Noninvasive strategies for surveillance of swine viral diseases: a review

Validation of a real-time PCR assay for the detection of African swine fever virus in fresh pork meat juice

African swine fever virus (ASFV) is the etiological agent of African swine fever (ASF), a disease with detrimental effects on the health, welfare, and production of domestic and wild pigs. The ASF laboratory confirmation is based on the analysis of blood, serum and organ samples. However, testing these samples could not be always convenient, economically feasible or possible. This study describes the validation process of a PCR-based assay targeting a portion of p72 gene, used for the molecular detection of ASFV, from meat juice samples obtained from pigs succumbed to ASFV. More specifically, we investigated the capability of a real-time PCR assay to detect ASFV DNA in meat juices obtained from the diaphragmatic muscle along with the correspondent spleens of 55 ASFV-positive pigs and wild boars sampled from confirmed outbreaks in Romania and from 73 ASFV-negative and regularly slaughtered healthy pigs collected in the Abruzzo region (Italy). The test was able to detect viral DNA in both types of samples, with lower Ct values in spleens (mean=21.11, median=20.61) than meat juices (mean=23.08, median=22.40). However, distributions of Ct values were strongly correlated each other (R2= 0.83, P<0.001). Considering the distribution of the observed Ct values in the 55 positive meat juice samples, a 1:10 dilution would be able to detect 90 % of positive samples, whereas a 1:100 dilution would reduce the detectability to 78 % of more contaminated samples. As meat juice could be obtained easily from muscles and considering the potential use of this test on pooled samples, it could represent a tool to aid the investigation of ASFV spread.

Concentrations of selected immunological parameters in the serum and processing fluid of suckling piglets and the serum and colostrum of their mothers

BACKGROUND

Blood sampling from neonatal piglets is related to multiple disadvantages. Therefore, a new, alternative matrix is required to assess piglets' early immune status efficiently. The present study aimed to assess the usefulness of processing fluid for determining selected piglets' immune parameters. 264 pigs - 31 sows, 146 male piglets, and 87 female piglets from commercial indoor farrow-to-finish pig herd were included in this study. 264 serum, 31 colostrum, and 146 processing fluid samples were collected. Serum was collected from all animals, colostrum was collected from sows, and processing fluid was collected from male piglets only. Using commercial ELISA tests, the concentration of various immunoglobulins, cytokines, and acute phase proteins was assessed in each matrix. Statistical analyses were employed to determine differences in the concentration of measured indices between piglets' serum and processing fluid and correlations in the concentration of tested indices between particular sets of matrices.

RESULTS

Statistical analyses did not reveal significant differences in the IgG, IgA, IL-1β, IL-4, IL-6, and IFN-γ concentration between piglets' serum and processing fluid (p > 0.05). A positive correlation (p < 0.05) regarding the concentration of some indices between processing fluid and samples collected from sows was also observed.

CONCLUSIONS

Processing fluid can be considered a promising alternative to blood for assessing some immunological indices in piglets, such as IgG, IgA, IL-1β, IL-4, IL-6, and IFN-γ, and, possibly, in the indirect assessment of some indices in lactating sows, including IgA, IL-1β, IL-4, IL-6, IL-8, IFN-γ, or Pig-MAP.

Dynamics of antibody response and bacterial shedding of Mycoplasma hyorhinis and M. hyosynoviae in oral fluids from experimentally inoculated pigs

Mycoplasma hyorhinis (Mhr) and M. hyosynoviae (Mhs) are commensal organisms of the upper respiratory tract and tonsils but may also cause arthritis in pigs. In this study, 8-week-old cesarean-derived colostrum-deprived (CDCD) pigs (n = 30; 3 groups, 10 pigs per group, 2 pigs per pen) were inoculated with Mhr, Mhs, or mock-inoculated with culture medium and then pen-based oral fluids were collected at different time points over the 56 days of the experimental study. Oral fluids tested by Mhr and Mhs quantitative real-time PCRs revealed Mhr DNA between day post inoculation (DPI) 5-52 and Mhs DNA between DPI 5-15. Oral fluids were likewise tested for antibody using isotype-specific (IgG, IgA, IgM) indirect ELISAs based on a recombinant chimeric polypeptide of variable lipoproteins (A-G) for Mhr and Tween 20-extracted surface proteins for Mhs. Mhr IgA was detected at DPI 7 and, relative to the control group, significant (p < 0.05) antibody responses were detected in the Mhr group between DPI 12-15 for IgM and DPI 36-56 for both IgA and IgG. In the Mhs group, IgM was detected at DPI 10 and significant (p < 0.05) IgG and IgA responses were detected at DPI 32-56 and DPI 44-56, respectively. This study demonstrated that oral fluid could serve as an effective and convenient antemortem sample for monitoring Mhr and Mhs in swine populations.

