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Pig production is increasing annually in Africa as it is recognized as a significant source of income, livelihood and food security, particularly in rural communities. Understanding the circulating swine pathogens is crucial for the success of this emerging industry. Although there is extensive data available on the African swine fever virus due to its devastating impact on pig production, knowledge about the presence of other viral swine pathogens on the continent is still extremely limited. This review discusses what is currently known about six swine pathogens in Africa: classical swine fever virus, porcine reproductive and respiratory syndrome virus, porcine circovirus-2, porcine circovirus-3, porcine parvovirus-1, and pseudorabies virus. Gaps in our knowledge are identified and topics of future focus discussed., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Since its discovery, Porcine circovirus type 2 has emerged as one of the most relevant swine infectious diseases, causing relevant economic losses for the pig industry. While four genotypes were identified, only three (PCV2a, PCV2b and PCV2d) are currently circulating and display a worldwide distribution. Another genotype, PCV2c, has been described only once in Danish archive samples collected between 1980 and 1990. In addition to commercial pigs, PCV2 has been demonstrated to infect wild boars and other wild species, which can potentially serve as a reservoir for domestic populations. In this study, eight sequences obtained from feral pigs in the Pantanal region (Mato Grosso do Sul State, Brazil) were compared with reference sequences and other Brazilian sequences, and the results revealed remarkable genetic diversity, with all four genotypes currently recognised being detected (PCV2a, PCV2b, PCV2c and PCV2d). This finding represents a remarkable discovery, as it is the first detection of PCV2c since 1990 and the first-ever detection of PCV2c in live animals. The peculiar population history and ecological scenario of feral pigs in the Pantanal coupled with the complex, and still only partially known relationship of feral pigs with other PCV2 susceptible species (i.e., domestic pigs, wild boars and peccaries), open exciting questions concerning PCV2 origin and evolution. Overall, the results of the present study led us to form the following hypothesis: the PCV2 strains found in feral pigs may be the last descent of the strains that circulated among European pigs in the past, or they may have infected these feral pigs more recently through a bridge species., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Introduction: Porcine circovirus 2 (PCV-2) is a key pathogen for the swine industry at a global level. Nine genotypes, differing in epidemiology and potentially virulence, emerged over time, with PCV-2a, -2b, and -2d being the most widespread and clinically relevant. Conversely, the distribution of minor genotypes appears geographically and temporally restricted, suggesting lower virulence and different epidemiological drivers. In 2022, PCV-2e, the most genetically and phenotypically divergent genotype, was identified in multiple rural farms in North-eastern Italy. Since rural pigs often have access to outdoor environment, the introduction from wild boars was investigated. Methods: Through a molecular and spatial approach, this study investigated the epidemiology and genetic diversity of PCV-2 in 122 wild boars across different provinces of North-eastern Italy. Results: Molecular analysis revealed a high PCV-2 frequency (81.1%, 99/122), and classified the majority of strains as PCV-2d (96.3%, 78/81), with sporadic occurrences of PCV-2a (1.2%, 1/81) and PCV-2b (2.5%, 2/81) genotypes. A viral flow directed primarily from domestic pigs to wild boars was estimated by phylogenetic and phylodynamic analyses. Discussion: These findings attested that the genotype replacement so far described only in the Italian domestic swine sector occurred also in wild boars. and suggested that the current heterogeneity of PCV-2d strains in Italian wild boars likely depends more on different introduction events from the domestic population rather than the presence of independent evolutionary pressures. While this might suggest PCV-2 circulation in wild boars having a marginal impact in the industrial sector, the sharing of PCV-2d strains across distinct wild populations, in absence of a consistent geographical pattern, suggests a complex interplay between domestic and wild pig populations, emphasizing the importance of improved biosecurity measures to mitigate the risk of pathogen transmission. [ABSTRACT FROM AUTHOR]

