NanoCoV19: An analytical pipeline for rapid detection of severe acute respiratory syndrome coronavirus 2.
Front Genet
; 13: 1008792, 2022.
Article
in English
| MEDLINE | ID: covidwho-2055015
ABSTRACT
Nanopore sequencing technology (NST) has become a rapid and cost-effective method for the diagnosis and epidemiological surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic. Compared with short-read sequencing platforms (e.g., Illumina's), nanopore long-read sequencing platforms effectively shorten the time required to complete the detection process. However, due to the principles and data characteristics of NST, the accuracy of sequencing data has been reduced, thereby limiting monitoring and lineage analysis of SARS-CoV-2. In this study, we developed an analytical pipeline for SARS-CoV-2 rapid detection and lineage identification that integrates phylogenetic-tree and hotspot mutation analysis, which we have named NanoCoV19. This method not only can distinguish and trace the lineages contained in the alpha, beta, delta, gamma, lambda, and omicron variants of SARS-CoV-2 but is also rapid and efficient, completing overall analysis within 1 h. We hope that NanoCoV19 can be used as an auxiliary tool for rapid subtyping and lineage analysis of SARS-CoV-2 and, more importantly, that it can promote further applications of NST in public-health and -safety plans similar to those formulated to address the COVID-19 outbreak.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Topics:
Variants
Language:
English
Journal:
Front Genet
Year:
2022
Document Type:
Article
Affiliation country:
Fgene.2022.1008792
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