Replicon-based genome-wide CRISPR knockout screening for the identification of host factors involved in viral replication
- Karen W. Cheng
- Madhura Bhave
- Andrew L. Markhard
- Duo Peng
- Karan D. Bhatt
- Katherine A. Travisano
- Josette V. Medicielo
- Astrid Anaya
- Sanae Lembirik
- Leila Njoya
- Manu Anantpadma
- Jens H. Kuhn
- Andreas S. Puschnik
- Amy L. Kistler
2025-12-10
We describe a viral replicon-based CRISPR knockout (KO) screening approach to specifically identify host factors essential for viral replication which are often missed in live virus screens. We benchmark the replicon screening using a stable fluorescent dengue virus type 2 (DENV-2) replicon cell line and successfully identify host genes known to be required for viral DENV-2 replication (e.g., endoplasmic reticulum membrane complex and oligosaccharyltransferase complex components), along with additional genes that have not been reported in prior CRISPR KO screens with DENV-2. We extend this replicon screening approach to chikungunya virus (CHIKV), a positive-sense RNA virus, and Ebola virus (EBOV), a negative-sense RNA virus, and identify distinct sets of genes required for replication of each virus. Our findings indicate that viral replicon-based CRISPR screens are a useful approach to identify host factors essential for replication of diverse viruses and to elucidate potential novel targets for host-directed medical countermeasures.