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Article ; Online: SARS-CoV-2 and other human coronavirus show genome patterns previously associated to reduced viral recognition and altered immune response

Giovanni Franzo

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 10

Abstract: Abstract A new pandemic caused by the betacoronavirus SARS-CoV-2 originated in China in late 2019. Although often asymptomatic, a relevant percentage of affected people can develop severe pneumonia. Initial evidence suggests that dysregulation of the ... ...

Abstract	Abstract A new pandemic caused by the betacoronavirus SARS-CoV-2 originated in China in late 2019. Although often asymptomatic, a relevant percentage of affected people can develop severe pneumonia. Initial evidence suggests that dysregulation of the immune response could contribute to the pathogenesis, as previously demonstrated for SARS-CoV. The presence of genome composition features involved in delaying viral recognition is herein investigated for human coronaviruses (HCoVs), with a special emphasis on SARS-CoV-2. A broad collection of HCoVs polyprotein, envelope, matrix, nucleocapsid and spike coding sequences was downloaded and several statistics representative of genome composition and codon bias were investigated. A model able to evaluate and test the presence of a significant under- or over-representation of dinucleotide pairs while accounting for the underlying codon bias and protein sequence was also implemented. The study revealed the significant under-representation of CpG dinucleotide pair in all HcoV, but especially in SARS-CoV and even more in SARS-CoV-2. The presence of forces acting to minimize CpG content was confirmed by relative synonymous codon usage pattern. Codons containing the CpG pair were severely under-represented, primarily in the polyprotein and spike coding sequences of SARS-CoV-2. Additionally, a significant under-representation of the TpA pair was observed in the N and S region of SARS-CoV and SARS-CoV-2. Increasing experimental evidence has proven that CpG and TpA are targeted by innate antiviral host defences, contributing both to RNA degradation and RIG-1 mediated interferon production. The low content of these dinucleotides could contribute to a delayed interferon production, dysregulated immune response, higher viral replication and poor outcome. Significantly, the RIG-1 signalling pathway was proven to be defective in elderlies, suggesting a likely interaction between limited viral recognition and lower responsiveness in interferon production that could justify the higher ...
Keywords	Medicine ; R ; Science ; Q
Subject code	572 ; 570
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Porcine Circovirus 2 Genotypes, Immunity and Vaccines

Giovanni Franzo / Joaquim Segalés

Pathogens, Vol 9, Iss 1049, p

Multiple Genotypes but One Single Serotype

2020 Volume 1049

Abstract: Identified for the first time in the 1990s, Porcine circovirus 2 (PCV-2) should not be considered an emerging virus anymore. Nevertheless, many aspects of its biology and epidemiology are still controversial. Particularly, its high evolutionary rate has ... ...

Abstract	Identified for the first time in the 1990s, Porcine circovirus 2 (PCV-2) should not be considered an emerging virus anymore. Nevertheless, many aspects of its biology and epidemiology are still controversial. Particularly, its high evolutionary rate has caused the emergence of several variants and genotypes, alternating on the worldwide proscenium. The biological and practical implications of such heterogenicity are unfortunately largely unknown. The effectiveness of currently available vaccines against new genotypes that have emerged over time has been the topic of an intense debate and often inconclusive or contradictory results between experimental, field, and epidemiological studies have been gathered. The challenge in establishing an effective PCV-2 disease model, the peculiarities in experimental design and settings and the strains involved could justify the observed differences. The present work aims to summarize and critically review the available knowledge on PCV-2 genetic heterogeneity, immunity, and vaccine efficacy, organizing and harmonizing the available data from different sources, shedding light on this complex field and highlighting current knowledge gaps and future perspectives. So far, all vaccines in the market have shown great efficacy in reducing clinical signs associated to diseases caused by PCV-2, independently of the genotype present in the farm. Moreover, experimental data demonstrated the cross-protection of PCV-2a vaccines against the most widespread genotypes (PCV-2a, PCV-2b, and PCV-2d). Therefore, despite the significant number of genotypes described/proposed (PCV-2a to PCV-2i), it seems one single PCV-2 serotype would exist so far.
Keywords	PCV-2 ; vaccine ; genotypes ; serotype ; evolution ; cross-protection ; Medicine ; R
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: When Everything Becomes Bigger

Giovanni Franzo / Matteo Legnardi / Giulia Faustini / Claudia Maria Tucciarone / Mattia Cecchinato

Animals, Vol 13, Iss 1804, p

Big Data for Big Poultry Production

2023 Volume 1804

Abstract: In future decades, the demand for poultry meat and eggs is predicted to considerably increase in pace with human population growth. Although this expansion clearly represents a remarkable opportunity for the sector, it conceals a multitude of challenges. ...