Porcine circovirus 4 (PCV-4) is a novel virus recently discovered (2019) in domestic pigs from China, although several studies have proven its circulation since 2008. Later, PCV-4 was also detected in wild boar populations from China and domestic pigs from South Korea and Thailand. Currently, Asia is so far the only continent where this novel virus has been reported; few studies carried out in South America and Europe failed in the attempt to detect it. The objective of this Comment is to communicate the first detection of PCV-4 in Europe, specifically in wild boar and domestic pigs from Mid-South-Western Spain. A retrospective study was carried out on wild boar and domestic pigs, both extensively (Iberian breed) and intensively raised, from Spain and Italy, sampled between 1998 and 2022. PCV-4 genome detection was attempted using different conventional or quantitative real time PCR (qPCR) protocols and some positive results were confirmed through Sanger sequencing. A total of 57 out of 166 (34.3%) Spanish wild boar and 9 out of 223 (4%) Iberian pigs (both geographically located in the Mid-South-Western Spain) were qPCR positive, while the rest of tested animals from North-Eastern Spain and Italy were negative. Partial sequences of Rep or Cap genes of selected samples confirmed the presence of PCV-4. The relatively high prevalence in wild boar and the low one in Iberian pigs from the same areas suggests intra- and interspecific transmission, being the wild boar a potential viral reservoir. The epidemiological and clinical importance of these findings are currently unknown, but guarantees further research on this novel virus. [ABSTRACT FROM AUTHOR]

Introduction: Porcine circovirus 3 (PCV-3) was firstly reported in 2017. Although evidence of its pathogenic role has been provided, its clinical relevance seems lower than Porcine circovirus 2 (PCV-2), as well as its evolutionary rate. Different studies have reported a high PCV-3 prevalence in wild boars, sometimes higher than the one observed in commercial pigs. Nevertheless, to date, few studies have objectively investigated the relationships between these populations when inhabiting the same area. Moreover, the role of small-scale, backyard pig production in PCV-3 epidemiology is still obscure. Methods: The present study investigated PCV-3 occurrence in 216 samples collected from the same area of Northern Italy from commercial and rural pigs, and wild boars. PCV-3 presence was tested by qPCR and complete genome or ORF2 sequences were obtained when possible and analysed using a combination of statistical, phylogenetic and phylodynamic approaches. Results: A higher infection risk in wild boars and rural pigs compared to the commercial ones was demonstrated. The phylodynamic analysis confirmed a larger viral population size in wild and rural populations and estimated a preferential viral flow from these populations to commercial pigs. A significant flow from wild to rural animals was also proven. The analysis of the Italian sequences and the comparison with a broader international reference dataset highlighted the circulation of a highly divergent clade in Italian rural pigs and wild boars only. Discussion: Overall, the present study results demonstrate the role of noncommercial pig populations in PCV-3 maintenance, epidemiology and evolution, which could represent a threat to intensive farming. [ABSTRACT FROM AUTHOR]

Like in many other African countries, pig production is increasing in Tanzania. To support farmers and stakeholders, it is important to increase our understanding of porcine pathogens present in the country. Currently, little is known about the circulation of porcine circovirus-2 (PCV-2) and porcine circovirus-3 (PCV-3). For this reason, samples from 124 pigs collected throughout the country between 2018 to 2022 were screened by PCR for the presence of PCV-2 and PCV-3. Sequencing and phylogenetic analysis of positive amplicons identified two PCV-2 genotypes (a and d). Limited genetic heterogenicity was observed among the PCV-3. This study provides important data on pathogens present in pigs in Tanzania and should be of use veterinary authorities involved in porcine disease management. [ABSTRACT FROM AUTHOR]

Porcine parvovirus 1 (PPV1) is recognized as a major cause of reproductive failure in pigs, leading to several clinical outcomes globally known as SMEDI. Despite being known since the late 1960s its circulation is still of relevance to swine producers. Additionally, the emergence of variants such as the virulent 27a strain, for which lower protection induced by vaccines has been demonstrated, is of increasing concern. Even though constant monitoring of PPV1 using molecular epidemiological approaches is of pivotal importance, viral sequence data are scarce especially in low-income countries. To fill this gap, a collection of 71 partial VP2 sequences originating from eight African countries (Burkina Faso, Côte d'Ivoire, Kenya, Mozambique, Namibia, Nigeria, Senegal, and Tanzania) during the period 2011–2021 were analyzed within the context of global PPV1 variability. The observed pattern largely reflected what has been observed in high-income regions, i.e., 27a-like strains were more frequently detected than less virulent NADL-8-like strains. A phylogeographic analysis supported this observation, highlighting that the African scenario has been largely shaped by multiple PPV1 importation events from other continents, especially Europe and Asia. The existence of such an international movement coupled with the circulation of potential vaccine-escape variants requires the careful evaluation of the control strategies to prevent new strain introduction and persistence. [ABSTRACT FROM AUTHOR]

