Genetic characterization of measles virus strains isolated during an epidemic cluster in Puglia, Italy 2006-2007.
Ontology highlight
ABSTRACT:
SUBMITTER: Chironna M
PROVIDER: S-EPMC2039735 | biostudies-literature | 2007
REPOSITORIES: biostudies-literature
Publications
Genetic characterization of measles virus strains isolated during an epidemic cluster in Puglia, Italy 2006-2007.
Chironna Maria M Prato Rosa R Sallustio Anna A Martinelli Domenico D Germinario Cinzia C Lopalco Pierluigi P Quarto Michele M
Virology journal 20070921
The genetic characterization of wild-type measles strains isolated during an epidemic cluster of measles occurred in Puglia (South Italy), between November 2006 and January 2007, was performed. Measles virus (MV) detection was carried out by a nested RT-PCR on 8 of 18 total cases. The viruses were analyzed using the standard genotyping protocols. The N gene sequences of the strains from outbreak were identical to each other, and sequence analysis revealed that the viruses belonged to genotype B3 ...[more]
Similar Datasets
Project description:Molecular characterization of wild-type measles viruses in China during 1995-2004 demonstrated that genotype H1 was endemic and widely distributed throughout the country. H1-associated cases and outbreaks caused a resurgence of measles beginning in 2005. A total of 210,094 measles cases and 101 deaths were reported by National Notifiable Diseases Reporting System (NNDRS) and Chinese Measles Laboratory Network (LabNet) from 2006 to 2007, and the incidences of measles were 6.8/100,000 population and 7.2/100,000 population in 2006 and 2007, respectively. Five hundred and sixty-five wild-type measles viruses were isolated from 24 of 31 provinces in mainland China during 2006 and 2007, and all of the wild type virus isolates belonged to cluster 1 of genotype H1. These results indicated that H1-cluster 1 viruses were the predominant viruses circulating in China from 2006 to 2007. This study contributes to previous efforts to generate critical baseline data about circulating wild-type measles viruses in China that will allow molecular epidemiologic studies to help measure the progress made toward China's goal of measles elimination by 2012.
| S-EPMC2887432 | biostudies-literature
Project description:Advances in the epidemiological tracing of pathogen transmission have been largely driven by the increasing characterisation of whole-genome sequence data obtained at a finer resolution from infectious disease outbreaks. Dynamic models that integrate genomic and epidemiological data further enhance inference on the evolutionary history and transmission dynamics of epidemic outbreaks by reconstructing the network of 'who-infected-whom'. Swine Vesicular Disease (SVD) was present in Italy from 1966 until 2015, and since the mid-1990s, it has mainly been circulating within Italy's central-southern regions with sporadic incursions to the north of the country. However, a recrudescence of SVD in northern Italy was recorded between November 2006 and October 2007, leading to a large-scale epidemic that significantly affected the intensive pig industry of the Lombardy region. In this study, by using whole-genome sequence data in combination with epidemiological information on disease occurrences, we report a retrospective epidemiological investigation of the 2006-2007 SVD epidemic, providing new insights into the transmission dynamics and evolutionary mode of the two phases that characterised the epidemic event. Our analyses support evidence of undetected premises likely missed in the chain of observed infections, of which the role as the link between the two phases is reinforced by the tempo of SVD virus evolution. These silent transmissions, likely resulting from the gradual loss of a clear SVD clinical manifestation linked to sub-clinical infections, may pose a risk of failure in the early detection of new cases. This study emphasises the power of joint inference schemes based on genomic and epidemiological data integration to inform the transmission dynamics of disease epidemics, ultimately aimed at better disease control.
| S-EPMC8310173 | biostudies-literature
Project description:BackgroundIn recent years, rotavirus genotyping by RT-PCR has provided valuable information about the diversity of rotaviruses (RV) circulating throughout the world.The purpose of the present study was to monitor the prevalence of the different G and P genotypes of rotaviruses circulating in Salento and detect any uncommon or novel types.MethodsDuring the period from January 2006 to December 2007, a total of 243 rotavirus positive stool samples were collected from children with diarrhoea admitted to four Hospitals in the province of Lecce (Copertino, Galatina, Gallipoli and Tricase).All the specimens were tested for RV by real time PCR and genotyped for VP7 (G-type) and VP4 (P-type) gene by reverse transcription (RT) and multiplex PCR using different type specific primers.ResultsIn course of this study we identified 4 common G&P combinations viz. G2P[8], G1P[8], G2P[4] and G9P[8] amongst 59.8% of the typeable rotavirus positives.Rotavirus G2P[8] was recognized as the most widespread genotype during the sentinel-based survey in Salento.The detection of other novel and unusual strains, such as G2P[10], G4P[10], G8P[4], G9P[11] and G10P[8] is noteworthy.Furthermore, a significant number of mixed infections were observed during the survey period but G3P[8] rotaviruses were not detected.ConclusionThis study highlights the genetic diversity among rotaviruses isolated from children in Salento and the emergence of some novel strains. Therefore, it is highly essential to continuously monitor for these strains so as to assess the impact of vaccines on RV strains circulating in Salento and understand the effect of strain variation on efficacy of presently available vaccines.
