NIRVANA for Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and Co-infections of Multiple Respiratory Viruses

Chongwei Bi; Gerardo Ramos-Mandujano; Mo Li

doi:10.1007/978-1-0716-2395-4_6

NIRVANA for Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and Co-infections of Multiple Respiratory Viruses

Methods Mol Biol. 2022:2511:79-88. doi: 10.1007/978-1-0716-2395-4_6.

Authors

Chongwei Bi^{1

2}, Gerardo Ramos-Mandujano¹, Mo Li³

Affiliations

¹ Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
² Shanghai ZhiYu Bio-technology Co., LTD, Shanghai, China.
³ Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. [email protected].

PMID: 35838953
DOI: 10.1007/978-1-0716-2395-4_6

Abstract

Detection and mutation surveillance of SARS-CoV-2 are crucial for combating the COVID-19 pandemic. Here we describe a lab-based method for multiplex isothermal amplification-based sequencing and real-time analysis of multiple viral genomes. It can simultaneously detect SARS-CoV-2, influenza A, human adenovirus, and human coronavirus and monitor mutations for up to 96 samples in real time. The method proved to be rapid and sensitive (limit of detection: 29 viral RNA copies/μL of extracted nucleic acid) in detecting SARS-CoV-2 in clinical samples. We expect it to offer a promising solution for rapid field-deployable detection and mutational surveillance of pandemic viruses.

Keywords: Multiplexing; Mutation surveillance; RPA; SARS-CoV-2; Virus detection.

MeSH terms

Adenoviruses, Human / genetics
COVID-19* / diagnosis
Coinfection* / diagnosis
Humans
Influenza A virus / genetics
Limit of Detection
Mutation
Nucleic Acid Amplification Techniques* / methods
Pandemics
RNA, Viral / analysis
RNA, Viral / genetics
SARS-CoV-2* / genetics
Sensitivity and Specificity

Substances

RNA, Viral