Detection and Isolation of Swine Influenza A Virus in Spiked Oral Fluid and Samples from Individually Housed, Experimentally Infected Pigs: Potential Role of Porcine Oral Fluid in Active Influenza A Virus Surveillance in Swine

Assessment of individual and population-based sampling for detection of influenza A virus RNA in breeding swine herds

Sample types currently used for Influenza A virus (IAV) surveillance in swine farms vary in sensitivity, convenience of collection, and herd representativeness. Family oral fluids are an effective population-based sample type for detecting porcine reproductive and respiratory syndrome virus (PRRSV) (ribonucleic acid) RNA by real-time reverse transcription-polymerase chain reaction (RT-rtPCR) in breeding herds. However, little is known about the efficacy of family oral fluids samples for detecting IAV RNA in these herds. This study compared the probability of IAV RNA detection among individual and population-based samples. A 3,500-sow breeding herd was sampled for matched sets (n = 57) of family oral fluids, udder wipes, sow nasal wipes, individual piglet nasal wipes, and drinker wipes, tested by RT-rtPCR for IAV RNA. Overall, 57.9 % (33/57) of family oral fluids, 49.1 % (28/57) of udder wipes, 28.1 % (16/57) of sow nasal wipes, 15.8 % (9/57) of drinker wipes, and 66.6 % (38/57) of individual piglet nasal wipes were positive. Family oral fluids showed a Kappa value of 0.81, indicating near-perfect agreement with individual piglet nasal wipes, while udder wipes had a substantial agreement (Kappa = 0.65). Other sample types showed fair agreement (Kappa < 0.28). These results validate family oral fluids as an efficient alternative population-based sample for IAV surveillance in breeding herds. The proportion of positive piglets within litters by room was 91 % in room A (20/22), 70 % in room B (17/24), and 9 % in room C (1/11). This study also highlights the importance of sampling different farrowing rooms within the same breeding herd to enhance IAV surveillance.

Evaluation of nasal swab and nasal wipe for detection of Influenza A in swine using Bayesian latent class analysis

Influenza A virus (IAV) is an important pathogen in Brazilian swine herds, and monitoring the viral circulation is essential to control and reduce the transmission. Surveillance programs for IAV are often based on individual piglets level sampling, making the evaluation of the available diagnostic tools crucial to assessing IAV circulation in herds. Thus, two sample collection methodologies were compared in pig herds in southern Brazil to detect IAV by RT-qPCR: nasal swab (NS) and nasal wipe (NW). A Bayesian latent class model (BLCM) was set for two tests and two populations. The NW and NS used are more specific (higher than 95 % for both) than sensitive. The sensitivity for NW was lower than the NS, 84.14 % (70 % - 95 %; posterior probability interval (PPI): 95 %) and 87.15 % (73 % - 97 %; PPI: 95 %), respectively, and the specificity was 95 % (90 % - 99 %; PPI: 95 %) and 99 % (96 % - 100 %; PPI: 95 %), respectively. Although the wipe sample collection loses both sensitivity and specificity compared with nasal swab, differences in test performance were very limited and PPIs largely overlapped. Therefore NW can also be considered a valuable tool. The decision about the use of both techniques should be based on the trade-off between their performance limitations and feasibility in routine monitoring.

Influenza surveillance in pigs: balancing act between broad diagnostic coverage and specific virus characterization

BACKGROUND

Monitoring of infectious diseases on swine farms requires a high diagnostic sensitivity and specificity of the test system. Moreover, particularly in cases of swine influenza A virus (swIAV) it is desirable to include characterization of the virus as precisely as possible. This is indispensable for strategies concerning prophylaxis of swIAV and furthermore, to meet the requirements of a purposeful monitoring of newly emerging swIAV strains in terms of vaccine design and public health. Within the present cross-sectional study, we compared the diagnostic value of group samples (wipes of surfaces with direct contact to mouth/nose, dust wipes, udder skin wipes, oral fluids) to individual samples (nasal swabs, tracheobronchial swabs) for both swIAV identification and characterization. Sampling included different stages of pig production on 25 sow farms with attached nursery considered as enzootically infected with swIAV. Firstly, samples were analyzed for IAV genome and subsequently samples with Ct-values < 32 were subtyped by multiplex RT-qPCR.