| S-EPMC2676288 | biostudies-literature
Project description:BackgroundThe European Regional Office of the World Health Organization (WHO/Europe) developed a strategic approach to halt the indigenous transmission of measles in its 53 Member States by 2015. In view of the goal of measles elimination, it is of great importance to assess the circulation of wild-type measles virus (MV). Genetic analysis is indispensable to understand the epidemiology of measles.MethodsUrine and saliva samples were collected between May 2002 and December 2007, in order to find the origins and routes of wild type measles virus circulation. RT-PCR was performed on a total of 414 clinical samples of patients from different Italian regions. The results confirmed the genome presence in 199 samples, out of which 179 were sequenced. The sequences were genotyped by comparing the fragment coding for the carboxyl terminus of the nucleoprotein (450 nucleotides) with that one of the WHO reference strains.ResultsFrom the year 2002 to the year 2007 phylogenetic analysis of measles sequences showed a predominant circulation of the D7 genotype in the Italian territory for the years 2002-2004. This genotype was replaced by D4 and B3 genotypes in the biennium 2006-2007. During the same period C2, A, D5 and D8 genotypes were also detected.ConclusionsGenetic characterization of wild-type MV provides a means to study the transmission pathways of the virus, and is an essential component of laboratory-based surveillance. Knowledge of currently circulating measles virus genotype in Italy will help in monitoring the success of the measles elimination programme and will contribute to evaluate the effectiveness of future vaccination campaigns.
| S-EPMC3568056 | biostudies-literature
Project description:In Italy, between 2003 and 2010, 8/21 Regions recommended varicella routine vaccination (URV). The National Immunization Plan (PNPV) 2012-2014 scheduled the introduction of URV nationwide in 2015, following the results achieved by the eight Regions. Puglia adopted varicella URV in 2006. This study describes epidemiology and costs of varicella in Puglia between 2003 and 2012. One-dose Vaccine Effectiveness (VE) against varicella of any severity and severe hospitalized cases in children was also evaluated. Vaccination coverage (VC) was estimated from the regional immunization registry. Incidence and hospitalization rates were calculated from computerised surveillance system for communicable diseases and hospital discharge registry (ICD9-CM codes: 052.x), respectively. URV impact was assessed by Incidence Rate Ratios (IIRs) and Hospitalization Risk Ratios (HRRs). Hospitalization costs were also evaluated. VE was estimated using the screening method, where PPV was VC in children aged <72 months and PCV was the proportion of cases vaccinated among notified or hospitalized cases, respectively. One-dose VC in children aged ≤ 24 months increased from 49% in the birth cohort 2006 to 91.1% in the cohort 2010; 2-dose VC was 64.8% and 28.8% in the 2005 and 1997 cohort, respectively. Comparing pre and post-vaccination era, incidence declined from 122.5 ×100 000 in 2003-2005 to 13.7 in 2009-2012 (IRR = 0.11, 95% CI = 0.10-0.12), hospitalization rate from 3.9 ×100 000 to 1.1 (HRR = 0.29, 95% CI = 0.21-0.4), hospitalization costs from 319 000 Euros/year to 106 000. One-dose VE against varicella of any severity and severe hospitalized disease was 98.8% and 99%, respectively. Our findings strongly support varicella URV introduction into the Italian Essential Health Interventions, as scheduled by 2015.
| S-EPMC4514359 | biostudies-other
Project description:A study of the distribution of orchid species in Puglia, based on an analysis of 2084 bibliographic reports from 2000 to 2022, was carried out with the aim of revising and updating the information on the consistency of the Orchidaceae family in Puglia, with a special focus on assessing threatened species occurring inside and outside protected areas. The work presents a checklist of the Orchidaceae taxa (genera, species, and subspecies) found in the region, including observations on genera and species that present taxonomic challenges. A total of 113 taxa (i.e., species and subspecies), distributed across 16 genera, are listed in alphabetical order. The most representative genera were Ophrys (51 taxa), Serapias (15 taxa), and Epipactis (11 taxa). Additionally, 49 taxa (43.4%) were found to be endemic to Italy, with 21 of these, mostly belonging to the Ophrys genus, being exclusive to Puglia. Our study notes two different trends of distribution: a predominantly coastal distribution for orchid records located in southern Puglia (the Salento peninsula) and a more widespread distribution for the other provinces. Our study also shows that the greatest number of records locate orchids in protected areas with a positive correlation between their presence and habitats cited in Directive 92/43/EEC.
