Comparative genomic analysis of pigs differing in survival following African swine fever virus infection

Impact of African swine fever virus genotype II on the porcine female reproductive system.

African swine fever virus (ASFV) genotype II is a highly virulent pathogen; however, its effects on the female reproductive system remain poorly understood. This study investigated the pathogenesis of ASFV genotype II in female pigs, focusing on viral dynamics and reproductive tissue damage. Pigs were intramuscularly inoculated with a highly pathogenic ASFV strain (103 HAD50). Clinical signs developed rapidly, with fever exceeding 41 °C at 3-4 days post-infection (dpi), followed by 100% mortality within 9 dpi. Viraemia was detected at 3 dpi, peaked at 6 dpi, and remained high until death, indicating rapid systemic dissemination. ASFV-specific antibodies were undetectable at 6 dpi, with only limited seroconversion observed at the terminal stage. ASFV DNA was detected in all reproductive organs (real-time PCR Ct values: 21.89-27.9). Severe gross and histopathological lesions were identified, including vascular congestion, haemorrhage, inflammatory infiltration, endometrial desquamation, glandular necrosis, and ovarian follicular degeneration. The co-occurrence of high viral loads and marked tissue damage, particularly in the ovaries and endometrium, indicates direct viral involvement in reproductive pathology. These findings demonstrate that ASFV genotype II causes rapid systemic infection and significant reproductive tissue damage, highlighting its potential impact on reproductive performance in swine.

Pathological insights of Porcine circovirus 2 infection in domestic pigs and molecular characterization of field virus.

Porcine circovirus type 2 (PCV2) poses a major threat to global pig industry by causing growth retardation, immunosuppression, co-infections and mortality. PCV2 has high mutation rate and it causes several clinical manifestations and diverse pathological lesions. Therefore, routine disease surveillance is necessary to understand epidemiology, genetic variations and pathology. The study was conducted to investigate occurrence, pathology and genetic diversity of PCV2 circulating among pigs at Bareilly district, Uttar Pradesh, India. Tissue samples (n=130) from pigs were screened using PCR during 2023-2024. Pathological studies were carried out alongwith mutational and structural annotations of ORF2 gene of circulating PCV2. Total 36.15% samples found positive (47/130) for PCV2, with 14.89% showing co-infections with Streptococcus suis and Haemophilus parasuis. There were interstitial and bronchointerstitial pneumonia with inclusion bodies and lymphoid depletion in lymph nodes. PCV2 antigens were detected by IHC in alveolar macrophages, lymphoid follicles of bronchial lymph nodes and tonsils. Apoptotic lymphocytes were demonstrated by TUNEL assay. Two PCV2 isolates were sequenced and compared with an American strain. Phylogenetic analysis of ORF2 gene, revealed that the circulating virus belongs to PCV 2d genotype. Three amino acid substitutions were identified (Y8F, A59T/K, F154Y). Structural modeling based on the bat circovirus capsid protein (PDB ID: 6RPO) showed that these mutations may have altered local polarity but did not alter linear epitope landscape. Study has revealed high occurrence of PCV2 infections in nursing piglets in study area causing diverse pathological lesions and the circulating virus belonged to PCV2d genotype with three amino acid substitutions.

Global transmission pathways and adaptive molecular evolution of avian infectious bronchitis GI-23 (Variant 2)

The infectious bronchitis virus (IBV) causes significant losses in commercial poultry egg and meat production. Since its first emergence, the genotype GI-23 (Variant 2) has progressively increased its geographical distribution, shown a significant virulence, and challenged the vaccine efficacy. Global viral transmission could be attributed to multiple factors including human related activities such as poultry and vaccine trades while other contributing factors such as the role of wild birds cannot be neglected. Therefore, A total 260 full S1 GI-23 sequences were obtained from Genebank, structured and intensively analyzed. The recombination analyses were conducted using RDP5 and GARD on the total dataset to identify the possible recombinant events. The recombinant-free dataset (214 sequences) was phylogeographically analyzed using BEAST 1.10, then selection pressure analyses to identify the possible migration routes and selection pressure markers, respectively. Recombination analyses showed multiple internal recombination events in 17.6% of the sequences. Phylogeographic analysis suggested Central and Eastern European (CEE) countries (i.e., particularly Poland and Romania) as likely sources of American GI-23-like virus outbreaks. Interestingly, the selection pressure analyses indicated positive selection signals, identifying five codons in some previously distinguished critical positions such as 61, 94, 119, 127, and 197. The virus extended geographical spread as well as molecular evolution through recombination and positive selection in the spike gene poses a major concern for increased adaptation and enhanced pathogenicity in susceptible domesticated and probably wild birds. Further studies on the impact of both recombination events and the identified positive selection codons are highly recommended to elucidate the molecular evolution mechanisms of IBV GI-23.

