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State-of-the-Art Porcine Viruses Research in Europe

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A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: closed (30 May 2023) | Viewed by 20189

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Special Issue Editor

Prof. Dr. Grzegorz Wozniakowski

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Guest Editor

Department of Diagnosis and Clinical Sciences, Faculty of Biological and Veteterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
Interests: veterinary virology; epidemiology; poultry and swine viruses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Taking into account the importance of pig production in numerous countries of Europe, the purpose of the forthcoming Special Issue is to discuss the most important topics related to swine diseases, including the aspects of prevention, epidemiology, control, and food safety. Therefore, I cordially to invite you to submit your relevant papers to the upcoming Special Issue of Viruses. Your valuable input will hopefully enrich the current state of knowledge and practical approach to the global production of pigs.

Prof. Dr. Grzegorz Wozniakowski
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

swine production
porcine viruses
biosecurity
welfare in swine production

Published Papers (11 papers)

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12 pages, 2027 KiB

Open AccessArticle

Evidence of Porcine Circovirus Type 2 (PCV2) Genetic Shift from PCV2b to PCV2d Genotype in Sardinia, Italy

by Silvia Dei Giudici, Lorena Mura, Piero Bonelli, Salwa Hawko, Pier Paolo Angioi, Anna Maria Sechi, Stefano Denti, Antonella Sulas, Giovanni Pietro Burrai, Maria Paola Madrau, Elisabetta Antuofermo and Annalisa Oggiano

Viruses 2023, 15(11), 2157; https://doi.org/10.3390/v15112157 - 26 Oct 2023

Viewed by 906

Abstract

Porcine Circovirus type 2 (PCV2) is the etiological agent of a disease syndrome named Porcine Circovirus disease (PCVD), representing an important threat for the pig industry. The increasing international trade of live animals and the development of intensive pig farming seem to have sustained the spreading of PCVD on a global scale. Recent classification criteria allowed the identification of nine different PCV2 genotypes (PCV2a–i). PCV2a was the first genotype detected with the highest frequency from the late 1990s to 2000, which was then superseded by PCV2b (first genotype shift). An ongoing genotype shift is now determining increasing prevalence rates of PCV2d, in replacement of PCV2b. In Italy, a complete genotype replacement was not evidenced yet. The present study was carried out on 369 samples originating from domestic pigs, free-ranging pigs, and wild boars collected in Sardinia between 2020 and 2022, with the aim to update the last survey performed on samples collected during 2009–2013. Fifty-seven complete ORF2 sequences were obtained, and the phylogenetic and network analyses evidenced that 56 out of 57 strains belong to the PCV2d genotype and only one strain to PCV2b, thus showing the occurrence of a genotype shift from PCV2b to PCV2d in Sardinia. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

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7 pages, 257 KiB

Open AccessCommunication

Detection of African Swine Fever Virus and Blood Meals of Porcine Origin in Hematophagous Insects Collected Adjacent to a High-Biosecurity Pig Farm in Lithuania; A Smoking Gun?

by Ann Sofie Olesen, Jonno Jorn Stelder, Kirsten Tjørnehøj, Camille Melissa Johnston, Louise Lohse, Lene Jung Kjær, Anette Ella Boklund, Anette Bøtner, Graham J. Belsham, René Bødker and Thomas Bruun Rasmussen

Viruses 2023, 15(6), 1255; https://doi.org/10.3390/v15061255 - 26 May 2023

Viewed by 1100

Abstract

A seasonal trend of African swine fever (ASF) outbreaks in domestic pig farms has been observed in affected regions of Eastern Europe. Most outbreaks have been observed during the warmer summer months, coinciding with the seasonal activity pattern of blood-feeding insects. These insects may offer a route for introduction of the ASF virus (ASFV) into domestic pig herds. In this study, insects (hematophagous flies) collected outside the buildings of a domestic pig farm, without ASFV-infected pigs, were analyzed for the presence of the virus. Using qPCR, ASFV DNA was detected in six insect pools; in four of these pools, DNA from suid blood was also identified. This detection coincided with ASFV being reported in the wild boar population within a 10 km radius of the pig farm. These findings show that blood from ASFV-infected suids was present within hematophagous flies on the premises of a pig farm without infected animals and support the hypothesis that blood-feeding insects can potentially transport the virus from wild boars into domestic pig farms. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