RESULTS

Nasal swabs of suckling piglets and nursery pigs resulted in a higher odds to detect swIAV (p < 0.001) and to identify swIAV subtypes by RT-qPCR (p < 0.05) compared to nasal swabs of sows. In suckling piglets, significant higher rates of swIAV detection could be observed for nasal swabs (p = 0.007) and sow udder skin wipes (p = 0.036) compared to contact wipes. In the nursery, group sampling specimens were significantly more often swIAV positive compared to individual samples (p < 0.01), with exception of the comparison between contact wipes and nasal swabs (p = 0.181). However, in general nasal swabs were more likely to have Ct-value < 32 and thus, to be suitable for subtyping by RT-qPCR compared to dust wipes, contact wipes, udder skin wipes and tracheobronchial swabs (p < 0.05). Interestingly, different subtypes were found in different age groups as well as in different specimens in the same holding.

CONCLUSION

Although population-based specimens are highly effective for swIAV monitoring, nasal swabs are still the preferable sampling material for the surveillance of on-farm circulating strains due to significantly higher virus loads. Remarkably, sampling strategies should incorporate suckling piglets and different age groups within the nursery to cover as many as possible of the on-farm circulating strains.

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

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.

A systematic review of influenza A virus prevalence and transmission dynamics in backyard swine populations globally

Background

Backyard swine farming is critical to generating subsistence and food security in rural and peri-urban households in several developing countries. The objective of this systematic review was to analyze the molecular and serological prevalence of influenza A virus (IAV) in backyard swine populations globally.

Results

We identified 34 full-text research articles in NCBI-PubMed and Google Scholar databases that have reported IAV sero- and/or virological prevalence in backyard swine up to 11 July 2021. The highest number of studies were reported from Asia (n = 11) followed by North America (n = 10), South America (n = 6), Africa (n = 6), and Europe (n = 1). While the maximum number of studies (44.12%) reported human-to-swine transmission of IAV, swine-to-human (5.88%), poultry-to-swine (5.88%), and wild birds-to-swine (2.94%) transmissions were also reported. An overall higher IAV seroprevalence (18.28%) in backyard swine was detected compared to the virological prevalence (1.32%). The human-origin pandemic A(H1N1)pdm09 virus clade 1A.3.3.2 was the more frequently detected IAV subtype in virological studies (27.27%) than serological studies (18.92%). In addition, the avian-origin highly pathogenic H5N1 and H5N8 viruses were also detected, which further substantiated the evidence of avian–swine interactions in the backyards.

Conclusion

Human–swine and avian–swine interactions in backyards may transmit IAV between species. Monitoring the circulation and evolution of IAV in backyard swine would help stakeholders make informed decisions to ensure sustainable backyard swine farming and public safety.

Detection of Porcine Respirovirus 1 (PRV1) in Poland: Incidence of Co-Infections with Influenza A Virus (IAV) and Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in Herds with a Respiratory Disease

Porcine respirovirus 1 (PRV1) is also known as porcine parainfluenza virus 1 (PPIV1). The prevalence and the role of PRV1 infections for pig health is largely unknown. In order to assess the PRV1 prevalence in Poland, nasal swabs and oral fluids collected from pigs from 30 farms were examined with RT real-time PCR. Additionally, IAV and PRRSV infection statuses of PRV1-positive samples were examined. The results showed that the virus is highly prevalent (76.7% farms positive) and different patterns of PRV1 circulation in herds with mild–moderate respiratory disease were observed. Co-infections with IAV and PRRSV were infrequent and detected in 8 (23.5%) and 4 (11.8%) out of 34 PRV1-positive nasal swab pools from diseased pens, respectively. In one pen PRV1, IAV, and PRRSV were detected at the same time. Interestingly, PRV1 mean Ct value in samples with co-infections was significantly lower (29.8 ± 3.1) than in samples with a single PRV1 infection (32.5 ± 3.6) (p < 0.05), which suggested higher virus replication in these populations. On the other hand, the virus detection in pig populations exhibiting respiratory clinical signs, negative for PRRSV and IAV, suggests that PRV1 should be involved in differential diagnosis of respiratory problems.