Abstract	In future decades, the demand for poultry meat and eggs is predicted to considerably increase in pace with human population growth. Although this expansion clearly represents a remarkable opportunity for the sector, it conceals a multitude of challenges. Pollution and land erosion, competition for limited resources between animal and human nutrition, animal welfare concerns, limitations on the use of growth promoters and antimicrobial agents, and increasing risks and effects of animal infectious diseases and zoonoses are several topics that have received attention from authorities and the public. The increase in poultry production must be achieved mainly through optimization and increased efficiency. The increasing ability to generate large amounts of data (“big data”) is pervasive in both modern society and the farming industry. Information accessibility—coupled with the availability of tools and computational power to store, share, integrate, and analyze data with automatic and flexible algorithms—offers an unprecedented opportunity to develop tools to maximize farm profitability, reduce socio-environmental impacts, and increase animal and human health and welfare. A detailed description of all topics and applications of big data analysis in poultry farming would be infeasible. Therefore, the present work briefly reviews the application of sensor technologies, such as optical, acoustic, and wearable sensors, as well as infrared thermal imaging and optical flow, to poultry farming. The principles and benefits of advanced statistical techniques, such as machine learning and deep learning, and their use in developing effective and reliable classification and prediction models to benefit the farming system, are also discussed. Finally, recent progress in pathogen genome sequencing and analysis is discussed, highlighting practical applications in epidemiological tracking, and reconstruction of microorganisms’ population dynamics, evolution, and spread. The benefits of the objective evaluation of the effectiveness ...
Keywords	poultry ; big data ; sensors ; machine learning ; deep learning ; sequencing ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Subject code	670
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Conflicting Evidence between Clinical Perception and Molecular Epidemiology

Giovanni Franzo / Giulia Faustini / Claudia Maria Tucciarone / Daniela Pasotto / Matteo Legnardi / Mattia Cecchinato

Animals, Vol 13, Iss 24, p

The Case of Fowl Adenovirus D

2023 Volume 3851

Abstract: Fowl adenoviruses (FAdVs, species FAdV-A/-E) are responsible for several clinical syndromes reported with increasing frequency in poultry farms in the last decades. In the present study, a phylodynamic analysis was performed on a group of FAdV-D Hexon ... ...

Abstract	Fowl adenoviruses (FAdVs, species FAdV-A/-E) are responsible for several clinical syndromes reported with increasing frequency in poultry farms in the last decades. In the present study, a phylodynamic analysis was performed on a group of FAdV-D Hexon sequences with adequate available metadata. The obtained results demonstrated the long-term circulation of this species, at least several decades before the first identification of the disease. After a period of progressive increase, the viral population showed a high-level circulation from approximately the 1960s to the beginning of the new millennium, mirroring the expansion of intensive poultry production and animal trade. At the same time, strain migration occurred mainly from Europe to other continents, although other among-continent connections were estimated. Thereafter, the viral population declined progressively, likely due to the improved control measures, potentially including the development and application of FAdV vaccines. An increase in the viral evolutionary rate featured this phase. A role of vaccine-induced immunity in shaping viral evolution could thus be hypothesized. Accordingly, several sites of the Hexon, especially those targeted by the host response were proven under a significant pervasive or episodic diversifying selection. The present study results demonstrate the role of intensive poultry production and market globalization in the rise of FAdV. The applied control strategies, on the other hand, were effective in limiting viral circulation and shaping its evolution.
Keywords	FAdV ; hexon ; evolution ; epidemiology ; phylogenesis ; phylogeography ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Subject code	630
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: First detection and molecular characterization of porcine reproductive and respiratory syndrome virus in Namibia, Africa

Umberto Molini / Lauren M. Coetzee / Maria Y. Hemberger / Bernard Chiwome / Siegfried Khaiseb / William G. Dundon / Giovanni Franzo

Frontiers in Veterinary Science, Vol

2024 Volume 10

Abstract: IntroductionThe swine sector in Africa plays an important role in local economies, contributing to poverty alleviation and community subsistence. In addition, intensive farming is progressively becoming more important in the region. Therefore, any ... ...