Porcine circovirus type 2 (PCV2) is one of the most relevant infectious agents affecting domestic pigs. Recently, a surprising PCV2 genetic heterogenicity has been reported in Africa. Nevertheless, the knowledge of the epidemiology of PCV2 in African countries, in both domestic and wild species, is limited and sparse. Having this in mind, in the present study, the PCV2 circulation and its molecular epidemiology in Southwestern Ethiopia have been investigated by collecting 64 samples from domestic pigs, wild boars, and warthogs. PCV2 genome presence was detected and quantified using qPCR and ORF2 sequencing was attempted on positive samples. Ten samples, 8 wild boars, 1 domestic pig, and 1 warthog, tested PCV2 positive. Complete ORF2 sequences were obtained from 5 wild boars; 4 of those were classified as PCV2d and 1 as PCV2b. Both PCV2b and PCV2d were related to strains of Asian origin, most commonly from China. The role of this country in the exportation of PCV2 strains in Ethiopia, and Africa in general, might be supported by the crescent economic relationship between the two continents. The obtained evidence also testifies to the inadequacy and/or poor application of biosecurity measures separating wild and domestic animals. Further, extensive and systematic studies should be performed to more deeply characterize the molecular epidemiology of PCV2 in this region, in order to improve our understanding of these ecological niches in the evolution and dispersal of PCV2. [ABSTRACT FROM AUTHOR]

Porcine circovirus‐2 (PCV‐2) is associated with several disease syndromes in domestic pigs that have a significant impact on global pig production and health. Currently, little is known about the status of PCV‐2 in Africa. In this study, a total of 408 archived DNA samples collected from pigs in Burkina Faso, Cameroon, Cape Verde, Ethiopia, the Democratic Republic of the Congo, Mozambique, Nigeria, Senegal, Tanzania and Zambia between 2000 and 2018 were screened by PCR for the presence of PCV‐2. Positive amplicons of the gene encoding the viral capsid protein (ORF2) were sequenced to determine the genotypes circulating in each country. Four of the nine currently known genotypes of PCV‐2 were identified (i.e. PCV‐2a, PCV‐2b, PCV‐2d and PCV‐2 g) with more than one genotype being identified in Burkina Faso, Ethiopia, Nigeria, Mozambique, Senegal and Zambia. Additionally, a phylogeographic analysis which included 38 additional ORF2 gene sequences of PCV‐2s previously identified in Mozambique, Namibia and South Africa from 2014 to 2016 and 2019 to 2020 and available in public databases, demonstrated the existence of several African‐specific clusters and estimated the approximate time of introduction of PCV‐2s into Africa from other continents. This is the first in‐depth study of PCV‐2 in Africa and it has important implications for pig production at both the small‐holder and commercial farm level on the continent. [ABSTRACT FROM AUTHOR]

Archival swine DNA samples from Indonesia and Mongolia, some of which were previously shown to be positive for African swine fever virus, were screened for the presence of porcine circovirus 2 (PCV-2) and porcine circovirus 3 (PCV-3) by PCR. Samples from both countries were positive for PCV-2 (three from Mongolia and two from Indonesia), while none were positive for PCV-3. The PCV-2 amplicons were sequenced, and phylogenetic analysis revealed that the PCV-2 strains belonged to four different genotypes: PCV-2a (Mongolia), PCV-2b (Mongolia and Indonesia), PCV-2d (Indonesia), and PCV-2g (Mongolia). This is the first report of ASFV/PCV-2 coinfection in pigs and the first report of the presence of PCV-2 in Mongolia. [ABSTRACT FROM AUTHOR]