Comparative Susceptibility of Madin–Darby Canine Kidney (MDCK) Derived Cell Lines for Isolation of Swine Origin Influenza A Viruses from Different Clinical Specimens

Madin–Darby canine kidney (MDCK) cells are commonly used for the isolation of mammalian influenza A viruses. The goal of this study was to compare the sensitivity and suitability of the original MDCK cell line in comparison with MDCK-derived cell lines, MDCK.2, MDCK SIAT-1 and MDCK-London for isolation of swine-origin influenza A viruses (IAV-S) from clinical specimens. One-hundred thirty clinical specimens collected from pigs in the form of nasal swabs, lung tissue and oral fluids that were positive by PCR for the presence of IAV-S RNA were inoculated in the cell cultures listed above. MDCK-SIAT1 cells yielded the highest proportion of positive IAV-S isolations from all specimen types. For nasal swabs, 58.62% of the specimens were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (36.21%), and conventional MDCK and MDCK.2 cells (27.5%). For lung specimens, 59.38% were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (40.63%), and conventional MDCK and MDCK.2 cells (18.75–31.25%). Oral fluids yielded the lowest number of positive virus isolation results, but MDCK-SIAT1 cells were still had the highest rate (35%) of IAV-S isolation, whereas the isolation rate in other cells ranged from 5–7.5%. Samples with lower IAV-S PCR cycle threshold (Ct) values were more suitable for culturing and isolation. The isolated IAV-S represented H1N1-β, H1N2-α, H1N1pdm and H3N2 cluster IV and cluster IVB viruses. The result of the current study demonstrated the importance of using the most appropriate MDCK cells when isolating IAV-S from clinical samples.

An evaluation of the InDevR FluChip-8G insight microarray assay in characterizing influenza a viruses

Influenza viruses are an important cause of disease in both humans and animals, and their detection and characterization can take weeks. In this study, we sought to compare classical virology techniques with a new rapid microarray method for the detection and characterization of a very diverse, panel of animal, environmental, and human clinical or field specimens that were molecularly positive for influenza A alone (n = 111), influenza B alone (n = 3), both viruses (n = 13), or influenza negative (n = 2) viruses. All influenza virus positive samples in this study were first subtyped by traditional laboratory methods, and later evaluated using the FluChip-8G Insight Assay (InDevR Inc. Boulder, CO) in laboratories at Duke University (USA) or at Duke Kunshan University (China). The FluChip-8G Insight multiplexed assay agreed with classical virologic techniques 59 (54.1%) of 109 influenza A-positive, 3 (100%) of the 3 influenza B-positive, 0 (0%) of 10 both influenza A- and B-positive samples, 75% of 24 environmental samples including those positive for H1, H3, H7, H9, N1, and N9 strains, and 80% of 22 avian influenza samples. It had difficulty with avian N6 types and swine H3 and N2 influenza specimens. The FluChip-8G Insight assay performed well with most human, environmental, and animal samples, but had some difficulty with samples containing multiple viral strains and with specific animal influenza strains. As classical virology methods are often iterative and can take weeks, the FluChip-8G Insight Assay rapid results (time range 8 to 12 h) offers considerable time savings. As the FluChip-8G analysis algorithm is expected to improve over time with addition of new subtypes and sample matrices, the FluChip-8G Insight Assay has considerable promise for rapid characterization of novel influenza viruses affecting humans or animals.

A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide

The global anxiety and a significant threat to public health due to the current COVID-19 pandemic reiterate the need for active surveillance for the zoonotic virus diseases of pandemic potential. Influenza virus due to its wide host range and zoonotic potential poses such a significant threat to public health. Swine serve as a “mixing vessel” for influenza virus reassortment and evolution which as a result may facilitate the emergence of new strains or subtypes of zoonotic potential. In this context, the currently available scientific data hold a high significance to unravel influenza virus epidemiology and evolution. With this objective, the current systematic review summarizes the original research articles and case reports of all the four types of influenza viruses reported in swine populations worldwide. A total of 281 articles were found eligible through screening of PubMed and Google Scholar databases and hence were included in this systematic review. The highest number of research articles (n = 107) were reported from Asia, followed by Americas (n = 97), Europe (n = 55), Africa (n = 18), and Australia (n = 4). The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were the most common influenza A virus subtypes reported in swine in most countries across the globe, however, few strains of influenza B, C, and D viruses were also reported in certain countries. Multiple reports of the avian influenza virus strains documented in the last two decades in swine in China, the United States, Canada, South Korea, Nigeria, and Egypt provided the evidence of interspecies transmission of influenza viruses from birds to swine. Inter-species transmission of equine influenza virus H3N8 from horse to swine in China expanded the genetic diversity of swine influenza viruses. Additionally, numerous reports of the double and triple-reassortant strains which emerged due to reassortments among avian, human, and swine strains within swine further increased the genetic diversity of swine influenza viruses. These findings are alarming hence active surveillance should be in place to prevent future influenza pandemics.

