Text S1 - Multiple Immune Factors Are Involved in Controlling Acute and Chronic Chikungunya Virus Infection

This file contains supporting information tables and figures. Table S1. The effect of age of mice within a 6–12 week old age range on peak foot swelling. Table S2. List of all the mice strains used in the current study. Table S3. Table of 192 genes identified by microarray as up-regulated in feet on day 30 post infection. Table S4. Table showing the full data set for upstream regulators shown in Table 1. Table S5. Attempts to isolate replication competent virus from foot tissues of CHIKV infected C57BL/6 mice≥30 days post infection. Figure S1 A. Foot swelling and/or viraemia in C57BL/6 mice infected with CHIKV isolates recovered from Rag1−/− mice days 100 and 429 post infection. Figure S1 B. Mutations identified in CHIKV recovered from Rag1−/− mice day 100 post infection. Figure S1 C. IGV display of deep sequencing output for parental and Rag100 viruses. Figure S2 A. H&E staining of feet after CHIKV infection of NOD mice showing inflammatory infiltrates in synovial membrane, muscle and dermis. Figure S2 B. Quantitation of cellular infiltrates in C57BL/6, Rag1−/−, µMT, and MHCII Δ/Δ mice. Figure S3. Early loss of viraemia control in B cell deficient mice, and neutralising antibody responses in C57BL/6 mice. Figure S4. Viraemia and foot swelling in FcγR−/− mice. Figure S5. Histopathological modifications in spleens of chronically CHIKV infected Rag1−/− mice. Figure S6. Survival of NRG mice post CHIKV infection. Figure S7 A. Brain lesions in NRG mice with neurological symptoms requiring euthanasia. Figure S7 B. Immunohistochemical staining of CHIKV capsid protein in brain tissue of NRG mice with neurological symptoms requiring euthanasia. Figure S8 A. No persistent CHIKV RNA in spleen. Figure S8 B. Curve fitting of decline in persistent post-viraemic CHIKV RNA in wild-type mouse feet over time. FigureS9. Persistence of viral antigen in feet of CHIKV infected mice. Figure S10 A. Principal component analysis of 4,805 filtered genes identified by microarray analysis of feet of wild-type mice day 0 and 30 post infection. Figure S10 B. Heat map of 192 significantly up-regulated genes identified by microarray analysis of feet of wild-type mice day 30 post infection. Figure S10 C. qRT PCR of granzyme B and FcγR4 at days 0, 7 and 30 post infection with CHIKV. Figure S11. Ingenuity Pathway Analysis showing canonical pathways associated with the 192 genes up-regulated in feet of mice at day 30 post infection.
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