Lineage-Specific Transcriptional Response to Chikungunya ECSA and West African Lineages in Primary Human Chondrocytes

Abstract Chikungunya virus (CHIKV) causes long-term arthritis in about a third of infected people. It circulates as three main lineages. The East/Central/South African (ECSA) lineage and its derivatives have led to outbreaks in the Indian Ocean, South America, Pakistan, and most recently China, while the West African (WA) lineage is restricted to West Africa. Here we characterized CHIKV lineage-specific differences in human chondrocyte infection, the cartilage secreting cell type central to joint function. We compared transcriptional responses to ECSA and WA in chondrocytes isolated from eight donors undergoing clinically indicated orthopedic surgical procedures. We used serial viral dilutions so that each donor line included at least one ECSA and one WA infection with a similar proportion of infected cells. We performed RNA-Seq 24 hours post-infection. ECSA and WA induced substantially different transcriptional programs in chondrocytes. Compared to matched uninfected controls, we identified 1,235 genes significantly differentially regulated in ECSA and 842 in WA infection, with 604 overlapping. Infection with both lineages upregulated interferon response genes, and reduced expression of cell cycle-associated genes. However, only ECSA significantly reduced expression of NF-κB response genes, while WA infection strongly increased SOX2 expression, and uniquely increased NOTCH1 and reduced SOX9 expression, a pattern broadly consistent with a chondrocyte de-differentiation or loss of cartilage identity. These results show that CHIKV lineages elicit distinct transcriptional programs, with potential implications for lineage-specific joint pathology and disease course. Author Summary Chikungunya virus (CHIKV) infection often causes severe joint pain and arthritis that can persist for months or years. Different viral lineages of CHIKV circulate globally but the effect of viral lineage on the cellular responses in relevant infected cell types remains poorly understood. Here we infected primary human chondrocytes, the cells responsible for maintaining cartilage, with two major CHIKV lineages under matched infection conditions. Although both viruses replicated similarly and triggered strong antiviral interferon responses, they induced distinct transcriptional programs, with only ECSA suppressing the inflammatory NF-κB response and WA infection resulting in a chondrocyte gene expression pattern more consistent with de-differentiation. These lineage-specific effects on cartilage cell biology may contribute to differences in joint outcomes following infection.