Probing the mutation independent interaction of DNA probes with SARS-CoV-2 variants through a combination of surface-enhanced Raman scattering and machine learning
Abid Hasan, Syed Mohammad
Gartia, Manas Ranjan
JournalBiosensors & Bioelectronics
MetadataShow full item record
AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has been characterized by the emergence of sets of mutations impacting the virus characteristics, such as transmissibility and antigenicity, presumably in response to the changing immune profile of the human population. The presence of mutations in the SARS-CoV-2 virus can potentially impact therapeutic and diagnostic test performances. We design and develop here a unique set of DNA probes i.e., antisense oligonucleotides (ASOs) which can interact with genetic sequences of the virus irrespective of its ongoing mutations. The probes, developed herein, target a specific segment of the nucleocapsid phosphoprotein (N) gene of SARS-CoV-2 with high binding efficiency which do not mutate among the known variants. Further probing into the interaction profile of the ASOs reveals that the ASO-RNA hybridization remains unaltered even for a hypothetical single point mutation at the target RNA site and diminished only in case of the hypothetical double or triple point mutations. The mechanism of interaction among the ASOs and SARS-CoV-2 RNA is then explored with a combination of surface-enhanced Raman scattering (SERS) and machine learning techniques. It has been observed that the technique, described herein, could efficiently discriminate between clinically positive and negative samples with ∼100% sensitivity and ∼90% specificity up to 63 copies/mL of SARS-CoV-2 RNA concentration. Thus, this study establishes N gene targeted ASOs as the fundamental machinery to efficiently detect all the current SARS-CoV-2 variants regardless of their mutations.
Rights/TermsCopyright © 2022 Elsevier B.V. All rights reserved.
surface-enhanced Raman scattering
selective and ultrasensitive diagnosis
mutation resistant probe
Identifier to cite or link to this itemhttp://hdl.handle.net/10713/18539
- Selective Naked-Eye Detection of SARS-CoV-2 Mediated by N Gene Targeted Antisense Oligonucleotide Capped Plasmonic Nanoparticles.
- Authors: Moitra P, Alafeef M, Dighe K, Frieman MB, Pan D
- Issue date: 2020 Jun 23
- Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results.
- Authors: Lesbon JCC, Poleti MD, de Mattos Oliveira EC, Patané JSL, Clemente LG, Viala VL, Ribeiro G, Giovanetti M, de Alcantara LCJ, de Lima LPO, Martins AJ, Dos Santos Barros CR, Marqueze EC, de Souza Todão Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Slavov SN, Dos Santos RB, Rodrigues ES, Santos EV, Borges JS, de La Roque DGL, Kitajima JP, Santos B, Assato PA, da Silva da Costa FA, Banho CA, Sacchetto L, Moraes MM, Palmieri M, da Silva FEV, Grotto RMT, Souza-Neto JA, Nogueira ML, Coutinho LL, Calado RT, Neto RM, Covas DT, Kashima S, Elias MC, Sampaio SC, Fukumasu H
- Issue date: 2021 Dec 10
- Surface-enhanced Raman scattering-based immunoassay for severe acute respiratory syndrome coronavirus 2.
- Authors: Cha H, Kim H, Joung Y, Kang H, Moon J, Jang H, Park S, Kwon HJ, Lee IC, Kim S, Yong D, Yoon SW, Park SG, Guk K, Lim EK, Park HG, Choo J, Jung J, Kang T
- Issue date: 2022 Apr 15
- Deepening of In Silico Evaluation of SARS-CoV-2 Detection RT-qPCR Assays in the Context of New Variants.
- Authors: Gand M, Vanneste K, Thomas I, Van Gucht S, Capron A, Herman P, Roosens NHC, De Keersmaecker SCJ
- Issue date: 2021 Apr 13
- A Recent Update on Advanced Molecular Diagnostic Techniques for COVID-19 Pandemic: An Overview.
- Authors: Roberts A, Chouhan RS, Shahdeo D, Shrikrishna NS, Kesarwani V, Horvat M, Gandhi S
- Issue date: 2021