Porcine circovirus 3 (PCV‐3) was discovered in 2015 using next‐generation sequencing (NGS) methods. Since then, the virus has been detected worldwide in pigs displaying several clinical–pathological outcomes as well as in healthy animals. The objective of this review is to critically discuss the evidence existing so far regarding PCV‐3 as a swine pathogen. In fact, a significant number of publications claim PCV‐3 as a disease causal infectious agent, but very few of them have shown strong evidence of such potential causality. The most convincing proofs of disease association are those that demonstrate a clinical picture linked to multisystemic lymphoplasmacytic to lymphohistiocytic perivascular inflammation and presence of viral nucleic acid within these lesions. Based on these evidence, individual case definitions for PCV‐3‐reproductive disease and PCV‐3‐systemic disease are proposed to standardize diagnostic criteria for PCV‐3‐associated diseases. However, the real frequency of these clinical–pathological conditions linked to the novel virus is unknown, and the most frequent outcome of PCV‐3 infection is likely subclinical based on its worlwide distribution. [ABSTRACT FROM AUTHOR]

Porcine circovirus 2 (PCV-2) is the causative agent of porcine circovirus diseases (PCVD). A study was undertaken to determine whether PCV-2 was present in samples collected from commercial pigs (n = 46) and warthogs (n = 42) in Namibia between 2019 and 2020. Twenty-three of the collected samples were positive by PCR (13 from pigs and 10 from warthogs), and a phylogenetic analysis of ORF2 identified three genotypes (PCV-2b and PCV-2d in pigs and PCV-2c in warthogs). This is the first time that PCV-2 has been identified in warthogs and in Namibia. It is also the first report of PCV-2c in Africa. [ABSTRACT FROM AUTHOR]

Since the identification of species Porcine circovirus 2, the relevance of genus Circovirus has increased given its impact on the swine industry. A new species (Porcine circovirus 3, PCV-3) has been detected in association with various clinical conditions. Consequently, there is an urgent need for reliable and widely accessible tests for both routine diagnostic and research purposes. We developed a direct PCR (requiring no DNA extraction) and a quantitative (q)PCR targeting the conserved rep gene to detect the PCV-3 genome. Test performance was assessed by testing 120 field samples within different matrices. Both methods were sensitive (detection of 10 viral genome/µL), specific, and repeatable. The substantially perfect agreement between the 2 assays strongly supports their high sensitivity and specificity. The low cost and short processing time of the direct PCR protocol, together with the reliable quantitative results provided by qPCR, support the establishment of common testing guidelines. [ABSTRACT FROM AUTHOR]

Simple Summary: Although often considered host-specific, there is increasing evidence of a broader-than-expected host tropism for different circoviruses, including porcine circovirus 2 (PCV-2). In this study, the presence of PCV-2 in the lung lymph nodes of Namibian jackals has been demonstrated. The complete genome of the viruses was generated, and they were classified as PCV-2b and shown to have a close genetic relationship with South African and Namibian strains collected from domestic pigs. Since contact between jackals and domestic swine is highly unlikely, one of the most plausible explanations for the infection of the jackals with PCV-2b would involve the dispersal of pig-derived products in the wild environment during recreational activities or the scavenging activity of jackals living in peri-urban areas. However, further studies are required to properly assess how PCV-2 is acquired and maintained in the wild canids and its potential impact on other wild and domestic species. Members of the genus Circovirus have been identified in several host species. While initially considered host-specific, there is growing evidence of their presence in unexpected hosts. Porcine circovirus 2 (PCV-2) is no exception, having been reported in animals belonging to different orders, including carnivores. Recently, PCV-2 was detected in domestic pigs, warthogs and antelopes in Namibia. Considering the potential contact between these populations and wild carnivores, the presence of PCV-2 was investigated in 32 black-backed jackals (Lupulella mesomelas) shot between February and July 2021 as part of predator control operations in Namibia. Two lung lymph nodes tested positive for PCV-2 by PCR, confirming the broader-than-expected PCV-2 host tropism and the susceptibility of canids. Sequence analysis demonstrated a close association between the PCV-2s identified in the jackals and PCV-2b strains collected from South African domestic pigs. Although several hypotheses regarding the source of the jackal's infection are proposed, further studies should be performed to properly assess how PCV-2 is acquired and maintained in the wild and its potential impact on wild and domestic species. [ABSTRACT FROM AUTHOR]

