Transcriptome profile of spleen tissues from locally-adapted Kenyan pigs (Sus scrofa) experimentally infected with three varying doses of a highly virulent African swine fever virus genotype IX isolate: Ken12/busia.1 (ken-1033)

Abstract

Background African swine fever (ASF) is a lethal hemorrhagic disease affecting domestic pigs resulting in up to 100% mortality rates caused by the ASF virus (ASFV). The locally-adapted pigs in South-western Kenya have been reported to be resilient to disease and harsh climatic conditions and tolerate ASF; however, the mechanisms by which this tolerance is sustained remain largely unknown. We evaluated the gene expression patterns in spleen tissues of these locally-adapted pigs in response to varying infective doses of ASFV to elucidate the virus-host interaction dynamics. Methods Locally adapted pigs (n = 14) were experimentally infected with a high dose (1x106HAD50), medium dose (1x104HAD50), and low dose (1x102HAD50) of the highly virulent genotype IX ASFV Ken12/busia.1 (Ken-1033) isolate diluted in PBS and followed through the course of infection for 29 days. The in vivo pig host and ASFV pathogen gene expression in spleen tissues from 10 pigs (including three from each infective group and one uninfected control) were analyzed in a dual-RNASeq fashion. We compared gene expression between three varying doses in the host and pathogen by contrasting experiment groups against the naïve control. Results A total of 4954 differentially expressed genes (DEGs) were detected after ASFV Ken12/1 infection, including 3055, 1771, and 128 DEGs in the high, medium, and low doses, respectively. Gene ontology and KEGG pathway analysis showed that the DEGs were enriched for genes involved in the innate immune response, inflammatory response, autophagy, and apoptosis in lethal dose groups. The surviving low dose group suppressed genes in pathways of physiopathological importance. We found a strong association between severe ASF pathogenesis in the high and medium dose groups with upregulation of proinflammatory cytokines and immunomodulation of cytokine expression possibly induced by overproduction of prostaglandin E synthase (4-fold; p < 0.05) or through downregulation of expression of M1-activating receptors, signal transductors, and transcription factors. The host-pathogen interaction resulted in induction of expression of immune-suppressive cytokines (IL-27), inactivation of autophagy and apoptosis through up-regulation of NUPR1 [5.7-fold (high dose) and 5.1-fold (medium dose) [p < 0.05] and IL7R expression. We detected repression of genes involved in MHC class II antigen processing and presentation, such as cathepsins, SLA-DQB1, SLA-DOB, SLA-DMB, SLA-DRA, and SLA-DQA in the medium and high dose groups. Additionally, the host-pathogen interaction activated the CD8+ cytotoxicity and neutrophil machinery by increasing the expression of neutrophils/CD8+ T effector cell-recruiting chemokines (CCL2, CXCL2, CXCL10, CCL23, CCL4, CXCL8, and CXCL13) in the lethal high and medium dose groups. The recovered pigs infected with ASFV at a low dose significantly repressed the expression of CXCL10, averting induction of T lymphocyte apoptosis and FUNDC1 that suppressed neutrophilia. Conclusions We provide the first in vivo gene expression profile data from locally-adapted pigs from south-western Kenya following experimental infection with a highly virulent ASFV genotype IX isolate at varying doses that mimic acute and mild disease. Our study showed that the locally-adapted pigs induced the expression of genes associated with tolerance to infection and repression of genes involved in inflammation at varying levels depending upon the ASFV dose administered.

African Swine Fever Virus Infection and Cytokine Response In Vivo: An Update

“…Upregulation of pro-inflammatory cytokine genes was also observed in the spleen of pigs infected with high doses of the genotype IX virulent isolate Ken12/busia.1 [ 146 ]. In detail, groups of pigs were immunized with high (10 6 ), medium (10 4 ) or low doses (10 2 ) of Ken12/busia.1 alongside an uninfected control group, and clinical signs were monitored until day 29 pi.…”

“…On the contrary, pigs belonging to the low-dose group and control pigs did not show ASF clinical signs and were killed at the end of the experiment (29 dpi). Spleens were collected after death and RNA-seq analysis revealed a marked association with severe ASF pathogenesis (especially in the high-dose group) with the upregulation of several pro-inflammatory interleukins (especially IL-6 and IL-17), chemokines (CCL2, CCL4, CXCL2, CXCL10) and VEGFA [ 146 ]. These results support the hypothesis that the massive release of pro-inflammatory cytokines is not a sign of a coordinated immune response, but rather evidence of an aberrant “cytokine storm” which is related to ASF pathogenesis.…”

The transcriptomic insight into the differential susceptibility of African Swine Fever in inbred pigs

“…In our study, RELA was downregulated only one-week post-infection. Machuka et al (2022) reported The down-regulation of RELA has been reported in the high-and medium doses of ASFV but was not differentially expressed in the low dose. It can be concluded the gene modi cations of RELA 43,[45][46][47] and CD163 43 genes have not been successful for ASFV resistance compared with gene editing for PRRSV 48 or TGEV 49 .…”

“…Four studies have already investigated the transcriptome pro ling of the host in response to ASF. Two studies compared the pathogenesis of different strains 13,14 , one study investigated the effect of varied doses of the inoculated virus on host transcriptome pro ling 15 , and one studied features of immune response of acutely infected, dead, and asymptomatic infection of ASFV in pigs 16 . To our knowledge this is the rst report of the transcriptomic pro le of pigs immunized with a low virulent isolate of ASFV before and after challenge with virulent virus.…”

“…The transcriptome of the various genotypes of ASF virus isolate [6][7][8] , its vector-borne tick 9 , and infected swine macrophages as the host-pathogen interaction [10][11][12] have already been studied. A few studies have surveyed the response to the infection in the host [13][14][15][16] . None of the latter studies have designed an infection challenge to study the transcriptome signatures of the immunization.…”