Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes

Timothy A Brown; Katherine S Schaefer; Arthur Tsang; Hyun Ah Yi; Jonathan B Grimm; Andrew L Lemire; Fadi M Jradi; Charles Kim; Kevin McGowan; Kimberly Ritola; Derek T Armstrong; Heba H Mostafa; Wyatt Korff; Ronald D Vale; Luke D Lavis

doi:10.7171/jbt.21-3203-007

Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes

J Biomol Tech. 2021 Sep;32(3):121-133. doi: 10.7171/jbt.21-3203-007.

Authors

Affiliations

¹ Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147.
² Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287-7093.

Abstract

The worldwide coronavirus disease 2019 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce 2 pH-sensitive "LAMPshade" dyes as novel readouts in an isothermal Reverse Transcriptase Loop-mediated isothermal AMPlification amplification assay for severe acute respiratory syndrome coronavirus 2 RNA. The resulting JaneliaLAMP assay is robust, simple, inexpensive, and has low technical requirements, and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.

Keywords: LAMPshade; RT-LAMP; Si-fluorescein; carbofluorescein.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19*
Coloring Agents
Humans
Hydrogen-Ion Concentration
Molecular Diagnostic Techniques
Nucleic Acid Amplification Techniques
RNA, Viral* / genetics
SARS-CoV-2
Sensitivity and Specificity
Social Structure

Substances

Coloring Agents
RNA, Viral