Publications by authors named "Gianpiero Zamperin"

25 Publications

  • Page 1 of 1

Interface between Bats and Pigs in Heavy Pig Production.

Viruses 2020 12 22;13(1). Epub 2020 Dec 22.

Laboratory for Viral Emerging Zoonoses, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro PD, Italy.

Bats are often claimed to be a major source for future viral epidemics, as they are associated with several viruses with zoonotic potential. Here we describe the presence and biodiversity of bats associated with intensive pig farms devoted to the production of heavy pigs in northern Italy. Since chiropters or signs of their presence were not found within animal shelters in our study area, we suggest that fecal viruses with high environmental resistance have the highest likelihood for spillover through indirect transmission. In turn, we investigated the circulation of mammalian orthoreoviruses (MRVs), coronaviruses (CoVs) and astroviruses (AstVs) in pigs and bats sharing the same environment. Results of our preliminary study did not show any bat virus in pigs suggesting that spillover from these animals is rare. However, several AstVs, CoVs and MRVs circulated undetected in pigs. Among those, one MRV was a reassortant strain carrying viral genes likely acquired from bats. On the other hand, we found a swine AstV and a MRV strain carrying swine genes in bat guano, indicating that viral exchange at the bat-pig interface might occur more frequently from pigs to bats rather than the other way around. Considering the indoor farming system as the most common system in the European Union (EU), preventive measures should focus on biosecurity rather than displacement of bats, which are protected throughout the EU and provide critical ecosystem services for rural settings.
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http://dx.doi.org/10.3390/v13010004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7822039PMC
December 2020

Multifactorial Causes of Chronic Mortality in Juvenile Sturgeon ().

Animals (Basel) 2020 Oct 13;10(10). Epub 2020 Oct 13.

Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy.

This investigation focused on an episode of chronic mortality observed in juvenile sturgeons. The examined subjects underwent pathological, microbiological, molecular, and chemical investigations. Grossly severe body shape deformities, epaxial muscle softening, and multifocal ulcerative dermatitis were the main observed findings. The more constant histopathologic findings were moderate to severe rarefaction and disorganization of the lymphohematopoietic lymphoid tissues, myofiber degeneration, atrophy and interstitial edema of skeletal epaxial muscles, and degeneration and atrophy of the gangliar neurons close to the myofibers. Chemical investigations showed a lower selenium concentration in affected animals, suggesting nutritional myopathy. Other manifestations were nephrocalcinosis and splenic vessel wall hyalinosis. Septicemia due to bacteria such as , , sp., and pigmented hyphae were found. No major sturgeon viral pathogens were detected by classical methods. Next-generation sequencing (NGS) analysis confirmed the absence of viral pathogens, with the exception of herpesvirus, at the order level; also, the presence of and was confirmed at the family level by the metagenomic classification of NGS data. In the absence of a primary yet undetected biological cause, it is supposed that environmental stressors, including nutritional imbalances, may have led to immune system impairment, facilitating the entry of opportunistic bacteria and mycotic hyphae.
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http://dx.doi.org/10.3390/ani10101866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7602020PMC
October 2020

Unexpected Genetic Diversity of Two Novel Swine MRVs in Italy.

Viruses 2020 05 22;12(5). Epub 2020 May 22.

Diagnostic Virology Laboratory, Department of Animal Health, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, Legnaro, 35020 Padua, Italy.

Mammalian Orthoreoviruses (MRV) are segmented dsRNA viruses in the family . MRVs infect mammals and cause asymptomatic respiratory, gastro-enteric and, rarely, encephalic infections. MRVs are divided into at least three serotypes: MRV1, MRV2 and MRV3. In Europe, swine MRV (swMRV) was first isolated in Austria in 1998 and subsequently reported more than fifteen years later in Italy. In the present study, we characterized two novel reassortant swMRVs identified in one same Italian farm over two years. The two viruses shared the same genetic backbone but showed evidence of reassortment in the S1, S4, M2 segments and were therefore classified into two serotypes: MRV3 in 2016 and MRV2 in 2018. A genetic relation to pig, bat and human MRVs and other unknown sources was identified. A considerable genetic diversity was observed in the Italian MRV3 and MRV2 compared to other available swMRVs. The S1 protein presented unique amino acid signatures in both swMRVs, with unexpected frequencies for MRV2. The remaining genes formed distinct and novel genetic groups that revealed a geographically related evolution of swMRVs in Italy. This is the first report of the complete molecular characterization of novel reassortant swMRVs in Italy and Europe, which suggests a greater genetic diversity of swMRVs never identified before.
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http://dx.doi.org/10.3390/v12050574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7290992PMC
May 2020

Characterization of novel, pathogenic field strains of infectious bronchitis virus (IBV) in poultry in Trinidad and Tobago.