| S-EPMC10255703 | biostudies-literature
Project description:Brucellosis is a major public health problem still prevalent as a neglected endemic zoonosis requiring proactive attention in many communities worldwide. The present study involved analysis of Brucella field strains submitted for typing to the Italian National Reference Laboratory for Brucellosis from 2007 to 2015. Strains were identified at the species and biovar levels by classic and molecular techniques according to the World Organisation for Animal Health Manual. In total, 5,784 strains were typed: 3,089 Brucella abortus (53.4%), 2,497 B. melitensis (43.2%), 10 B. ovis (0.2%), 181 B. suis (3.1%), and 7 B. ceti (0.1%). The 2,981 strains from cattle were typed as B. abortus biovars 1, 3, and 6 (90.1%) and B. melitensis biovar 3 (9.9%). The 318 strains from water buffalo were typed as B. abortus biovars 1, 3 (95.9%) and B. melitensis biovar 3 (4.1%). The 2,279 strains from sheep and goats were typed as B. abortus biovars 1 and 3 (4.3%); B. melitensis biovars 1, 3, (95.3%); and B. ovis (0.4%). The 173 strains from wild boar were typed as B. suis biovar 2 (98.3%) and B. melitensis biovar 3 (1.7%). The 11 strains from pigs were typed as B. suis biovar 2. The 13 strains from humans were typed as B. melitensis biovar 3. The two strains from horses were typed as B. abortus biovar 1, while the seven strains from dolphins were typed as B. ceti. This additional knowledge on the epidemiology of brucellosis in Italy may be useful to formulate policies and strategies for the control and eradication of the disease in animal populations. The animal species affected, biovars typed, geographical origins, and spatial distributions of isolates are herein analyzed and discussed.
| S-EPMC6430384 | biostudies-literature
Project description:Porcine circovirus 3 (PCV3) is an emerging virus that was first identified in the United States in 2016. Since its first detection, PCV3 has already been found in America, Asia, and Europe. Although PCV3 has already been described in Brazil, knowledge of its detection and sequence variation before 2016 is limited, as well as its distribution in the main swine producing regions of Brazil. In this study, 67 porcine clinical samples collected from nine states in Brazil between 2006 and 2007 were analyzed for PCV3 infection by PCR. Results showed that 47.8% of the samples were PCV3 positive, across all nine states. Of the PCV3-positive samples, 37.5% were also positive for PCV2. Interestingly, no clinical signs were associated with samples that were detected singularly with PCV3 infection. Moreover, the positive PCV3 rate in healthy pigs was higher (29.8%) than that found in unhealthy pigs (17.9%), suggesting that most pigs could live with PCV3 infection without any clinical sign in the analyzed samples. Nucleotide sequence analysis showed that PCV3 strains obtained in this study shared 94.44% to 99.83% sequence identity at the open reading frame 2 (ORF2) gene level with available strains from different countries. PCV3 Brazilian sequences collected in 2006 and 2007 shared 97.94% to 99.62% identity with the strains obtained in 2016. The results of neutrality and selective pressure tests indicated that the PCV3 Cap protein seems unable to tolerate high levels of variation on its sequence. Phylogenetic analysis grouped the Brazilian strains in PCV3a and PCV3b genotypes clusters, both including strains collected in America, Asia, and Europe. Taking the results together, multiple events of introduction of PCV3 may have occurred in Brazil, and Brazilian PCV3 strains may show genetic stability over the past 10 years.
| S-EPMC6466443 | biostudies-literature
Project description:In 2006 and 2007 pig farming in the region of Lombardy, in the north of Italy, was struck by an epidemic of Swine Vesicular Disease virus (SVDV). In fact this epidemic could be viewed as consisting of two sub-epidemics, as the reported outbreaks occurred in two separate time periods. These periods differed in terms of the provinces or municipalities that were affected and also in terms of the timing of implementation of movement restrictions. Here we use a simple mathematical model to analyse the epidemic data, quantifying between-farm transmission probability as a function of between-farm distance. The results show that the distance dependence of between-farm transmission differs between the two periods. In the first period transmission over relatively long distances occurred with higher probability than in the second period, reflecting the effect of movement restrictions in the second period. In the second period however, more intensive transmission occurred over relatively short distances. Our model analysis explains this in terms of the relatively high density of pig farms in the area most affected in this period, which exceeds a critical farm density for between-farm transmission. This latter result supports the rationale for the additional control measure taken in 2007 of pre-emptively culling farms in that area.
| S-EPMC3647039 | biostudies-literature
Project description:Interest in local landraces has unfortunately decreased over, the last decades, in which they have been continuously subjected to a high genetic erosion in favour of new modern varieties. Within the Puglia region (S-E Italy), Foggia province was found to be the richest in vegetable landraces. In the present study, six garlic landraces collected from this area have been assessed for their chemical composition (minerals, organic acids, free sugars, volatile, and phenolic compounds) along with their main morpho-biometrical traits. A commercial genotype was also considered as a reference standard. The landraces show a large variability, but in general high morphological standards, high levels of cations and phenols, and low levels of volatile-(S)-compounds in comparison with the commercial genotype and the literature values. 'Aglio di Peschici' and 'Aglio Rosso di Monteleone di Puglia' are very rich in minerals and phenols (mainly ferulic acid and iso-rhamnetin). This increase in knowledge on the chemical properties of these garlic landraces could represent a tool for encouraging the consumption of a food product. At the same time, the consumption of these landraces would stimulate their cultivation and could highly contribute to protection against the risk of erosion of agro-biodiversity by their in situ/on-farm conservation.
| S-EPMC7404550 | biostudies-literature