ABSTRACT
The COVID-19 pandemic has created an urgent need for rapid, effective, and low-cost SARS-CoV-2 diagnostic testing. Here, we describe COV-ID, an approach that combines RT-LAMP with deep sequencing to detect SARS-CoV-2 in unprocessed human saliva with a low limit of detection (5-10 virions). Based on a multi-dimensional barcoding strategy, COV-ID can be used to test thousands of samples overnight in a single sequencing run with limited labor and laboratory equipment. The sequencing-based readout allows COV-ID to detect multiple amplicons simultaneously, including key controls such as host transcripts and artificial spike-ins, as well as multiple pathogens. Here, we demonstrate this flexibility by simultaneous detection of 4 amplicons in contrived saliva samples: SARS-CoV-2, influenza A, human STATHERIN, and an artificial SARS calibration standard. The approach was validated on clinical saliva samples, where it showed excellent agreement with RT-qPCR. COV-ID can also be performed directly on saliva absorbed on filter paper, simplifying collection logistics and sample handling.
Subject(s)
COVID-19 , Orthomyxoviridae , COVID-19/diagnosis , Humans , Pandemics , RNA, Viral/analysis , SARS-CoV-2/genetics , Saliva , Sensitivity and SpecificityABSTRACT
COVID-19 has killed over 6 million people worldwide. Currently available methods to detect SARS-CoV-2 are limited by their cost and need for multistep sample preparation and trained personnel. Therefore, there is an urgent need to develop fast, inexpensive, and scalable point-of-care diagnostics that can be used for mass testing. Between January and March 2021, we obtained 321 anterior nare swab samples from individuals in Philadelphia (PA, USA). For the Real-time Accurate Portable Impedimetric Detection prototype 1.0 (RAPID) test, anterior nare samples were tested via an electrochemical impedance spectroscopy (EIS) approach. The overall sensitivity, specificity, and accuracy of RAPID in this cohort study were 80.6%, 89.0%, and 88.2%, respectively. We present a rapid, accurate, inexpensive (<$5.00 per unit), and scalable test for diagnosing COVID-19 at the point-of-care. We anticipate that further iterations of this approach will enable widespread deployment, large-scale testing, and population-level surveillance.