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Rajkhowa S, Sonowal J, Pegu SR, Sanger GS, Deb R, Das PJ, Doley J, Paul S, Gupta VK. Natural co-infection of pigs with African swine fever virus and porcine reproductive and respiratory syndrome virus in India. Braz J Microbiol 2024; 55:1017-1022. [PMID: 38041718 PMCID: PMC10920511 DOI: 10.1007/s42770-023-01203-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) and African swine fever (ASF) are economically important diseases of pigs throughout the world. During an outbreak, all age groups of animals except piglets < 1 month of age were affected with symptoms of high fever, cutaneous hemorrhages, vomition with blood, diarrhea, poor appetite, ataxia, and death. The outbreak was confirmed by the detection of the N gene of the porcine reproductive and respiratory syndrome virus (PRRSV) and the VP72 gene of the African swine fever virus (ASFV) by PCR in representative blood samples from affected pigs followed by Sanger sequencing. Mixed infection was also confirmed by simultaneous detection of both the viruses using multiplex PCR. Phylogenetic analysis of both the viruses revealed that the outbreak was related to ASFV and PRRSV strains from China which were also closely related to the PRRSV and ASFV strains from the recent outbreak from India. The study confirmed the involvement of genotype II of ASFV and genotype 2 of PRRSV in the present outbreak. Interestingly, PRRSV associated with the present outbreak was characterized as a highly pathogenic PRRSV. Therefore, the present study indicates the possibility of future waves or further outbreaks of these diseases (PRRS and ASF) in this region. This is the first report of ASFV and PRRSV co-infection in pigs from India.
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Affiliation(s)
- Swaraj Rajkhowa
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India.
| | - Joyshikh Sonowal
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Seema Rani Pegu
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | | | - Rajib Deb
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Pranab Jyoti Das
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Juwar Doley
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Souvik Paul
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Vivek Kumar Gupta
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
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Deb R, Sengar GS, Sonowal J, Pegu SR, Das PJ, Singh I, Chakravarti S, Selvaradjou A, Attupurum N, Rajkhowa S, Gupta VK. Transcriptome signatures of host tissue infected with African swine fever virus reveal differential expression of associated oncogenes. Arch Virol 2024; 169:54. [PMID: 38381218 DOI: 10.1007/s00705-023-05959-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/27/2023] [Indexed: 02/22/2024]
Abstract
African swine fever (ASF) has emerged as a threat to swine production worldwide. Evasion of host immunity by ASF virus (ASFV) is well understood. However, the role of ASFV in triggering oncogenesis is still unclear. In the present study, ASFV-infected kidney tissue samples were subjected to Illumina-based transcriptome analysis. A total of 2463 upregulated and 825 downregulated genes were differentially expressed (p < 0.05). A literature review revealed that the majority of the differentially expressed host genes were key molecules in signaling pathways involved in oncogenesis. Bioinformatic analysis indicated the activation of certain oncogenic KEGG pathways, including basal cell carcinoma, breast cancer, transcriptional deregulation in cancer, and hepatocellular carcinoma. Analysis of host-virus interactions revealed that the upregulated oncogenic RELA (p65 transcription factor) protein of Sus scrofa can interact with the A238L (hypothetical protein of unknown function) of ASFV. Differential expression of oncogenes was confirmed by qRT-PCR, using the H3 histone family 3A gene (H3F3A) as an internal control to confirm the RNA-Seq data. The levels of gene expression indicated by qRT-PCR matched closely to those determined through RNA-Seq. These findings open up new possibilities for investigation of the mechanisms underlying ASFV infection and offer insights into the dynamic interaction between viral infection and oncogenic processes. However, as these investigations were conducted on pigs that died from natural ASFV infection, the role of ASFV in oncogenesis still needs to be investigated in controlled experimental studies.
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Affiliation(s)
- Rajib Deb
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India.
| | | | - Joyshikh Sonowal
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
- Multidisciplinary Research Unit, Jorhat Medical College and Hospital, Jorhat, Assam, 785001, India
| | - Seema Rani Pegu
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Pranab Jyoti Das
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India.
| | | | - Soumendu Chakravarti
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
- Pirbright Institute, Ash Road, Pirbright, Surrey, United Kingdom
| | | | - Nitin Attupurum
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Swaraj Rajkhowa
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Vivek Kumar Gupta
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India.
