenerate (aFT9d) version of the rotavirus G9-specific primer (aFT9) allowed strains that were previously untypable, because of point mutations accumulating at the primer binding site, to be G typed by reverse transcription-polymerase chain reaction. The strains were collected during 2001-2002 in Italy in hospitals of the Apulia region, from children affected by severe rotavirus-associated enteritis. Using a wide selection of G9 rotaviruses detected worldwide, sequencing of the G9 untypable strains, sequence comparison, and phylogenetic analysis showed that the Italian strains have strong genetic similarity (< or =99.4%) to G9 rotaviruses identified recently in man…
Analysis of early strains of the norovirus pandemic variant GII.4 Sydney 2012 identifies mutations in adaptive sites of the capsid protein.
2014
AbstractGlobal surveillance for norovirus identified in 2012 the emergence of a novel pandemic GII.4 variant, termed Sydney 2012. In Italy, the novel pandemic variant was identified as early as November 2011 but became predominant only in the winter season 2012–2013. Upon sequencing and comparison with strains of global origin, the early Sydney 2012 strains were found to differ from those spreading in 2012–2013 in the capsid (ORF2) putative epitopes B, C and D, segregating into a distinct phylogenetic clade. At least three residues (333, 340 and 393, in epitopes B, C and D, respectively) of the VP1 varied among Sydney 2012 strains of different clades. These findings suggest that the spread …
Nationwide surveillance study of human astrovirus infections in an Italian paediatric population
2012
SUMMARYThe study investigated the genetic diversity of human astroviruses (HAstVs) detected in children hospitalized with gastroenteritis in Italy in 2008–2009. A total of 1321 faecal samples were collected in Parma (northern Italy), Bari (southern Italy), and Palermo (Sicily) and screened for the presence of HAstVs. RT–PCR amplification of a portion at the 5′-end of ORF2 allowed the detection of HAstVs in 3·95% of the patients. Four different genotypes (HAstV-1, HAstV-2, HAstV-4, HAstV-5) were found to be circulating during the study period, with HAstV-1 being the predominant type. Interestingly, a novel lineage, proposed as HAstV-2d, was found to have emerged in Parma in 2009. Investigati…
Evaluation of the diagnostic performances of two commercially available assays for the detection of enteric adenovirus antigens
2021
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 signific…
Molecular Analysis of the VP7, VP4, VP6, NSP4, and NSP5/6 Genes of a Buffalo Rotavirus Strain: Identification of the Rare P[3] Rhesus Rotavirus-Like …
2003
ABSTRACT We report the detection and molecular characterization of a rotavirus strain, 10733, isolated from the feces of a buffalo calf affected with diarrhea in Italy. Strain 10733 was classified as a P[3] rotavirus, as the VP8* trypsin cleavage product of the VP4 protein revealed a high amino acid identity (96.2%) with that of rhesus rotavirus strain RRV (P5B[3]), used as the recipient virus in the human-simian reassortant vaccine. Analysis of the VP7 gene product revealed that strain 10733 possessed G6 serotype specificity, a type common in ruminants, with an amino acid identity to G6 rotavirus strains ranging from 88 to 98%, to Venezuelan bovine strain BRV033, and Hungarian human strain…
Recombinant GII.P16 genotype challenges RT-PCR-based typing in region A of norovirus genome
2021
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 2016–2…
Relationships among porcine and human P[6] rotaviruses: Evidence that the different human P[6] lineages have originated from multiple interspecies tr…
2005
AbstractPorcine rotavirus strains (PoRVs) bearing human-like VP4 P[6] gene alleles were identified. Genetic characterization with either PCR genotyping or sequence analysis allowed to determine the VP7 specificity of the PoRVs as G3, G4, G5 and G9, and the VP6 as genogroup I, that is predictive of a subgroup I specificity. Sequence analysis of the VP8* trypsin-cleavage product of VP4 allowed PoRVs to be characterized further into genetic lineages within the P[6] genotype. Unexpectedly, the strains displayed significantly higher similarity (up to 94.6% and 92.5% at aa and nt level, respectively) to human M37-like P[6] strains (lineage I), serologically classifiable as P2A, or to the atypical…
Sentinel hospital-based surveillance for norovirus infection in children with gastroenteritis between 2015 and 2016 in Italy
2018
Noroviruses are one of the leading causes of gastro-enteric diseases worldwide in all age groups. Novel epidemic noroviruses with GII.P16 polymerase and GII.2 or GII.4 capsid type have emerged worldwide in late 2015 and in 2016. We performed a molecular epidemiological study of the noroviruses circulating in Italy to investigate the emergence of new norovirus strains. Sentinel hospital-based surveillance, in three different Italian regions, revealed increased prevalence of norovirus infection in children (<15 years) in 2016 (14.4% versus 9.8% in 2015) and the emergence of GII.P16 strains in late 2016, which accounted for 23.0% of norovirus infections. The majority of the strains with a GII.…
Seroprevalence of Norovirus Genogroup IV Antibodies among Humans, Italy, 2010–2011
2014
Antibodies specific to genogroup IV identified in human specimens suggest zoonotic exposure.