Transbound Emerg Dis 2020 Nov 13;67(6):2775-2788. Epub 2020 Jun 13.

Department of Basic Veterinary Sciences, School of Veterinary Medicine, The University of the West Indies (St. Augustine), Mount Hope, Republic of Trinidad and Tobago.

Avian coronaviruses, including infectious bronchitis virus (IBV) and turkey coronavirus (TCoV), are economically important viruses affecting poultry worldwide. IBV is responsible for causing severe losses to the commercial poultry sector globally. The objectives of this study were to identify the viruses that were causing outbreaks of severe respiratory disease in chickens in Trinidad and Tobago (T&T) and to characterize the strains. Swab samples were collected from birds showing severe respiratory signs in five farms on the island of Trinidad. Samples were tested for the presence of IBV, as well as avian influenza virus (AIV), Newcastle disease virus (NDV) and avian metapneumovirus (aMPV) by real-time reverse transcription polymerase chain reaction (qRT-PCR). All samples from the five farms tested negative for AIV, NDV and aMPV; however, samples from clinically affected birds in all five of the farms tested positive for IBV. Genetic data revealed the presence of TCoV in chickens on two of the farms. Interestingly, these two farms had never reared turkeys. Phylogenetic analysis showed that IBV S1 sequences formed two distinct clusters. Two sequences grouped with vaccine strains within the GI-1 lineage, whereas three sequences grouped together, but separately from other defined lineages, forming a likely new lineage of IBV. Pairwise comparison revealed that the three unique variant strains within the distinct lineage of IBV were significantly different in their S1 nucleotide coding regions from viruses in the closest lineage (16% difference) and locally used vaccine strains (>20% difference). Results also suggested that one of the samples was a recombinant virus, generated from a recombination event between a Trinidad virus of the GI-1 lineage and a Trinidad virus of the newly defined lineage. Many amino acid differences were also observed between the S1 coding regions of the circulating field and vaccine strains, indicating that the IBV vaccines may not be protective. Vaccine-challenge studies are however needed to prove this.
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http://dx.doi.org/10.1111/tbed.13637DOI Listing
November 2020

Unexpected rabies variant identified in kinkajou (), Mato Grosso, Brazil.

Emerg Microbes Infect 2020 Dec;9(1):851-854

FAO and National Reference Centre for rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy.

A second case of a novel rabies variant described once in a capuchin monkey from Mato Grosso, Brazil, was discovered in a rabid wild kinkajou from the same region, indicating a public health risk following exposure to either of the two animals.
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http://dx.doi.org/10.1080/22221751.2020.1759380DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7269027PMC
December 2020

Spatial spread and emergence of reassortant H5 highly pathogenic avian influenza viruses in Iran.

Infect Genet Evol 2020 09 27;83:104342. Epub 2020 Apr 27.

EU/OIE/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'università 10, 35020 Legnaro, Padova, Italy. Electronic address:

Since 2005, H5Nx highly pathogenic avian influenza (HPAI) viruses of the Goose/Guangdong (Gs/GD) lineage have spread worldwide, affecting poultry and wild birds in Asia, Europe, Africa and North America. So far, the role of Western Asia and the Middle East in the diffusion dynamics of this virus has been poorly explored. In order to investigate the genetic diversity and the role of Iran in the transmission dynamics of the Gs/GD lineage, we sequenced the complete genome of twenty-eight H5Nx viruses which were circulating in the country between 2016 and 2018. We reported the first characterization of the HPAI H5N6 subtype of clade 2.3.4.4B in Iran and gave evidence of the high propensity of the Gs/GD H5 AIVs to reassort, describing six novel H5N8 genotypes of clade 2.3.4.4B, some of them likely generated in this area, and one H5N1 reassortant virus of clade 2.3.2.1c. Our spatial analyses demonstrated that the viruses resulted from different viral introductions from Asia and Europe and provided evidence of virus spread from Iran to the Middle East. Therefore, Iran may represent a hot-spot for virus introduction, dissemination and for the generation of new genetic variability. Increasing surveillance efforts in this high-risk area is of utmost importance for the early detection of novel emerging strains with zoonotic potential.
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http://dx.doi.org/10.1016/j.meegid.2020.104342DOI Listing
September 2020

Genomic Sequence of a New Detected in Comber (Serranus cabrilla).

