biostudies-literatureWilson JAQueensland GovernmentUniversity of QueenslandNational Health and Medical Research Council (AU)Programme d'Investissements d'Avenir'Queensland Tropical Health Alliancee1006155https://www.ebi.ac.uk/biostudies/studies/S-EPMC5312928biostudies-literatureUnknown13(2)Chikungunya virus (CHIKV) is an arthritogenic alphavirus causing epidemics of acute and chronic arthritic disease. Herein we describe a comprehensive RNA-Seq analysis of feet and lymph nodes at peak viraemia (day 2 post infection), acute arthritis (day 7) and chronic disease (day 30) in the CHIKV adult wild-type mouse model. Genes previously shown to be up-regulated in CHIKV patients were also up-regulated in the mouse model. CHIKV sequence information was also obtained with up to ≈8% of the reads mapping to the viral genome; however, no adaptive viral genome changes were apparent. Although day 2, 7 and 30 represent distinct stages of infection and disease, there was a pronounced overlap in up-regulated host genes and pathways. Type I interferon response genes (IRGs) represented up to ≈50%PLoS pathogensRNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation.PMC5312928Principal Research FellowANR-11-INBS-0008; Intergrated Chikungunya Research project 261202Australian Postgraduate AwardAdvance Queensland Research FellowshipBSL3 equipmentAPP613622Prow NAEllis JJSuhrbier ATang BGearing LJGardner JWilson JASchroder WAHueston LLe Grand RMahalingam SRoques PPoo YSLe TTTaylor AHertzog PJBird PICumming HEDi Giallonardo FfalseRNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation.Chikungunya virus (CHIKV) is an arthritogenic alphavirus causing epidemics of acute and chronic arthritic disease. Herein we describe a comprehensive RNA-Seq analysis of feet and lymph nodes at peak viraemia (day 2 post infection), acute arthritis (day 7) and chronic disease (day 30) in the CHIKV adult wild-type mouse model. Genes previously shown to be up-regulated in CHIKV patients were also up-regulated in the mouse model. CHIKV sequence information was also obtained with up to ≈8% of the reads mapping to the viral genome; however, no adaptive viral genome changes were apparent. Although day 2, 7 and 30 represent distinct stages of infection and disease, there was a pronounced overlap in up-regulated host genes and pathways. Type I interferon response genes (IRGs) represented up to ≈50%2017-01-01T00:00:00Z2017 Feb2026-05-04T20:12:08.779Z2019-03-26T22:49:14ZS-EPMC53129282820789610.1371/journal.ppat.1006155