Evidence for recombination between the pandemic GII.4 norovirus strains New Orleans 2009 and Sydney 2012
2013
ABSTRACT During 2012, a novel pandemic GII.4 norovirus variant, Sydney 2012, emerged worldwide. A signature of the variant was a GII.Pe ORF1, in association with GII.4 Apeldoorn 2008-like ORF2-ORF3 genes. We report the detection of recombinant GII.4 Sydney 2012 strains, possessing the ORF1 gene of the former pandemic variant New Orleans 2009.
Are Human P[14] Rotavirus Strains the Result of Interspecies Transmissions from Sheep or Other Ungulates That Belong to the Mammalian Order Artiodact…
2009
ABSTRACT A limited number of human G6P[14] rotavirus strains that cause gastroenteritis in humans have been isolated in Europe and Australia. The complete genome sequences were determined for five of these human strains—B10925-97 (isolated in Belgium in 1997), 111/05-27 (Italy, 2005), PA169 (Italy, 1987), MG6 (Australia, 1993), and Hun5 (Hungary, 1997)—and their genetic relatedness to animal rotavirus strains was evaluated by sequencing the complete genome of the sheep rotavirus OVR762 (G8P[14]; Spain, 2002), the guanaco ( Lama guanicoe ) rotavirus strains Arg/Chubut/99 and Arg/Río Negro/98 (G8P[14] and G8P[1], respectively; Argentina, 1999 and 1998), the sable antelope strain RC-18/08 (G6…
Novel recombinant GII.P16_GII.13 and GII.P16_GII.3 norovirus strains in Italy.
2014
Novel norovirus strains are continuously emerging worldwide. Molecular investigation and phylogenetic analysis identified GII.P16 recombinant noroviruses from the stools of four Italian children with gastroenteritis. The capsid gene was characterized as either GII.13 or GII.3. The GII.P16_GII.13 Italian strains were closely related to German strains involved in a large outbreak in the second half of 2012 and the Italian strains are the first recorded occurrence of GII.P16_GII.13 in Europe.
Norovirus GII.4/Sydney/2012 in Italy, Winter 2012–2013
2013
To the Editor: Noroviruses (NoVs) are the major cause of acute gastroenteritis in children and adults; they are responsible for sporadic cases and outbreaks of gastroenteritis in various epidemiologic settings. NoVs can be classified genetically into at least 5 genogroups, GI to GV (1). Although >30 genotypes within genogroups GI, GII, and GIV can infect humans (2), a single genotype, GII.4, has been associated with most NoV-related outbreaks and sporadic cases of gastroenteritis worldwide (3). GII.4 NoV strains continuously undergo genetic/antigenic diversification and periodically generate novel strains through accumulation of punctate mutations or recombination. New GII.4 variants emerge…
Genetic heterogeneity of porcine enteric caliciviruses identified from diarrhoeic piglets
2008
Enteric caliciviruses (noroviruses and sapoviruses) are responsible for the majority of non-bacterial gastroenteritis in humans of all age groups. Analysis of the polymerase and capsid genes has provided evidence for a huge genetic diversity, but the understanding of their ecology is limited. In this study, we investigated the presence of porcine enteric caliciviruses in the faeces of piglets with diarrhoea. A total of 209 samples from 118 herds were analysed and calicivirus RNA was detected by RT-PCR in 68 sample (32.5%) and in 46 herds (38.9%), alone or in mixed infection with group A and C rotaviruses. Sequence and phylogenetic analysis of the calicivirus-positive samples characterized t…
Identification of a multi-reassortant G12P[9] rotavirus with novel VP1, VP2, VP3 and NSP2 genotypes in a child with acute gastroenteritis.
