A Robust, Safe, and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Wastewater Samples

Abstract

Molecular diagnosis and surveillance of pathogens such as SARS‐CoV‐2 depend on nucleic acid isolation. Pandemics at the scale of COVID‐19 can cause a global shortage of proprietary commercial reagents and BSL‐2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. An open‐source method, magnetic‐nanoparticle‐aided viral RNA isolation from contagious samples (MAVRICS), built upon readily available reagents, and easily assembled in any basically equipped laboratory, is thus developed. The performance of MAVRICS is evaluated using validated pathogen detection assays and real‐world and contrived samples. Unlike conventional methods, MAVRICS works directly in samples inactivated in phenol‐chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. MAVRICS allows wastewater biomass immobilized on membranes to be directly inactivated and lysed in TRIzol followed by RNA extraction by magnetic nanoparticles, thereby greatly reducing biohazard risk and simplifying processing procedures. Using 39 COVID‐19 patient samples and two wastewater samples, it is shown that MAVRICS rivals commercial kits in detection of SARS‐CoV‐2, influenza viruses, and respiratory syncytial virus. Therefore, MAVRICS is safe, fast, and scalable. It is field‐deployable with minimal equipment requirements and could become an enabling technology for widespread testing and wastewater monitoring of diverse pathogens.

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

“…It is worth noting that the sensitivity of SARS-CoV-2 detection of multi-virus multiplex NIRVANA is lower than that of singleplex rRT-PCR assays achieved in our hands. 27 Further optimization of the RPA primer combination may improve the sensitivity, and the ability of NIRVANA to identify multiple viruses and to detect variants could partially offset the reduced sensitivity.…”

Uncoupling Molecular Testing for SARS-CoV-2 From International Supply Chains

“…RNA extraction from nasopharyngeal swabs was not specifically trialed as part of the HB initiative although supply of RNA extraction reagents was a critical concern at the beginning of the pandemic. The BOMB.bio protocol for making magnetic RNA extraction beads from easily obtained laboratory materials ( 8 ) has proved successful for COVID-19 screening at centers both in NZ and the UK and as part of modified diagnostic systems for viral testing [e.g., ( 26 , 27 )]. Use of BOMB.bio for RNA extraction from clinical samples meets the goals of self-sufficiency for NZ onshore production in case traditional supplies of RNA extraction reagent become unavailable.…”

Therapeutic and diagnostic applications of nanoparticles in the management of COVID-19: a comprehensive overview

“…Nucleic acids are liberated from viral particles before adhering to the column membrane, followed by repeated centrifugation steps to allow binding, cleaning, and elution of the extracted nucleic acids. Techniques based on magnetic NPs have been proven to be easy-to-use, automated, and high-throughput alternatives to centrifugation [ 47 – 50 ]. Traditional Magnetic NPs (MNPs) based methods may selectively absorb nucleic acids from lysed materials due to surface-modified functional groups (Fig.…”