Assessing the value of PCR assays in oral fluid samples for detecting African swine fever, classical swine fever, and foot-and-mouth disease in U.S. swine

INTRODUCTION

Oral fluid sampling and testing offers a convenient, unobtrusive mechanism for evaluating the health status of swine, especially grower and finisher swine. This assessment evaluates the potential testing of oral fluid samples with real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) to detect African swine fever, classical swine fever, or foot-and-mouth disease for surveillance during a disease outbreak and early detection in a disease-free setting.

METHODS

We used a series of logical arguments, informed assumptions, and a range of parameter values from literature and industry practices to examine the cost and value of information provided by oral fluid sampling and rRT-PCR testing for the swine foreign animal disease surveillance objectives outlined above.

RESULTS

Based on the evaluation, oral fluid testing demonstrated value for both settings evaluated. The greatest value was in an outbreak scenario, where using oral fluids would minimize disruption of animal and farm activities, reduce sample sizes by 23%-40%, and decrease resource requirements relative to current individual animal sampling plans. For an early detection system, sampling every 3 days met the designed prevalence detection threshold with 0.95 probability, but was quite costly.

LIMITATIONS

Implementation of oral fluid testing for African swine fever, classical swine fever, or foot-and-mouth disease surveillance is not yet possible due to several limitations and information gaps. The gaps include validation of PCR diagnostic protocols and kits for African swine fever, classical swine fever, or foot-and-mouth disease on swine oral fluid samples; minimal information on test performance in a field setting; detection windows with low virulence strains of some foreign animal disease viruses; and the need for confirmatory testing protocol development.

Comparison of individual, group and environmental sampling strategies to conduct influenza surveillance in pigs

BACKGROUND

Influenza A virus (IAV) is an important pathogen in pigs that affects productivity and has important public health implications because of its zoonotic nature. Surveillance is central to the control of influenza, however, detection of IAV infections can be challenging in endemically infected herds with low prevalence of infection.

METHODS

In groups of suckling (18-21 days of age) and growing (35-45 days of age) pigs, we compared various sampling approaches to detect, isolate and sequence IAV using individual (nasal swabs, nasal wipes and oropharyngeal swabs), group (oral fluids, surface wipes and sow udder skin wipes) and environmental (airborne particles deposited on surfaces and air samples) sampling approaches. All samples were tested by IAV rRT-PCR and a subset was used for virus isolation and direct sequencing.

RESULTS

In general, environmental and group samples resulted in higher odd ratios (range = 3.87-16.5, p-value < 0.05) of detecting a positive sample by rRT-PCR compared to individual pooled samples, except for oropharyngeal swabs (OR = 8.07, p-value < 0.05). In contrast, individual samples were most likely to yield a viral isolate by cell culture. Oropharyngeal swabs in suckling pigs (78.4%), and nasal swabs (47.6%) or nasal wipes (45%) in growing pigs, and udder wipes in lactating sows (75%) were the preferred samples to obtain an isolate.

CONCLUSIONS

Our findings indicate that group and environmental sampling strategies should be considered in influenza surveillance programs in particular if the goal is just to detect infection. This study provides new information on sampling approaches to conduct effective influenza surveillance in pigs and identifies udder wipes from lactating sows as a novel sample type that offers a convenient, cheap and sensitive manner to monitor IAV in litters prior to weaning.