16 pages, 634 KiB

Open AccessArticle

Risk Factor Impact on African Swine Fever Transmission in Different Extensive Pig Production Settings in Serbia

by Jan Plut, Melita Hajdinjak, Jasna Prodanov-Radulović, Siniša Grubač, Biljana Djurdjević and Marina Štukelj

Viruses 2023, 15(6), 1232; https://doi.org/10.3390/v15061232 - 24 May 2023

Cited by 1 | Viewed by 1772

Abstract

The first case of ASF in a domestic pig population in Serbia was confirmed in 2019 in a backyard population. Today, outbreaks in wild boar and, more importantly, in domestic pigs are still occurring, although the government measures for ASF prevention are in place. The aim of this study was to determine critical risk factors and identify the possible reasons for ASF introduction into different extensive pig farms. The study was conducted on 26 extensive pig farms with confirmed ASF outbreaks, with data collected from beginning of 2020 to the end of 2022. Collected epidemiological data were divided into 21 main categories. After identifying specific values of variables as critical for ASF transmission, we identified nine important ASF transmission indicators as those variables for which at least 2/3 of the observed farms reported values critical for ASF transmission. Among them were type of holding, distance to hunting ground, farm/yard fencing, and home slaughtering; however, the hunting activity of pig holders, swill feeding, and feeding with mowed green mass were not included. We represented the data in the form of contingency tables to study associations between pairs of variables using Fisher’s exact test. All pairs of variables in the group including type of holding, farm/yard fencing, domestic pig–wild boar contact, and hunting activity were significantly related; hunting activity of pig holders, holding pigs in backyards, unfenced yards, and domestic pig–wild boar contact were observed on the same farms. Free-range pig farming led to observed domestic pig–wild boar contact on all farms. The identified critical risk factors need to be strictly addressed to prevent the further spread of ASF to extensive farms and backyards in Serbia and elsewhere. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

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15 pages, 6744 KiB

Open AccessArticle

Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds

by Nick Vereecke, Aleksandra Woźniak, Marthe Pauwels, Sieglinde Coppens, Hans Nauwynck, Piotr Cybulski, Sebastiaan Theuns and Tomasz Stadejek

Viruses 2023, 15(2), 435; https://doi.org/10.3390/v15020435 - 4 Feb 2023

Cited by 2 | Viewed by 2439

Abstract

Influenza A virus (IAV) is a single-stranded, negative-sense RNA virus and a common cause of seasonal flu in humans. Its genome comprises eight RNA segments that facilitate reassortment, resulting in a great variety of IAV strains. To study these processes, the genetic code of each segment should be unraveled. Fortunately, new third-generation sequencing approaches allow for cost-efficient sequencing of IAV segments. Sequencing success depends on various factors, including proper sample storage and processing. Hence, this work focused on the effect of storage of oral fluids and swIAV sequencing. Oral fluids (n = 13) from 2017 were stored at −22 °C and later transferred to −80 °C. Other samples (n = 21) were immediately stored at −80 °C. A reverse transcription quantitative PCR (RT-qPCR) pre- and post-storage was conducted to assess IAV viral loads. Next, samples were subjected to two IAV long-read nanopore sequencing methods to evaluate success in this complex matrix. A significant storage-associated loss of swIAV loads was observed. Still, a total of 17 complete and 6 near-complete Polish swIAV genomes were obtained. Genotype T, (H1avN2, seven herds), P (H1N1pdm09, two herds), U (H1avN1, three herds), and A (H1avN1, 1 herd) were circulated on Polish farms. In conclusion, oral fluids can be used for long-read swIAV sequencing when considering appropriate storage and segment amplification protocols, which allows us to monitor swIAV in an animal-friendly and cost-efficient manner. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

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20 pages, 3090 KiB

Open AccessArticle

Rotavirus A in Domestic Pigs and Wild Boars: High Genetic Diversity and Interspecies Transmission

by Dragan Brnić, Daniel Čolić, Valentina Kunić, Nadica Maltar-Strmečki, Nina Krešić, Dean Konjević, Miljenko Bujanić, Ivica Bačani, Dražen Hižman and Lorena Jemeršić

