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

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.

SUBMITTER: Peng X

PROVIDER: S-EPMC9000099 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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

Peng Xinxin X Luo Yikai Y Li Hongyue H Guo Xuejiao X Chen Hu H Ji Xuwo X Liang Han H

PLoS genetics 20220330 3

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 ...[more]

PMID: 35353808

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

Publications

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

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