Porcine rotavirus A (PoRVA) is an enteric pathogen capable of causing severe diarrhea in suckling piglets. Investigating the prevalence and molecular characteristics of PoRVA in the world, including China, is of significance for disease prevention. In 2022, a total of 25,768 samples were collected from 230 farms across China, undergoing porcine RVA positivity testing. The results showed that 86.52% of the pig farms tested positive for porcine RVA, with an overall positive rate of 51.15%. Through the genetic evolution analysis of VP7, VP4 and VP6 genes, it was revealed that G9 is the predominant genotype within the VP7 segment, constituting 56.55%. VP4 genotypes were identified as P[13] (42.22%), P[23] (25.56%) and P[7] (22.22%). VP6 exhibited only two genotypes, namely I5 (88.81%) and I1 (11.19%). The prevailing genotype combination for RVA was determined as G9P[23]I5. Additionally, some RVA strains demonstrated significant homology between VP7, VP4 and VP6 genes and human RV strains, indicating the potential for human RV infection in pigs. Based on complete genome sequencing analysis, a special PoRVA strain, CHN/SD/LYXH2/2022/G4P[6]I1, had high homology with human RV strains, revealing genetic reassortment between human and porcine RV strains in vivo. Our data indicate the high prevalence, major genotypes, and cross-species transmission of porcine RVA in China. Therefore, the continuous monitoring of porcine RVA prevalence is essential, providing valuable insights for virus prevention and control, and supporting the development of candidate vaccines against porcine RVA.

Duck Tembusu virus (DTMUV) has recently appeared in ducks in China and the key cellular determiners for DTMUV replication in host cells remain unknown. Autophagy is an evolutionarily conserved cellular process that has been reported to facilitate flavivirus replication. In this study, we utilized primary duck embryo fibroblast (DEF) as the cell model and found that DTMUV infection triggered LC3-II increase and polyubiquitin-binding protein sequestosome 1 (p62) decrease, confirming that complete autophagy occurred in DEF cells. The induction of autophagy by pharmacological treatment increased DTMUV replication in DEF cells, whereas the inhibition of autophagy with pharmacological treatments or RNA interference decreased DTMUV replication. Inhibiting autophagy enhanced the activation of the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and interferon regulatory factor 7 (IRF7) pathways and increased the p62 protein level in DTMUV-infected cells. We further found that the overexpression of p62 decreased DTMUV replication and inhibited the activation of the NF-κB and IRF7 pathways, and changes in the NF-κB and IRF7 pathways were consistent with the level of phosphorylated TANK-binding kinase 1 (p-TBK1). Opposite results were found in p62 knockdown cells. In summary, we found that autophagy-mediated p62 degradation acted as a new strategy for DTMUV to evade host innate immunity.

Porcine circoviruses (PCVs), encompassing porcine circovirus type 1 (PCV1), porcine circovirus type 2 (PCV2), porcine circovirus type 3 (PCV3), and porcine circovirus type 4 (PCV4), have been documented in China and represent a significant threat to the swine industry. Nevertheless, there is a paucity of data regarding the infection characteristics of PCVs across different age groups within intensive pig farming operations. In this investigation, a systematic cross-sectional methodology was employed to collect 415 testicular processing fluid samples and 1583 serum samples from 30 breeding farms and 27 fattening farms in China. All samples underwent analysis using real-time quantitative polymerase chain reaction (qPCR). Among the testicular fluid samples from suckling pigs, the detection rates for PCV1, PCV2, PCV3, and PCV4 were 56.9%, 31.1%, 75.4%, and 2.2%, respectively. The lowest mean cycle threshold (Ct) values for PCV1 and PCV3 were observed in testicular fluid as opposed to serum samples. At the individual level, the detection rate of PCV1 was significantly higher in fattening pigs (28.7%) and sows (28.7%) compared to nursery pigs (8.5%). The detection rate of PCV2 was highest in fattening pigs (43.1%) and lowest in sows (19.2%). The infection profile of PCV3 contrasted markedly with that of PCV2, exhibiting the lowest prevalence in fattening pigs (8.1%) and the highest in sows (46.1%). PCV4 was infrequently detected across all age groups, with prevalence rates ranging from 0% to 1.7%. Furthermore, the incidence of mixed infections involving the four PCV types was observed to be 12.7% in nursery pigs, 16.8% in fattening pigs, and 22.4% in sows. Notably, no strong correlation was identified between any two co-detected PCV types across all pig age categories. The findings of this study contribute valuable insights into the infection dynamics of PCVs across different pig age groups. Additionally, this research offers critical reference information for devising strategies to prevent PCV infections in intensive pig farming operations in China.

