Discovery of Widespread Host Protein Interactions with the Pre-Replicated Genome of CHIKV using VIR-CLASP

We evaluated the extent of BHK21 RNA that is packaged within the viral particle, which may lead to identification of interactions with passenger non-viral RNAs from a previous infection rather than interactions with the pre-replicated viral genome. We performed RNA-seq with RNA from purified CHIKV viral particles and found that of the 378.6 million reads across two replicates, over 340 million reads (>90%) mapped to either the CHIKV genome or to Mesocricetus auratus (golden hamster). From the mapped reads, 98.8% map to CHIKV genomic sequences and approximately 1% are from golden hamster RNA.