Viruses 2022, 14(9), 2028; https://doi.org/10.3390/v14092028 - 13 Sep 2022

Cited by 6 | Viewed by 2431

Abstract

Rotavirus A (RVA) is an important pathogen for porcine health. In comparison to humans, RVA in domestic animals and especially in wildlife is under researched. Therefore, the aim of the present study was to investigate the prevalence, genetic diversity, molecular epidemiology and interspecies transmission of RVA in domestic pigs and wild boars. During the three consecutive RVA seasons (2018–2021) we collected 445 and 441 samples from domestic pigs and wild boars, respectively. Samples were tested by real-time RT-PCR, and RVA-positive samples were genotyped in VP7 and VP4 segments. Our results report an RVA prevalence of 49.9% in domestic pigs and 9.3% in wild boars. Outstanding RVA genetic diversity was observed in VP7 and VP4 segments, especially in domestic pigs exhibiting a striking 23 different RVA combinations (G5P[13] and G9P[23] prevailed). Interspecies transmission events were numerous between domestic pigs and wild boars, sharing G3, G5, G6, G9, G11 and P[13] genotypes. Furthermore, our data indicate that such transmission events involved even bovines (G6, P[11]) and, intriguingly, humans (G1P[8]). This study contributes to the basic knowledge that may be considered important for vaccine development and introduction, as a valuable and currently missing tool for efficient pig health management in the EU. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

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13 pages, 2451 KiB

Open AccessArticle

Allele-Specific Dual PCRs to Identify Members of the 27a Cluster of PPV

by Vivien Tamás, István Mészáros, Ferenc Olasz, István Kiss, Zalán G. Homonnay, Preben Mortensen and Zoltán Zádori

Viruses 2022, 14(7), 1500; https://doi.org/10.3390/v14071500 - 8 Jul 2022

Viewed by 1333

Abstract

Porcine Parvovirus (PPV) is one of the most important infectious agents causing severe reproductive failure in pigs. In the last two decades a particular, a novel genotype emerged in Europe and PPV-27a was named as the prototype of this genetic cluster. It was suggested that members of the PPV-27a cluster may adversely influence effective vaccination against PPV. For a reliable updated 27a definition, we aligned 93 databank-deposited partial or full nucleotide and protein sequences of the VP2 of different PPV isolates. We confirmed that the 27a cluster could indeed be distinguished from other members of the species, however, some divergences were identified compared to earlier defined genetic markers. Based on genetic differences, we developed a dual allele-specific polymerase chain reaction for the easy and quick discrimination of members of the 27a cluster from other PPV strains. The detection limit of dual PCR was found <1.66 × 10⁴ copies/reaction. To sensitize and make it more user friendly, the method was further developed for qPCR application with fluorescent probes. Regarding the detection limit of the two PCRs (<1.66 × 10⁴ copies/reaction of the dual PCR versus <2.40 × 10² copy/reaction of the dual qPCR), approximately two log improvement was achieved in the sensitivity of the method. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

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18 pages, 2219 KiB

Open AccessArticle

Changes in Estimating the Wild Boar Carcasses Sampling Effort: Applying the EFSA ASF Exit Strategy by Means of the WBC-Counter Tool

by Stefano Cappai, Ileana Baldi, Pietro Desini, Antonio Pintore, Daniele Denurra, Marcella Cherchi, Sandro Rolesu, Daniela Mandas, Giulia Franzoni, Mariangela Stefania Fiori, Annalisa Oggiano, Francesco Feliziani, Vittorio Guberti and Federica Loi

Viruses 2022, 14(7), 1424; https://doi.org/10.3390/v14071424 - 28 Jun 2022

Cited by 5 | Viewed by 1819

Abstract

African swine fever (ASF) is a devastating disease, resulting in the high mortality of domestic and wild pigs, spreading quickly around the world. Ensuring the prevention and early detection of the disease is even more crucial given the absence of licensed vaccines. As suggested by the European Commission, those countries which intend to provide evidence of freedom need to speed up passive surveillance of their wild boar populations. If this kind of surveillance is well-regulated in domestic pig farms, the country-specific activities to be put in place for wild populations need to be set based on wild boar density, hunting bags, the environment, and financial resources. Following the indications of the official EFSA opinion 2021, a practical interpretation of the strategy was implemented based on the failure probabilities of wrongly declaring the freedom of an area even if the disease is still present but undetected. This work aimed at providing a valid, applicative example of an exit strategy based on two different approaches: the first uses the wild boar density to estimate the number of carcasses need to complete the exit strategy, while the second estimates it from the number of wild boar hunted and tested. A practical free access tool, named WBC-Counter, was developed to automatically calculate the number of needed carcasses. The practical example was developed using the ASF data from Sardinia (Italian island). Sardinia is ASF endemic from 43 years, but the last ASFV detection dates back to 2019. The island is under consideration for ASF eradication declaration. The subsequent results provide a practical example for other countries in approaching the EFSA exit strategy in the best choices for its on-field application. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

