TMEM41B is a host factor required for the replication of diverse coronaviruses including SARS-CoV-2

Antiviral therapeutics are a front-line defense against virally induced diseases. Because viruses frequently mutate to escape direct inhibition of viral proteins, there is interest in targeting the host proteins that the virus must co-opt to complete its replication cycle. However, a detailed understanding of the interactions between the virus and the host cell is necessary in order to facilitate development of host-directed therapeutics. As a first step, we performed a genome-wide loss of function screen using the alphacoronavirus HCoV-229E to better define the interactions between coronaviruses and host-factors. We report the identification and validation of an ER-resident host protein, TMEM41B, as an essential host factor for not only HCoV-229E but also genetically distinct coronaviruses including the pandemic beta-coronavirus SARS-CoV-2. We show that the protein is required at an early, but post-receptor engagement, stage of the viral lifecycle. Further, mechanistic studies revealed that although the protein was not enriched at replication complexes, it likely contributes to viral replication complex formation via mobilization of cholesterol and other lipids to facilitate host membrane expansion and curvature. Continued study of TMEM41B and the development of approaches to prevent its function may lead to broad spectrum anti-coronavirus therapeutics. Author summary The COVID-19 pandemic has highlighted the burden that emerging coronaviruses can place on global health systems. Due to difficulty in predicting the characteristics of future pandemic viruses, pan-coronaviral therapeutics are highly desired. While many antivirals directly target viral proteins to inhibit their functions, targeting broadly required host-dependency factors represents an orthogonal approach that may have the added benefit of lower susceptibly to the emergence of viral escape mutants. One limitation of this approach, however, is that essential host factors for viral replication must be identified and characterized prior to development of novel therapeutics. In this work, we performed a genome-wide host-dependency factor screen with the endemic seasonal human coronavirus HCoV-229E. We identified TMEM41B, an ER-resident protein, as a critical host-dependency factor for not only HCoV-229E but also distantly related coronaviruses as well. Mechanistic studies revealed that TMEM41B is likely required to facilitate appropriate membrane composition for the establishment of intracellular viral replication complexes. Thus, the conserved requirement for TMEM41B is likely due to the fact that all coronaviruses establish similar structures for RNA replication. Future studies understanding how to pharmacologically target TMEM41B and its associated lipid mobilization pathways may lead to the development of broad-spectrum anti-coronavirus therapeutics.

Automated summary

The ER-resident host protein TMEM41B has been identified as an essential factor for multiple coronaviruses, including HCoV-229E and SARS-CoV-2. It likely contributes to viral replication complex formation by mobilizing cholesterol and other lipids to facilitate host membrane expansion and curvature. Targeting TMEM41B and its associated pathways may lead to the development of broad-spectrum anti-coronavirus therapeutics.