Microbiol Resour Announc 2020 Jan 9;9(2). Epub 2020 Jan 9.

Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Department of Comparative Biomedical Sciences, Legnaro, Padua, Italy

The comber alphavirus was isolated from a fish cell line from the brain of an apparently healthy specimen collected during wild fish surveillance in southern Italy. The comber alphavirus is a new member of the genus , family .
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http://dx.doi.org/10.1128/MRA.01294-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6952657PMC
January 2020

Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza.

Nat Commun 2019 11 22;10(1):5310. Epub 2019 Nov 22.

Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy.

The role of Africa in the dynamics of the global spread of a zoonotic and economically-important virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx intercontinental epidemic waves and demonstrate that Africa mainly acted as an ecological sink of the HPAI H5Nx viruses. A joint analysis of host dynamics and continuous spatial diffusion indicates that poultry trade as well as wild bird migrations have contributed to the virus spreading into Africa, with West Africa acting as a crucial hotspot for virus introduction and dissemination into the continent. We demonstrate varying paths of avian influenza incursions into Africa as well as virus spread within Africa over time, which reveal that virus expansion is a complex phenomenon, shaped by an intricate interplay between avian host ecology, virus characteristics and environmental variables.
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http://dx.doi.org/10.1038/s41467-019-13287-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874648PMC
November 2019

Sequencing of animal viruses: quality data assurance for NGS bioinformatics.

Virol J 2019 11 21;16(1):140. Epub 2019 Nov 21.

Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), viale dell'Università 10, 35120, Legnaro (PD), Italy.

Background: Next generation sequencing (NGS) is becoming widely used among diagnostics and research laboratories, and nowadays it is applied to a variety of disciplines, including veterinary virology. The NGS workflow comprises several steps, namely sample processing, library preparation, sequencing and primary/secondary/tertiary bioinformatics (BI) analyses. The latter is constituted by a complex process extremely difficult to standardize, due to the variety of tools and metrics available. Thus, it is of the utmost importance to assess the comparability of results obtained through different methods and in different laboratories. To achieve this goal, we have organized a proficiency test focused on the bioinformatics components for the generation of complete genome sequences of salmonid rhabdoviruses.

Methods: Three partners, that performed virus sequencing using different commercial library preparation kits and NGS platforms, gathered together and shared with each other 75 raw datasets which were analyzed separately by the participants to produce a consensus sequence according to their own bioinformatics pipeline. Results were then compared to highlight discrepancies, and a subset of inconsistencies were investigated more in detail.

Results: In total, we observed 526 discrepancies, of which 39.5% were located at genome termini, 14.1% at intergenic regions and 46.4% at coding regions. Among these, 10 SNPs and 99 indels caused changes in the protein products. Overall reproducibility was 99.94%. Based on the analysis of a subset of inconsistencies investigated more in-depth, manual curation appeared the most critical step affecting sequence comparability, suggesting that the harmonization of this phase is crucial to obtain comparable results. The analysis of a calibrator sample allowed assessing BI accuracy, being 99.983%.

Conclusions: We demonstrated the applicability and the usefulness of BI proficiency testing to assure the quality of NGS data, and recommend a wider implementation of such exercises to guarantee sequence data uniformity among different virology laboratories.
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http://dx.doi.org/10.1186/s12985-019-1223-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868765PMC
November 2019

Complete Genome Sequences of Three Rabbit Endogenous Lentivirus Type K Viruses Obtained from Commercial Meat Rabbits in Italy.

Microbiol Resour Announc 2019 Oct 10;8(41). Epub 2019 Oct 10.

Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy.

Rabbit endogenous lentivirus type K (RELIK) was discovered in the genome of the European rabbit (). In our study, we present three complete genome sequences of RELIK viruses generated using a target amplification approach performed on the RNA of commercial rabbits from Italy.
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http://dx.doi.org/10.1128/MRA.00669-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6787314PMC
October 2019

First whole genome characterization of porcine astrovirus detected in swine faeces in Italy.

Vet Ital 2019 Sep 30;55(3):221-229. Epub 2019 Sep 30.

