Center for dynamic RNA epitranscriptomes - Covid 19 Supplement Version 2

AbstractQuantitative sequencing of SARS-CoV-2 viral RNA modifications and identification of hostmodification enzymes critical to viral RNA replicationA new coronavirus disease (known as COVID-19) has swept 200 countries and was declared apandemic. The causative agent is named severe acute respiratory syndrome coronavirus 2(SARS-CoV-2). There is no effective vaccine currently available for SARS-CoV-2. FDA hasapproved two anti-malaria drugs, chloroquine and hydroxychloroquine, for emergency use fortreatment of COVID-19. In addition, remdesivir, a nucleotide analog used for treatment of Ebolavirus disease, is now in clinical trials and clinical use for COVID-19 treatment. Understandingproperties of SARS-CoV-2 and revealing cellular components essential to its infection are criticalto development of effective therapies and vaccines in the near future.SARS-CoV-2 is an RNA virus. Its viral RNAs have been shown to be chemically modified.Previous studies from us and others have revealed crucial roles of viral RNA modifications in viralreplication and immune evasion. Our most recent data indicate that an RNA m5Cmethyltransferase NSUN2 plays a vital role in human coronavirus replication inside host cells. Inthis administrative supplement application we propose to apply quantitative sequencing methodsdeveloped by our CEGS to map N6-methyladenosine (m6A), 5-methylcytosine (m5C),pseudouridine (Ψ), 2'-O-methylation (Nm), N7-methylguanosine (m7G) and N1-methyladenosine(m1A) in SARS-CoV-2 RNA. We will also assign modification enzymes and test their effects onviral infection using established infection models of SARS-CoV-2. We will specifically examinedNSUN2 and its effect on viral RNA m5C methylation, and test known inhibitors for inhibition of viralinfection. We will also examine potential roles of m6A and related modifications in protecting viralRNA from host innate immune responses.