Porcine reproductive and respiratory syndrome (PRRS) is probably the most relevant viral disease affecting pig farming. Despite the remarkable efforts paid in terms of vaccination administration and biosecurity, eradication and long-term control have often been frustrated. Unfortunately, few studies are currently available that objectively link, using a formal statistical approach, viral molecular epidemiology to the risk factors determining the observed scenario. The purpose of the present study is to contribute to filling this knowledge gap taking advantage of the advancements in the field of phylodynamics. Approximately one-thousand ORF7 sequences were obtained from strains collected between 2004 and 2021 from the largest Italian pig company, which implements strict compartmentalization among independent three-sites (i.e., sow herds, nurseries and finishing units) pig flows. The history and dynamics of the viral population and its evolution over time were reconstructed and linked to managerial choices. The viral fluxes within and among independent pig flows were evaluated, and the contribution of other integrated pig companies and rurally risen pigs in mediating such spreading was investigated. Moreover, viral circulation in Northern Italy was reconstructed using a continuous phylogeographic approach, and the impact of several environmental features on PRRSV strain persistence and spreading velocity was assessed. The results demonstrate that PRRSV epidemiology is shaped by a multitude of factors, including pig herd management (e.g., immunization strategy), implementation of strict-independent pig flows, and environmental features (e.g., climate, altitude, pig density, road density, etc.) among the others. Small farms and rurally raised animals also emerged as a potential threat for larger, integrated companies. These pieces of evidence suggest that none of the implemented measures can be considered effective alone, and a multidimensional approach, ranging from individual herd management to collaboration and information sharing among different companies, is mandatory for effective infection control. [ABSTRACT FROM AUTHOR]

For several years after its discovery, Porcine circovirus 2 (PCV-2) represented a major threat to the swine industry through economic losses due to the associated clinical syndromes, decreased production performances in both symptomatic and asymptomatic animals and disease management costs. Widespread vaccination administration has largely reduced the impact of this infection and represents the most effective control measure. The efficacy of vaccination is threatened by the emergence of novel (or uncommon) PCV-2 genotypes. In addition to domestic pigs, PCV-2 has been detected in several other species, a fact which could have an impact on new variant emergence and maintenance. Considering this, the present study assessed the distribution of the minor PCV-2c genotype in non-Suidae ungulates in Namibia. Red hartebeests (Alcelaphus buselaphus caama) (n = 44), kudus (Tragelaphus strepsiceros) (n = 10) and oryxes (Oryx gazella) (n = 54), whose mediastinal lymph nodes were sampled after slaughtering during the period 2019–2021, were included in the study. Two oryxes (3.7%; 95% CI = 0.45–12.75%) were PCV-2-positive by PCR. Complete genome sequence was obtained for the two samples identifying them as PCV-2c genotype. The sequences were identical and shared a high percentage of identity (~99.9%) with those recently obtained from warthogs living in the same area. The present study confirms the presence of the PCV-2c genotype (previously considered extinct) in Namibian wild animal populations and demonstrates greater than expected PCV-2 host plasticity. Because of the role these niches can have in the maintenance and evolution of minor PCV-2 genotypes, more extensive and dedicated studies should be performed to prepare authorities to promptly react to potential emerging threats from these viruses. [ABSTRACT FROM AUTHOR]