Diagnostic Virology Laboratory, Department of Animal Health, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, 35020, Legnaro (PD), Italy.

Porcine astroviruses (PoAstV) are found in the gastrointestinal tract of healthy and diseased pigs worldwide. However, their role in causing enteric disease in pigs and other animals has not been elucidated. In the present report, we describe for the first time in Italy, the identification and genetic characterization, through whole genome sequencing, of a PoAstV2 in pigs in Northeast Italy in 2015. This instance is the first detection of PoAstV2 in pigs in Italy. The phylogenetic analysis of the complete ORF2 segment highlights the high similarity of this virus to those circulating that same year in Japan. There are very few full astrovirus genomes available, and the present data represent an important contribution towards a better understanding of the characteristics and evolution of these viruses.
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http://dx.doi.org/10.12834/VetIt.1873.9956.1DOI Listing
September 2019

Complete Genome Sequence of Psittacine Adenovirus 1, Identified from Poicephalus senegalus in Italy.

Microbiol Resour Announc 2018 Sep 20;7(11). Epub 2018 Sep 20.

Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (Padua), Italy.

Using a metagenomics approach, we were able to determine for the first time the full-genome sequence of a psittacine adenovirus 1 isolate that was recovered from the liver of a dead Senegal parrot (Poicephalus senegalus) in Italy. The results of the phylogenetic investigations revealed the existence of high genetic diversity among adenoviruses circulating in psittacine birds.
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http://dx.doi.org/10.1128/MRA.01037-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256658PMC
September 2018

Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout.

Virus Evol 2018 Jul 18;4(2):vey019. Epub 2018 Jul 18.

Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università 10, Legnaro, Padova, Italy.

Infectious pancreatic necrosis virus (IPNV) is a naked double-stranded RNA virus with a bi-segmented genome that is classified within the family , genus . IPNV was first detected in Italian trout farms in the late 1970s and ultimately became endemic. To characterize the evolution of IPNV circulating in Italy, particularly whether there is a link between evolutionary rate and virulence, we obtained and analyzed the VP1 (polymerase) and the pVP2 (major capsid protein precursor) sequences from 75 IPNV strains sampled between 1978 and 2017. These data revealed that the Italian IPNV exhibit relatively little genetic variation over the sampling period, falling into four genetic clusters within a single genogroup (group 2 for VP1 and genogroup V for pVP2) and contained one example of inter-segment reassortment. The mean evolutionary rates for VP1 and pVP2 were estimated to be 1.70 and 1.45 × 10 nucleotide substitutions per site, per year, respectively, and hence significantly lower than those seen in other . Similarly, the relatively low ratios of non-synonymous () to synonymous () nucleotide substitutions per site in both genes indicated that IPNV was subject to strong selective constraints, again in contrast to other RNA viruses infecting salmonids that co-circulate in the same area during the same time period. Notably, all the Italian IPNV harbored a proline at position 217 (P) and a threonine at position 221 (T) in pVP2, both of which are associated with a low virulence phenotype. We therefore suggest the lower virulence of IPNV may have resulted in reduced rates of virus replication and hence lower rates of evolutionary change. The data generated here will be of importance in understanding the factors that shape the evolution of in nature.
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http://dx.doi.org/10.1093/ve/vey019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054257PMC
July 2018

Highly Pathogenic Avian Influenza A(H5N8) Virus, Cameroon, 2017.

Emerg Infect Dis 2018 07;24(7):1367-1370

Highly pathogenic avian influenza A(H5N8) viruses of clade 2.3.4.4 spread into West Africa in late 2016 during the autumn bird migration. Genetic characterization of the complete genome of these viruses detected in wild and domestic birds in Cameroon in January 2017 demonstrated the occurrence of multiple virus introductions.
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http://dx.doi.org/10.3201/eid2407.172120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6038759PMC
July 2018

Highly Pathogenic Avian Influenza A(H5N8) Virus, Democratic Republic of the Congo, 2017.

Emerg Infect Dis 2018 07;24(7):1371-1374

In 2017, highly pathogenic avian influenza A(H5N8) virus was detected in poultry in the Democratic Republic of the Congo. Whole-genome phylogeny showed the virus clustered with H5N8 clade 2.3.4.4B strains from birds in central and southern Asia. Emergence of this virus in central Africa represents a threat for animal health and food security.
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http://dx.doi.org/10.3201/eid2407.172123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6038760PMC
July 2018

Identification of a newly described OsHV-1 µvar from the North Adriatic Sea (Italy).

