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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.

Franzo, Giovanni

2021 Volume 11, Issue 1, Page(s) 10696

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 ... ...

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 disease severity and mortality in older patients.
MeSH term(s)	COVID-19/genetics ; COVID-19/immunology ; CpG Islands/immunology ; Genome, Viral/immunology ; Humans ; RNA Stability/immunology ; RNA, Viral/genetics ; RNA, Viral/immunology ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	RNA, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-05-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-90278-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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 3 (PCV-3) variability: Is it in the virus or in the classification criteria?

Franzo, Giovanni / Segalés, Joaquim

Virology journal

2023 Volume 20, Issue 1, Page(s) 26

Abstract: The continuous discovery of new viruses during the last decades has increased the need for new classification approaches and rules. Currently, the International Committee on Taxonomy of Viruses classifies viruses up to the species level. However, because ...

Abstract	The continuous discovery of new viruses during the last decades has increased the need for new classification approaches and rules. Currently, the International Committee on Taxonomy of Viruses classifies viruses up to the species level. However, because of the higher variability of most of these infectious agents, a below-species categorization is often required for proper epidemiological investigations. Unfortunately, variable criteria are typically proposed by different research groups, leading to misleading and poorly reproducible results. This scenario occurred for the recently identified Porcine circovirus 3. Although genotype definition standards had been defined by a group of experts in the field, recent articles have been published introducing new genotypes, whose classification rules are not reported. We therefore would like to stress the usefulness of defining and maintaining a common language to allow proper results comparison among groups. We consider the consensus opinion of a heterogeneous expert team as the most valuable approach. Nevertheless, if other approaches are proposed, the disclosure of the criteria and the comparison with previous literature should be deemed mandatory to allow effective results reproducibility, interpretation and sharing.
MeSH term(s)	Swine ; Animals ; Circovirus/genetics ; Reproducibility of Results ; Swine Diseases/diagnosis ; Genotype ; Circoviridae Infections/veterinary
Language	English
Publishing date	2023-02-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-01984-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Porcine circovirus 3 (PCV-3) variability: Is it in the virus or in the classification criteria?

Franzo, Giovanni / Segalés, Joaquim

Virol J. 2023 Dec., v. 20, no. 1 p.26-26

2023

Abstract	The continuous discovery of new viruses during the last decades has increased the need for new classification approaches and rules. Currently, the International Committee on Taxonomy of Viruses classifies viruses up to the species level. However, because of the higher variability of most of these infectious agents, a below-species categorization is often required for proper epidemiological investigations. Unfortunately, variable criteria are typically proposed by different research groups, leading to misleading and poorly reproducible results. This scenario occurred for the recently identified Porcine circovirus 3. Although genotype definition standards had been defined by a group of experts in the field, recent articles have been published introducing new genotypes, whose classification rules are not reported. We therefore would like to stress the usefulness of defining and maintaining a common language to allow proper results comparison among groups. We consider the consensus opinion of a heterogeneous expert team as the most valuable approach. Nevertheless, if other approaches are proposed, the disclosure of the criteria and the comparison with previous literature should be deemed mandatory to allow effective results reproducibility, interpretation and sharing.
Keywords	Porcine circovirus-3 ; genotype ; taxonomy ; viruses
Language	English
Dates of publication	2023-12
Size	p. 26.
Publishing place	BioMed Central
Document type	Article ; Online
Note	Letter
ZDB-ID	2160640-7
ISSN	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-01984-6
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Not Asian Anymore: Reconstruction of the History, Evolution, and Dispersal of the "Asian" Lineage of CPV-2c.

Franzo, Giovanni / Mira, Francesco / Schirò, Giorgia / Canuti, Marta

Viruses

2023 Volume 15, Issue 9

Abstract: Variability has been one of the hallmarks of canine parvovirus type 2 (CPV-2) since its discovery, and several lineages and antigenic variants have emerged. Among these, a group of viruses commonly called Asian CPV-2c has recently been reported with ... ...

