RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells

Xinxin Peng, Yikai Luo, Hongyue Li, Xuejiao Guo, Hu Chen, Xuwo Ji, Han Liang

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

SARS-CoV-2 is a positive-sense, single-stranded RNA virus responsible for the COVID-19 pandemic. It remains unclear whether and to what extent the virus in human host cells undergoes RNA editing, a major RNA modification mechanism. Here we perform a robust bioinformatic analysis of metatranscriptomic data from multiple bronchoalveolar lavage fluid samples of COVID-19 patients, revealing an appreciable number of A-to-I RNA editing candidate sites in SARS-CoV-2. We confirm the enrichment of A-to-I RNA editing signals at these candidate sites through evaluating four characteristics specific to RNA editing: the inferred RNA editing sites exhibit (i) stronger ADAR1 binding affinity predicted by a deep-learning model built from ADAR1 CLIP-seq data, (ii) decreased editing levels in ADAR1-inhibited human lung cells, (iii) local clustering patterns, and (iv) higher RNA secondary structure propensity. Our results have critical implications in understanding the evolution of SARS-CoV-2 as well as in COVID-19 research, such as phylogenetic analysis and vaccine development.

Original languageEnglish (US)
Article numbere1010130
JournalPLoS genetics
Volume18
Issue number3
DOIs
StatePublished - Mar 30 2022

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

MD Anderson CCSG core facilities

  • Bioinformatics Shared Resource

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