Carabelli, A. M. et al. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat. Rev. Microbiol. 21, 162–177 (2023).CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Amicone, M. et al. Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Evol. Med. Public Health 10, 142–155 (2022).ArticleÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Meng, B. et al. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity. Nature 603, 706–714 (2022).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Escalera, A. et al. Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell Host Microbe 30, 373–387.e377 (2022).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
DeGrace, M. M. et al. Defining the risk of SARS-CoV-2 variants on immune protection. Nature 605, 640–652 (2022).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Tomalka, J. A., Suthar, M. S., Deeks, S. G. & Sekaly, R. P. Fighting the SARS-CoV-2 pandemic requires a global approach to understanding the heterogeneity of vaccine responses. Nat. Immunol. 23, 360–370 (2022).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Garcia-Beltran, W. F. et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 184, 2372–2383.e2379 (2021).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Petherick, A. Developing antibody tests for SARS-CoV-2. Lancet 395, 1101–1102 (2020).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Peeling, R. W., Heymann, D. L., Teo, Y.-Y. & Garcia, P. J. Diagnostics for COVID-19: moving from pandemic response to control. Lancet 399, 757–768 (2022).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Vogels, C. B. F. et al. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets. Nat. Microbiol. 5, 1299–1305 (2020).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Bokelmann, L. et al. Point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP. Nat. Commun. 12, 1467 (2021).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Qian, J. et al. An enhanced isothermal amplification assay for viral detection. Nat. Commun. 11, 5920 (2020).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Osório, N. S. & Correia-Neves, M. Implication of SARS-CoV-2 evolution in the sensitivity of RT–qPCR diagnostic assays. Lancet Infect. Dis. 21, 166–167 (2021).ArticleÂ
PubMedÂ
Google ScholarÂ
Robishaw, J. D. et al. Genomic surveillance to combat COVID-19: challenges and opportunities. Lancet Microbe 2, e481–e484 (2021).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Li, P., de Vries, A. C., Kamar, N., Peppelenbosch, M. P. & Pan, Q. Monitoring and managing SARS-CoV-2 evolution in immunocompromised populations. Lancet Microbe 3, e325–e326 (2022).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Zhang, T. et al. A paper-based assay for the colorimetric detection of SARS-CoV-2 variants at single-nucleotide resolution. Nat. Biomed. Eng. 6, 957–967 (2022).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Zhang, T. et al. Precise in-field molecular diagnostics of crop diseases by smartphone-based mutation-resolved pathogenic RNA analysis. Nat. Commun. 14, 4327 (2023).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Dao Thi, V. L. et al. A colorimetric RT–LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples. Sci. Transl. Med. 12, eabc7075 (2020).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Wu, Q. et al. INSIGHT: a population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing. Sci. Adv. 7, eabe5054 (2021).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Yelagandula, R. et al. Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq. Nat. Commun. 12, 3132 (2021).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Garg, A. et al. Evaluation of seven commercial RT–PCR kits for COVID-19 testing in pooled clinical specimens. J. Med. Virol. 93, 2281–2286 (2021).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Panpradist, N. et al. Harmony COVID-19: a ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection. Sci. Adv. 7, eabj1281 (2021).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Alafeef, M., Moitra, P., Dighe, K. & Pan, D. RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19. Nat. Protoc. 16, 3141–3162 (2021).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Mohammadniaei, M. et al. A non-enzymatic, isothermal strand displacement and amplification assay for rapid detection of SARS-CoV-2 RNA. Nat. Commun. 12, 5089 (2021).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Broughton, J. P. et al. CRISPR–Cas12-based detection of SARS-CoV-2. Nat. Biotechnol. 38, 870–874 (2020).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Casati, B. et al. Rapid, adaptable and sensitive Cas13-based COVID-19 diagnostics using ADESSO. Nat. Commun. 13, 3308 (2022).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Patchsung, M. et al. Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA. Nat. Biomed. Eng. 4, 1140–1149 (2020).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Joung, J. et al. Detection of SARS-CoV-2 with SHERLOCK one-pot testing. N. Engl. J. Med. 383, 1492–1494 (2020).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Xun, G., Lane, S. T., Petrov, V. A., Pepa, B. E. & Zhao, H. A rapid, accurate, scalable, and portable testing system for COVID-19 diagnosis. Nat. Commun. 12, 2905 (2021).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Ding, X. et al. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR–Cas12a assay. Nat. Commun. 11, 4711 (2020).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Chandrasekaran, S. S. et al. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nat. Biomed. Eng. 6, 944–956 (2022).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