Abstract	Variability has been one of the hallmarks of canine parvovirus type 2 (CPV-2) since its discovery, and several lineages and antigenic variants have emerged. Among these, a group of viruses commonly called Asian CPV-2c has recently been reported with increasing frequency in different regions. Currently, its global epidemiology and evolution are essentially unknown. The present work deals with this information gap by evaluating, via sequence, phylodynamic, and phylogeographic analyses, all the complete coding sequences of strains classified as Asian CPV-2c based on a combination of amino acid markers and phylogenetic analysis. After its estimated origin around 2008, this lineage circulated undetected in Asia until approximately 2012, when an expansion in viral population size and geographical distribution occurred, involving Africa, Europe, and North America. Asia was predicted to be the main nucleus of viral dispersal, leading to multiple introduction events in other continents/countries, where infection establishment, persistence, and rapid evolution occurred. Although the dog is the main host, other non-canine species were also involved, demonstrating the host plasticity of this lineage. Finally, although most of the strains showed an amino acid motif considered characteristic of this lineage, several exceptions were observed, potentially due to convergent evolution or reversion phenomena.
MeSH term(s)	Animals ; Dogs ; Phylogeny ; Africa ; Antigenic Variation ; Asia ; Europe
Language	English
Publishing date	2023-09-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15091962
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Molecular survey of feline immunodeficiency virus (FIV) infection in Namibian cats.

Franzo, Giovanni / de Villiers, Lourens / Coetzee, Lauren M / Villiers, Mari de / Molini, Umberto

Acta tropica

2024 Volume 253, Page(s) 107184

Abstract: Feline Immunodeficiency Virus (FIV) is one of the most important infectious diseases of cats, with potential implications in wildlife conservation. Unfortunately, FIV screening and surveillance in domestic cats remains limited in several African ... ...

Abstract	Feline Immunodeficiency Virus (FIV) is one of the most important infectious diseases of cats, with potential implications in wildlife conservation. Unfortunately, FIV screening and surveillance in domestic cats remains limited in several African countries, including Namibia. In this study, 279 blood samples from domestic cats in Namibia were analyzed for FIV diagnosis by PCR. The cats represented various regions and were cared for by people largely from rural areas with limited financial means. Only 1.43 % of the samples tested positive, unexpectedly low given their outdoor lifestyles. The infected cats, primarily adult and unsterilized, showed no typical FIV symptoms, suggesting subclinical infections. Genetic analysis of the detected strains indicated a unique FIV strain cluster in Namibia, although with a certain within-country variability, in the absence of consistent geographical clustering. The present study represents the first detection and genetic characterization of FIV in the Namibian domestic cat population. Although the infection frequency was low, also in the rural free-roaming population, the features of the enrolled population could have biased the estimation, suggesting the need for more extensive surveys involving diseased and older cats as well. Additionally, because of the long-lasting subclinical nature of the infection, frequent monitoring activities should be performed that allow prompt isolation of infected animals and the implementation of appropriate control measures if necessary.
MeSH term(s)	Humans ; Animals ; Cats ; Immunodeficiency Virus, Feline/genetics ; Feline Acquired Immunodeficiency Syndrome/epidemiology ; Animals, Wild ; Cluster Analysis ; Africa ; Cat Diseases/epidemiology
Language	English
Publishing date	2024-03-11
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	210415-5
ISSN	1873-6254 ; 0001-706X
ISSN (online)	1873-6254
ISSN	0001-706X
DOI	10.1016/j.actatropica.2024.107184
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Molecular Survey on Porcine Parvoviruses (PPV1-7) and Their Association with Major Pathogens in Reproductive Failure Outbreaks in Northern Italy.

Faustini, Giulia / Tucciarone, Claudia Maria / Franzo, Giovanni / Donneschi, Anna / Boniotti, Maria Beatrice / Alborali, Giovanni Loris / Drigo, Michele

Viruses

2024 Volume 16, Issue 1

Abstract: Successful reproductive performance is key to farm competitiveness in the global marketplace. Porcine parvovirus 1 (PPV1) has been identified as a major cause of reproductive failure, and since 2001 new species of porcine parvoviruses, namely PPV2-7, ... ...

