Bioproject ID: PRJNA359221

bioproject id PRJNA359221      to NCBI
key word Challenge; GCRV; Grass carp; Grass carp reovirus; Transcriptome sequencing; Immune response; Hemorrhage; HEMATOPOIETIC NECROSIS VIRUS; COMPLETE GENOME SEQUENCE; INNATE IMMUNE-RESPONSE; PROKARYOTIC EXPRESSION; COMPLEMENT ACTIVATION; RNA-SEQ; FISH; GENE; INFECTION; PATHWAY
experiment type challenge
publication He L et al., "Differences in responses of grass carp to different types of grass carp reovirus (GCRV) and the mechanism of hemorrhage revealed by transcriptome sequencing" BMC Genomics, 2017; 18: 452.
description transcriptome sequencing of grass carp that infeceted with two types of GCRV
abstract Background: Grass carp is an important farmed fish in China that is affected by serious disease, especially hemorrhagic disease caused by grass carp reovirus (GCRV). The mechanism underlying the hemorrhagic symptoms in infected fish remains to be elucidated. Although GCRV can be divided into three distinct subtypes, differences in the pathogenesis and host immune responses to the different subtypes are still unclear. The aim of this study was to provide a comprehensive insight into the grass carp response to different GCRV subtypes and to elucidate the mechanism underlying the hemorrhagic symptoms. Results: Following infection of grass carp, GCRV-I was associated with a long latent period and low mortality (42.5%), while GCRV-II was associated with a short latent period and high mortality (81.4%). The relative copy number of GCRV-I remained consistent or decreased slightly throughout the first 7 days post-infection, whereas a marked increase in GCRV-II high copy number was detected at 5 days post-infection. Transcriptome sequencing revealed 211 differentially expressed genes (DEGs) in Group I (66 up-regulated, 145 down-regulated) and 670 (386 up-regulated, 284 down-regulated) in Group II. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed significant enrichment in the terms or pathways involved in immune responses and correlating with blood or platelets. Most of the DEGs in Group I were also present in Group II, although the expression profiles differed, with most DEGs showing mild changes in Group I, while marked changes were observed in Group II, especially the interferon-related genes. Many of the genes involved in the complement pathway and coagulation cascades were significantly up-regulated at 7 days post-infection in Group II, suggesting activation of these pathways. Conclusion: GCRV-I is associated with low virulence and a long latent period prior to the induction of a mild host immune response, whereas GCRV-II is associated with high virulence, a short latent period and stimulates a strong and extensive host immune response. The complement and coagulation pathways are significantly activated at 7 days post-infection, leading to the endothelial cell and blood cell damage that result in hemorrhagic symptoms.