Abstract	IntroductionThe swine sector in Africa plays an important role in local economies, contributing to poverty alleviation and community subsistence. In addition, intensive farming is progressively becoming more important in the region. Therefore, any disease affecting swine populations can have detrimental effects on local communities. Porcine Reproductive and Respiratory Syndrome (PRRS) is among the most important infectious diseases affecting swine worldwide, but information on its epidemiology in Africa is extremely limited.Material and methodsIn the present study, 147 healthy butchered pigs, originating from 15 Namibian intensive and rural farms were tested by RT-PCR and the ORF7 genes of positive samples were sequenced for further genetic characterization and phylogenetic analysis. Additionally, 55 warthogs were also evaluated using the same approach.ResultsOverall, 7 out of 147 pigs (4.76%) tested positive, all originating from 3 rural farms (with a within-herd detection frequency higher than 14%) characterized by strong epidemiological links. All industrial pig and warthog samples were negative. Sequence analysis revealed that all strains belonged to the Betaarterivirus suid1 species, previously known as PRRSV type I, and were likely imported from Europe at least 6 years ago, evolving independently thereafter. When and how the first introduction occurred could not be determined due to the absence of other African sequences for comparison.DiscussionThe present work provides the first detection and characterization of PRRSV molecular epidemiology in Namibia. Based on the present findings, the presence of the PPRSV appears marginal and limited to backyard farms. While biosecurity measures applied in industrial farms appear to be effective in preventing viral introduction, PRRSV circulation in rural settings still represents a potential threat, and considering the socio-economical implication of livestock diseases decreasing animal performances in rural areas, active monitoring should be encouraged to promptly ...
Keywords	PRRSV ; Namibia ; Africa ; molecular epidemiology ; phylogenetics ; virus ; Veterinary medicine ; SF600-1100
Subject code	630
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Porcine circovirus 2 (PCV-2) genotype update and proposal of a new genotyping methodology.

Giovanni Franzo / Joaquim Segalés

PLoS ONE, Vol 13, Iss 12, p e

2018 Volume 0208585

Abstract: Porcine circovirus 2 (PCV-2) is one of the most widespread viral infections of swine, causing a remarkable economic impact because of direct losses and indirect costs for its control. As other ssDNA viruses, PCV-2 is characterized by a high evolutionary ... ...

Abstract	Porcine circovirus 2 (PCV-2) is one of the most widespread viral infections of swine, causing a remarkable economic impact because of direct losses and indirect costs for its control. As other ssDNA viruses, PCV-2 is characterized by a high evolutionary rate, leading to the emergence of a plethora of variants with different biological and epidemiological features. Over time, several attempts have been made to organize PCV-2 genetic heterogeneity in recognized genotypes. This categorization has clearly simplified the epidemiological investigations, allowing to identify different spatial and temporal patterns among genotypes. Additionally, variable virulence and vaccine effectiveness have also been hypothesized. However, the rapid increase in sequencing activity, coupled with the per se high viral variability, has challenged the previously established nomenclature, leading to the definition of several study-specific genotypes and hindering the capability of performing comparable epidemiological studies. Based on these premises, an updated classification scheme is herein reported. Recognizing the impossibility of defining a clear inter-cluster p-distance cut-off, the present study proposes a phylogeny-grounded genotype definition based on three criteria: maximum intra-genotype p-distance of 13% (calculated on the ORF2 gene), bootstrap support at the corresponding internal node higher than 70% and at least 15 available sequences. This scheme allowed defining 8 genotypes (PCV-2a to PCV-2h), which six of those had been previously proposed. To minimize the inconvenience of implementing a new classification, the most common names already adopted have been maintained when possible. The analysis of sequence-associated metadata highlighted a highly unbalanced sequencing activity in terms of geographical, host and temporal distribution. The PCV-2 molecular epidemiology scenario appears therefore characterized by a severe bias that could lead to spurious associations between genetic and epidemiological/biological viral ...
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Investigation of Serotype Prevalence of Escherichia coli Strains Isolated from Layer Poultry in Greece and Interactions with Other Infectious Agents

Dimitrios Koutsianos / Labrini V. Athanasiou / Dimitris Mossialos / Giovanni Franzo / Mattia Cecchinato / Konstantinos C. Koutoulis

Veterinary Sciences, Vol 9, Iss 4, p

2022 Volume 152

Abstract: Colibacillosis is the most common bacterial disease in poultry and it is caused by avian pathogenic Escherichia coli (APEC), which is assigned to various O-serogroups. Previous studies have shown that APEC strains are more often related to certain O- ... ...