A Diagnostic Device for In-Situ Detection of Swine Viral Diseases: The SWINOSTICS Project

In this paper, we present the concept of a novel diagnostic device for on-site analyses, based on the use of advanced bio-sensing and photonics technologies to tackle emerging and endemic viruses causing swine epidemics and significant economic damage in farms. The device is currently under development in the framework of the EU Commission co-funded project. The overall concept behind the project is to develop a method for an early and fast on field detection of selected swine viruses by non-specialized personnel. The technology is able to detect pathogens in different types of biological samples, such as oral fluids, faeces, blood or nasal swabs. The device will allow for an immediate on-site threat assessment. In this work, we present the overall concept of the device, its architecture with the technical requirements, and all the used innovative technologies that contribute to the advancements of the current state of the art.

Overhang molecular beacons encapsulated in tethered cationic lipoplex nanoparticles for detection of single-point mutation in extracellular vesicle-associated RNAs

Detection of specific extracellular RNAs has been developed for non-invasive cancer diagnosis. However, accurate and efficient identification of RNAs with single-point mutation in cancer cells-derived extracellular vesicles (EVs) is challenging. Herein, we present a unique overhang molecular beacon with internal dye (Ohi-MB) with a stable hairpin structure, fast hybridization kinetics and single mismatch specificity. Ohi-MBs are encapsulated in cationic lipoplex nanoparticles (CLNs) that are tethered on a gold coated glass slide as a chip, which can capture circulating EVs and detect encapsulated target RNAs in-situ in a single step. The capability of detection of single-point mutation by CLN-Ohi-MB is demonstrated in artificial EVs and cancer cells. This CLN-Ohi-MB biochip could quantify single-point mutations in KRAS mRNA (G12C, G12D, G12V) in pancreatic cancer cell-derived EVs and single-point mutations in EGFR mRNA (L858R and T790M) in lung cancer cell-derived EVs with high specificity, not achievable by conventional molecular probes. We show that CLN-Ohi-MB biochip could selectively and sensitively identify single-point mutations in KRAS mRNA in human serum EVs, distinguishing pancreatic cancer patients with different mutations.

Assessment of abattoir based monitoring of PRRSV using oral fluids

Various porcine reproductive and respiratory syndrome virus (PRRSV) regional elimination projects have been implemented in the U.S., but none have yet succeeded. In part, this reflects the need for efficient methods to monitor over time the progress of PRRSV status of participating herds. This study assessed the feasibility of monitoring PRRSV using oral fluids collected at the abattoir. A total of 36 pig lots were included in the study. On-farm oral fluid (n = 10) and serum (n = 10) collected within two days of shipment to the abattoir were used to establish the reference PRRSV status of the population. Oral fluids (n = 3 per lot) were successfully collected from 32 lots (89%) at the lairage. Three veterinary diagnostic laboratories (VDLs) tested the sera (VDL1 and VDL3: n = 316, VDL2: n = 315) and oral fluids (VDL1 and VDL3: n = 319, VDL2: n = 320) for PRRSV antibodies (ELISA) and RNA (rRT-PCR). Environmental samples (n = 64, 32 before and 32 after pigs were placed in lairage) were tested for PRRSV RNA at one VDL. All oral fluids (farm and abattoir) tested positive for PRRSV antibody at all VDLs. PRRSV positivity frequency on serum ranged from 92.4% to 94.6% among VDLs, with an overall agreement of 97.6%. RNA was detected on 1.3% to 1.9%, 8.1% to 17.7%, and 8.3% to 17.7% of sera, on-farm and abattoir oral fluids, respectively. Between-VDLs rRT-PCR agreement on sera and oral fluids (farm and abattoir) ranged from 97.8% to 99.0%, and 79.0% to 81.2%, respectively. Between-locations agreement of oral fluids varied from 31.3% to 50% depending on the VDL. This study reported the application of swine oral fluids collected at the abattoir for monitoring PRRSV, and describes the between-VDL agreement for PRRS testing of serum and oral fluid field samples.