Shifts in Genetic Diversity of Porcine Reproductive and Respiratory Syndrome Virus 2 in Vietnam Before and After African Swine Fever: Increased Diversity and Novel Sub-lineages

Whole-genome sequencing and molecular characterization of Newcastle disease virus isolates from Kazakhstan

Newcastle disease virus (NDV) remains an important threat to poultry health, while complete genome data from Kazakhstan remain limited. In this study, two NDV-positive samples obtained from domestic chicken carcasses in the Almaty region were propagated in embryonated chicken eggs and characterized by diagnostic PCR/RT-PCR, infectivity assessment, whole-genome sequencing, phylogenetic analysis, and comparative molecular analysis. Both isolates replicated efficiently in embryonated eggs, reaching 9.6–9.7 log10 EID50/mL, with HA titers of 1:128–1:256 and no virus-attributable embryo mortality or marked embryo lesions. The complete consensus genomes of NDV_KZ_I and NDV_KZ_II were 15,186 bp and contained six major coding sequences arranged in the canonical 3′-N-P-M-F-HN-L-5′ order. Both isolates were closely related to the lentogenic vaccine-like strain AVIVAK-NDV-LaSota, and the F protein cleavage site motif was 112GRQGRL117, consistent with a lentogenic molecular profile. The F and HN proteins were identical between the isolates, with conserved predicted N-linked glycosylation motifs and predicted linear B-cell epitope profiles. The complete genome sequences were submitted to GenBank under submission number SUB16299204. Because the vaccination history of the source birds was unavailable and ICPI/MDT assays were not performed, the isolates should be interpreted as vaccine-like NDV detected during diagnostic investigation rather than confirmed causative agents of mortality. These data expand available NDV genomic information from Kazakhstan and support future molecular surveillance.

Genomic characterization and pathogenicity validation of Mycoplasma ovipneumoniae strains from diseased sheep: insights into potential pathogenic mechanisms of GSWW364

Mycoplasma ovipneumoniae (Mo) is the primary etiological agent of mycoplasmal pneumonia of sheep in China, posing a significant threat to the sheep industry. In this study, 18 strains of Mo were isolated from nasal swab samples collected from diseased Hu sheep at nine farms in Gansu Province. Nine representative strains were selected for whole-genome sequencing (WGS) and analysis to explore the genetic relationships between the isolates and reference strains from different regions and hosts. On the basis of the cultural characteristics and the genetic variability among regional strains, strain GSWW364 was chosen for further experiments. A total of 100 healthy 2-month-old Hu sheep were challenged experimentally with strain GSWW364 at a dose of 1 × 107 color change units (CCU). Fifty-four sheep exhibited typical clinical symptoms, including elevated body temperature, coughing, and pulmonary lesions, confirming the pathogenicity of GSWW364. Transcriptomic analyses at both the tissue and cellular levels revealed three infection-associated differentially expressed genes (DEGs): HIF1A, SLC2A3, and SLC38A1. Validation confirmed significantly upregulated expression of these genes in diseased lung tissues. Knockdown of these genes in sheep alveolar epithelial type II cells significantly reduced Mo adhesion. These findings suggest that these genes may promote pathogen adhesion and inflammatory responses by regulating hypoxia-responsive and metabolic pathways during infection. Collectively, this study provides a scientific basis for the prevention and control of mycoplasmal pneumonia of sheep and lays the groundwork for further investigation into the disease’s pathological mechanisms. It also offers valuable insights for vaccine development and disease-resistant breeding programs.