Abstract	Colibacillosis is the most common bacterial disease in poultry and it is caused by avian pathogenic Escherichia coli (APEC), which is assigned to various O-serogroups. Previous studies have shown that APEC strains are more often related to certain O-serogroups such asO78, O2 and O1. E. coli has been reported to act either as a primary or secondary agent in complicating other infections. The aim of this study was to investigate the occurrence of and characterize the O-serogroups of E. coli strains isolated from commercial layer and layer breeder flocks showing macroscopic lesions of colibacillosis and increased or normal mortality in Greece. Furthermore, we attempted to assess the interaction between infectious agents such as Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), infectious bronchitis (IBV) and infectious laryngotracheitis (ILT) with E. coli infections in layer flocks with increased mortality. Our study revealed that in addition to the common serogroups (O78, O2), many other, and less common serogroups were identified, including O111. The O78, O111 and O2 serogroups were frequently detected in flocks with lesions of colibacillosis and increased mortality whereas O2, O88 and O8 were reported more commonly in birds with colibacillosis lesions but normal mortality rates. These data provide important information for colibacillosis monitoring and define preventative measures, especially by using effective vaccination programs because E. coli vaccines are reported to mainly offer homologous protection. Finally, concerning the association of the four tested infectious agents with E. coli mortality, our study did not reveal a statistically significant effect of the above infectious agents tested with E. coli infection mortality.
Keywords	commercial layers ; Escherichia coli ; layer breeder ; predisposing factor ; O-serogroup ; Veterinary medicine ; SF600-1100
Subject code	630
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular survey of Cytauxzoon spp. and Hepatozoon spp. in felids using a novel real-time PCR approach

Marika Grillini / Paola Beraldo / Antonio Frangipane di Regalbono / Giorgia Dotto / Cinzia Tessarin / Giovanni Franzo / Erica Marchiori / David Modrý / Giulia Simonato

Frontiers in Veterinary Science, Vol

2023 Volume 10

Abstract: Tick-transmitted apicomplexans of the genera Cytauxzoon and Hepatozoon affect a wide range of felids worldwide, but little is known about them. Recently, several studies addressed the species circulating in Europe, their distribution, and their hosts. ... ...

Abstract	Tick-transmitted apicomplexans of the genera Cytauxzoon and Hepatozoon affect a wide range of felids worldwide, but little is known about them. Recently, several studies addressed the species circulating in Europe, their distribution, and their hosts. Molecular assays are the method of choice for their detection. Unfortunately, conventional PCRs already described are time- and cost-consuming and specific for either Hepatozoon or Cytauxzoon detection. This study was developed to evaluate (i) the occurrence of Cytauxzoon and Hepatozoon in felids using a fast and cost-saving real-time PCR capable of detecting both protozoa simultaneously, (ii) the distribution of Cytauxzoon and Hepatozoon species in north-eastern Italy, and (iii) the involvement of other susceptible felid hosts in the same area. An SYBR® Green-based real-time PCR with primers targeting the 18S-rRNA was validated and applied to 237 felid samples, i.e., whole blood from 206 domestic cats and 12 captive exotic felids, and tissues from 19 wildcats. Positive results were obtained by melting temperature curve analysis due to the specific melting peak (i.e., 81°C Cytauxzoon spp.; 78–78.5°C Hepatozoon spp.). Positive samples were subjected to conventional PCR, followed by sequencing for species identification. Phylogenetic analyses were performed to assess relatedness among European isolates. Data on domestic cats (age class, sex, origin, management, and lifestyle) were recorded, and statistical analyses were performed to identify potential risk factors. A total of 31 (15%) domestic cats were positive for Hepatozoon spp. (i.e., 12 for H. felis, 19 for H. silvestris), while six (2.9%) for C. europaeus. The prevalence of Hepatozoon felis was significantly (p < 0.05) higher in domestic cats, while H. silvestris was higher in strays and animals from the Eastern region (i.e., Friuli-Venezia Giulia). Cytauxzoon europaeus was detected only in stray cats from Friuli-Venezia Giulia (province of Trieste). Among captive felids, one tiger was infected with H. felis ...
Keywords	real-time PCR ; Hepatozoon ; Cytauxzoon ; cat ; wildcat ; exotic felids ; Veterinary medicine ; SF600-1100
Subject code	590 ; 630
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Feline Parvovirus Lethal Outbreak in a Group of Adult Cohabiting Domestic Cats

