Genome-scale CRISPR screen identifies TMEM41B as a multi-function host factor required for coronavirus replication

Emerging coronaviruses (CoVs) pose a severe threat to human and animal health worldwide. To identify host factors required for CoV infection, we used α-CoV transmissible gastroenteritis virus (TGEV) as a model for genome-scale CRISPR knockout (KO) screening. Transmembrane protein 41B (TMEM41B) was found to be a bona fide host factor involved in infection by CoV and three additional virus families. We found that TMEM41B is critical for the internalization and early-stage replication of TGEV. Notably, our results also showed that cells lacking TMEM41B are unable to form the double-membrane vesicles necessary for TGEV replication, indicating that TMEM41B contributes to the formation of CoV replication organelles. Lastly, our data from a mouse infection model showed that the KO of this factor can strongly inhibit viral infection and delay the progression of a CoV disease. Our study revealed that targeting TMEM41B is a highly promising approach for the development of broad-spectrum anti-viral therapeutics.
Author summary Coronaviruses (CoVs) pose a severe threat to human and animal health. Identification of host genes essential for transmissible gastroenteritis virus (TGEV) infection may reveal novel therapeutic targets and strengthen our understanding of CoV disease pathogenesis. We performed genome-wide and sub-pooled CRISPR screens in porcine kidney cells with TGEV. We identified numerous candidate host factors for TGEV infection. Considering its extremely strong effect on TGEV infection, we focused our efforts on characterizing the roles that TMEM41B play in the virus replication cycle. Our results revealed that TMEM41B contributed to CoV internalization and the formation of replication organelles. TMEM41B is critical for the replication of TGEV and other RNA viruses. Our mouse infection model provides strong evidence that knocking out the TMEM41B gene can inhibit viral infection and delay the progression of a CoV disease. Our study identified potential therapeutic targets for common RNA viruses and reveals host factors that regulate susceptibility to highly pathogenic CoVs.