Subtyping of Swine Influenza Viruses Using a High-Throughput Real-Time PCR Platform

A New Sampling Approach for the Detection of Swine Influenza a Virus on European Sow Farms

Simple Summary

Due to concerns in public health and its negative impact on the pig industry the need for Influenza A virus (IAV) surveillance is rising. The gold standard procedure for detecting IAV is to sample acutely diseased pigs. Endemic infections with unspecific clinical signs and low disease prevalence need new approaches. Our study aimed to evaluate a standardized sampling procedure for the detection of IAV in epidemically and endemically infected farms. We performed a cross-sectional study in 131 farms investigating three different age groups per farm in 12 European countries. The results of our investigation indicate that 10 nasal swabs each in suckling piglets, weaners and middle of nursery is a valuable tool for influenza detection and identification of subtypes. However, for farms with a lower prevalence than 15% it is advisable to either increase the number of nasal swabs in each age group or to use group sampling methods. Interestingly, different subtypes were found in different age groups. Thus, our study underlines that sampling of different age groups is mandatory to obtain a comprehensive overview on all circulating variants on farm. In addition, our results highlight that sampling strategies should also consider piglets without obvious clinical signs for IAV infection.

Abstract

Swine influenza A virus (swIAV), which plays a major role in the porcine respiratory disease complex (PRDC), is eliminated from the respiratory tract within 7–9 days after infection. Therefore, diagnosis is complicated in endemically infected swine herds presenting no obvious clinical signs. This study aimed to investigate the right time point for sampling to detect swIAV. A cross-sectional study was performed in 131 farms from 12 European countries. The sampling protocol included suckling piglets, weaners, and nursery pigs. In each age group, 10 nasal swabs were collected and further examined in pools of 5 for swIAV by Matrix rRT-PCR, followed by a multiplex RT-PCR to determine the influenza subtype. SwIAV was detected in 284 (37.9%) of the samples and on 103 (78.6%) farms. Despite the highest number of animals with clinical signs being found in the nursery, the weaners were significantly more often virus-positive compared to nursery pigs (p = 0.048). Overall, the swIAV detection rate did not significantly differ between diseased or non-diseased suckling and nursery piglets, respectively; however, diseased weaners had significantly more positive pools than the non-diseased animals. Interestingly, in 9 farms, different subtypes were detected in different age groups. Our findings indicate that to detect all circulating swIAV subtypes on a farm, different age groups should be sampled. Additionally, the sampling strategy should also aim to include non-diseased animals, especially in the suckling period.

[Challenges in Influenza diagnostics in a swine herd - a case report]

In a gilt producing farm in Lower Austria, respiratory diseases occurred over the previous years in self-reared gilts after being introduced into the sow herd. In addition, fertility disorders in terms of late abortions and re-breeders were observed in the fall of 2019. Nasal swabs of 3 gilts with respiratory signs and fever were tested positive for influenza A virus (IAV) subtype H1avN1 by PCR. However, examination of serum samples from these animals at 2 different time points did not detect antibodies using the standard hemagglutination inhibition (HI) test of the laboratory. Examination of additional age groups likewise failed to detect H1avN1 antibody titers. In consequence to the extension of the diagnostic panel of the HI test by 7 additional H1avN1 test antigens, a clear seroconversion of the PCR positive sows against 2 different H1avN1 isolates could be measured. In addition, high antibody titers against these 2 H1avN1 strains were also detectable in the majority of the remaining age groups tested. Following the administration of the trivalent influenza vaccine, which has been approved throughout Europe, a significant improvement of the clinical presentation in the herd was achieved. The present case report illustrates that direct and indirect pathogen detection should be used in combination for targeted influenza diagnostics. In addition, it was shown that the continuous adaptation of test antigens to the isolates circulating in the field would be extremely crucial for the significance of the HI test.

