“Nano COVID-19”: Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern
Issued Date
2023-01-01
Resource Type
ISSN
15353702
eISSN
15353699
Scopus ID
2-s2.0-85170852718
Journal Title
Experimental Biology and Medicine
Rights Holder(s)
SCOPUS
Bibliographic Citation
Experimental Biology and Medicine (2023)
Suggested Citation
Nimsamer P., Sawaswong V., Klomkliew P., Kaewsapsak P., Puenpa J., Poovorawan Y., Payungporn S. “Nano COVID-19”: Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern. Experimental Biology and Medicine (2023). doi:10.1177/15353702231190931 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/90167
Title
“Nano COVID-19”: Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern
Author's Affiliation
Other Contributor(s)
Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide pandemic infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). World Health Organization (WHO) has defined the viral variants of concern (VOC) which cause more severe disease, higher transmissibility, and reduced vaccine efficacy. In this study, the “Nano COVID-19” workflow based on Oxford nanopore sequencing of the full-length spike gene combined with flexible data analysis options was developed to identify SARS-CoV-2 VOCs. The primers were designed to cover the full-length spike gene and can amplify all VOC strains. The results of VOC identification based on phylogenetic analysis of the full-length spike gene were comparable to the whole genome sequencing (WGS). Compared to the standard VOC identification pipeline, the fast analysis based on Read Assignment, Mapping, and Phylogenetic Analysis in Real Time (RAMPART) and the user-friendly method based on EPI2ME yielded 89.3% and 97.3% accuracy, respectively. The EPI2ME pipeline is recommended for researchers without bioinformatic skills, whereas RAMPART is more suitable for bioinformaticians. This workflow provides a cost-effective, simplified pipeline with a rapid turnaround time. Furthermore, it is portable to point-of-care SARS-CoV-2 VOC identification and compatible with large-scale analysis. Therefore, “Nano COVID-19” is an alternative viral epidemic screening and transmission tracking workflow.