<i>Sarbecovirus</i> ORF6 Proteins Hamper the Induction of Interferon Signaling by Blocking mRNA Nuclear Export

Abstract

The presence of an ORF6 gene distinguishes Sarbecoviruses such as SARS-CoV and SARS-CoV-2 from other Betacoronaviruses. Here, we show that ORF6 inhibits the induction of type I IFN upon viral infection, as well as IFN types I and III signaling. Intriguingly, the anti-IFN activity of ORF6 proteins of SARS-CoV-2 lineages is more potent than that of SARS-CoV lineages. Mutational analyses identified residues E46 and Q56 as determinants of the potent IFN-antagonistic activity of SARS-CoV-2 ORF6. Moreover, we show that ORF6 binds to RAE1 and NUP98 via its C-terminus, thereby inhibiting the nuclear export of IFNB1 mRNA. Finally, we identify natural occurring frameshift/nonsense mutations that result in an inactivating truncation of ORF6 in approximately 0.2% of SARS-CoV-2 isolates. Altogether, our findings suggest that ORF6 contributes to the poor IFN activation observed in COVID-19 patients. Furthermore, the emergence of SARS-CoV-2 variants without functional ORF6 may contribute to the attenuation of viral pathogenicity.Funding: This study was supported in part by AMED Research Program on Emerging and Re-emerging Infectious Diseases 20fk0108146 (to K.S.), 19fk0108171 (to S.N. and K.S.) and 20fk0108270 (to K.S.); AMED Research Program on HIV/AIDS 19fk0410019 (to K.S.) and 20fk0410014 (to K.S.); JST J-RAPID JPMJJR2007 (to K.S.); KAKENHI Grant-in-Aid for Scientific Research B 18H02662 (to K.S.), KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas 16H06429 (to S.N. and K.S.), 16K21723 (to S.N. and K.S.), 17H05823 (to S.N.), 17H05813 (to K.S.), 19H04843 (to S.N.) and 19H04826 (to K.S.), and Fund for the Promotion of Joint International Research (Fostering Joint International Research) 18KK0447 (to K.S.); JSPS Research Fellow DC1 19J20488 (to I.K.) and DC1 19J22914 (to Y.K.); ONO Medical Research Foundation (to K.S.); Ichiro Kanehara Foundation (to K.S.); Lotte Foundation (to K.S.); Mochida Memorial Foundation for Medical and Pharmaceutical Research (to K.S.); Daiichi Sankyo Foundation of Life Science (to K.S.); Sumitomo Foundation (to K.S.); Uehara Foundation (to K.S.); Takeda Science Foundation (to K.S.); JSPS Core-to-Core program (A. Advanced Research Networks) (to K.S.); the Canon Foundation in Europe (to. D.S. and K.S.); a COVID19 Research Grant of the Federal Ministry of Education and Research (MWK) Baden-Württemberg (to. D.S.); 2020 Tokai University School of Medicine Research Aid (to S.N.); and International Joint Research Project of the Institute of Medical Science, the University of Tokyo 2020-K3003 (to D.S. and K.S.). Conflict of Interest: The authors declare that no competing interests exist.