Herd-level infectious disease surveillance of livestock populations using aggregate samples

All sectors of livestock production are in the process of shifting from small populations on many farms to large populations on fewer farms. A concurrent shift has occurred in the number of livestock moved across political boundaries. The unintended consequence of these changes has been the appearance of multifactorial diseases that are resistant to traditional methods of prevention and control. The need to understand complex animal health conditions mandates a shift toward the collection of longitudinal animal health data. Historically, collection of such data has frustrated and challenged animal health specialists. A promising trend in the evolution toward more efficient and effective livestock disease surveillance is the increased use of aggregate samples, e.g. bulk tank milk and oral fluid specimens. These sample types provide the means to monitor disease, estimate herd prevalence, and evaluate spatiotemporal trends in disease distribution. Thus, this article provides an overview of the use of bulk tank milk and pen-based oral fluids in the surveillance of livestock populations for infectious diseases.

Experimental infection of pigs with H1 and H3 influenza A viruses of swine by using intranasal nebulization

BACKGROUND

Experimental infection of pigs via direct intranasal or intratracheal inoculation has been mainly used to study the infectious process of influenza A viruses of swine (IAVs-S). Nebulization is known to be an alternative method for inoculating pigs with IAVs-S, because larger quantities of virus potentially can be delivered throughout the respiratory tract. However, there is very little data on the experimental infection of pigs by inhalation using nebulizer. In the current study, we used intranasal nebulization to inoculate pigs with 9 different IAVs-S-3 H1N1, 2 H1N2, and 4 H3N2 strains. We then assessed the process of infection by evaluating the clinical signs, nasal and oral viral shedding, and seroconversion rates of the pigs inoculated.

RESULTS

Lethargy and sneezing were the predominant clinical signs among pigs inoculated with 7 of the 9 strains evaluated; the remaining 2 strains (1 H1N1 and 1 H1N2 isolate) failed to induce any clinical signs throughout the experiments. Significantly increased rectal temperatures were observed with an H1N1 or H3N2 strains between 1 and 3 days post-inoculation (dpi). In addition, patterns of nasal viral shedding differed among the strains: nasal viral shedding began on 1 dpi for 6 strains, with all 9 viruses being shed from 2 to 5 dpi. The detection of viral shedding was less sensitive from oral samples than nasal secretions. Viral shedding was not detected in either nasal or oral swabs after 10 dpi. According to hemagglutination-inhibition assays, all inoculated pigs had seroconverted to the inoculating virus by 14 dpi, with titers ranging from 10 to 320.

CONCLUSIONS

Our current findings show that intranasal nebulization successfully established IAV-S infections in pigs and demonstrate that clinical signs, viral shedding, and host immune responses varied among the strains inoculated.

Comparison of serum pools and oral fluid samples for detection of porcine circovirus type 2 by quantitative real-time PCR in finisher pigs

Background

Porcine circovirus type 2 (PCV2) diagnostics in live pigs often involves pooled serum and/or oral fluid samples for group-level determination of viral load by quantitative real-time polymerase chain reaction (qPCR). The purpose of the study was to compare the PCV2 viral load determined by qPCR of paired samples at the pen level of pools of sera (SP) from 4 to 5 pigs and the collective oral fluid (OF) from around 30 pigs corresponding to one rope put in the same pen. Pigs in pens of 2 finishing herds were sampled by cross-sectional (Herd 1) and cross-sectional with follow-up (Herd 2) study designs. In Herd 1, 50 sample pairs consisting of SP from 4 to 5 pigs and OF from around 23 pigs were collected. In Herd 2, 65 sample pairs consisting of 4 (SP) and around 30 (OF) pigs were collected 4 times at 3-week intervals.

Results

A higher proportion of PCV2-positive pens (86% vs. 80% and 100% vs. 91%) and higher viral loads (mean difference: 2.10 and 1.83 log(10) PCV2 copies per ml) were found in OF versus SP in both herds. The OF cut-off value corresponding to a positive SP (>3 log(10) PCV2 copies per ml) was estimated to 6.5 and 7.36 log(10) PCV2 copies per ml for Herds 1 and 2, respectively. Significant correlations between SP and OF results were found in Herd 1 (rho = 0.69) and the first sampling in Herd 2 (rho = 0.39), but not for the subsequent consecutive 3 samplings in Herd 2.