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14 pages, 2513 KiB

Open AccessArticle

High Prevalence of Porcine Circovirus 3 in Hungarian Pig Herds: Results of a Systematic Sampling Protocol

by Barbara Igriczi, Lilla Dénes, Imre Biksi, Ervin Albert, Tamás Révész and Gyula Balka

Viruses 2022, 14(6), 1219; https://doi.org/10.3390/v14061219 - 3 Jun 2022

Cited by 6 | Viewed by 1811

Abstract

Porcine circovirus type 3 (PCV3) is an emerging pathogen that has been reported worldwide in all ages of healthy and clinically ill pigs. The presence of this virus in Hungary has been confirmed in a commercial farm experiencing reproductive failures, but there were no data on the circulation of PCV3 in the country. Here we report the prevalence and the genetic diversity of PCV3 in Hungarian herds. To estimate the prevalence, 1855 serum samples, 176 oral fluid and 97 processing fluid samples were collected in a systematic, cross-sectional method from 20 large scale swineherds and tested by real-time qPCR. PCV3 was present in at least one type of diagnostic matrix in 19 out of the 20 (95%) pig farms. The highest detection rates were observed in the processing fluid samples (61%), but 41% of the oral fluid and 23% of the serum samples were positive. The virus was found in all age groups, and slightly more adult animals were infected than growing pigs, but the viral burden was lower amongst them. Phylogenetic analysis of nine complete genomes, obtained from either the sampled herds or organ samples of PCV3-positive carcasses, showed high nucleotide identity between the detected sequences, which all belonged to the PCV3a genotype. Our results indicate that PCV3 is widespread in Hungary, but in most cases, the virus seems to circulate subclinically, infecting all age groups and production phases without the presence of apparent clinical disease. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

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20 pages, 2745 KiB

Open AccessArticle

Point-of-Care and Label-Free Detection of Porcine Reproductive and Respiratory Syndrome and Swine Influenza Viruses Using a Microfluidic Device with Photonic Integrated Circuits

by Georgios Manessis, Maciej Frant, Grzegorz Wozniakowski, Lapo Nannucci, Martina Benedetti, Lilla Denes, Balka Gyula, Athanasios I. Gelasakis, Clare Squires, Sara Recuero, Carlos Sanchez, Amadeu Griol, Alessandro Giusti and Ioannis Bossis

Viruses 2022, 14(5), 988; https://doi.org/10.3390/v14050988 - 7 May 2022

Cited by 1 | Viewed by 1932

Abstract

Swine viral diseases challenge the sector’s sustainability by affecting productivity and the health and welfare of the animals. The lack of antiviral drugs and/or effective vaccines renders early and reliable diagnosis the basis of viral disease management, underlining the importance of point-of-care (POC) diagnostics. A novel POC diagnostic device utilizing photonic integrated circuits (PICs), microfluidics, and information and communication technologies for the detection of porcine reproductive and respiratory syndrome virus (PRRSV) and swine influenza A (SIV) was validated using spiked and clinical oral fluid samples. Metrics including sensitivity, specificity, accuracy, precision, positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR) were calculated to assess the performance of the device. For PRRSV, the device achieved a sensitivity of 83.5%, specificity of 77.8%, and DOR values of 17.66, whereas the values for SIV were 81.8%, 82.2%, and 20.81, respectively. The POC device and PICs can be used for the detection of PRRSV and SIV in the field, paving the way for the introduction of novel technologies in the field of animal POC diagnostics to further optimize livestock biosecurity. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

