Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses

Jaing, Crystal; Rowland, Raymond R. R.; Allen, Jonathan; Certoma, Andrea; Thissen, James B.; Bingham, John; Rowe, Brenton; White, John R.; Wynne, James W.; Johnson, Dayna A.; Gaudreault, Natasha N.; Williams, David T.

doi:10.1038/s41598-017-10186-4

Cited by 43 publications

(79 citation statements)

References 95 publications

(79 reference statements)

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“…The recent advances in genomics, the state of knowledge in computational biology and comprehensive profiling of immune system (Zak & Aderem, ) would be a possible approach to probe unknown gene functions. Recently, Jaing et al () carried out transcriptomic study using RNA sequencing in pigs infected with OURT88/3 (a low‐virulent strain of ASFV) and Georgia 2007/1 (a highly pathogenic isolate). As a result, the expression of ASFV genes only from the virulent strain was reported.…”

Section: Future Perspectives and Recommendations: The Next‐generationmentioning

confidence: 99%

Current status and evolving approaches to African swine fever vaccine development

Teklue

Sun

Abid

et al. 2019

Transbound Emerg Dis

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African swine fever (ASF) is a highly lethal haemorrhagic disease of swine caused by African swine fever virus (ASFV), a unique and genetically complex virus. The disease continues to be a huge burden to the pig industry in Africa, Europe and recently in Asia, especially China. The purpose of this review was to recapitulate the current scenarios and evolving trends in ASF vaccine development. The unavailability of an applicable ASF vaccine is partly due to the complex nature of the virus, which encodes various proteins associated with immune evasion. Moreover, the incomplete understanding of immune protection determinants of ASFV hampers the rational vaccine design. Developing an effective ASF vaccine continues to be a challenging task due to many undefined features of ASFV immunobiology. Recent attempts on DNA and live attenuated ASF vaccines have been reported with promising efficacy, and especially live attenuated vaccines have been proved to provide complete homologous protection. Single‐cycle viral vaccines have been developed for various diseases such as Rift Valley fever and bluetongue, and the rational extension of these strategies could be helpful for developing single‐cycle ASF vaccines. Therefore, live attenuated vaccines in short term and single‐cycle vaccines in long term would be the next generation of ASF vaccines.

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Section: Future Perspectives and Recommendations: The Next‐generationmentioning

confidence: 99%

Current status and evolving approaches to African swine fever vaccine development

Teklue

Sun

Abid

et al. 2019

Transbound Emerg Dis

View full text Add to dashboard Cite

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“…The transcribed RNAs have 5'-cap structures and 3'-poly(A) tails with an average length of 33 nucleotides added by the viral capping enzyme complex and the poly(A) polymerase, respectively [27]. Jaing and coworkers have carried out a survey on the entire ASFV transcriptome using RNA-seq [28]. Approximately 60% of the ORFs (109 genes) were detected from the circulating monocytes of highly pathogenic Georgia 2007/1 infected pigs.…”

Section: Introductionmentioning

confidence: 99%

Combined short and long-read sequencing reveals a complex transcriptomic architecture of African swine fever virus

Torma

Tombácz

Csabai

et al. 2020

Preprint

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African swine fever virus (ASFV) is a large DNA virus belonging to the Asfarviridae family. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen. Understanding of genetic regulation provides new insights into the virus pathogenicity, which can help prevent epidemics. Short-read sequencing (SRS) is able to produce a huge amount of high-precision sequencing reads for transcriptomic profiling, but it is inefficient for the comprehensive annotation of transcriptomes. Long-read sequencing (LRS) is able to overcome some of the limitations of SRS, but they also have drawbacks, such as low-coverage and high error rate. The limitations of the two approaches can be surmounted by the combined use of these techniques. In this study, we used Illumina SRS and Oxford Nanopore Technologies LRS platforms with multiple library preparation methods (amplified and direct cDNA sequencings and native RNA sequencing) for constructing the transcriptomic atlas of ASFV. This work identified a large number of novel genes, transcripts and RNA isoforms, and annotated the precise termini of previously described RNA molecules. In contrast to the current view that the ASFV transcripts are monocistronic, we detected a significant extent of polycistronism. A multifaceted meshwork of transcriptional overlaps is also discovered.

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“…Interestingly, in a recent and exhaustive work carried out by Jaing et al about gene expression in blood of ASFV-infected pigs, wherein some DE host miRNA have been identified, viral miRNAs are not described [36]. In the literature, there are examples in which were indicated that certain viruses encode miRNAs that were initially considered as non coding miRNAs, e.g.…”

Section: Discussionmentioning

confidence: 99%

African swine fever virus does not express viral microRNAs in experimentally infected pigs

et al. 2018

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BackgroundAfrican swine fever virus (ASFV) is the etiological agent of African swine fever (ASF), a re-expanding devastating and highly lethal hemorrhagic viral disease. microRNAs (miRNAs) are a new class of small non-coding RNAs that regulate gene expression post-transcriptionally. The discovery of virus specific miRNAs has increased both in number and importance in the past few years. We have recently described the differential expression of several porcine miRNAs during in vivo infection with attenuated and virulent ASFV strains. Here, we have extended these studies trying to identify the presence of viral miRNAs encoded by ASFV in an in vivo infection in pigs.ResultsSixteen small RNA libraries were analyzed from spleen and submandibular lymph nodes obtained from eight pigs, seven infected with either the virulent E75 ASFV strain or its attenuated counterpart E75CV1, or from pigs surviving E75CV1-infection and challenged with BA71 (heterologous challenge) and one non infected as negative control. Samples were recovered at different times post-infection. Libraries were analyzed by next-generation sequencing. Some viral miRNA candidates were initially identified, which did not correspond to porcine miRNAs. Further structural analyses were carried out in order to confirm if they met the conformational requirements to be considered a viral miRNA.ConclusionsThe analysis of sixteen small RNA libraries prepared from two different tissues obtained from pigs experimentally infected with E75, E75CV1 or with E75CV1 plus BA71, revealed the presence of six potential miRNA sequences but none of them met the requirements to be considered as viral miRNAs. Thus, we can conclude that ASFV does not express miRNAs in vivo, at least under the experimental conditions described here.

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Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses

Cited by 43 publications

References 95 publications

Current status and evolving approaches to African swine fever vaccine development

Current status and evolving approaches to African swine fever vaccine development

Combined short and long-read sequencing reveals a complex transcriptomic architecture of African swine fever virus

African swine fever virus does not express viral microRNAs in experimentally infected pigs

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