2015
The G12 rotavirus genotype is globally emerging to cause severe gastroenteritis in children. Common G12 rotaviruses have either a Wa-like or DS-1-like genome constellation, while some G12 strains may have unusual genome composition. In this study, we determined the full-genome sequence of a G12P[9] strain (ME848/12) detected in a child hospitalized with acute gastroenteritis in Italy in 2012. Strain ME848/12 showed a complex genetic constellation (G12-P[9]-I17-R12-C12-M11-A12-N12-T7-E6-H2), likely derived from multiple reassortment events, with the VP1, VP2, VP3 and NSP2 genes being established as novel genotypes R12, C12, M11 and N12, respectively. Gathering sequence data on human and anim…
Identification of group A porcine rotavirus strains bearing a novel VP4 (P) genotype in Italian swine herds.
2007
ABSTRACT The VP4 gene of a G5 Italian porcine rotavirus strain, 344/04-1, was nontypeable by PCR genotyping. The amino acid sequence of the full-length VP4 protein had low identity (≤76.6%) with the homologous sequences of representative strains of the remaining P genotypes, providing evidence for a novel P genotype.
Epidemiological dynamics of norovirus GII.4 variant New Orleans 2009.
2015
Norovirus (NoV) is one of the major causes of diarrhoeal disease with epidemic, outbreak and sporadic patterns in humans of all ages worldwide. NoVs of genotype GII.4 cause nearly 80–90 % of all NoV infections in humans. Periodically, some GII.4 strains become predominant, generating major pandemic variants. Retrospective analysis of the GII.4 NoV strains detected in Italy between 2007 and 2013 indicated that the pandemic variant New Orleans 2009 emerged in Italy in the late 2009, became predominant in 2010–2011 and continued to circulate in a sporadic fashion until April 2013. Upon phylogenetic analysis based on the small diagnostic regions A and C, the late New Orleans 2009 NoVs circulati…
Emergence in 2017-2019 of novel reassortant equine-like G3 rotavirus strains in Palermo, Sicily.
2021
Rotavirus A (RVA) is a major etiologic agent of gastroenteritis in children worldwide. Hospital-based surveillance of viral gastroenteritis in paediatric population in Palermo (Italy) from 2017 onwards revealed a sharp increase in G3P[8] RVAs, accounting for 71% of all the RVAs detected in 2019. This pattern had not been observed before in Italy, with G3 RVA usually being detected at rates lower than 3%. In order to investigate this unique epidemiological pattern, the genetic diversity of G3 RVAs identified during a 16-year long surveillance (2004-2019) was explored by systematic sequencing of the VP7 and VP4 genes and by whole genome sequencing of selected G3 strains, representative of the…
G2 rotavirus infections in an infantile population of the South of Italy: variability of viral strains over time.
2005
Rotavirus positive samples collected in Palermo, Italy, during 2002–2004 did not react with the G2 type-specific RV5:3 monoclonal antibodies (MAbs) and could be identified as G2 only by RT-PCR genotyping. The genetic variation of VP7 and VP4 antigenic proteins was studied in 14 G2 samples including a selection of both those successfully characterized by serotyping and those failing to be serotyped. The phylogenetic analysis performed on partial VP7 sequences showed a temporal clustering of these strains, with those isolated in Palermo in 2003 belonging to the same lineage of G2 MAbs-unreactive strains identified in UK in 1996–1997 and in Bari, Italy, in 2003–2004. A single amino acid substi…
Genetic heterogeneity and recombination in human type 2 astroviruses
2012
ABSTRACT Novel lineages of human astrovirus (HAstV) types 2, 2c, and 2d have been identified. Upon sequencing of the 3′ end of the genome, the type 2c and 2d HAstVs were found to be open reading frame 1b (ORF1b)-ORF2 recombinant, with ORF1b being derived from type 3 and type 1 HAstVs, respectively. An ORF2 interlineage recombinant strain, 2c/2b, was also identified.