De Puig, H. et al. Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants. Sci. Adv. 7, eabh2944 (2021).ArticleÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Welch, N. L. et al. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat. Med. 28, 1083–1094 (2022).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Arizti-Sanz, J. et al. Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Nat. Biomed. Eng. 6, 932–943 (2022).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Metsky, H. C. et al. Designing sensitive viral diagnostics with machine learning. Nat. Biotechnol. 40, 1123–1131 (2022).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Fozouni, P. et al. Amplification-free detection of SARS-CoV-2 with CRISPR–Cas13a and mobile phone microscopy. Cell 184, 323–333.e329 (2021).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Wang, D. et al. Rapid lateral flow immunoassay for the fluorescence detection of SARS-CoV-2 RNA. Nat. Biomed. Eng. 4, 1150–1158 (2020).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Phillips, E. A. et al. Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes. Nat. Biomed. Eng. https://doi.org/10.1038/s41551-41023-01028-y (2023).ArticleÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Puhach, O., Meyer, B. & Eckerle, I. SARS-CoV-2 viral load and shedding kinetics. Nat. Rev. Microbiol. 21, 147–161 (2023).CASÂ
PubMedÂ
Google ScholarÂ
Yuasa, S. et al. Viral load of SARS-CoV-2 Omicron is not high despite its high infectivity. J. Med. Virol. 94, 5543–5546 (2022).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
La Scola, B. et al. Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards. Eur. J. Clin. Microbiol. 39, 1059–1061 (2020).ArticleÂ
Google ScholarÂ
Gallichotte, E. N. et al. Early adoption of longitudinal surveillance for SARS-CoV-2 among staff in long-term care facilities: prevalence, virologic and sequence analysis. Microbiol. Spectr. 9, e01003–e01021 (2021).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Wölfel, R. et al. Virological assessment of hospitalized patients with COVID-2019. Nature 581, 465–469 (2020).ArticleÂ
PubMedÂ
Google ScholarÂ
Fu, E. & Downs, C. Progress in the development and integration of fluid flow control tools in paper microfluidics. Lab Chip 17, 614–628 (2017).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Wu, K. & Green, A. A. Sensitive detection of SARS-CoV-2 on paper. Nat. Biomed. Eng. 6, 928–929 (2022).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Sakuma, T., Barry, Michael, A. & Ikeda, Y. Lentiviral vectors: basic to translational. Biochem. J. 443, 603–618 (2012).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Myhrvold, C. et al. Field-deployable viral diagnostics using CRISPR–Cas13. Science 360, 444–448 (2018).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Weickmann, J. L. & Glitz, D. G. Human ribonucleases. Quantitation of pancreatic-like enzymes in serum, urine, and organ preparations. J. Biol. Chem. 257, 8705–8710 (1982).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Laue, T., Emmerich, P. & Schmitz, H. Detection of dengue virus RNA in patients after primary or secondary dengue infection by using the TaqMan automated amplification system. J. Clin. Microbiol. 37, 2543–2547 (1999).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Simmel, F. C., Yurke, B. & Singh, H. R. Principles and applications of nucleic acid strand displacement reactions. Chem. Rev. 119, 6326–6369 (2019).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Chen, S. X. & Seelig, G. An engineered kinetic amplification mechanism for single nucleotide variant discrimination by DNA hybridization probes. J. Am. Chem. Soc. 138, 5076–5086 (2016).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Martinez, A. W., Phillips, S. T., Butte, M. J. & Whitesides, G. M. Patterned paper as a platform for inexpensive, low-volume, portable bioassays. Angew. Chem. Int. Ed. 46, 1318–1320 (2007).ArticleÂ
CASÂ
Google ScholarÂ
Martinez, A. W., Phillips, S. T., Wiley, B. J., Gupta, M. & Whitesides, G. M. FLASH: a rapid method for prototyping paper-based microfluidic devices. Lab Chip 8, 2146–2150 (2008).ArticleÂ
CASÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Dungchai, W., Chailapakul, O. & Henry, C. S. A low-cost, simple, and rapid fabrication method for paper-based microfluidics using wax screen-printing. Analyst 136, 77–82 (2011).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Yamada, K., Henares, T. G., Suzuki, K. & Citterio, D. Paper-based inkjet-printed microfluidic analytical devices. Angew. Chem. Int. Ed. 54, 5294–5310 (2015).ArticleÂ
CASÂ
Google ScholarÂ
Apilux, A., Ukita, Y., Chikae, M., Chailapakul, O. & Takamura, Y. Development of automated paper-based devices for sequential multistep sandwich enzyme-linked immunosorbent assays using inkjet printing. Lab Chip 13, 126–135 (2013).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Ghosh, R., Gopalakrishnan, S., Savitha, R., Renganathan, T. & Pushpavanam, S. Fabrication of laser printed microfluidic paper-based analytical devices (LP-µPADs) for point-of-care applications. Sci. Rep. 9, 7896 (2019).ArticleÂ
PubMedÂ
PubMed CentralÂ
Google ScholarÂ
Almeida, M. I. G. S., Jayawardane, B. M., Kolev, S. D. & McKelvie, I. D. Developments of microfluidic paper-based analytical devices (μPADs) for water analysis: a review. Talanta 177, 176–190 (2018).ArticleÂ
CASÂ
PubMedÂ
Google ScholarÂ
Smereka, M. & DulÄ™ba, I. Circular object detection using a modified hough transform. Int. J. Appl. Math. Comput. Sci. 18, 85–91 (2008).ArticleÂ
Google ScholarÂ
Hoo, Z. H., Candlish, J. & Teare, D. What is an ROC curve? Emerg. Med. J. 34, 357–359 (2017).ArticleÂ
PubMedÂ
Google ScholarÂ