Viral and Bacterial Profiles in Endemic Influenza A Virus Infected Swine Herds Using Nanopore Metagenomic Sequencing on Tracheobronchial Swabs

Porcine respiratory coronavirus genome sequences; comparisons and relationships to transmissible gastroenteritis viruses

Porcine respiratory coronavirus (PRCV) was initially detected in Europe, and later in the United States of America (US), in the 1980s. In this study we obtained and compared PRCV sequences from Europe and the US, and investigated how these are related to transmissible gastroenteritis virus (TGEV) sequences. The whole genome sequences of Danish (1/90-DK), Italian (PRCV15087/12 III NPTV Parma), and Belgian PRCV (91V44) strains are presented. These sequences were aligned with nine other PRCV sequences from Europe and the US, and 43 TGEV sequences. Following alignment of the PRCV sequences, it was apparent that multiple amino acid variations in the structural proteins were distinct between the European and US strains. The alignments were used to build phylogenetic trees to infer the evolutionary relationships between the strains. In these trees, the European PRCV strains clustered as a separate group, whereas the US strains of PRCV all clustered with TGEVs.

Recombinant Viruses from the Picornaviridae Family Occurring in Racing Pigeons

Viruses from Picornaviridae family are known pathogens of poultry, although the information on their occurrence and pathogenicity in pigeons is scarce. In this research, efforts are made to broaden the knowledge on Megrivirus B and Pigeon picornavirus B prevalence, phylogenetic relationship with other avian picornaviruses and their possible connection with enteric disease in racing pigeons. As a result of Oxford Nanopore Sequencing, five Megrivirus and two pigeon picornavirus B-like genome sequences were recovered, among which three recombinant strains were detected. The recombinant fragments represented an average of 10.9% and 25.5% of the genome length of the Pigeon picornavirus B and Megrivirus B reference strains, respectively. The phylogenetic analysis revealed that pigeons are carriers of species-specific picornaviruses. TaqMan qPCR assays revealed 7.8% and 19.0% prevalence of Megrivirus B and 32.2% and 39.7% prevalence of Pigeon picornavirus B in the group of pigeons exhibiting signs of enteropathy and in the group of asymptomatic pigeons, respectively. In turn, digital droplet PCR showed a considerably higher number of genome copies of both viruses in sick than in asymptomatic pigeons. The results of quantitative analysis leave the role of picornaviruses in enteropathies of pigeons unclear.

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.

Metagenomics to Identify Viral Communities Associated with Porcine Respiratory Disease Complex in Tibetan Pigs in the Tibetan Plateau, China

Tibetan pig is a unique pig breed native to the Qinghai-Tibet Plateau. To investigate viral communities associated with porcine respiratory disease complex (PRDC), 167 respiratory samples were collected from Tibetan pigs in the Ganzi Tibetan autonomous prefecture of Sichuan province. Following library construction and Illunima Novaseq sequencing, 18 distinct viruses belonging to 15 viral taxonomic families were identified in Tibetan pigs with PRDC. Among the 18 detected viruses, 3 viruses were associated with PRDC, including porcine circovirus type 2 (PCV-2), Torque teno sus virus (TTSuV), and porcine cytomegalovirus (PCMV). The genomic sequences of two PCV-2 strains, three TTSuV strains, and one novel Porprismacovirus strain were assembled by SOAPdenovo software (v2). Sequence alignment and phylogenetic analysis showed that both PCV-2 strains belonged to PCV-2d, three TTSuVs were classified to TTSuV2a and TTSuV2b genotypes, and the Porprismacovirus strain PPMV-SCgz-2022 showed a close genetic relationship with a virus of human origin. Recombination analysis indicated that PPMV-SCgz-2022 may have originated from recombination events between Human 16,806 × 66-213 strain and Porcine 17,668 × 82-593 strain. Furthermore, the high proportion of single infection or co-infection of PCV2/TTSuV2 provides insight into PRDC infection in Tibetan pigs. This is the first report of the viral communities in PRDC-affected Tibetan pigs in this region, and the results provides reference for the prevention and control of respiratory diseases in these animals.

Overview of Modern Commercial Kits for Laboratory Diagnosis of African Swine Fever and Swine Influenza A Viruses

Rapid and early detection of infectious diseases in pigs is important, especially for the implementation of control measures in suspected cases of African swine fever (ASF), as an effective and safe vaccine is not yet available in most of the affected countries. Additionally, analysis for swine influenza is of significance due to its high morbidity rate (up to 100%) despite a lower mortality rate compared to ASF. The wide distribution of swine influenza A virus (SwIAV) across various countries, the emergence of constantly new recombinant strains, and the danger of human infection underscore the need for rapid and accurate diagnosis. Several diagnostic approaches and commercial methods should be applied depending on the scenario, type of sample and the objective of the studies being implemented. At the early diagnosis of an outbreak, virus genome detection using a variety of PCR assays proves to be the most sensitive and specific technique. As the disease evolves, serology gains diagnostic value, as specific antibodies appear later in the course of the disease (after 7-10 days post-infection (DPI) for ASF and between 10-21 DPI for SwIAV). The ongoing development of commercial kits with enhanced sensitivity and specificity is evident. This review aims to analyse recent advances and current commercial kits utilised for the diagnosis of ASF and SwIAV.