Canine-Origin G3P[3] Rotavirus Strain in Child with Acute Gastroenteritis
2007
Infection by an animal-like strain of rotavirus (PA260/97) was diagnosed in a child with gastroenteritis in Palermo, Italy, in 1997. Sequence analysis of VP7, VP4, VP6, and NSP4 genes showed resemblance to a G3P[3] canine strain identified in Italy in 1996. Dogs are a potential source of human viral pathogens.
Genomic characterization of a novel group A lamb rotavirus isolated in Zaragoza, Spain.
2008
An ovine rotavirus (OVR) strain, 762, was isolated from a 30-day-old lamb affected with severe gastroenteritis, in Zaragoza, Spain, and the VP4, VP7, VP6, NSP4, and NSP5/NSP6 genes were subsequently characterized molecularly. Strain OVR762 was classified as a P[14] rotavirus, as the VP4 and VP8* trypsin-cleavage product of the VP4 protein revealed the highest amino acid (aa) identity (94% and 97%, respectively) with that of the P11[14] human rotavirus (HRV) strain PA169, isolated in Italy. Analysis of the VP7 gene product revealed that OVR762 possessed G8 serotype specificity, a type common in ruminants, with the highest degree of aa identity (95–98%) shared with serotype G8 HRV, bovine rot…
Genetic Variability among Serotype G4 Italian Human Rotaviruses
2005
ABSTRACT A total of 254 serotype GH rotavirus strains were detected in Palermo, Italy, from 1985 to 2003. Out of 38 serotype G4 strains selected for genetic analysis, 14 were recognized by genotyping as type G9. Strains confirmed to belong to the G4 type showed temporal patterns of genetic evolution in their VP7 and VP4 gene sequences, and the latest Italian G4 strains were distantly related to the reference vaccinal ST3 strain.
Identification of a novel VP4 genotype carried by a serotype G5 porcine rotavirus strain
2006
AbstractRotavirus genome segment 4, encoding the spike outer capsid VP4 protein, of a porcine rotavirus (PoRV) strain, 134/04-15, identified in Italy was sequenced, and the predicted amino acid (aa) sequence was compared to those of all known VP4 (P) genotypes. The aa sequence of the full-length VP4 protein of the PoRV strain 134/04-15 showed aa identity values ranging from 59.7% (bovine strain KK3, P8[11]) to 86.09% (porcine strain A46, P[13]) with those of the remaining 25 P genotypes. Moreover, aa sequence analysis of the corresponding VP8* trypsin cleavage fragment revealed that the PoRV strain 134/04-15 shared low identity, ranging from 37.52% (bovine strain 993/83, P[17]) to 73.6% (po…
Detection of the norovirus variants GGII.4 hunter and GGIIb/hilversum in Italian children with gastroenteritis.
2006
Noroviruses (NoVs) are important enteric pathogens of humans. Although they exhibit an impressive genetic diversity, few NoV strains appear to predominate worldwide. Limited epidemiological data are available on NoV gastroenteritis in Italy. In this study, we assessed the prevalence of human NoV in Italian children with gastroenteritis by using a reverse-transcription nested polymerase chain reaction (RT-PCR) assay specific for the RNA-dependent RNA polymerase (RdRp) on faecal samples collected throughout the 2004 surveillance activity in Palermo, Italy. NoVs were detected in 47% of the stool samples obtained from children <5 years age, admitted to hospital with acute non-bacterial gastroen…
Molecular characterization of the genotype G9 human rotavirus strains recovered in Palermo, Italy, during the winter of 1999-2000
2004
Among the known human rotavirus serotypes, types G1–G4 are ubiquitous and account for >80% of global human rotavirus strains. Since 1994 an increase in reports of G9 serotype isolates has been observed in both developed and developing countries. In the winter season of 1999–2000 we detected the appearance of G9 rotavirus in Palermo, Italy, accounting for 19% of all rotaviruses circulating in our geographical area. Some of these Italian G9 isolates have been submitted to partial sequencing of their VP7 gene. All of them showed complete nucleotide identity suggesting a clonal origin. The Italian VP7 sequences were found to be very closely related to that of other G9 strains recently isolat…
Evolution of DS-1-like human G2P[4] rotaviruses assessed by complete genome analyses
2013
Group A rotaviruses (RVAs) are a leading cause of viral gastroenteritis in children, with G2P[4] RVA being one of the most common human strain worldwide. The complete genome sequences of nine G2P[4] RVA strains, selected from a 26-year archival collection (1985-2011) established in Palermo/Italy, were determined. A strain associated with a peak of G2P[4] RVA activity in 1996 resembled a reassortant strain identified in Kenya in 1982 and completely differed in the genomic make up from more recent strains that circulated during 2004-2011. Conversely, the 2004-2011 G2P[4] RVAs were genetically more similar to contemporary RVA strains circulating globally. Recent G2P[4] strains possessed either…
Prevalence of group C rotaviruses in weaning and post-weaning pigs with enteritis.