Vaccination against porcine circovirus 2 (PCV-2) is a common practice all over the world. Vaccines can prevent PCV-2-systemic disease (PCV-2-SD) outbreaks but not PCV-2 infection, which can be detectable in a percentage of vaccinated animals. Occasionally, PCV-2-SD is diagnosed in vaccinated farms. The objective of this study was to genotype the PCV-2 strains detected in vaccinated animals diagnosed with PCV-2-SD. Additionally, the evolution of the frequency of PCV-2 genotype detection at Spanish, European, and world levels was assessed. Fifty cases diagnosed as PCV-2-SD between 2009 and 2020 were included in this study. PCV-2 genotype was determined by sequencing the Cap gene region. Among them, only PCV-2b (23/50, 46%) and PCV-2d (27/50, 54%) genotypes were detected. Although the frequency of detection of these two genotypes was similar, their temporal distribution was different. Whereas most PCV-2b sequences (17/23, 74%) were detected between 2009 and 2012, PCV-2d sequences were obtained from 2013 to 2020. Indeed, a predominance of the PCV-2d genotype was observed from 2013 onwards, a trend also noticed at European and world levels. The results suggest that detection of particular genotypes in vaccinated animals probably reflects the general prevalence of the genotypes over time rather than genotype-specific vaccine-immunity escaping. [ABSTRACT FROM AUTHOR]

Porcine circovirus type 3 (PCV-3) infection is widely distributed in domestic pig populations in America, Europe, and Asia. However, no data is currently available about its presence and distribution in Africa. This study investigated the presence of PCV-3 in pigs (n = 122) in Namibia, by means of biomolecular methods. The pig samples collected (n = 122) were representative of the swine industry in Namibia, covering the major pig production facilities in the country. All of the samples tested were negative for PCV-3, and this indicated that the virus was either not present in the country or was circulating at low levels. Further studies are needed to better understand the distribution, if any, of PCV-3 in Namibia. [ABSTRACT FROM AUTHOR]

Differently from alpha- and betaherpesviruses affecting swine, interest in the recently discovered Suid gammaherpesvirus 3, Suid gammaherpesvirus 4, and Suid gammaherpesvirus 5, also known as porcine lymphotropic herpesviruses (PLHV-1, PLHV-2, and PLHV-3), has largely focused on their role as potential zoonotic agents in cases of xenotransplantation. However, their role as primary pathogens of swine or as co-factors for other lymphotropic infections has essentially been neglected. The present study aims at filling this gap, evaluating the association between PLHVs infection and different clinical conditions and/or porcine circovirus (PCV) co-infection. One hundred seventy-six samples were obtained from different animals located in a high-density pig area of Northern Italy in the period 2017–2020. The presence of PLHVs and PCVs was tested and quantified by specific real-time PCR: PLHVs were widespread among pigs (PLHV-1, PLHV-2, and PLHV-3 prevalence was 28.97%, 10.79%, and 4.54%, respectively) and detected in all considered tissues and clinical conditions. Frequent co-infections were also observed among PLHVs and with PCVs, although a significant association was not detected with the exception of a positive interaction between PLHV-1 and PLHV-3, and a negative one between PLHV-2 and PCV-2. Significantly, no association between PLHVs, alone or in co-infection, emerged with any of the considered clinical signs, their frequency being comparable between healthy and diseased animals. Based on these pieces of evidence and despite their high prevalence, PLHVs' relevance for the swine industry appears negligible, either as primary pathogens or as predisposing factors for circovirus-induced diseases. [ABSTRACT FROM AUTHOR]

The genus Circovirus includes several species and mostly causes asymptomatic infections. Porcine circovirus 2 (PCV-2) and, with increasing evidence, Porcine circovirus 3 (PCV-3), have been associated with different clinical conditions all over the world. In 2019, a new porcine circovirus (PCV-4) was identified from diseased animals in China. Because of the lessons learned from PCV-2 and PCV-3, it appears mandatory to investigate the actual distribution of this new virus and its potential association with clinical outcomes. To this purpose, an exploratory study to detect PCV-4 by molecular methods was performed in Italy and Spain by testing more than 300 samples of different types (serum and tissues), collected from both healthy and diseased pigs and wild boar as well. All samples, independently from the country, type, health status and host, tested PCV-4 negative. Therefore, no evidence of PCV-4 presence was found in Italy and Spain through this exploratory study. Considering the dense pig trade among European countries, its presence in the continent can similarly be considered unlikely. The reasons behind the restricted PCV-4 distribution compared to other porcine circoviruses will require further investigations. Careful surveillance might nevertheless be important since prompt recognition of PCV-4 would allow the implementation of effective countermeasures to prevent its spreading and potential economic losses. [ABSTRACT FROM AUTHOR]

