Smartphone-Based SARS-CoV‑2 and Variants Detection System using Colorimetric DNAzyme Reaction Triggered by Loop-Mediated Isothermal Amplification (LAMP) with Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)

• Published in: ACS nano Vol. 16; no. 7; pp. 11300 - 11314
• Main Authors: Song, Jayeon, Cha, Baekdong, Moon, Jeong, Jang, Hyowon, Kim, Sunjoo, Jang, Jieun, Yong, Dongeun, Kwon, Hyung-Jun, Lee, In-Chul, Lim, Eun-Kyung, Jung, Juyeon, Park, Hyun Gyu, Kang, Taejoon
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 26.07.2022
• Subjects: Colorimetry; COVID-19 - diagnosis; DNA, Catalytic - genetics; Humans; Molecular Diagnostic Techniques - methods; Nucleic Acid Amplification Techniques - methods; SARS-CoV-2 - genetics; Sensitivity and Specificity; Smartphone; SARS-CoV-2; smartphone; variants; machine learning; CRISPR-Cas9
• ISSN: 1936-0851; 1936-086X
• DOI: 10.1021/acsnano.2c04840

Coronavirus disease (COVID-19) has affected people for over two years. Moreover, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has raised concerns regarding its accurate diagnosis. Here, we report a colorimetric DNAzyme reaction triggered by loop-mediated isothermal amplification (LAMP) with clustered regularly interspaced short palindromic repeats (CRISPR), referred to as DAMPR assay for detecting SARS-CoV-2 and variants genes with attomolar sensitivity within an hour. The CRISPR-associated protein 9 (Cas9) system eliminated false-positive signals of LAMP products, improving the accuracy of DAMPR assay. Further, we fabricated a portable DAMPR assay system using a three-dimensional printing technique and developed a machine learning (ML)-based smartphone application to routinely check diagnostic results of SARS-CoV-2 and variants. Among blind tests of 136 clinical samples, the proposed system successfully diagnosed COVID-19 patients with a clinical sensitivity and specificity of 100% each. More importantly, the D614G (variant-common), T478K (delta-specific), and A67V (omicron-specific) mutations of the SARS-CoV-2 S gene were detected selectively, enabling the diagnosis of 70 SARS-CoV-2 delta or omicron variant patients. The DAMPR assay system is expected to be employed for on-site, rapid, accurate detection of SARS-CoV-2 and its variants gene and employed in the diagnosis of various infectious diseases.