First assessment of weeks-to-negative processing fluids in breeding herds after a Senecavirus A outbreak

Senecavirus A (SVA) causes vesicular disease in swine and has been responsible for a rampant increase in the yearly number of foreign animal disease investigations conducted in the United States. Diagnostic investigations for SVA are typically performed by sampling animals individually, which is labor-intensive and stressful. Developing an alternative aggregate sampling method would facilitate the detection of this virus at the population level. In a preliminary study, SVA was detected in processing fluids (PF) collected in a breeding herd before and after outbreak detection. The objective of this study was to estimate the average number of weeks PF remain SVA-positive after an SVA outbreak. Ten farrow-to-wean breeding herds volunteered to participate in this studyby longitudinally collecting PF samples after an SVA outbreak was detected and submitting samples for RT-rtPCR testing. The PF samples from the 10 farms were SVA-positive for an average of 11.8 weeks after the outbreak. Here, we show that testing of PF may be a cost-effective method to detect SVA and help halt its spread in SVA-endemic regions.

Emergent Molecular Techniques Applied to the Detection of Porcine Viruses

Molecular diagnostic tests have evolved very rapidly in the field of human health, especially with the arrival of the recent pandemic caused by the SARS-CoV-2 virus. However, the animal sector is constantly neglected, even though accurate detection by molecular tools could represent economic advantages by preventing the spread of viruses. In this regard, the swine industry is of great interest. The main viruses that affect the swine industry are described in this review, including African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), and porcine circovirus (PCV), which have been effectively detected by different molecular tools in recent times. Here, we describe the rationale of molecular techniques such as multiplex PCR, isothermal methods (LAMP, NASBA, RPA, and PSR) and novel methods such as CRISPR-Cas and microfluidics platforms. Successful molecular diagnostic developments are presented by highlighting their most important findings. Finally, we describe the barriers that hinder the large-scale development of affordable, accessible, rapid, and easy-to-use molecular diagnostic tests. The evolution of diagnostic techniques is critical to prevent the spread of viruses and the development of viral reservoirs in the swine industry that impact the possible development of future pandemics and the world economy.

A cross-sectional assessment of PRRSV nucleic acid detection by RT-qPCR in serum, ear-vein blood swabs, nasal swabs, and oral swabs from weaning-age pigs under field conditions

Introduction

The porcine reproductive and respiratory syndrome virus (PRRSV) continues to challenge swine production in the US and most parts of the world. Effective PRRSV surveillance in swine herds can be challenging, especially because the virus can persist and sustain a very low prevalence. Although weaning-age pigs are a strategic subpopulation in the surveillance of PRRSV in breeding herds, very few sample types have been validated and characterized for surveillance of this subpopulation. The objectives of this study, therefore, were to compare PRRSV RNA detection rates in serum, oral swabs (OS), nasal swabs (NS), ear-vein blood swabs (ES), and family oral fluids (FOF) obtained from weaning-age pigs and to assess the effect of litter-level pooling on the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of PRRSV RNA.

Methods

Three eligible PRRSV-positive herds in the Midwestern USA were selected for this study. 666 pigs across 55 litters were sampled for serum, NS, ES, OS, and FOF. RT-qPCR tests were done on these samples individually and on the litter-level pools of the swabs. Litter-level pools of each swab sample type were made by combining equal volumes of each swab taken from the pigs within a litter.