Introduction: Porcine neurological disorders represent a prevalent clinical condition that leads to significant mortality and economic losses within the swine industry. Pseudorabies virus (PRV), porcine teschovirus 1 (PTV1), and Streptococcus suis 2 (SS2) are key viral and bacterial pathogens implicated in the manifestation of neurological symptoms in pig populations. The overlapping clinical presentations and pathological alterations associated with these pathogens pose challenges in their clinical differentiation. Therefore, it is essential to develop a diagnostic method with high sensitivity and specificity that can simultaneously detect and differentiate these viral and bacterial agents.Materials and methods: A triplex real-time PCR assay using TaqMan probes was developed to simultaneously detect PRV, PTV1, and SS2. To assess the efficacy of the established assay, 30 clinical samples of animals with nervous symptoms were used to compare the results obtained from the triplex real-time PCR assay with those obtained from commercial singleplex real-time PCR kits. Furthermore, a total of 282 samples were tested and analyzed to validate the utility of the assay.Results: The triplex real-time PCR assay exhibited high sensitivity, specificity, and repeatability, with a detection limit of 1.0 × 10⁰ copy/μL. The triplex real-time PCR method and commercial singleplex real-time PCR kits showed complete concordance in detecting PRV, PTV1, and SS2. Clinical data indicated single infection rates of 8.16% for PRV, 26.95% for PTV1, and 7.80% for SS2. The observed co-infection rates were 7.45% for PRV + PTV1, 0.71% for PRV + SS2, 1.42% for PTV1 + SS2, and 1.77% for PRV + PTV1 + SS2, respectively.Conclusion: The triplex real-time PCR method developed in this study effectively distinguishes PRV, PTV1, and SS2 simultaneously, serving as a valuable diagnostic tool. This method is anticipated to play a crucial role in preventing and controlling infectious disease spread and supporting epidemiological investigations.

This study aimed to characterize the mitochondrial (MT) genome of Tibetan fragrant chickens along an altitudinal gradient and to relate it to meat quality. Eighteen 150-day-old male chickens were selected from three groups (LX, 1500 m; MX, 2800 m; HX, 3500 m; n = 6 each; six birds were randomly chosen from 30 reared per group) and subjected to whole-genome resequencing (reference: Gallus gallus GCA_000002315.5). Ninety MT variants (85 polymorphic; transition/transversion 83:7) were identified, comprising 58 coding (42 synonymous, 16 non-synonymous), 20 D-loop/non-coding, 10 rRNA and 2 tRNA sites; no MT insertions/deletions or structural variants were found. The 18 birds clustered into three maternal lineages (A, B, C) that were only partially structured by altitude (A more frequent at low altitude; B at mid and high altitude). A neighbour-joining tree with 12 Gallus mitogenomes placed the population close to Gallus gallus gallus and Chinese local breeds. Fifteen heteroplasmic sites were detected, with 16S rRNA nt3946 (G/C/A) heteroplasmic in all birds. Relative mtDNA copy number did not differ among groups (p = 0.52). Meat quality varied with altitude (highest protein and lowest fat at 2800 m; highest inosine monophosphate at 3500 m) but not with maternal lineage, suggesting that the observed phenotypic differences are associated mainly with altitude of rearing rather than with maternal mitochondrial lineage, and that the MT genome contributes standing genetic variation rather than a direct functional basis for these differences.

This study aimed to characterize the mitochondrial (MT) genome of Tibetan fragrant chickens along an altitudinal gradient and to relate it to meat quality. Eighteen 150-day-old male chickens were selected from three groups (LX, 1500 m; MX, 2800 m; HX, 3500 m; n = 6 each; six birds were randomly chosen from 30 reared per group) and subjected to whole-genome resequencing (reference: Gallus gallus GCA_000002315.5). Ninety MT variants (85 polymorphic; transition/transversion 83:7) were identified, comprising 58 coding (42 synonymous, 16 non-synonymous), 20 D-loop/non-coding, 10 rRNA and 2 tRNA sites; no MT insertions/deletions or structural variants were found. The 18 birds clustered into three maternal lineages (A, B and C) that were only partially structured by altitude (A more frequent at low altitude; B at mid and high altitude). A neighbour-joining tree with 12 Gallus mitogenomes placed the population close to Gallus gallus gallus and Chinese local breeds. Fifteen heteroplasmic sites were detected, with 16S rRNA nt3946 (G/C/A) heteroplasmic in all birds. Relative mtDNA copy number did not differ among groups (P = 0.52). Meat quality varied with altitude (highest protein and lowest fat at 2800 m; highest inosine monophosphate at 3500 m) but not with maternal lineage, indicating that high-altitude adaptation is driven mainly by nuclear genes and environment, whereas the MT genome mainly harbours standing variation.