Conclusions

The proportion and viral loads of PCV2 positive pens were higher in collective OF (including up to 30 pigs) compared to SP (including 4–5 pigs) of the same pens. Also, OF seemed to detect the PCV2 infection earlier with OF values just below 6.5 (Herd 1) and 7.36 (Herd 2) log(10) being associated with a negative SP for the same pen. Nevertheless, a statistically significant correlation between SP and OF could not be found for all sampling time points, probably due to a high within-pen variation in individual pig viral load becoming very evident in SP of only four or five pigs. Consequently, the results imply that OF is well suited for detecting presence of PCV2 but less so for determining the specific viral load of pigs in a pen.

Molecular epidemiology of swine influenza A viruses in the Southeastern United States, highlights regional differences in circulating strains

Swine influenza A virus (IAV) can cause widespread respiratory disease with high morbidity, low mortality, and have a substantial economic impact to the swine industry. Swine infection may contribute to pandemic IAV given their susceptibility to both avian and human IAVs. Currently, three IAV subtypes (H1N1, H3N2 and H1N2) circulate in swine in North America frequently combining gene segments from avian or human viruses. This study investigated the prevalence of IAV in commercial swine herds. A total of 1878 oral fluid samples were collected from pigs of all ages from 201 commercial farms located in North Carolina and South Carolina. Sixty-eight oral fluid samples from 35 farms were positive by MP gene PCR with an overall IAV-positivity of 3.6%. On the herd level, the percentage of IAV positivity was 17.4%. Fifty-six viruses were subtyped, while 12 were partly subtyped or not subtyped at all. Using de novo assembly, complete sequences were obtained for 59 HA genes. The majority of IAVs subtyped had an H1 HA demonstrating a considerable prevalence over H3 viruses. Furthermore, only six out of eleven HA types were detected which has implications for the selection of vaccines used by swine producers in the region.

Influenza Herd-Level Prevalence and Seasonality in Breed-to-Wean Pig Farms in the Midwestern United States

Influenza is a costly disease for pig producers and understanding its epidemiology is critical to control it. In this study, we aimed to estimate the herd-level prevalence and seasonality of influenza in breed-to-wean pig farms, evaluate the correlation between influenza herd-level prevalence and meteorological conditions, and characterize influenza genetic diversity over time. A cohort of 34 breed-to-wean farms with monthly influenza status obtained over a 5-year period in piglets prior to wean was selected. A farm was considered positive in a given month if at least one oral fluid tested influenza positive by reverse transcriptase polymerase chain reaction. Influenza seasonality was assessed combining autoregressive integrated moving average (ARIMA) models with trigonometric functions as covariates. Meteorological conditions were gathered from local land-based weather stations, monthly aggregated and correlated with influenza herd-level prevalence. Influenza herd-level prevalence had a median of 28% with a range from 7 to 57% and followed a cyclical pattern with levels increasing during fall, peaking in both early winter (December) and late spring (May), and decreasing in summer. Influenza herd-level prevalence was correlated with mean outdoor air absolute humidity (AH) and temperature. Influenza genetic diversity was substantial over time with influenza isolates belonging to 10 distinct clades from which H1 delta 1 and H1 gamma 1 were the most common. Twenty-one percent of farms had three different clades co-circulating over time, 18% of farms had two clades, and 41% of farms had one clade. In summary, our study showed that influenza had a cyclical pattern explained in part by air AH and temperature changes over time, and highlighted the importance of active surveillance to identify high-risk periods when strategic control measures for influenza could be implemented.

Etiology of acute respiratory disease in fattening pigs in Finland

Background

The objective of our study was to clinically and etiologically investigate acute outbreaks of respiratory disease in Finland. Our study also aimed to evaluate the clinical use of various methods in diagnosing respiratory infections under field conditions and to describe the antimicrobial resistance profile of the main bacterial pathogen(s) found during the study.

Methods

A total of 20 case herds having finishing pigs showing acute respiratory symptoms and eight control herds showing no clinical signs suggesting of respiratory problems were enrolled in the study. Researchers visited each herd twice, examining and bleeding 20 pigs per herd. In addition, nasal swab samples were taken from 20 pigs and three pigs per case herd were necropsied during the first visit. Serology was used to detect Actinobacillus pleuropneumoniae (APP), swine influenza virus (SIV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine respiratory coronavirus (PRCV) and Mycoplasma hyopneumoniae antibodies. Polymerase chain reaction (PCR) was used to investigate the presence of porcine circovirus type 2 (PCV2) in serum and SIV in the nasal and lung samples. Pathology and bacteriology, including antimicrobial resistance determination, were performed on lung samples obtained from the field necropsies.