Abstract	Successful reproductive performance is key to farm competitiveness in the global marketplace. Porcine parvovirus 1 (PPV1) has been identified as a major cause of reproductive failure, and since 2001 new species of porcine parvoviruses, namely PPV2-7, have been identified, although their role is not yet fully understood yet. The present study aimed to investigate PPVs' presence in reproductive failure outbreaks occurring in 124 farms of northern Italy. Fetuses were collected from 338 sows between 2019 and 2021 and tested for PPVs by real-time PCR-based assays and for other viruses responsible for reproductive disease. At least one PPV species was detected in 59.7% (74/124) of the tested farms. In order, PPV1, PPV5, PPV6, PPV7 and PPV4 were the most frequently detected species, whereas fewer detections were registered for PPV2 and PPV3. Overall, the new PPV2-7 species were detected in 26.6% (90/338) of the cases, both alone or in co-infections: PCV-2 (7.1%, 24/338), PCV-3 (8.2%, 28/338), and PRRSV-1 (6.2%, 21/338) were frequently identified in association with PPVs. Single PPVs detections or co-infections with other agents commonly responsible for reproductive failure should encourage future studies investigating their biological, clinical, and epidemiological role, for a better preparedness for potential emerging challenges in intensive pig production.
MeSH term(s)	Swine ; Animals ; Female ; Parvovirus, Porcine/genetics ; Swine Diseases/epidemiology ; Coinfection ; Parvoviridae Infections/epidemiology ; Parvoviridae Infections/veterinary ; Prevalence ; Porcine respiratory and reproductive syndrome virus/genetics
Language	English
Publishing date	2024-01-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v16010157
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: First genetic detection and characterization of canine parvovirus type 2 (Carnivore protoparvovirus 1) in southwestern Ethiopia.

Tegegne, Dechassa / Tsegaye, Girma / Faustini, Giulia / Franzo, Giovanni

Veterinary research communications

2022 Volume 47, Issue 2, Page(s) 975–980

Abstract: The species Carnivore protoparvovirus 1 includes viruses, e.g. canine parvovirus (CPV-2) and feline panleukopenia virus (FPV), which are among the most relevant for pets, causing extremely severe clinical signs and high fatality rate in dogs and cats. ... ...

Abstract	The species Carnivore protoparvovirus 1 includes viruses, e.g. canine parvovirus (CPV-2) and feline panleukopenia virus (FPV), which are among the most relevant for pets, causing extremely severe clinical signs and high fatality rate in dogs and cats. Moreover, a broad range of wild hosts, including endangered ones, were proven to be susceptible. Currently, no data on CPV-2 molecular epidemiology and strain characterization are available in Ethiopia, also considering the frequent contacts between domestic and wild populations. In the present study, a molecular epidemiology survey was performed on 92 fecal samples collected from domestic (n = 84) and stray (n = 8) dogs in southwestern Ethiopia in 2021. Approximately, 10% of the samples tested positive and the complete VP2 sequences of 5 strains were obtained, classified within the CPV-2a (n = 1) and CPV-2c (n = 4) antigenic variants. In most instances, the closest genetic relatives were strains of Chinese origin, which is fully compatible with the intense relationships that have been developing between the two countries, involving human being travels and their pets as well. Considering the clinical relevance of this infection and the risk it poses to local domestic and wild carnivore populations, especially endangered ones, much stronger monitoring and surveillance activity on foreign incoming animals should be performed. More strict constraints on animal introduction, e.g. compulsory vaccination, should also be considered.
MeSH term(s)	Humans ; Animals ; Cats ; Dogs ; Parvovirus, Canine/genetics ; Cat Diseases/epidemiology ; Ethiopia/epidemiology ; Parvoviridae Infections/epidemiology ; Parvoviridae Infections/veterinary ; Phylogeny ; Dog Diseases/epidemiology ; Parvovirus/genetics
Language	English
Publishing date	2022-11-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	406735-6
ISSN	1573-7446 ; 0165-7380
ISSN (online)	1573-7446
ISSN	0165-7380
DOI	10.1007/s11259-022-10027-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Porcine Circovirus 2 Genotypes, Immunity and Vaccines: Multiple Genotypes but One Single Serotype.

Franzo, Giovanni / Segalés, Joaquim

Pathogens (Basel, Switzerland)

2020 Volume 9, Issue 12

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.
Language	English
Publishing date	2020-12-14
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens9121049
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Porcine Circovirus 2 Genotypes, Immunity and Vaccines: Multiple Genotypes but One Single Serotype

Franzo, Giovanni / Segalés, Joaquim

Pathogens. 2020 Dec. 14, v. 9, no. 12

2020

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	Porcine circovirus-2 ; cross immunity ; disease models ; epidemiological studies ; experimental design ; farms ; genetic heterogeneity ; genotype ; knowledge ; light ; markets ; pathogens ; serotypes ; signs and symptoms (animals and humans) ; vaccines ; viruses
Language	English
Dates of publication	2020-1214
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-light
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens9121049
Database	NAL-Catalogue (AGRICOLA)

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