2006
Diarrheic fecal specimens collected from porcine herds were screened for the presence of group C rotaviruses using a reverse transcription-polymerase chain reaction (RT-PCR) assay. A total of 188 samples were tested and 54 were positive. When compiled these data with diagnostic results on group A rotaviruses and enteric caliciviruses we found that all but 5 group C rotavirus positive samples contained at least one additional virus. A subset of samples were subjected to nucleotide sequencing. The selected strains showed an unexpectedly wide range of nucleotide sequence heterogeneity (88.6-100%) to each other and to the reference porcine group C rotavirus strain, Cowden. The nucleotide sequen…
Impact of Vaccination on Rotavirus Genotype Diversity: A Nearly Two-Decade-Long Epidemiological Study before and after Rotavirus Vaccine Introduction…
2022
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 th…
Assessing the burden of viral co-infections in acute gastroenteritis in children: An eleven-year-long investigation.
2020
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 presen…
Norovirus in captive lion cub (Panthera leo)
2007
African lions (Panthera leo) are susceptible to viral diseases of domestic carnivores, including feline calici-virus infection. We report the identification of a novel enteric calicivirus, genetically related to human noroviruses of genogroup IV, in a lion cub that died of severe hemorrhagic enteritis.
Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-cl…
2014
Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5' or 3' end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established. Three main lineages could be defined in HAstV-1, four in HAstV-2, two in HAstV-…
Introduction and prolonged circulation of G12 rotaviruses in Sicily
2016
SUMMARYGenotype G12 strains are now considered to be the sixth most prevalent human rotaviruses worldwide. In two Sicilian cities, Palermo and Messina, surveillance of rotavirus circulation performed since 1985 and 2009, respectively, did not detect G12 strains until 2012. From 2012 to 2014 rotavirus infection was detected in 29·7% of 1647 stool samples collected from children admitted for acute gastroenteritis to three Sicilian hospitals in Palermo, Messina and Ragusa. In 2012, G12P[8] was first detected in Palermo and then in Messina where it represented the second most frequent genotype (20% prevalence) after G1P[8]. Thereafter, G12 strains continued to circulate in Sicily, showing a mar…
Data mining from a 27-years rotavirus surveillance in Palermo, Italy.
2014
Uninterrupted surveillance conducted in Palermo, Sicily, for 27 years (1985–2012) detected rotavirus infection in 32.7% of 6522 children <5 years of age, hospitalised at the “G. Di Cristina” Children’s Hospital of Palermo. Increased rotavirus activity usually occurred from the beginning of winter to mid-spring. G1P[8] rotaviruses were the prevalent strains in most of the years and were only occasionally overcome by G9P[8], G4P[8] or G2P[4]. The circulation of non-G1P[8] strains was discontinuous and fluctuating. Phylogenetic analyses revealed an heterogeneous population of viruses within each genotype, with different lineages and sublineages emerging over the time. Amino acid substitutions …
Full-genome sequencing of a Hungarian canine G3P[3] Rotavirus A strain reveals high genetic relatedness with a historic Italian human strain
2015
A canine Rotavirus A strain was identified in the fecal specimen of a young dog during 2012 in Hungary. The strain RVA/Dog-wt/HUN/135/2012/G3P[3] shared complete genotype constellation (G3-P[3]-I3-R3-C3-M3-A15-N2-T3-E3-H6) and high genome sequence similarity (nt, 98.8 %) with a historic human strain, RVA/Human-tc/ITA/PA260-97/1997/G3P[3]. This study provides evidence for the canine origin of the unusual NSP1 genotype, A15, and reinforces the hypothesis of direct interspecies transmission of canine rotaviruses to humans.