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15 pages, 1863 KiB

Open AccessArticle

Genetic Diversity of Porcine Circovirus 2 in Wild Boar and Domestic Pigs in Ukraine

by Nataliia Rudova, Jeremy Buttler, Ganna Kovalenko, Mykola Sushko, Vitaliy Bolotin, Larysa Muzykina, Oleksandr Zinenko, Borys Stegniy, Yurii Dunaiev, Mykola Sytiuk, Anton Gerilovych, Devin M. Drown, Eric Bortz and Oleksii Solodiankin

Viruses 2022, 14(5), 924; https://doi.org/10.3390/v14050924 - 28 Apr 2022

Cited by 8 | Viewed by 2198

Abstract

Porcine circovirus type 2 (PCV2) is responsible for a number of porcine circovirus-associated diseases (PCVAD) that can severely impact domestic pig herds. For a non-enveloped virus with a small genome (1.7 kb ssDNA), PCV2 is remarkably diverse, with eight genotypes (a–h). New genotypes of PCV2 can spread through the migration of wild boar, which are thought to infect domestic pigs and spread further through the domestic pig trade. Despite a large swine population, the diversity of PCV2 genotypes in Ukraine has been under-sampled, with few PCV2 genome sequences reported in the past decade. To gain a deeper understanding of PCV2 genotype diversity in Ukraine, samples of blood serum were collected from wild boars (n = 107) that were hunted in Ukraine during the November–December 2012 hunting season. We found 34/107 (31.8%) prevalence of PCV2 by diagnostic PCR. For domestic pigs, liver samples (n = 16) were collected from a commercial market near Kharkiv in 2019, of which 6 out of 16 (37%) samples were positive for PCV2. We sequenced the genotyping locus ORF2, a gene encoding the PCV2 viral capsid (Cap), for 11 wild boar and six domestic pig samples in Ukraine using an Oxford Nanopore MinION device. Of 17 samples with resolved genotypes, the PCV2 genotype b was the most common in wild boar samples (10 out of 11, 91%), while the domestic pigs were infected with genotypes b and d. We also detected genotype b/d and b/a co-infections in wild boars and domestic pigs, respectively, and for the first time in Ukraine we detected genotype f in a wild boar from Poltava. Building a maximum-likelihood phylogeny, we identified a sublineage of PCV2 genotype b infections in both wild and domestic swine, suggesting a possible epizootic cluster and an ecological interaction between wild boar and domestic pig populations in northeastern Ukraine. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

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9 pages, 1333 KiB

Open AccessBrief Report

A Serological Investigation of Porcine Reproductive and Respiratory Syndrome and Three Coronaviruses in the Campania Region, Southern Italy

by Gianmarco Ferrara, Emanuele D’Anza, Antonella Rossi, Elvira Improda, Valentina Iovane, Ugo Pagnini, Giuseppe Iovane and Serena Montagnaro

Viruses 2023, 15(2), 300; https://doi.org/10.3390/v15020300 - 20 Jan 2023

Cited by 7 | Viewed by 1400

Abstract

Porcine coronaviruses and reproductive and respiratory syndrome (PRRS) are responsible for severe outbreaks that cause huge economic losses worldwide. In Italy, three coronaviruses have been reported historically: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus (PRCV). Although repeated outbreaks have been described, especially in northern Italy, where intensive pig farming is common, there is a worrying lack of information on the spread of these pathogens in Europe. In this work, we determined the seroprevalence of three porcine coronaviruses and PRRSV in the Campania region, southern Italy. A total of 443 samples were tested for the presence of antibodies against porcine coronaviruses and PRRSV using four different commercial ELISAs. Our results indicated that PEDV is the most prevalent among porcine coronaviruses, followed by TGEV, and finally PRCV. PRRSV appeared to be the most prevalent virus (16.7%). For coronaviruses, seroprevalence was higher in pigs raised in intensive farming systems. In terms of distribution, TGEV is more widespread in the province of Avellino, while PEDV and PRRSV are more prevalent in the province of Naples, emphasizing the epidemic nature of both infections. Interestingly, TGEV-positive animals are more common among growers, while seropositivity for PEDV and PRRSV was higher in adults. Our research provides new insights into the spread of swine coronaviruses and PRRSV in southern Italy, as well as a warning about the need for viral surveillance. Full article

(This article belongs to the Special Issue State-of-the-Art Porcine Viruses Research in Europe)

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