Swine influenza A virus subtypes circulating in Brazilian commercial pig herds from 2012 to 2019

The swine influenza A virus (SIAV) subtypes/lineages H1N1pdm09, H3N2, H1N2, and H1N1 of seasonal human origin are widespread in Brazilian swine herds. A monovalent inactivated H1N1pdm09 vaccine was licensed in Brazil in 2014. However, there are concerns about its efficacy due to the limited vaccine cross-protection against heterologous viruses and the potential for exacerbated reactions against vaccine strains. Thus, monitoring SIAVs subtypes/lineages that are circulating in the Brazilian swine population is important, by applying a fast and efficient diagnostic test in herd field samples. A RT-PCR assay was developed, using primers specific for HA subtyping of Brazilian SIAV, and was used to evaluate the occurrence of subtypes from samples collected between 2012 and 2019. From 167 field samples positive for influenza A, 117 were subtyped by nested RT-PCR assay. A higher occurrence of H1N1pdm was observed from 2012 to 2015, H3N2 in 2017, and H1hu in 2017 to 2019. A hemagglutination inhibition test was performed in serum samples received from 2017 to 2019, confirming these data. The molecular data highlights the importance of H1hu and H3N2 detection since there are no vaccines available for the subtypes/lineages and raises an alert of H1hu for its potential to infect humans. Serological data suggest a cyclical profile of occurrence between the H3N2 and H1N1pdm over time. Monitoring SIAVs circulating in Brazilian swine herds is necessary, which provides the relevant information for field veterinarians to apply effective control measures on the properties.

Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses

Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018. In total, 3800 submissions were received with a steady increase in swIAV-positive submissions, reaching 56% in 2018. Full-genome sequences were obtained from 129 swIAV-positive samples. Altogether, 17 different circulating genotypes were identified including six novel reassortants harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx (clade 1A.3.3.2) viruses. The results provide essential data for the control of swIAV in pigs and emphasize the importance of contemporary surveillance for discovering novel swIAV strains posing a potential threat to the human population.

Design of a High-Throughput Real-Time PCR System for Detection of Bovine Respiratory and Enteric Pathogens

Bovine respiratory and enteric diseases have a profound negative impact on animal, health, welfare, and productivity. A vast number of viruses and bacteria are associated with the diseases. Pathogen detection using real-time PCR (rtPCR) assays performed on traditional rtPCR platforms are costly and time consuming and by that limit the use of diagnostics in bovine medicine. To diminish these limitations, we have developed a high-throughput rtPCR system (BioMark HD; Fluidigm) for simultaneous detection of the 11 most important respiratory and enteric viral and bacterial pathogens. The sensitivity and specificity of the rtPCR assays on the high-throughput platform was comparable with that of the traditional rtPCR platform. Pools consisting of positive and negative individual field samples were tested in the high-throughput rtPCR system in order to investigate the effect of an individual sample in a pool. The pool tests showed that irrespective of the size of the pool, a high-range positive individual sample had a high influence on the cycle quantification value of the pool compared with the influence of a low-range positive individual sample. To validate the test on field samples, 2,393 nasal swab and 2,379 fecal samples were tested on the high-throughput rtPCR system as pools in order to determine the occurrence of the 11 pathogens in 100 Danish herds (83 dairy and 17 veal herds). In the dairy calves, Pasteurella multocida (38.4%), rotavirus A (27.4%), Mycoplasma spp. (26.2%), and Trueperella pyogenes (25.5%) were the most prevalent pathogens, while P. multocida (71.4%), Mycoplasma spp. (58.9%), Mannheimia haemolytica (53.6%), and Mycoplasma bovis (42.9%) were the most often detected pathogens in the veal calves. The established high-throughput system provides new possibilities for analysis of bovine samples, since the system enables testing of multiple samples for the presence of different pathogens in the same analysis test even with reduced costs and turnover time.