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Bharati J, Kumar S, Mohan NH, Pegu SR, Borah S, Gupta VK, Sarkar M. CRISPR/Cas genome editing revealed non-angiogenic role of VEGFA gene in porcine luteal cells: a preliminary report. Mol Biol Rep 2024; 51:195. [PMID: 38270707 DOI: 10.1007/s11033-023-09115-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND The angiogenic cytokine vascular endothelial growth factor A (VEGFA) also exerts non-angiogenic effects on endocrine functionality of porcine luteal cells critical for progesterone (P4) production. METHOD AND RESULTS The expression dynamics of VEGFA-FLT/KDR system were investigated using RT-qPCR during luteal stages and VEGFA gene knock out (KO) porcine luteal cells were generated using CRISPR/Cas9 technology. The downstream effects of VEGFA ablation were studied using RT-qPCR, Annexin V, MTT, ELISA for P4 estimation and scratch wound assay. Bioinformatics analysis of RNA-Seq data of porcine mid-luteal stage was conducted for exploring protein-protein interaction network, KEGG pathways, transcription factors and kinase mapping for VEGFA-FLT/KDR interactomes. The VEGFA-FLT/KDR system expressed throughout the luteal stages with highest expression during mid- luteal stage. Cellular morphology, structure and oil-red-o staining for lipid droplets did not differ significantly between VEGFA KO and wild type cells, however, VEGFA KO significantly decreased (p < 0.05) viability and proliferation efficiency of edited cells on subsequent passages. Expression of apoptotic gene, CASP3 and hypoxia related gene, HIF1A were significantly (p < 0.05) upregulated in KO cells. The relative mRNA expression of VEGFA and steroidogenic genes STAR, CYP11A1 and HSD3B1 decreased significantly (p < 0.05) upon KO, which was further validated by the significant (p < 0.05) decrease in P4 output from KO cells. Bioinformatics analysis mapped VEGFA-FLT/KDR system to signalling pathways associated with steroidogenic cell functionality and survival, which complemented the findings of the study. CONCLUSION The ablation of VEGFA gene resulted in decreased steroidogenic capability of luteal cells, which suggests that VEGFA exerts additional non-angiogenic regulatory effects in luteal cell functionality.
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Affiliation(s)
- Jaya Bharati
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India.
- Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, 243122, India.
| | - Satish Kumar
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - N H Mohan
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Seema Rani Pegu
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Sanjib Borah
- Lakhimpur College of Veterinary Science, Assam Agricultural University, North Lakhimpur, Assam, India
| | - Vivek Kumar Gupta
- Lakhimpur College of Veterinary Science, Assam Agricultural University, North Lakhimpur, Assam, India
| | - Mihir Sarkar
- ICAR-National Research Centre On Yak, Dirang, Arunachal Pradesh, 790101, India.
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Bharati J, Kumar S, Mohan NH, Chandra Das B, Devi SJ, Gupta VK. Ovarian follicle transcriptome dynamics reveals enrichment of immune system process during transition from small to large follicles in cyclic Indian Ghoongroo pigs. J Reprod Immunol 2023; 160:104164. [PMID: 37924675 DOI: 10.1016/j.jri.2023.104164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023]
Abstract
Ovarian follicular development is a critical determinant of reproductive performance in litter bearing species like pigs, wherein economic gains depend on litter size. The study aimed to gain insight into the differentially expressed genes (DEGs) and signalling pathways regulating follicular growth and maturation in Ghoongroo pigs. Transcriptome profiling of porcine small follicles (SF) and large follicles (LF) was conducted using NovaSeq600 sequencing platform and DEGs were identified using DESeq2 with threshold of Padj. < 0.05 and log2 fold change cut off 0.58 (LF vs. SF). Functional annotations and bioinformatics analysis of DEGs were performed to find out biological functions, signalling pathways and hub genes regulating follicular dynamics. Transcriptome analysis revealed 709 and 479 genes unique to SF and LF stages, respectively, and 11,993 co-expressed genes in both the groups. In total, 507 DEGs (284 upregulated and 223 downregulated) were identified, which encoded for diverse proteins including transcription factors (TFs). These DEGs were functionally linked to response to stimulus, lipid metabolic process, developmental process, extracellular matrix organisation along with the immune system process, indicating wide-ranging mechanisms associated with follicular transition. The enriched KEGG pathways in LF stage consisted of ovarian steroidogenesis, cholesterol and retinol metabolism, cell adhesion molecules, cytokine receptor interaction and immune signalling pathways, depicting intra-follicular control of varied ovarian function. The hub gene analysis revealed APOE, SCARB1, MMP9, CYP17A1, TYROBP as key regulators of follicular development. This study identified candidate genes and TFs providing steroidogenic advantage to LFs which makes them fit for selection into the ovulatory pool of follicles.
