Human norovirus hyper-mutation revealed by ultra-deep sequencing

• Published in: Infection, genetics and evolution Vol. 41; pp. 233 - 239
• Main Authors: Cuevas, José M., Combe, Marine, Torres-Puente, Manoli, Garijo, Raquel, Guix, Susana, Buesa, Javier, Rodríguez-Díaz, Jesús, Sanjuán, Rafael
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.07.2016; Elsevier
• Subjects: Bacteriology; Base Sequence; Biodiversity and Ecology; Caliciviridae Infections - virology; Cloning, Molecular; Ecology, environment; Ecosystems; Emerging diseases; Environmental Sciences; Feces - virology; Gastroenteritis - virology; Gene Expression; Genètica humana; Global Changes; Health; HEK293 Cells; High-Throughput Nucleotide Sequencing; Human genetics; Human health and pathology; Humans; Hyper-mutation; Infectious diseases; Life Sciences; Microbiology and Parasitology; Mutation Rate; Next-generation sequencing; Norovirus; Norovirus - genetics; Norovirus - growth & development; Norovirus - isolation & purification; RNA virus; RNA, Viral - genetics; Transfection; Viral Proteins - genetics; Virologia; Virology; Virus Replication; Next-generation sequencing; Norovirus; Hyper-mutation; RNA virus
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2016.04.017

Human noroviruses (NoVs) are a major cause of gastroenteritis worldwide. It is thought that, similar to other RNA viruses, high mutation rates allow NoVs to evolve fast and to undergo rapid immune escape at the population level. However, the rate and spectrum of spontaneous mutations of human NoVs have not been quantified previously. Here, we analyzed the intra-patient diversity of the NoV capsid by carrying out RT-PCR and ultra-deep sequencing with 100,000-fold coverage of 16 stool samples from symptomatic patients. This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. This confirmed the presence of sequences with multiple U-to-C/A-to-G transitions, and suggested that hyper-mutation contributed a large fraction of the total NoV spontaneous mutation rate. The type of changes produced and their sequence context are compatible with ADAR-mediated editing of the viral RNA. •Norovirus U-to-C hyper-mutants are present in patient samples.•Analysis of hyper-mutants in cell culture suggests ADAR-mediated RNA edition.•Hyper-mutation may contribute to norovirus diversity and evolution.