Versatile and flexible microfluidic qPCR test for high-throughput SARS-CoV-2 and cellular response detection in nasopharyngeal swab samples

The emergence and quick spread of SARS-CoV-2 has pointed at a low capacity response for testing large populations in many countries, in line of material, technical and staff limitations. The traditional RT-qPCR diagnostic test remains the reference method and is by far the most widely used test. These assays are limited to a few probe sets, require large sample PCR reaction volumes, along with an expensive and time-consuming RNA extraction step. Here we describe a quantitative nanofluidic assay that overcomes some of these shortcomings, based on the BiomarkTM instrument from Fluidigm. This system offers the possibility of performing 4608 qPCR end-points in a single run, equivalent to 192 clinical samples combined with 12 pairs of primers/probe sets in duplicate, thus allowing the monitoring of SARS-CoV-2 including the detection of specific SARS-CoV-2 variants, as well as the detection other pathogens and/or host cellular responses (virus receptors, response markers, microRNAs). The 10 nL-range volume of BiomarkTM reactions is compatible with sensitive and reproducible reactions that can be easily and cost-effectively adapted to various RT-qPCR configurations and sets of primers/probe. Finally, we also evaluated the use of inactivating lysis buffers composed of various detergents in the presence or absence of proteinase K to assess the compatibility of these buffers with a direct reverse transcription enzymatic step and we propose several protocols, bypassing the need for RNA purification. We advocate that the combined utilization of an optimized processing buffer and a high-throughput real-time PCR device would contribute to improve the turn-around-time to deliver the test results to patients and increase the SARS-CoV-2 testing capacities.

Label-free fluorometric detection of influenza viral RNA by strand displacement coupled with rolling circle amplification

Since influenza occurs globally every year, it is important to develop a facile and accurate method to detect the influenza virus. This study aimed at developing a sensitive fluorometric assay for detecting influenza viral RNA through tandem gene amplification methods including reverse transcription PCR (RT-PCR), followed by strand displacement amplification (SDA) coupled with rolling circle amplification (RCA). Influenza viral RNA was initially amplified by RT-PCR with a tailed reverse primer containing an additional sequence for SDA. The RT-PCR amplicon was then subjected to SDA, yielding multiple copies of single-stranded DNA (ssDNA) that can be used as a primer for subsequent RCA. Thereafter, a long ssDNA segment harboring tandem repeated G-quadruplexes that were generated through RCA was intercalated by Thioflavin T, yielding a strong fluorescence signal indicating the presence of the target viral RNA. Fluorometric analysis detected influenza viral RNA ranging from 50 pg to 500 pg with a limit of detection of 6.2 pg with a signal-to-background ratio of 10 and identified each influenza virus strain (H1N1, H3N2, and influenza B). Thus, the present method for the label-free fluorometric detection of viral RNA via tandem gene amplifications combining RT-PCR-coupled SDA and G-quadruplex-generating RCA would facilitate the efficient diagnosis of influenza infection.

Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018

This study evaluated the genetic and antigenic evolution of swine influenza A viruses (swIAV) of the two main enzootic H1 lineages, i.e., HA-1C (H1_av) and -1B (H1_hu), circulating in France between 2000 and 2018. SwIAV RNAs extracted from 1220 swine nasal swabs were hemagglutinin/neuraminidase (HA/NA) subtyped by RT-qPCRs, and 293 virus isolates were sequenced. In addition, 146 H1_avNy and 105 H1_huNy strains were submitted to hemagglutination inhibition tests. H1_avN1 (66.5%) and H1_huN2 (25.4%) subtypes were predominant. Most H1 strains belonged to HA-1C.2.1 or -1B.1.2.3 clades, but HA-1C.2, -1C.2.2, -1C.2.3, -1B.1.1, and -1B.1.2.1 clades were also detected sporadically. Within HA-1B.1.2.3 clade, a group of strains named "Δ146-147" harbored several amino acid mutations and a double deletion in HA, that led to a marked antigenic drift. Phylogenetic analyses revealed that internal segments belonged mainly to the "Eurasian avian-like lineage", with two distinct genogroups for the M segment. In total, 17 distinct genotypes were identified within the study period. Reassortments of H1_av/H1_hu strains with H1N1pdm virus were rarely evidenced until 2018. Analysis of amino acid sequences predicted a variability in length of PB1-F2 and PA-X proteins and identified the appearance of several mutations in PB1, PB1-F2, PA, NP and NS1 proteins that could be linked to virulence, while markers for antiviral resistance were identified in N1 and N2. Altogether, diversity and evolution of swIAV recall the importance of disrupting the spreading of swIAV within and between pig herds, as well as IAV inter-species transmissions.

Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses

The degree of antigenic drift in swine influenza A viruses (swIAV) has historically been regarded as minimal compared to that of human influenza A virus strains. However, as surveillance activities on swIAV have increased, more isolates have been characterized, revealing a high level of genetic and antigenic differences even within the same swIAV lineage. The objective of this study was to investigate the level of genetic drift in one enzootically infected swine herd over one year. Nasal swabs were collected monthly from sows (n = 4) and piglets (n = 40) in the farrowing unit, and from weaners (n = 20) in the nursery. Virus from 1-4 animals were sequenced per month. Analyses of the sequences revealed that the hemagglutinin (HA) gene was the main target for genetic drift with a substitution rate of 7.6 × 10^-3 substitutions/site/year and evidence of positive selection. The majority of the mutations occurred in the globular head of the HA protein and in antigenic sites. The phylogenetic tree of the HA sequences displayed a pectinate typology, where only a single lineage persists and forms the ancestor for subsequent lineages. This was most likely caused by repeated selection of a single immune-escape variant, which subsequently became the founder of the next wave of infections.

Subtyping of Swine Influenza Using a High-Throughput Real-Time PCR Platform and a Single Microfluidics Device

Reverse transcription real-time PCR (RT-qPCR) is one of several techniques used to determine the presence and level of infectious veterinary pathogens in diagnostic laboratories. Here we describe how automation of PCR reactions using integrated fluidic circuits (IFCs), an IFC controller MX and a Biomark HD instrument allows for the testing of 48 field samples with swine influenza for up to 48 different subtypes simultaneously in nanoliter volumes.

Development of a high-throughput real-time PCR system for detection of enzootic pathogens in pigs

Respiratory and intestinal diseases in pigs can have significant negative influence on productivity and animal welfare. A wide range of real-time PCR (rtPCR) assays are used in our laboratory (National Veterinary Institute, Technical University of Denmark) for pathogen detection, and PCR analyses are performed on traditional rtPCR platforms in which a limited number of samples can be analyzed per day given limitations in equipment and personnel. To mitigate these restrictions, rtPCR assays have been optimized for the high-throughput rtPCR BioMark platform (Fluidigm). Using this platform, we developed a high-throughput detection system that can be used for simultaneous examination of 48 samples with detection specificity for 18 selected respiratory and enteric viral and bacterial pathogens of high importance to Danish pig production. The rtPCR assays were validated and optimized to run under the same reaction conditions using a BioMark 48.48 dynamic array (DA) integrated fluidic circuit chip, and the sensitivity and specificity were assessed by testing known positive samples. Performance of the 48.48DA was similar to traditional rtPCR analysis, and the specificity of the 48.48DA was high. Application of the high-throughput platform has resulted in a significant reduction in cost and working hours and has provided production herds with a new innovative service with the potential to facilitate the optimal choice of disease control strategies such as vaccination and treatment.

Longitudinal field studies reveal early infection and persistence of influenza A virus in piglets despite the presence of maternally derived antibodies

A longitudinal study was performed in three Danish farrow to grower (30 kilos) herds over a 4-month period to investigate the dynamics and clinical impacts of influenza A virus (IAV) infections. In each herd, four batches consisting of four sows each with five ear-tagged piglets were included. Nasal swabs and/or blood were sampled from the sows and/or the piglets prior to farrowing and at weeks 1, 3, and 5 and at the end of the nursery period. Clinical examinations were performed at each sampling time. The sows and piglets were tested for IAV and IAV antibodies in nasal swabs and blood samples, respectively. The results revealed three enzootically infected herds, where the majority of the pigs were infected during the first 5 weeks after birth. Infected piglets of only 3 days of age were detected in the farrowing unit, where the sows were also shedding virus. In all herds, low to moderate numbers of infected pigs (ranging from 3.6 to 20.7%) were found to be virus positive in nasal swabs at two consecutive sampling times. Furthermore, clinical signs of respiratory disease were associated with IAV detection. The findings of this study documented that IAV can persist in herds and that piglets as young as 3 days can be infected despite the presence of maternally derived antibodies.