Unusual Assortment of Segments in 2 Rare Human Rotavirus Genomes
2010
Using full-length genome sequence analysis, we investigated 2 rare G3P[9] human rotavirus strains isolated from children with diarrhea. The genomes were recognized as assortments of genes closely related to rotaviruses originating from cats, ruminants, and humans. Results suggest multiple transmissions of genes from animal to human strains of rotaviruses.
Rare AU-1-like G3P[9] human rotaviruses with a Kun-like NSP4 gene in children with diarrhea in Italy
2007
ABSTRACT Three G3P[9] rotaviruses, detected in children hospitalized with gastroenteritis in Palermo, Italy, were found to be genetically related to strains of either human or feline origin in the VP7, VP4, and VP6 genes. In contrast, in the NSP4 gene the viruses resembled G2P[4] human strains, suggesting a reassortment between AU-1-like and Kun-like strains.
Review of group A rotavirus strains reported in swine and cattle
2013
Group A rotavirus (RVA) infections cause severe economic losses in intensively reared livestock animals, particularly in herds of swine and cattle. RVA strains are antigenically heterogeneous, and are classified in multiple G and P types defined by the two outer capsid proteins, VP7 and VP4, respectively. This study summarizes published literature on the genetic and antigenic diversity of porcine and bovine RVA strains published over the last 3 decades. The single most prevalent genotype combination among porcine RVA strains was G5P[7], whereas the predominant genotype combination among bovine RVA strains was G6P[5], although spatiotemporal differences in RVA strain distribution were observ…
Heterogeneity and temporal dynamics of evolution of G1 human rotaviruses in a settled population.
2006
ABSTRACT A rotavirus sample collection from 19 consecutive years was used to investigate the heterogeneity and the dynamics of evolution of G1 rotavirus strains in a geographically defined population. Phylogenetic analysis of the VP7 gene sequences of G1P[8] human rotavirus strains showed the circulation of a heterogeneous population comprising three lineages and seven sublineages. Increases in the circulation of G1 rotaviruses were apparently associated with the introduction of novel G1 strains that exhibited multiple amino acid changes in antigenic regions involved in rotavirus neutralization compared to the strains circulating in the previous years. The emergence and/or introduction of G…
Genetic characterization of G3 rotaviruses detected in Italian children in the years 1993–2005
2009
International audience; In recent years an apparent increase in the frequency of detection of G3P[8] rotaviruses has been observed worldwide. Similarly, in Italy G3P[8] strains have been detected sporadically and in a scattered fashion over 20 years, whereas in 2003 and 2005 G3P[8] rotavirus activity increased markedly. By analysis of the VP7, VP4, VP6 and NSP4 genes of a selection of G3P[8] rotaviruses detected between 1993 and 2005, a remarkable sequence conservation was observed in the VP7, VP4 and VP6 genes. By converse, after 2002 the Italian G3P[8] strains were found to possess unique mutations in significant regions of the NSP4 protein.
MLB1 Astrovirus in Children with Gastroenteritis, Italy
2014
To the Editor: Astroviruses are notable agents of gastroenteritis in many mammalian and avian hosts. Astroviruses are nonenveloped RNA small, round, viruses (SRVs) with a single-stranded, positive sense RNA of 6.1 to 7.9 kb (1). The genome contains 2 nonstructural genes, open reading frame (ORF) 1a and 1b, and a capsid gene, ORF2, with short 5′ and 3′ untranslated regions. Human astroviruses, a major cause of gastroenteritis, are classified in the human astrovirus species, comprising 8 serotypes (1). Recently, astroviruses genetically unrelated to canonical human astroviruses have been identified in human stools in several countries. These unusual astroviruses form 2 main genetic clades. On…
Temporal variation in the distribution of type-1 human astrovirus lineages in a settled population over 14 years.