Maria Irene Pacini / Mario Forzan / Giovanni Franzo / Claudia Maria Tucciarone / Milena Fornai / Fabrizio Bertelloni / Micaela Sgorbini / Carlo Cantile / Maurizio Mazzei

Pathogens, Vol 12, Iss 822, p

2023 Volume 822

Abstract: Feline panleukopenia is a highly contagious and often fatal disease in cats. The virus, known as feline panleukopenia virus (FPV), primarily affects kittens and unvaccinated cats. It is transmitted through contact with infected cats or their bodily ... ...

Abstract	Feline panleukopenia is a highly contagious and often fatal disease in cats. The virus, known as feline panleukopenia virus (FPV), primarily affects kittens and unvaccinated cats. It is transmitted through contact with infected cats or their bodily fluids, as well as contaminated objects and environments. The diagnosis of FPV infection can be confirmed through a combination of clinical signs, blood tests, and fecal testing. Prevention through vaccination is recommended for all cats. This case report describes an outbreak of feline panleukopenia in a group of unvaccinated domestic cats that resulted in acute mortality. The lesions were evaluated using histopathology, and the specific viral strain was characterized using molecular techniques. The clinical course of the outbreak was peracute, with a hemorrhagic pattern and 100% of lethality. The observed clinical-pathological pattern was unusual; nevertheless, molecular studies did not highlight peculiar genomic features of the parvovirus isolate. The outbreak affected 3 out of 12 cats in a very short time. However, the prompt application of biosecurity measures and vaccination resulted in an effective interruption of virus spread. In conclusion, we could assume that the virus found the ideal conditions to infect and replicate at high titers, resulting in a particularly aggressive outbreak.
Keywords	Felis catus ; feline panleukopenia virus ; Protoparvovirus carnivoran1 ; lethal outbreak ; Medicine ; R
Subject code	630
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Phylodynamic analysis of current Porcine circovirus 4 sequences: Does the porcine circoviruses evolutionary history repeat itself?

Faustini, Giulia / Drigo, Michele / Menandro, Maria Luisa / Pasotto, Daniela / Giovanni, Franzo

Transboundary and emerging diseases. 2022 Sept., v. 69, no. 5

2022

Abstract: Four porcine circoviruses (PCVs) have been discovered over time and seem to share a common history, particularly for PCV‐2 and ‐3. Despite being reported as apparently new viruses, rapidly emerging as a threat for the worldwide swine industry, they were ... ...

Abstract	Four porcine circoviruses (PCVs) have been discovered over time and seem to share a common history, particularly for PCV‐2 and ‐3. Despite being reported as apparently new viruses, rapidly emerging as a threat for the worldwide swine industry, they were then proven to have been circulating and coexisting with domestic pigs undetected for decades, without causing relevant health issues. A similar scenario could be true for the most recently identified PCV‐4. However, its detection in Asia only and the limited genetic variability could suggest a truly recent origin. To investigate which of the above‐mentioned scenarios is more plausible, a phylodynamic analysis was performed on all available PCV‐4 sequences for which adequate metadata were available to reconstruct the viral history and evolution. Obtained results suggest an ancient origin, at least decades ago, followed by a prolonged low‐level circulation and a moderate increase in viral population size after the second half of the XX century, in parallel with a progressive rise in pig population and farming intensification. A relevant local geographical clustering was also highlighted. The reason behind such low spreading capacity and limited geographical distribution compared to other circoviruses is currently obscure and will require dedicated studies, involving a more extensive sampling and sequencing activity.
Keywords	Porcine circovirus ; evolution ; genetic variation ; geographical distribution ; metadata ; population size ; pork industry ; swine ; Asia
Language	English
Dates of publication	2022-09
Size	p. e3363-e3369.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2414822-2
ISSN	1865-1682 ; 1865-1674
ISSN (online)	1865-1682
ISSN	1865-1674
DOI	10.1111/tbed.14638
Database	NAL-Catalogue (AGRICOLA)

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