Impact of bronchoalveolar lavage from influenza A virus diseased pigs on neutrophil functions and growth of co-infecting pathogenic bacteria

Introduction

Influenza A viruses (IAVs) infect the respiratory tract of mainly humans, poultry, and pigs. Co-infections with pathogenic lung bacteria are a common event and contribute to the severity of disease progression. Neutrophils are a major cell type of the innate immune system and are rapidly recruited to the site of infection. They have several effector functions to fight invading pathogens such as the secretion of reactive oxygen species (ROS) or the release of neutrophil extracellular traps (NETs). NETs are known to promote the growth of Pasteurellaceae bacteria, especially if degraded by nucleases.

Methods

In this study, bronchoalveolar lavage fluid (BALF) from 45 field-infected pigs was analyzed for 1) NET markers, 2) influence on growth of lung bacteria, and 3) impact on neutrophil functions. BALF samples from 21 IAV-positive pigs and 24 lung diseased but IAV-negative pigs were compared.

Results

Here, we show that neutrophils in the lungs of IAV-positive pigs release vesicular NETs. Several NET markers were increased in the BALF of IAV-positive pigs compared with the BALF from IAV-negative pigs. The amount of NET markers positively correlated with the viral load of the IAV infection. Interestingly, the BALF of IAV-positive pigs enhanced the growth of bacteria belonging to the family of Pasteurellaceae as potential coinfecting bacteria. These effects were weaker with the BALF derived from IAV-negative pigs with other lung infections. The intensity of oxidative burst in neutrophils was significantly decreased by BALF from IAVpositive pigs, indicating impaired antimicrobial activity of neutrophils. Finally, the lung milieu reflected by IAV-positive BALF does not enable neutrophils to kill Actinobacillus pleuropneumoniae but rather enhances its growth.

Discussion

In summary, our data show that an IAV infection is affecting neutrophil functions, in particular the release of NETs and ROS. Furthermore, IAV infection seems to provide growth-enhancing factors for especially coinfecting Pasteurellaceae and reduces the killing efficiency of neutrophils.

Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencing

During the last decade, porcine rotavirus H was detected in the USA, Asian regions, South Africa, Brazil, and a couple of European countries. In the presented study, the virus was identified in piglets on a farrow-to-finish farm in Russia during metagenomic surveillance. Currently, it is the first identification of this species in the country. As a diagnostic method, nanopore-based metagenomic sequencing was applied. The obtained nanopore reads allowed for the assembly of 10 genome segments out of 11. The phylogenetic analysis revealed the virus belonged to the porcine cluster and had GX-P3-I3-R3-C3-M8-A7-N1-T5-E3-H3 genome constellation. Moreover, three potential new genotype groups for VP3, NSP1, and NSP3 genes were determined. Additionally, a recombination between RVH and RVC in the NSP3 gene was detected. The study provides significant information about a novel RVH strain.

Porcine ear necrosis: characterization of lesions and associated pathogens

Porcine ear necrosis (PEN) is characterized by ulcerative lesions of the ear auricle. To investigate that problem, three farms with PEN in nursery pigs were included, and the study aim was to characterize PEN and the potential role of pathogens and mycotoxins. Within each farm, one batch of weaned piglets was included and the prevalence and severity of PEN were monitored for 6-7 weeks. Within each batch, 30 PEN-affected/non-affected animals were randomly selected. Blood samples were taken from these animals, to assess the systemic presence of pathogens and mycotoxins, as well as punch biopsies from the ear auricle for histopathological examination. From 10 animals, scrapings and swabs from the lesions were subjected to nanopore metagenomic sequencing and bacteriological cultivation, respectively. In all three farms, lesions appeared within 3-4 weeks post-weaning. The prevalence at the end of the nursery was 33%, 24%, and 46% for farms A, B, and C, respectively. Most affected pigs had mild to moderate lesions. Blood samples revealed low to very low levels of pathogens and mycotoxins. Different bacteria such as Staphylococcus, Streptococcus, Fusobacterium, Mycoplasma, and Clostridium species were identified by sequencing in the scrapings. The first two pathogens were also most often identified in bacterial cultures. Mycoplasma hyopharyngis was only found in PEN-affected pigs. Histopathological changes were primarily observed in the outer layer of the epidermis. The results suggest that PEN lesions develop by damage to the outer part of the skin e.g. by ear suckling or biting, followed by multiplication of opportunistic pathogens.