Sample Information

sample id sample name tissue strain treatment description
1. SRR5145951 I-1(1) spleen grass carp infected with GCRV-I for one day infected with GCRV-I 1 day post infected with GCRV-I, replicate 1.
2. SRR5145952 I-1(2) spleen grass carp infected with GCRV-I for one day infected with GCRV-I 1 day post infected with GCRV-I, replicate 2.
3. SRR5145953 I-1(3) spleen grass carp infected with GCRV-I for one day infected with GCRV-I 1 day post infected with GCRV-I, replicate 3.
4. SRR5145954 I-3(1) spleen grass carp infected with GCRV-I for three days infected with GCRV-I 3 days post infected with GCRV-I, replicate 1.
5. SRR5145955 I-3(2) spleen grass carp infected with GCRV-I for three days infected with GCRV-I 3 days post infected with GCRV-I, replicate 2.
6. SRR5145957 I-3(3) spleen grass carp infected with GCRV-I for three days infected with GCRV-I 3 days post infected with GCRV-I, replicate 3.
7. SRR5145958 I-5(1) spleen grass carp infected with GCRV-I for five days infected with GCRV-I 5 days post infected with GCRV-I, replicate 1.
8. SRR5145959 I-5(2) spleen grass carp infected with GCRV-I for five days infected with GCRV-I 5 days post infected with GCRV-I, replicate 2.
9. SRR5145960 I-5(3) spleen grass carp infected with GCRV-I for five days infected with GCRV-I 5 days post infected with GCRV-I, replicate 3.
10. SRR5145961 I-7(1) spleen grass carp infected with GCRV-I for seven days infected with GCRV-I 7 days post infected with GCRV-I, replicate 1.
11. SRR5145962 I-7(2) spleen grass carp infected with GCRV-I for seven days infected with GCRV-I 7 days post infected with GCRV-I, replicate 2.
12. SRR5145963 I-7(3) spleen grass carp infected with GCRV-I for seven days infected with GCRV-I 7 days post infected with GCRV-I, replicate 3.
13. SRR5145996 II-1(1) spleen grass carp infected with GCRV-II for one day infected with GCRV-II 1 day post infected with GCRV-II, replicate 1.
14. SRR5145997 II-1(2) spleen grass carp infected with GCRV-II for one day infected with GCRV-II 1 day post infected with GCRV-II, replicate 2.
15. SRR5145998 II-1(3) spleen grass carp infected with GCRV-II for one day infected with GCRV-II 1 day post infected with GCRV-II, replicate 3.
16. SRR5145999 II-3(1) spleen grass carp infected with GCRV-II for three days infected with GCRV-II 3 days post infected with GCRV-II, replicate 1.
17. SRR5146000 II-3(2) spleen grass carp infected with GCRV-II for three days infected with GCRV-II 3 days post infected with GCRV-II, replicate 2.
18. SRR5146001 II-3(3) spleen grass carp infected with GCRV-II for three days infected with GCRV-II 3 days post infected with GCRV-II, replicate 3.
19. SRR5146003 II-5(1) spleen grass carp infected with GCRV-II for five days infected with GCRV-II 5 days post infected with GCRV-II, replicate 1.
20. SRR5146004 II-5(2) spleen grass carp infected with GCRV-II for five days infected with GCRV-II 5 days post infected with GCRV-II, replicate 2.
21. SRR5146005 II-5(3) spleen grass carp infected with GCRV-II for five days infected with GCRV-II 5 days post infected with GCRV-II, replicate 3.
22. SRR5146006 II-7(1) spleen grass carp infected with GCRV-II for seven days infected with GCRV-II 7 days post infected with GCRV-II, replicate 1.
23. SRR5146007 II-7(2) spleen grass carp infected with GCRV-II for seven days infected with GCRV-II 7 days post infected with GCRV-II, replicate 2.
24. SRR5146008 II-7(3) spleen grass carp infected with GCRV-II for seven days infected with GCRV-II 7 days post infected with GCRV-II, replicate 3.
25. SRR5146010 C-1(1) spleen control sample for one day control 1 day post injected with PBS, replicate 1 (Control).
26. SRR5146011 C-1(2) spleen control sample for one day control 1 day post injected with PBS, replicate 2 (Control).
27. SRR5146012 C-1(3) spleen control sample for one day control 1 day post injected with PBS, replicate 3 (Control).
28. SRR5146013 C-3(1) spleen control sample for three days control 3 days post injected with PBS, replicate 1 (Control).
29. SRR5146014 C-3(2) spleen control sample for three days control 3 days post injected with PBS, replicate 2 (Control).
30. SRR5146015 C-3(3) spleen control sample for three days control 3 days post injected with PBS, replicate 3 (Control).
31. SRR5146017 C-5(1) spleen control sample for five days control 5 days post injected with PBS, replicate 1 (Control).
32. SRR5146018 C-5(2) spleen control sample for five days control 5 days post injected with PBS, replicate 2 (Control).
33. SRR5146019 C-5(3) spleen control sample for five days control 5 days post injected with PBS, replicate 3 (Control).
34. SRR5146020 C-7(1) spleen control sample for seven days control 7 days post injected with PBS, replicate 1 (Control).
35. SRR5146031 C-7(2) spleen control sample for seven days control 7 days post injected with PBS, replicate 2 (Control).
36. SRR5146032 C-7(3) spleen control sample for seven days control 7 days post injected with PBS, replicate 3 (Control).