Results

Ninety-six piglets distributed across 22 litters were positive by PRRSV RT-qPCR on serum, 80 piglets distributed across 15 litters were positive on ES, 80 piglets distributed across 17 litters were positive on OS, and 72 piglets distributed across 14 litters were positive on NS. Cohen's kappa analyses showed near-perfect agreement between all paired ES, OS, NS, and serum comparisons (). The serum RT-qPCR cycle threshold values (Ct) strongly predicted PRRSV detection in swab samples. There was a ≥ 95% probability of PRRSV detection in ES-, OS-, and NS pools when the proportion of positive swab samples was ≥ 23%, ≥ 27%, and ≥ 26%, respectively.

Discussion

ES, NS, and OS can be used as surveillance samples for detecting PRRSV RNA by RT-qPCR in weaning-age pigs. The minimum number of piglets to be sampled by serum, ES, OS, and NS to be 95% confident of detecting ≥ 1 infected piglet when PRRSV prevalence is ≥ 10% is 30, 36, 36, and 40, respectively.

In-silico characterization of the relationship between the Porcine reproductive and respiratory syndrome virus prevalence at the piglet and litter levels in a farrowing room

BACKGROUND

Family oral fluids (FOF) sampling has been described as a sampling technique where a rope is exposed to sows and respective suckling litters and thereafter wrung to obtain fluids. PCR-based testing of FOF reveals presence of PRRS virus RNA only at the litter level, as opposed to conventional individual-animal-based sampling methods that demonstrate PRRSV RNA at the piglet level. The relationship between the PRRSV prevalence at the individual piglet level and at the litter level in a farrowing room has not been previously characterized. Using Monte Carlo simulations and data from a previous study, the relationship between the proportion of PRRSV-positive (viremic) pigs in the farrowing room, the proportion of litters in the farrowing room with at least one viremic pig, and the likely proportion of litters to be positive by a FOF RT-rtPCR test in a farrowing room was characterized, taking into account the spatial distribution (homogeneity) of viremic pigs within farrowing rooms.

RESULTS

There was a linear relationship between piglet-level- and litter-level prevalence, where the latter was always larger than the former. When the piglet-level prevalence was 1%, 5%, 10%, 20%, and 50%, the true-litter level prevalence was 5.36%, 8.93%, 14.29%, 23.21%, and 53.57%, respectively. The corresponding apparent-litter prevalence by FOF was 2.06%, 6.48%, 11.25%, 21.60%, and 51.56%, respectively.

CONCLUSION

This study provides matching prevalence estimates to help guide sample size calculations. It also provides a framework to estimate the likely proportion of viremic pigs, given the PRRSV RT-rtPCR positivity rate of FOF samples submitted from a farrowing room.

Evaluation of Non-Invasive Sampling Methods for Detection of Hepatitis E Virus Infected Pigs in Pens

Pigs are a reservoir of hepatitis E virus (HEV), which causes hepatitis in humans. To study the epidemiology of HEV in pig farms, sampling methods are currently used that cause discomfort to pigs, such as rectal sampling. In line with the 3Rs principle, we aimed to evaluate non-invasive methods to detect pens with HEV-shedding pigs. Twenty-eight pens of one farm were sampled cross-sectionally. Individual rectal swabs (IRS) were collected to determine prevalence within pens. Four pen-level samples were compared: a pool of IRS per pen (P), boot socks (BS), oral fluid (OF) and pooled faecal droppings (FD). Each sample was tested by RT-PCR and the sensitivity and specificity of each method was determined by Bayesian latent class analysis. According to IRS, 19/28 pens were HEV positive. BS had a sensitivity of 95% and detected HEV in pens with 10% of pigs shedding; however, specificity was below 30%. FD were comparably accurate to P, with a sensitivity and specificity of 94% and 86%, respectively. BS sampling is thus advised to detect early shedding of HEV or pen contamination, and FD to determine the duration of shedding. This study demonstrates that non-invasive sampling can replace rectal swabs in research on HEV in pigs.