Porcine circovirus 2 (PCV-2) is one of the most impactful and widespread pathogens of the modern swine industry. Unlike other DNA viruses, PCV-2 is featured by a remarkable genetic variability, which has led to the emergence and recognition of different genotypes, some of which (PCV-2a, 2b, and 2d) have alternated over time. Currently, PCV-2d is considered the most prevalent genotype, and some evidence of differential virulence and vaccine efficacy have been reported. Despite the potential practical relevance, the data on PCV-2 epidemiology in Italy are quite outdated and do not quantify the actual circulation of this genotype in Italy. In the present study, 82 complete ORF2 sequences were obtained from domestic pigs and wild boars sampled in Northern Italy in the period 2013–2018 and merged with those previously obtained from Italy and other countries. A combination of phylogenetic, haplotype network, and phylodynamic analyses were used to genotype the collected strains and evaluate the temporal trend and the spatial and host spread dynamics. A rising number of PCV-2d detections was observed in domestic pigs, particularly since 2013, reaching a detection frequency comparable to PCV-2b. A similar picture was observed in wild boars, although a lower sequence number was available. Overall, the present study demonstrates the extreme complexity of PCV-2 molecular epidemiology in Italy, the significant spread across different regions, the recurrent introduction from foreign countries, and the frequent occurrence of recombination events. Although a higher viral flux occurred from domestic to wild populations than vice versa, wild boars seem to maintain PCV-2 infection and spread it over relatively long distances. [ABSTRACT FROM AUTHOR]

The identification of a new circovirus (Porcine circovirus 3, PCV‐3) has raised a remarkable concern because of some analogies with Porcine circovirus 2 (PCV‐2). Preliminary results suggest an extremely recent PCV‐3 emergence and high mutation rate. Retrospective studies prove its circulation at least since the early 1990s, revealing that PCV‐3 could have been infecting pigs for an even longer period. Therefore, a new evaluation, based on an updated collection of PCV‐3 sequences spanning more than 20 years, is performed using a phylodynamic approach. The obtained results overrule the previous PCV‐3 history concept, indicating an ancient origin. These evidences are associated with an evolutionary rate far lower (10−5–10−6 substitution/site/year) than the PCV‐2 one. Accordingly, the action of selective pressures on PCV‐3 open reading frames (ORFs) seems to be remarkably lower compared to those acting on PCV‐2, suggesting either a reduced PCV‐3 plasticity or a less efficient host‐induced natural selection. A complex and not‐directional viral flow network is evidenced through phylogeographic analysis, indicating a long lasting circulation rather than a recent emergence followed by spreading. Being recent emergence has been ruled out, efforts should be devoted to understand whether its recent discovery is simply due to improved detection capabilities or to the breaking of a previous equilibrium. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Sixteen outbreaks of diarrhoea in suckling piglets and sows were investigated. • Deep-sequencing was performed on 24 rotavirus A positive faecal samples. • A new strain was introduced in Spain shortly before the onset of the outbreaks. • A high diversification of the VP7 and VP4 genes occurred in a short time. • A high number of changes in the epitopes compared to vaccine strains was reported. Abstract Since early 2017, in Spain there was an apparent increase in reports on rotavirus involvement in neonatal diarrhoea outbreaks, affecting also adult sows. In this study, 16 unrelated outbreaks of diarrhoea in suckling pigs and sows, where rotavirus A was the only pathogen detected, were investigated. Deep-sequencing was performed on total RNA from twenty-four positive faecal samples. Genotyping, phylogenetic and bayesian analyses showed that all isolates had a common ancestor of porcine, or human porcine-like, origin. The new strain was introduced in the population shortly before the onset of the outbreaks. Besides, a high diversification of the VP7 and VP4 genes occurred in a short time. Isolates presented a high number of amino acid changes in the neutralizing epitopes compared to vaccine sequences. The present report illustrates how a new rotavirus A strain may disseminate rapidly and the extremely high diversification that this pathogen may undergo in a short period. [ABSTRACT FROM AUTHOR]