Strategies That Facilitate Extraction-Free SARS-CoV-2 Nucleic Acid Amplification Tests

Abstract

The COVID-19 pandemic has resulted in an unprecedented global demand for in vitro diagnostic reagents. Supply shortages and hoarding have impacted testing capacity which has led to inefficient COVID-19 case identification and transmission control, predominantly in developing countries. Traditionally, RNA extraction is a prerequisite for conducting SARS-CoV-2 nucleic acid amplification tests (NAAT); however, simplified methods of sample processing have been successful at bypassing typical nucleic acid extraction steps, enabling extraction-free SARS-CoV-2 NAAT workflows. These methods involve chemical and physical approaches that are inexpensive and easily accessible alternatives to overcome extraction kit supply shortages, while offering acceptable test performance. Here we provide an overview of three main sample preparation strategies that have been shown to facilitate extraction-free SARS-CoV-2 NAATs.

Keywords: COVID-19; NAAT; RT-PCR; SARS-CoV-2; diagnostics; isothermal amplification; nucleic acid extraction.

Figure 1

Standard vs. extraction-free SARS-CoV-2 NAATs. Standard SARS-CoV-2 NAAT workflows involve the collection, elution, and lysis of respiratory samples, and extraction of their RNA prior to reverse transcription and amplification of the target (A,B). Alternative workflows that bypass the extraction step and streamline the procedure involve chemical and physical treatment methods that inactivate inhibitory or interfering substances but do not impact the integrity of the nucleic acid or the amplification of the target.