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Affiliation(s)
- Jaya Bharati
- Animal Physiology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India.
| | - Satish Kumar
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - N H Mohan
- Animal Physiology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - Bikash Chandra Das
- Animal Physiology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - Salam Jayachitra Devi
- Computer Applications and Information Technology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - Vivek Kumar Gupta
- Director, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
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Mei Q, Zheng R, Li J, Ma X, Wang L, Wei Y, Luo X, Guan J, Zhang X. Transcriptomic analysis reveals differentially expressed genes and key immune pathways in the spleen of the yak (Bos grunniens) at different growth stage. Gene 2023; 884:147743. [PMID: 37640116 DOI: 10.1016/j.gene.2023.147743] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Yak is one of the rare and unique cattle species on the Qinghai-Tibetan Plateau, which has strong adaptability to the extreme environment of the plateau. The spleens are important functional organs that enable animals to adapt to their external environment and are vital in the growth and development process. To further investigate changes in immune function during yak development, we compared the transcriptome profiles of spleen tissues among juvenile (1-day old), youth (15-months old), and prime (5-years old) yaks. Immunology of spleen development was evaluated based on histological analyses and global gene expression was examined by using RNA-sequencing (RNA-seq) technology. In this work, we found 6378 genes with significant differences between the spleen of juvenile yak and youth yak, with the largest difference between groups. There were 3144 genes with significant differences between the spleen of young yak and prime yak, with the smallest differences between groups. Further, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for the functional annotation of these genes. GO and KEGG analysis showed that some of them were related to growth, disease, immune, and metabolism. However, the genetic mechanism underlying the adaptability of yak spleens at different ages to harsh plateau environments remains unknown. These findings are important for studying the mechanisms of spleen development in yaks of different age groups.
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Affiliation(s)
- Qundi Mei
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China.
| | - Rui Zheng
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China.
| | - Juan Li
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China.
| | - Xuefeng Ma
- Chongqing Institute for Food and Drug Control, Chongqing 404100, China.
| | - Li Wang
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China.
| | - Yong Wei
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Sciences Academy, Chengdu 610066, China.
| | - Xiaolin Luo
- Sichuan Academy of Grassland Sciences, Chengdu 610041, China.
| | - Jiuqiang Guan
- Sichuan Academy of Grassland Sciences, Chengdu 610041, China.
| | - Xiangfei Zhang
- Sichuan Academy of Grassland Sciences, Chengdu 610041, China.
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Maity HK, Samanta K, Deb R, Gupta VK. Revisiting Porcine Circovirus Infection: Recent Insights and Its Significance in the Piggery Sector. Vaccines (Basel) 2023; 11:1308. [PMID: 37631876 PMCID: PMC10457769 DOI: 10.3390/vaccines11081308] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/29/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023] Open
Abstract
Porcine circovirus (PCV), a member of the Circoviridae family within the genus Circovirus, poses a significant economic risk to the global swine industry. PCV2, which has nine identified genotypes (a-i), has emerged as the predominant genotype worldwide, particularly PCV2d. PCV2 has been commonly found in both domestic pigs and wild boars, and sporadically in non-porcine animals. The virus spreads among swine populations through horizontal and vertical transmission routes. Despite the availability of commercial vaccines for controlling porcine circovirus infections and associated diseases, the continuous genotypic shifts from a to b, and subsequently from b to d, have maintained PCV2 as a significant pathogen with substantial economic implications. This review aims to provide an updated understanding of the biology, genetic variation, distribution, and preventive strategies concerning porcine circoviruses and their associated diseases in swine.
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Affiliation(s)
- Hemanta Kumar Maity
- Department of Avian Science, Faculty of Veterinary & Animal Science, West Bengal University of Animal & Fishery Sciences, Kolkata 700037, West Bengal, India
| | - Kartik Samanta
- Department of Avian Science, Faculty of Veterinary & Animal Science, West Bengal University of Animal & Fishery Sciences, Kolkata 700037, West Bengal, India
| | - Rajib Deb
- ICAR-National Research Center on Pig, Rani, Guwahati 781131, Assam, India
| | - Vivek Kumar Gupta
- ICAR-National Research Center on Pig, Rani, Guwahati 781131, Assam, India
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