Correction to: Mechanism of interaction between virus and host is inferred from the changes of gene expression in macrophages infected with African swine fever virus CN/GS/2018 strain

Yang, Bo; Shen, Chao; Zhang, Dajun; Zhang, Ting; Shi, Xijuan; Yang, Jinke; Hao, Yu; Zhao, Dengshuai; Cui, Huimei; Yuan, Xingguo; Chen, Xuehui; Zhang, Keshan; Zheng, Haixue; Liu, Xiangtao

doi:10.1186/s12985-021-01654-5

Cited by 9 publications

(8 citation statements)

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“…In conclusion, the results of viral and host gene expression analysis during ASFV infection were consistent with previous data describing host responses to ASFV infection ( 21 , 59 ). Our study provides new knowledge regarding ASFV-infected hosts.…”

Section: Discussionsupporting

confidence: 91%

“…It is well known that RNA-Seq is an effective technique to address multiple clinical questions. Previous studies on ASFV transcriptome were based on the in vitro cell culture or experimental ASFV infection of animals and mainly analyzed for ASFV DEGs, but not paid close attention to host DEGs (18)(19)(20)(21). In this study, the samples for RNA-Seq were collected from naturally infected animals in a farm, thus more relevant information and DEGs for both virus and host from animal samples could be obtained which truly reflected the animals infected status.…”

Section: Discussionmentioning

confidence: 99%

“…RNA-Seq is a very powerful technique and has been widely used in the fields of oncology, immunology and cell biology in recent years; it is also used in the ASFV mechanisms and regulation of ASFV transcription (18)(19)(20)(21). To investigate the differential gene expression between acutely infected, dead, cohabiting asymptomatic and healthy pigs, we compared the gene expression at the transcriptional level by RNA-Seq technique.…”

Section: Transcriptome Analysis and Gene Expression Statisticsmentioning

confidence: 99%

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Transcriptome Profiling Reveals Features of Immune Response and Metabolism of Acutely Infected, Dead and Asymptomatic Infection of African Swine Fever Virus in Pigs

et al. 2021

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African swine fever virus (ASFV) infection can result in lethal disease in pigs. ASFV encodes 150-167 proteins, of which only approximately 50 encoded viral structure proteins are functionally known. ASFV also encodes some nonstructural proteins that are involved in the regulation of viral transcription, viral replication and evasion from host defense. However, the understanding of the molecular correlates of the severity of these infections is still limited. The purpose of this study was to compare host and viral gene expression differences and perform functional analysis in acutely infected, dead and cohabiting asymptomatic pigs infected with ASFV by using RNA-Seq technique; healthy pigs were used as controls. A total of 3,760 and 2,874 upregulated genes and 4,176 and 2,899 downregulated genes were found in healthy pigs vs. acutely infected, dead pigs or asymptomatic pigs, respectively. Additionally, 941 upregulated genes and 956 downregulated genes were identified in asymptomatic vs. acutely infected, dead pigs. Different alternative splicing (AS) events were also analyzed, as were gene chromosome locations, and protein-protein interaction (PPI) network prediction analysis was performed for significantly differentially expressed genes (DEGs). In addition, 30 DEGs were validated by RT-qPCR, and the results were consistent with the RNA-Seq results. We further analyzed the interaction between ASFV and its host at the molecular level and predicted the mechanisms responsible for asymptomatic pigs based on the selected DEGs. Interestingly, we found that some viral genes in cohabiting asymptomatic pigs might integrate into host genes (DP96R, I73R and L83L) or remain in the tissues of cohabiting asymptomatic pigs. In conclusion, the data obtained in the present study provide new evidence for further elucidating ASFV-host interactions and the ASFV infection mechanism and will facilitate the implementation of integrated strategies for controlling ASF spread.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Transcriptome Analysis and Gene Expression Statisticsmentioning

confidence: 99%

See 1 more Smart Citation

Transcriptome Profiling Reveals Features of Immune Response and Metabolism of Acutely Infected, Dead and Asymptomatic Infection of African Swine Fever Virus in Pigs

et al. 2021

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“…The latter microarray study indicated similar suppression of inflammatory response after 16 hpi as we observed in this study, with expression of many cytokines downregulated relative to noninfected macrophages ( 42 ). More recently, there have been several transcriptomic studies using classical RNA-seq of ASFV infections from Chinese isolates ( 44 – 46 ). Fan et al ( 44 ) investigated the transcriptomic and proteomic response within tissues of pigs following ASFV infection and death, though this was not directly comparable to our own analysis in PAMs, due to their observations being of a far later infection stage (postmortem) than our 16-h time point.…”

