The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for versatile diagnostic assays that can discriminate among emerging variants of the virus. Here we report the development and performance benchmarking of an inexpensive (approximately US$0.30 per test) assay for the rapid (sample-to-answer time within 30 min) colorimetric detection of SARS-CoV-2 variants. The assay, which we integrated into foldable paper strips, leverages nucleic acid strand-displacement reactions, the thermodynamic energy penalty associated with single-base-pair mismatches and the metal-ion-controlled enzymatic cleavage of urea to amplify the recognition of viral RNAs for the colorimetric readout of changes in pH via a smartphone. For 50 throat swab samples, the assay simultaneously detected the presence of SARS-CoV-2 and mutations specific to the SARS-CoV-2 variants Alpha, Beta and Gamma, with 100% concordance with real-time quantitative polymerase chain reaction and RNA sequencing. Customizable and inexpensive paper-based assays for the detection of viruses and their variants may facilitate viral surveillance.

严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 的演变凸显了对能够区分病毒新变种的多功能诊断检测的需求。在此，我们报告了一种廉价（每次测试约 0.30 美元）检测方法的开发和性能基准测试，用于快速（从样本到给出结果的时间在 30 分钟内）比色检测 SARS-CoV-2 变体。我们将这种检测方法集成到可折叠纸条中，利用核酸链置换反应、与单碱基对错配相关的热力学能量损失以及金属离子控制的尿素酶裂解来放大病毒 RNA 的识别通过智能手机比色读取 pH 值的变化。对于 50 份咽拭子样本，该检测同时检测到 SARS-CoV-2 的存在以及 SARS-CoV-2 变体 Alpha、Beta 和 Gamma 特有的突变，与实时定量聚合酶链反应和 RNA 测序的一致性达到 100% 。用于检测病毒及其变体的可定制且廉价的纸质检测可能有助于病毒监测。