2016
Human astroviruses (HAstVs) are important enteric pathogens that are genetically and antigenically heterogeneous and can be classified into eight sero/genotypes (HAstV-1 to -8) and different lineages within each HAstV type. This study describes the genetic diversity of HAstVs circulating in southern Italy over 14 years. Molecular analysis of HAstV-1 strains showed that three different lineages (1a, 1b and 1d) of the predominant genotype were circulating during the study period. The study of an archival collection of HAstV strains offers a unique opportunity to evaluate the patterns of variation of HAstV infections over the years and to correlate the observed epidemiological changes to the g…
Complete genome analysis of contemporary G12P[8] rotaviruses reveals heterogeneity within Wa-like genomic constellation
2016
G12 rotaviruses are globally emergent rotaviruses causing severe childhood gastroenteritis. Little is known about the evolution and diversity of G12P[8] rotaviruses and the possible role that widespread vaccine use, globally, has had on their emergence. In Sicily, Italy, surveillance activity for rotaviruses has been conducted uninterruptedly since 1985, thus representing a unique observatory for the study of human rotaviruses in the pre- and post-vaccine era. G12 rotaviruses were first detected only in 2012 and between 2012 and 2014 they accounted for 8.7% of all rotavirus-associated infections among children, with peaks of 27.8% in 2012/2013 and 21% in 2014. We determined and analyzed the…
Detection of a porcine-like rotavirus in a child with enteritis in Italy.
2008
ABSTRACT During a 1-year rotavirus surveillance of children hospitalized with acute gastroenteritis in Brescia Hospital, Italy, a chimerical rotavirus strain, G3P[6], was detected, displaying the VP7 and VP4 genes of porcine origin and the NSP4 and VP6 genes of human origin. The reassortant nature of the virus rules out a direct zoonotic event.
Norovirus GII.17 as Major Epidemic Strain in Italy, Winter 2015–16
2017
In winter 2015-16, norovirus GII.17 Kawasaki 2014 emerged as a cause of sporadic gastroenteritis in children in Italy. Median patient age was higher for those with GII.17 than GII.4 infection (55 vs. 24 months), suggesting limited cross-protection for older children.
Lineage diversification and recombination in type-4 human astroviruses.
2013
Abstract Human astroviruses (HAstVs) are important enteric pathogens and can be classified genetically and antigenically into eight types. During surveillance of HAstVs in Italy, type-4 HAstVs were detected only sporadically and found to cluster into two distinct genetic groups. Upon sequence analysis of the 3′ end of the polymerase gene (ORF1b) and of the full-length ORF2, the 2008 type-4 HAstV strains were characterised as a novel ORF2 genetic lineage, designated as 4c. The 2008 type-4 HAstVs also shared the ORF1b gene with similar HAstV-4c strains detected globally, thus displaying a conserved ORF1b/ORF2 asset. By interrogation of the databases, this novel lineage 4c accounted for 60.8% …
Diversity of human rotaviruses detected in Sicily, Italy, over a 5-years period (2001-2005).
2007
It is well known that the death of dopaminergic neurons of the substantia nigra pars compacta (SNc) is the pathological hallmark of Parkinson's disease (PD), the second most common and disabling condition in the expanding elderly population. Nevertheless, the intracellular cascade of events leading to dopamine cell death is still unknown and, consequently, treatment is largely symptomatic rather than preventive. Moreover, the mechanisms whereby nigral dopaminergic neurons may degenerate still remain controversial. Hitherto, several data have shown that the earlier cellular disturbances occurring in dopaminergic neurons include oxidative stress, excitotoxicity, inflammation, mitochondrial dy…
Assignment of the group A rotavirus NSP4 gene into genotypes using a hemi-nested multiplex PCR assay: a rapid and reproducible assay for strain surve…
2009
The rotavirus non-structural protein NSP4 has been implicated in a number of biological functions during the rotavirus cellular cycle and pathogenesis, and has been addressed as a target for vaccine development. The NSP4 gene has been classified into six genotypes (A–F). A semi-nested triplex PCR was developed for genotyping the major human NSP4 genotypes (A–C), which are common in human rotavirus strains but are also shared among most mammalian rotavirus strains. A total of 192 previously characterized human strains representing numerous G and P type specificities (such as G1P[8], G1P[4], G2P[4], G3P[3], G3P[8], G3P[9], G4P[6], G4P[8], G6P[4], G6P[9], G6P[14], G8P[10], G8P[14], G9P[8], G9P…
Analysis of GII.P7 and GII.6 noroviruses circulating in Italy during 2011-2016 reveals a replacement of lineages and complex recombination history.