Section: Discussionmentioning

confidence: 99%

“…There are two RNA-seq studies of whole blood or tissues isolated from pigs postmortem, which were either infected with a low pathogenic ASFV-OURT 88/3 or ASFV-GRG ( 43 ) or infected with a pathogenic Chinese isolate, ASFV-SY18 ( 44 ). Recently, two reports have been published about the transcriptomic response of porcine macrophages to infection with a virulent Chinese genotype II isolate using a low multiplicity of infection (MOI, 1) and classical RNA-seq ( 45 , 46 ), but due to different experimental conditions the various results are somewhat challenging to compare with other studies. It must also be remembered that neither these classical RNA-seq nor microarray analyses have sufficient resolution to accurately capture viral gene expression in the compact ASFV genome alongside that of the host.…”

Section: Introductionmentioning

confidence: 99%

African Swine Fever Virus and Host Response: Transcriptome Profiling of the Georgia 2007/1 Strain and Porcine Macrophages

Cackett

Portugal

Matelska

et al. 2022

J Virol

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African swine fever virus (ASFV) has a major global economic impact. With a case fatality in domestic pigs approaching 100%, it currently presents the largest threat to animal farming. Although genomic differences between attenuated and highly virulent ASFV strains have been identified, the molecular determinants for virulence at the level of gene expression have remained opaque. Here we characterise the transcriptome of ASFV genotype II Georgia 2007/1 (GRG) during infection of the physiologically relevant host cells, porcine macrophages. In this study we applied Cap Analysis Gene Expression sequencing (CAGE-seq) to map the 5’ ends of viral mRNAs at 5 and 16 hours post-infection. A bioinformatics analysis of the sequence context surrounding the transcription start sites (TSSs) enabled us to characterise the global early and late promoter landscape of GRG. We compared transcriptome maps of the GRG isolate and the lab-attenuated BA71V strain that highlighted GRG virulent-specific transcripts belonging to multigene families, including two predicted MGF 100 genes I7L and I8L. In parallel, we monitored transcriptome changes in the infected host macrophage cells. Of the 9,384 macrophage genes studied, transcripts for 652 host genes were differentially regulated between 5 and 16 hours-post-infection compared with only 25 between uninfected cells and 5 hours post-infection. NF-kB activated genes and lysosome components like S100 were upregulated, and chemokines such as CCL24, CXCL2, CXCL5 and CXCL8 downregulated. African swine fever virus (ASFV) causes haemorrhagic fever in domestic pigs with case fatality rates approaching 100%, and no approved vaccines or antivirals. The highly-virulent ASFV Georgia 2007/1 strain (GRG) was the first isolated when ASFV spread from Africa to the Caucasus region in 2007. Then spreading through Eastern Europe, and more recently across Asia. We used an RNA-based next generation sequencing technique called CAGE-seq to map the starts of viral genes across the GRG DNA genome. This has allowed us to investigate which viral genes are expressed during early or late stages of infection and how this is controlled, comparing their expression to the non-virulent ASFV-BA71V strain to identify key genes that play a role in virulence. In parallel we investigated how host cells respond to infection, which revealed how the ASFV suppresses components of the host immune response to ultimately win the arms race against its porcine host.

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Deoxycholic acid inhibits ASFV replication by inhibiting MAPK signaling pathway

Gao,

Xu,

Feng

et al. 2024

International Journal of Biological Macromolecules

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Correction to: Mechanism of interaction between virus and host is inferred from the changes of gene expression in macrophages infected with African swine fever virus CN/GS/2018 strain

Cited by 9 publications

References 1 publication

Transcriptome Profiling Reveals Features of Immune Response and Metabolism of Acutely Infected, Dead and Asymptomatic Infection of African Swine Fever Virus in Pigs

Transcriptome Profiling Reveals Features of Immune Response and Metabolism of Acutely Infected, Dead and Asymptomatic Infection of African Swine Fever Virus in Pigs

African Swine Fever Virus and Host Response: Transcriptome Profiling of the Georgia 2007/1 Strain and Porcine Macrophages

Deoxycholic acid inhibits ASFV replication by inhibiting MAPK signaling pathway

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