Results

According to the pathology and bacteriology of the lung samples, APP and Ascaris suum were the main causes of respiratory outbreaks in 14 and three herds respectively, while the clinical signs in three other herds had a miscellaneous etiology. SIV, APP and PCV2 caused concurrent infections in certain herds but they were detected serologically or with PCR also in control herds, suggesting possible subclinical infections. APP was isolated from 16 (80%) case herds. Marked resistance was observed against tetracycline for APP, some resistance was detected against trimethoprim/sulfamethoxazole, ampicillin and penicillin, and no resistance against florfenicol, enrofloxacin, tulathromycin or tiamulin was found. Serology, even from paired serum samples, gave inconclusive results for acute APP infection diagnosis.

Conclusions

APP was the most common cause for acute respiratory outbreaks in our study. SIV, A. suum, PCV2 and certain opportunistic bacteria were also detected during the outbreaks; however, viral pathogens appeared less important than bacteria. Necropsies supplemented with microbiology were the most efficient diagnostic methods in characterizing the studied outbreaks.

The use of oral fluids to monitor key pathogens in porcine respiratory disease complex

Background

The usefulness of oral fluid (OF) sampling for surveillance of infections in pig populations is already accepted but its value as a tool to support investigations of porcine respiratory disease complex (PRDC) has been less well studied. This study set out to describe detection patterns of porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV2), swine influenza virus type A (SIV) and Mycoplasma hyopneumoniae (M. hyo) among farms showing differing severity of PRDC.

The study included six wean-to-finish pig batches from farms with historical occurrence of respiratory disease. OF samples were collected from six pens every two weeks from the 5^th to the 21^st week of age and tested by real time PCR for presence of PRRSV, SIV and M. hyo and by quantitative real time PCR for PCV2. Data was evaluated alongside clinical and post-mortem observations, mortality rate, slaughter pathology, histopathology, and immunohistochemistry testing data for PCV2 antigen where available.

Results

PRRSV and M. hyo were detectable in OF but with inconsistency between pens at the same sampling time and within pens over sequential sampling times. Detection of SIV in clinical and subclinical cases showed good consistency between pens at the same sampling time point with detection possible for periods of 2–4 weeks. Quantitative testing of OF for PCV2 indicated different patterns and levels of detection between farms unaffected or affected by porcine circovirus diseases (PCVD). There was good correlation of PCR results for multiple samples collected from the same pen but no associations were found between prevalence of positive test results and pen location in the building or sex of pigs.

Conclusions

Detection patterns for PRRSV, SIV and M. hyo supported the effectiveness of OF testing as an additional tool for diagnostic investigation of PRDC but emphasised the importance of sampling from multiple pens and on multiple occasions. Preliminary evidence supported the measurement of PCV2 load in pooled OF as a tool for prediction of clinical or subclinical PCVD at farm level.

Detection of porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV) in oral fluid of pigs

Recently oral fluid has become a novel sample type for pathogen nucleic acid and antibody detection, as it is easy to obtain with non-invasive procedures. The objective of the study was to analyze porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV) circulation in growing pigs from three Polish production farms, using Real Time PCR and ELISA testing of oral fluid and serum. Oral fluids were collected every 2weeks, in the same 3-4 pens of pigs aged between 5 and 17weeks. Additionally, blood samples were collected every 4weeks from 4 pigs corresponding to the same pens as oral fluid and tested for the presence of PRRSV nucleic acid (pooled by 4) and antibodies. In farm A no PRRSV circulation was detected and only maternal antibodies were present. In farm B and farm C antibodies to PRRSV in serum and oral fluid were detected in most samples. In farm B PRRSV Type 1 was detected in 80.9% of oral fluid samples and in 58.3% of serum pools, and in farm C in 92.8% of oral fluid samples and 75% serum pools. Striking differences were observed between different pens in PRRSV detection patterns. In farms B and C ORF5 sequence analysis showed the presence of wild type strains which were about 84-85% identical to the modified live vaccine used. In all three farms two waves of IAV shedding with oral fluid were detected, in weaners and fatteners.