J Gen Virol 2018 05 26;99(5):693-703. Epub 2018 Mar 26.

Department of Biology, University of Padova, Padova (PD), Italy.

The surveillance activities for abnormal bivalve mortality events in Italy include the diagnosis of ostreid herpesvirus type 1 (OsHV-1) in symptomatic oysters. OsHV-1-positive oysters (Crassostrea gigas) were used as a source for in vivo virus propagation and a virus-rich sample was selected to perform shotgun sequencing based on Illumina technology. Starting from this unpurified supernatant sample from gills and mantle, we generated 3.5 million reads (2×300 bp) and de novo assembled the whole genome of an Italian OsHV-1 microvariant (OsHV-1-PT). The OsHV-1-PT genome encodes 125 putative ORFs, 7 of which had not previously been predicted in other sequenced Malacoherpesviridae. Overall, OsHV-1-PT displays typical microvariant OsHV-1 genome features, while few polymorphisms (0.08 %) determine its uniqueness. As little is known about the genetic determinants of OsHV-1 virulence, comparing complete OsHV-1 genomes supports a better understanding of the virus pathogenicity and provides new insights into virus-host interactions.
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http://dx.doi.org/10.1099/jgv.0.001042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994699PMC
May 2018

Detection and characterization of a rhabdovirus causing mortality in black bullhead catfish, Ameiurus melas.

J Fish Dis 2018 Jul 23;41(7):1063-1075. Epub 2018 Mar 23.

Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy.

This study fully describes a severe disease outbreak occurred in 2016 in black bullhead catfish farmed in Italy. Affected fish showed nervous clinical signs as well as emaciations and haemorrhagic petechiae on the skin at the fin bases, abdomen and gills. Viral isolation in cell culture allowed the subsequent identification of a rhabdovirus, tentatively named ictalurid rhabdovirus (IcRV), through electron microscopy, immunofluorescence and whole genome sequencing (WGS). The newly isolated virus, together with 14 additional viral strains stored in our repository and detected during similar mortality episodes in the period 1993-2016, was phylogenetically analysed on the basis of the nucleoprotein and the glycoprotein nucleotide and amino acid sequences. The genetic distances among Italian IcRV strains were also estimated. Our results show that all the IcRV strains belong to the genus Sprivivirus and are closely related to the tench rhabdovirus (TenRV). Italian catfish production is constantly decreasing, mainly due to viral infections, which include the newly characterized IcRV. Data presented in this work will assist to investigate the molecular epidemiology and the diffusive dynamics of this virus and to develop adequate surveillance activities.
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http://dx.doi.org/10.1111/jfd.12797DOI Listing
July 2018

Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses.

Infect Genet Evol 2018 03 30;58:279-289. Epub 2018 Jan 30.

National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy.

Coronaviruses (CoVs) have been documented in almost every species of bat sampled. Bat CoVs exhibit both extensive genetic diversity and a broad geographic range, indicative of a long-standing host association. Despite this, the respective roles of long-term virus-host co-divergence and cross-species transmission (host-jumping) in the evolution of bat coronaviruses are unclear. Using a phylogenetic approach we provide evidence that CoV diversity in bats is shaped by both species richness and their geographical distribution, and that CoVs exhibit clustering at the level of bat genera, with these genus-specific clusters largely associated with distinct CoV species. Co-phylogenetic analyses revealed that cross-species transmission has been more common than co-divergence across coronavirus evolution as a whole, and that cross-species transmission events were more likely between sympatric bat hosts. Notably, however, an analysis of the CoV RNA polymerase phylogeny suggested that many such host-jumps likely resulted in short-term spill-over infections, with little evidence for sustained onward transmission in new co-roosting host species.
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http://dx.doi.org/10.1016/j.meegid.2018.01.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106311PMC
March 2018

A two-year monitoring period of the genetic properties of clade 2.3.2.1c H5N1 viruses in Nigeria reveals the emergence and co-circulation of distinct genotypes.

Infect Genet Evol 2018 01 15;57:98-105. Epub 2017 Nov 15.

Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa.

