Characterization of m⁶ A modifications in the contemporary Zika virus genome and host cellular transcripts

Zika virus (ZIKV) suddenly evolved from a neglected arthropod-borne flavivirus into a pandemic pathogen during 2015-2016. A panel of amino acid mutations has been shown to be responsible for the enhanced neurovirulence and transmissibility of ZIKV. Recent studies have demonstrated that ZIKV genomic RNA is modified by host N6-methyladenosine (m⁶ A) machinery during viral replication in host cells, and the m⁶ A profiles vary among different isolates and different host cells. In the present study, using a contemporary Asian ZIKV strain isolated in 2019 (SZ1901) as a model, we profiled m⁶ A modifications on both the viral genome RNA and cellular transcripts from the ZIKV-infected human hepatocarcinoma cell line Huh7. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) identified a unique m⁶ A map in the genome of ZIKV strain SZ1901 that is different from all previous isolates. Meanwhile, ZIKV infection induced m⁶ A upregulation in the CDS regions but downregulation in the 3' untranslated region of host RNA transcripts. The m⁶ A peak intensity in the majority of host genes was downregulated, including ISG-related genes. Overall, our study describes unique viral and host m⁶ A profiles in contemporary ZIKV-infected Huh7 cells, highlighting the complexity and importance of m⁶ A modification during viral infection.