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Simultaneous detection and mutation surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by rapid field-deployable sequencing


Strategies for monitoring the COVID-19 infection are crucial for combating the pandemic. Here we describe a method for multiplex isothermal amplification-based sequencing and real-time analysis of multiple viral genomes. It can simultaneously detect SARS-CoV-2 and co-infecting respiratory viruses, and monitor mutations for up to 96 samples in real time.

The method, termed NIRVANA for Nanopore sequencing of Isothermal Rapid Viral Amplification for Near real-time Analysis, showed high sensitivity and specificity for SARS-CoV-2 in 70 clinical samples. It also simultaneously detected other viral pathogens (e.g. influenza A) in clinical and municipal wastewater samples. It provides a rapid field-deployable solution of COVID-19 and cos-infection detection and surveillance of the evolution of pandemic strains.

Authors: Chongwei Bi, Gerardo Ramos-Mandujano, Sharif Hala, Jinna Xu, Sara Mfarrej, Yeteng Tian, Concepcion Rodriguez Esteban, Estrella Nuñez Delicado, Fadwa S. Alofi, Asim Khogeer, Anwar M. Hashem, Naif A.M. Almontashiri, Arnab Pain, Juan Carlos Izpisua Belmonte, Mo Li

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