2019
Noroviruses are important human enteric pathogens and monitoring their genetic diversity is important for epidemiological surveillance, vaccine development, and understanding of RNA viruses evolution. Epidemiological investigations have revealed that genogroup II, genotype 6 noroviruses (GII.6) are common agents of gastroenteritis. Upon sequencing of the ORF2 (encoding the viral capsid), GII.6 viruses have been distinguished into three variants. Sentinel hospital-based surveillance in Italy revealed that GII.6 noroviruses were the second most common capsid genotype in 2015, mostly in association with a GII.P7 ORF1 (encoding the viral polymerase). Upon molecular characterization of the ORF1 …
Recombinant norovirus GII.g/GII.12 gastroenteritis in children.
2011
Recombinant GII.g/GII.12 norovirus (NoV) strains emerged in 2008 in Australia and subsequently have been associated with gastroenteritis outbreaks worldwide. In the winter season 2009-2010 GII.12 strains caused 16% of the NoV outbreaks in the United States. During 2009-2010 we also identified GII.g/GII.12 strains during surveillance of sporadic cases of gastroenteritis in Italian children. Severity scores were calculated for the GII.g/GII.12 NoV infections using the Vesikari scale and in two out of three paediatric cases they exceeded the median value calculated for concomitant GII.4 infections. Upon sequence analysis, the Italian strains were found to be recombinant viruses and displayed d…
Surveillance of human astrovirus circulation in Italy 2002-2005: emergence of lineage 2c strains.
2010
AbstractBy screening faecal samples collected over four consecutive years (2002-2005) from hospitalized children with diarrhoea in Palermo, Italy, astroviruses (HAstVs) were detected in 3.95% of the patients. The predominant type circulating was HAstV-1 but, in 2002, only HAstV-2 and -4 were identified. Interestingly, the HAstVs-2 detected appeared to be consistently different in 5′ end of their open reading frame 2 from the previously described subtypes. These novel type 2 strains were included in a new 2c lineage based on the phylogenetic analysis and the presence of nine peculiar substitutions.
Molecular characterization of genotype G6 human rotavirus strains detected in Italy from 1986 to 2009.
2011
Group A human rotavirus (HRV) strains with a bovine-like (G6) major outer capsid protein VP7 were first detected in Palermo, Italy, in the late 1980s, and subsequently worldwide. During a 25-year rotavirus surveillance period, additional HRV G6 strains, associated with either a P[9] or P[14] VP4 genotype, have been detected sporadically, but repeatedly, in Palermo. Whether these G6 HRVs were transmitted to humans directly from an animal reservoir or could have circulated at low prevalence in susceptible individuals is uncertain. Upon sequence analyses of the VP7, VP4, VP6, NSP4 and NSP5 gene segments, all the Italian HRV strains displayed a conserved genotype constellation, G6-P[9]/[14]-I2-…
Genotyping of GII.4 and GIIb norovirus RT-PCR amplicons by RFLP analysis
2007
GII.4 and GIIb/Hilversum norovirus (NoV) strains appear to have a prominent epidemiological role in outbreaks or sporadic cases of human gastroenteritis. Sequence analysis, although laborious, is the reference method used for characterization of noroviruses. In this study a screening test is proposed to characterize GIIb and GII.4 NoVs based on restriction fragment length polymorphism (RFLP) analysis of amplicons obtained from the RNA-dependent RNA polymerase (RdRp) region. Virtual analysis of 793 RdRp sequences of GGI and GGII NoVs, retrieved from GenBank, and representative of global geographical origins on a long-time period, permitted the selection of four restriction enzymes, XmnI, Ahd…
Molecular evolutionary analysis of type-1 human astroviruses identifies putative sites under selection pressure on the capsid protein
2017
Human astroviruses (HAstV) are important enteric pathogens that can be classified into eight sero/genotypes (HAstV-1 to -8). Although the various HAstV types show global spread, type-1 strains tend to be predominant. Molecular analysis of the genomic region encoding the capsid protein (ORF2) has revealed discrete sequence variation, with different lineages within each HAstV type and at least three major lineages have been identified within HAstV-1. Longitudinal epidemiological surveillance has revealed temporal shift of the various HAstV-1 lineages. Metadata analysis of HAstV-1 sequences available in the databases also revealed temporal shifts of the circulation of HAstV-1 lineages, suggest…