Phylogenetic analyses of the complete genomes of the highly pathogenic avian influenza (HPAI) 2.3.2.1c H5N1 virus strains causing outbreaks in Nigeria's poultry population from 2014 to 2016 showed evidence of distinct co-circulating genotypes and the emergence of reassortant viruses. One of these reassortants became the predominant strain by 2016, and the NA protein of this strain possessed the V96A substitution known to confer reduced susceptibility to neuraminidase inhibiting antiviral drugs. Our findings also demonstrated evolutionary relationships between Nigerian isolates and European and Middle Eastern strains of H5N1 which provides further evidence for the proposed role of migratory birds in spreading the virus, although the involvement of the live poultry trade cannot be excluded. Efforts must be directed towards improving biosecurity and gaining the cooperation of poultry farmers for more effective control of HPAI, in order to mitigate the emergence of HPAI strains in Nigeria with biological properties that are potentially even more dangerous to animals and humans.
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http://dx.doi.org/10.1016/j.meegid.2017.10.027DOI Listing
January 2018

Highly Pathogenic Avian Influenza H5N1 Clade 2.3.2.1c Virus in Lebanon, 2016.

Avian Dis 2017 Jun;61(2):271-273

B Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, 10, 35020, Legnaro, Padova, Italy.

We report the phylogenetic analysis of the first outbreak of H5N1 highly pathogenic avian influenza virus detected in Lebanon from poultry in April 2016. Our whole-genome sequencing analysis revealed that the Lebanese H5N1 virus belongs to genetic clade 2.3.2.1c and clusters with viruses from Europe and West Africa.
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http://dx.doi.org/10.1637/11544-113016-Case.1DOI Listing
June 2017

Vaccine immune pressure influences viral population complexity of avian influenza virus during infection.

Vet Microbiol 2017 May 27;203:88-94. Epub 2017 Feb 27.

Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy.

Vaccines are useful tools to control influenza A virus infection in poultry, but they need to be periodically reformulated to guarantee appropriate protection from infection and to limit viral replication and circulation, which could favour the emergence of new variants. In this study, a deep sequencing approach was used to characterize and follow the evolution of the hemagglutinin of the H5N1 highly pathogenic avian influenza viral population in infected animals vaccinated with two vaccines conferring different protection levels. Results from this preliminary investigation suggested that the evolution of the viral population, as well as the abundance and heterogeneity of minority variants could be influenced by the immune pressure conferred by vaccination.
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http://dx.doi.org/10.1016/j.vetmic.2017.02.016DOI Listing
May 2017

Unexpected Interfarm Transmission Dynamics during a Highly Pathogenic Avian Influenza Epidemic.

J Virol 2016 07 24;90(14):6401-6411. Epub 2016 Jun 24.

Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy.

Unlabelled: Next-generation sequencing technology is now being increasingly applied to study the within- and between-host population dynamics of viruses. However, information on avian influenza virus evolution and transmission during a naturally occurring epidemic is still limited. Here, we use deep-sequencing data obtained from clinical samples collected from five industrial holdings and a backyard farm infected during the 2013 highly pathogenic avian influenza (HPAI) H7N7 epidemic in Italy to unravel (i) the epidemic virus population diversity, (ii) the evolution of virus pathogenicity, and (iii) the pathways of viral transmission between different holdings and sheds. We show a high level of genetic diversity of the HPAI H7N7 viruses within a single farm as a consequence of separate bottlenecks and founder effects. In particular, we identified the cocirculation in the index case of two viral strains showing a different insertion at the hemagglutinin cleavage site, as well as nine nucleotide differences at the consensus level and 92 minority variants. To assess interfarm transmission, we combined epidemiological and genetic data and identified the index case as the major source of the virus, suggesting the spread of different viral haplotypes from the index farm to the other industrial holdings, probably at different time points. Our results revealed interfarm transmission dynamics that the epidemiological data alone could not unravel and demonstrated that delay in the disease detection and stamping out was the major cause of the emergence and the spread of the HPAI strain.

Importance: The within- and between-host evolutionary dynamics of a highly pathogenic avian influenza (HPAI) strain during a naturally occurring epidemic is currently poorly understood. Here, we perform for the first time an in-depth sequence analysis of all the samples collected during a HPAI epidemic and demonstrate the importance to complement outbreak investigations with genetic data to reconstruct the transmission dynamics of the viruses and to evaluate the within- and between-farm genetic diversity of the viral population. We show that the evolutionary transition from the low pathogenic form to the highly pathogenic form occurred within the first infected flock, where we identified haplotypes with hemagglutinin cleavage site of different lengths. We also identify the index case as the major source of virus, indicating that prompt application of depopulation measures is essential to limit virus spread to other farms.
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http://dx.doi.org/10.1128/JVI.00538-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936132PMC
July 2016

De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici.

