Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Feb;95(2):e28564.
doi: 10.1002/jmv.28564.

Whole-genome single molecule real-time sequencing of SARS-CoV-2 Omicron

Florence Nicot  1 , Pauline Trémeaux  1 , Justine Latour  1 , Romain Carcenac  1 , Sofia Demmou  1 , Nicolas Jeanne  1 , Noémie Ranger  1 , Clémentine De Smet  1 , Stéphanie Raymond  1   2 , Chloé Dimeglio  1   2 , Jacques Izopet  1   2
Affiliations

Whole-genome single molecule real-time sequencing of SARS-CoV-2 Omicron

Florence Nicot et al. J Med Virol. 2023 Feb.

Abstract

New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harboring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p < 0.001) on our data set, and the median genome coverage with the target capture protocol (98.6% [interquartile range (IQR): 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], [p < 0.001]). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p < 0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants.

Keywords: Omicron; SARS-CoV-2 genotyping; SMRT sequencing; long read sequencing; whole genome sequencing.

PubMed Disclaimer

References

REFERENCES

    1. Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265-269.
    1. Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579:270-273.
    1. Khailany RA, Safdar M, Ozaslan M. Genomic characterization of a novel SARS-CoV-2. Gene Rep. 2020;19:100682.
    1. Wan Y, Shang J, Graham R, Baric RS, Li F. Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. J Virol. 2020;94:e00127-20.
    1. Rotondo JC, Martini F, Maritati M, et al. SARS-CoV-2 infection: new molecular, phylogenetic, and pathogenetic insights. Efficacy of current vaccines and the potential risk of variants. Viruses. 2021;13:1687.

Supplementary concepts

LinkOut - more resources