Loss of host factor-mediated m ⁶ Am methylation of the viral RNA cap impairs SARS CoV-2 replication

Eukaryotic mRNAs are co-transcriptionally capped at the 5′ end with a methylated m ⁷ G moiety (cap0) ¹ , which in higher eukaryotes is further methylated on the ribose (Nm) of the transcription start site (TSS) nucleotide to create the cap1 structure (m ⁷ GpppNm). Coronaviruses that replicate in the cytoplasm encode their own capping enzymes to acquire this cap1 structure which facilitates translation and shields them from the host innate immune system ^2–5 . Here we report the identification of an additional N ⁶ -methyladenosine (m ⁶ A) methylation on the 5′ cap (m ⁷ Gpppm ⁶ Am) of the human coronavirus SARS-CoV-2 RNA. It is catalysed by the host m ⁶ A methylase PCIF1 ^6–9 following capping by virus-encoded non-structural protein NSP 14 and NSP16 ¹⁰ . Human cell cultures lacking PCIF1 accumulate reduced levels of the viral RNA and support reduced viral replication. Furthermore, Pcif1 mutant mice infected with SARS CoV-2 display milder symptoms. We identify the host RNA methyltransferase PCIF1 as a critical ally of SARS CoV-2 for viral replication.