BMC Genomics 2014 Apr 27;15:313. Epub 2014 Apr 27.

Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy.

Background: Pyrenochaeta lycopersici is a soil-dwelling ascomycete pathogen that causes corky root rot disease in tomato (Solanum lycopersicum) and other Solanaceous crops, reducing fruit yields by up to 75%. Fungal pathogens that infect roots receive less attention than those infecting the aerial parts of crops despite their significant impact on plant growth and fruit production.

Results: We assembled a 54.9Mb P. lycopersici draft genome sequence based on Illumina short reads, and annotated approximately 17,000 genes. The P. lycopersici genome is closely related to hemibiotrophs and necrotrophs, in agreement with the phenotypic characteristics of the fungus and its lifestyle. Several gene families related to host-pathogen interactions are strongly represented, including those responsible for nutrient absorption, the detoxification of fungicides and plant cell wall degradation, the latter confirming that much of the genome is devoted to the pathogenic activity of the fungus. We did not find a MAT gene, which is consistent with the classification of P. lycopersici as an imperfect fungus, but we observed a significant expansion of the gene families associated with heterokaryon incompatibility (HI).

Conclusions: The P. lycopersici draft genome sequence provided insight into the molecular and genetic basis of the fungal lifestyle, characterizing previously unknown pathogenic behaviors and defining strategies that allow this asexual fungus to increase genetic diversity and to acquire new pathogenic traits.
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http://dx.doi.org/10.1186/1471-2164-15-313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234444PMC
April 2014

The high polyphenol content of grapevine cultivar tannat berries is conferred primarily by genes that are not shared with the reference genome.

Plant Cell 2013 Dec 6;25(12):4777-88. Epub 2013 Dec 6.

Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, 11600 Montevideo, Uruguay.

The grapevine (Vitis vinifera) cultivar Tannat is cultivated mainly in Uruguay for the production of high-quality red wines. Tannat berries have unusually high levels of polyphenolic compounds, producing wines with an intense purple color and remarkable antioxidant properties. We investigated the genetic basis of these important characteristics by sequencing the genome of the Uruguayan Tannat clone UY11 using Illumina technology, followed by a mixture of de novo assembly and iterative mapping onto the PN40024 reference genome. RNA sequencing data for genome reannotation were processed using a combination of reference-guided annotation and de novo transcript assembly, allowing 5901 previously unannotated or unassembled genes to be defined and resulting in the discovery of 1873 genes that were not shared with PN40024. Expression analysis showed that these cultivar-specific genes contributed substantially (up to 81.24%) to the overall expression of enzymes involved in the synthesis of phenolic and polyphenolic compounds that contribute to the unique characteristics of the Tannat berries. The characterization of the Tannat genome therefore indicated that the grapevine reference genome lacks many genes that appear to be relevant for the varietal phenotype.
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http://dx.doi.org/10.1105/tpc.113.118810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903987PMC
December 2013

De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity.

BMC Genomics 2013 Jan 18;14:41. Epub 2013 Jan 18.

Biotechnology Department, University of Verona, Strada Le Grazie 15, I-37134, Verona, Italy.

Background: Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to disentangle genetic and environmental factors.

Results: We have shown that cDNA sequencing by RNA-seq is a robust approach for the characterization of varietal diversity between a local grapevine cultivar (Corvina) and the PN40024 reference genome. We detected 15,161 known genes including 9463 with novel splice isoforms, and identified 2321 potentially novel protein-coding genes in non-annotated or unassembled regions of the reference genome. We also discovered 180 apparent private genes in the Corvina genome which were missing from the reference genome.

Conclusions: The de novo assembly approach allowed a substantial amount of the Corvina transcriptome to be reconstructed, improving known gene annotations by robustly defining gene structures, annotating splice isoforms and detecting genes without annotations. The private genes we discovered are likely to be nonessential but could influence certain cultivar-specific characteristics. Therefore, the application of de novo transcriptome assembly should not be restricted to species lacking a reference genome because it can also improve existing reference genome annotations and identify novel, cultivar-specific genes.
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http://dx.doi.org/10.1186/1471-2164-14-41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556335PMC
January 2013