Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities.

Briefings in Bioinformatics
Matteo ChiaraGraziano Pesole

Abstract

Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic. Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes....Continue Reading

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Citations

Jun 21, 2021·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Carlos M DuarteIntikhab Alam
Jun 25, 2021·Nature Communications·Michele SimonettiNicola Crosetto
Jul 3, 2021·Cells·Zachary W Kockler, Dmitry A Gordenin
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Aug 4, 2021·MSystems·Alexandra RehnMathias C Walter
Aug 27, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Yao MengXiang Zhao
Aug 28, 2021·Biomolecules·Gabriel DoradoPilar Hernández

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Methods Mentioned

BETA
PCR
genotyping
RNA assay
amplicon sequencing
RNA-seq
PCRs
amplicon-sequencing
in vitro transcription
RNAseq
BioSample

Software Mentioned

Galaxy Europe
COV3D
GISAID
EpiCov
Illumina
UK
Galaxy
OpenAIRE
GISAID EpiCoV
Vipr

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