Immune status of piglets during the first week of life: Current knowledge, significance and assessment

The immune system of neonate piglets differs from adult pigs in structure and competence. Although piglets are born immunocompetent, they are genuinely immunologically defenceless. To survive in the environment, piglets need passive protection provided by sow’s colostrum and milk when constantly exposed to numerous pathogens. Early assessment of piglets’ immune status may enable rapid intervention in case of detection of any deficiencies or disorders. Moreover, awareness of the piglets’ immunocompetence and the level of maternally-derived antibodies (MDA) may allow the creation of a proper vaccine schedule. Hence, extending knowledge of prenatal ontogeny of the porcine immune system, the immune status of neonate piglets’ and the immunological components of porcine colostrum is crucial. Since animal welfare has become a more critical element of animal production, new, non-invasive sampling methodologies are highly desirable for the evaluation of piglets’ immune status.

Non-Invasive Sampling in the Aspect of African Swine Fever Detection-A Risk to Accurate Diagnosis

African swine fever remains one of the most economically important and dangerous diseases of the Suidae family. Until now, neither a safe vaccine nor a treatment against ASF has been available, which is why prevention of the disease involves biosecurity measures and early recognition based on accurate diagnosis. Nowadays, different strategies for ASF detection are discussed to reduce both animal suffering and the costs of ASF surveillance. This article aims to indicate the risk, with regard to non-invasive sampling, for the detection of ASFV. In this study, we analyzed data from three independent animal trials, in the framework of the detection of positive samples in different matrices (blood, sera, oral and rectal swabs) collected from nineteen domestic pigs infected with similar doses but under different scenarios, including different ASFV strains or routes of infection. Genetic material of ASFV was found in all matrices, but detection occurred earlier in the blood samples than in the oral and the rectal swabs. Furthermore, analyses revealed that at relevant sampling timepoints, PCR-positive blood samples were detected more frequently and reached higher percentages (up to 100% during fever) than oral and rectal swabs. Moreover, mean Ct values in blood samples collected from animals infected with virulent strains were significantly lower than in oral and rectal swabs, ensuring a higher probability of ASFV detection. High Ct values and occasional shedding in all tested matrices, in the cases of animals infected by an attenuated ASFV-strain, showed that blood sampling may be necessary to confirm the presence of anti-ASFV antibodies in sera. This study showed that during veterinary surveillance, blood sampling (for both PCR and serological analyses) is essential for the accurate diagnosis of ASF and provides the highest probability of detection of the disease.

Epidemiological Study on Salmonella Prevalence in Sow Herds Using Direct and Indirect Detection Methods

In piglet production, the beginning of pork production, Salmonella prevalence requires greater attention as having an impact on the subsequent production steps. The aim of this study was to investigate Salmonella prevalence in three sow herds with attached piglet rearing units. Salmonella prevalence was investigated either directly by boot swabs and feces or indirectly by serum samples taken during gilt integration, the peripartal period, and piglet rearing. Boot swabs and feces were analyzed by real-time PCR and subsequent microbiology. Results indicated that high biosecurity measures in sow husbandry do not necessarily result in a low Salmonella prevalence. Furthermore, the sow herds' Salmonella prevalence should not be used to infer the situation in the associated piglet rearing. The proportion of positive boot swabs was 10.5, 3.6, and 21.3% for sows (gilts and peripartal) with an inverse situation in piglet rearing with 50.0, 63.3, and 5.8% positive swabs for farms A, B, and C, respectively. Boot swabs are suitable as a direct sampling method to gain an overview of Salmonella prevalence in both sows and piglets. Indirect serum antibody testing can be useful, although it should be evaluated considering age-dependent levels of antibody titres.

Impact of maternally derived immunity on immune responses elicited by piglet early vaccination against the most common pathogens involved in porcine respiratory disease complex

Background

Newborn piglets can trigger an elementary immune response, but the acquirement of specific antibodies and/or cellular immunity against pathogens before they get infected post-natally is paramount to preserve their health. This is especially important for the pathogens involved in porcine respiratory disease complex (PRDC) as they are widespread, fairly resistant at environment, and genetically variable; moreover, some of them can cause intrauterine/early life infections.

Main body

Piglet protection can be achieved by either passive transfer of maternal derived immunity (MDI) and/or actively through vaccination. However, vaccinating piglets in the presence of remaining MDI might interfere with vaccine efficacy. Hence, the purpose of this work is to critically review the putative interference that MDI may exert on vaccine efficacy against PRDC pathogens. This knowledge is crucial to design a proper vaccination schedule.

Conclusion

MDI transferred from sows to offspring could potentially interfere with the development of an active humoral immune response. However, no conclusive interference has been shown regarding performance parameters based on the existing published literature.

Revisiting Porcine Circovirus Disease Diagnostic Criteria in the Current Porcine Circovirus 2 Epidemiological Context

Current knowledge on porcine circovirus diseases (PCVD) caused by Porcine circovirus 2 (PCV-2) includes the subclinical infection (PCV-2-SI), systemic (PCV-2-SD) and reproductive (PCV-2-RD) diseases, and porcine dermatitis and nephropathy syndrome (PDNS). Criteria to establish the diagnosis of these conditions have not changed over the years; thus, the triad composed by clinical signs, lesions and viral detection in lesions are still the hallmark for PCV-2-SD and PCV-2-RD. In contrast, PCV-2-SI diagnosis is not usually performed since this condition is perceived to be controlled by default through vaccination. PDNS is diagnosed by gross and histopathological findings, and PCV-2 detection is not recognized as a diagnostic criterion. Molecular biology methods as a proxy for PCVD diagnoses have been extensively used in the last decade, although these techniques should be mainly considered as monitoring tools rather than diagnostic ones. What has changed over the years is the epidemiological picture of PCV-2 through the massive use of vaccination, which allowed the decrease in infectious pressure paralleled with a decrease in overall herd immunity. Consequently, the need for establishing the diagnosis of PCVD has increased lately, especially in cases with a PCV-2-SD-like condition despite vaccination. Therefore, the objective of the present review is to update the current knowledge on diagnostic criteria for PCVDs and to contextualize the interest of using molecular biology methods in the overall picture of these diseases within variable epidemiological scenarios of PCV-2 infection.

Reappraisal of PRRS Immune Control Strategies: The Way Forward

The control of porcine reproductive and respiratory syndrome (PRRS) is still a major issue worldwide in the pig farming sector. Despite extensive research efforts and the practical experience gained so far, the syndrome still severely affects farmed pigs worldwide and challenges established beliefs in veterinary virology and immunology. The clinical and economic repercussions of PRRS are based on concomitant, additive features of the virus pathogenicity, host susceptibility, and the influence of environmental, microbial, and non-microbial stressors. This makes a case for integrated, multi-disciplinary research efforts, in which the three types of contributing factors are critically evaluated toward the development of successful disease control strategies. These efforts could be significantly eased by the definition of reliable markers of disease risk and virus pathogenicity. As for the host's susceptibility to PRRSV infection and disease onset, the roles of both the innate and adaptive immune responses are still ill-defined. In particular, the overt discrepancy between passive and active immunity and the uncertain role of adaptive immunity vis-à-vis established PRRSV infection should prompt the scientific community to develop novel research schemes, in which apparently divergent and contradictory findings could be reconciled and eventually brought into a satisfactory conceptual framework.

A multiplex assay for the detection of antibodies to relevant swine pathogens in serum

Livestock industry supports the livelihood of around 1.3 billion people in the world, with swine industry contributing with 30% of total livestock production worldwide. To maintain and guarantee this production, a pivotal point according to the OIE is addressing potential biohazards. To control them, permanent sero-surveillance is crucial to achieve more focused veterinary public health intervention and prevention strategies, to break the chains of transmission, and to enable fast responses against outbreaks. Within this context, multiplex assays are powerful tools with the potential to simplify surveillance programs, since they reduce time, labour, and variability within analysis. In the present work, we developed a multiplex bead-based assay for the detection of specific antibodies to six relevant pathogens affecting swine: ASFV, CSFV, PRRSV, SIV, TB and HEV. The most immunogenic target antigen of each pathogen was selected as the target protein to coat different microsphere regions in order to develop this multiplex assay. A total of 1544 serum samples from experimental infections as well as field samples were included in the analysis. The 6-plex assay exhibited credible diagnostic parameters with sensitivities ranging from 87.0% to 97.5% and specificities ranging from 87.9% to 100.0%, demonstrating it to be a potential high throughput tool for surveillance of infectious diseases in swine.