Targeted accurate RNA consensus sequencing (tARC-seq) reveals mechanisms of replication error affecting SARS-CoV-2 divergence.

Autor: Bradley CC; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.; Baylor College of Medicine Medical Scientist Training Program, Houston, TX, USA.; Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars program, Houston, TX, USA., Wang C; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Gordon AJE; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Wen AX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.; Baylor College of Medicine Medical Scientist Training Program, Houston, TX, USA.; Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars program, Houston, TX, USA., Luna PN; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Cooke MB; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Kohrn BF; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Kennedy SR; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Avadhanula V; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA., Piedra PA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA., Lichtarge O; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA., Shaw CA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Ronca SE; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.; Feigin Biosafety Level 3 Facility, Texas Children's Hospital, Houston, TX, USA.; National School of Tropical Medicine, Department of Pediatrics Tropical Medicine, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA., Herman C; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. herman@bcm.edu.; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA. herman@bcm.edu.; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA. herman@bcm.edu.
Jazyk: angličtina
Zdroj: Nature microbiology [Nat Microbiol] 2024 May; Vol. 9 (5), pp. 1382-1392. Date of Electronic Publication: 2024 Apr 22.
DOI: 10.1038/s41564-024-01655-4
Abstrakt: RNA viruses, like SARS-CoV-2, depend on their RNA-dependent RNA polymerases (RdRp) for replication, which is error prone. Monitoring replication errors is crucial for understanding the virus's evolution. Current methods lack the precision to detect rare de novo RNA mutations, particularly in low-input samples such as those from patients. Here we introduce a targeted accurate RNA consensus sequencing method (tARC-seq) to accurately determine the mutation frequency and types in SARS-CoV-2, both in cell culture and clinical samples. Our findings show an average of 2.68 × 10 -5 de novo errors per cycle with a C > T bias that cannot be solely attributed to APOBEC editing. We identified hotspots and cold spots throughout the genome, correlating with high or low GC content, and pinpointed transcription regulatory sites as regions more susceptible to errors. tARC-seq captured template switching events including insertions, deletions and complex mutations. These insights shed light on the genetic diversity generation and evolutionary dynamics of SARS-CoV-2.
(© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)
Databáze: MEDLINE
Externí odkaz: