References
- Habibzadeh P, Stoneman EK. The novel coronavirus: a bird's eye view. Int J Occup Environ Med. 2020;11(2):65–71.
- Scientific Brief: SARS-CoV-2 and Potential Airborne Transmission: CDC; 2020 [cited 2020 Nov 2]. Available from: https://www.cdc.gov/coronavirus/2019-ncov/more/scientific-brief-sars-cov-2.html
- Wiersinga WJ, Rhodes A, Cheng AC, et al. Pathophysiology, transmission, diagnosis, and treatment of coronavirus disease 2019 (COVID-19): a review. JAMA. 2020;324(8):782–793.
- Arons MM, Hatfield KM, Reddy SC, et al. Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. N Engl J Med. 2020 May 28;382(22):2081–2090.
- Bai Y, Yao L, Wei T, et al. Presumed asymptomatic carrier transmission of COVID-19. JAMA. 2020;323(14):1406–1407.
- CDC’s Diagnostic Test for COVID-19 Only and Supplies: CDC; 2020 [updated 2020 Jul 15; 2020 Sep 30]. Available from: https://www.cdc.gov/coronavirus/2019-ncov/lab/virus-requests.html
- Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265–269.
- Wu A, Peng Y, Huang B, et al. Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host Microbe. 2020;27(3):325–328.
- Malik YS, Sircar S, Bhat S, et al. Emerging novel coronavirus (2019-nCoV)-current scenario, evolutionary perspective based on genome analysis and recent developments. Vet Q. 2020;40(1):68–76.
- Sevajol M, Subissi L, Decroly E, et al. Insights into RNA synthesis, capping, and proofreading mechanisms of SARS-coronavirus. Virus Res. 2014;194:90–99.
- Fauver JR, Petrone ME, Hodcroft EB, et al. Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States. Cell. 2020;181(5):990.e5–996.e5.
- Korber B, Fischer WM, Gnanakaran S, et al. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. 2020;182(4):812–827.
- Yurkovetskiy L, Wang X, Pascal KE, et al. SARS-CoV-2 spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain. bioRxiv. 2020. DOI:https://doi.org/10.1101/2020.07.04.187757
- WHO. SARS-CoV-2 Variants: WHO; 2020. Available from: https://www.who.int/csr/don/31-december-2020-sars-cov2-variants/en/
- Leung K, Shum MH, Leung GM, et al. Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom. Euro Surveill. 2021;26:2002106.
- Interim guidelines for collecting, handling, and testing clinical specimens for COVID-19: CDC; 2020 [updated 2020 Jul 8]. Available from: https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html
- Wang W, Xu Y, Gao R, et al. Detection of SARS-CoV-2 in different types of clinical specimens. JAMA. 2020;323(18):1843–1844.
- Cohen J. Chinese researchers reveal draft genome of virus implicated in Wuhan pneumonia outbreak. Science; 2020. Available from: https://www.sciencemag.org/news/2020/01/chinese-researchers-reveal-draft-genome-virus-implicated-wuhan-pneumonia-outbreak
- Park M, Won J, Choi BY, et al. Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCR and real-time PCR. Exp Mol Med. 2020;52(6):963–977.
- Corman VM, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3):2000045.
- VanGuilder HD, Vrana KE, Freeman WM. Twenty-five years of quantitative PCR for gene expression analysis. Biotechniques. 2008;44(5):619–626.
- Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270–273.
- Chu DKW, Pan Y, Cheng SMS, et al. Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia. Clin Chem. 2020;66(4):549–555.
- Shi J, Han D, Zhang R, et al. Molecular and serological assays for SARS-CoV-2: insights from genome and clinical characteristics. Clin Chem. 2020;66(8):1030–1046.
- Chan JF, Yip CC, To KK, et al. Improved molecular diagnosis of COVID-19 by the Novel, highly sensitive and specific COVID-19-RdRp/Hel real-time reverse transcription-PCR assay validated in vitro and with clinical specimens. J Clin Microbiol. 2020;58(5):e00310-20.
- Accelerated Emergency Use Authorization (EUA) Summary Orig3n 2019 Novel Coronavirus (COVID-19) Test (ORIG3N, INC.) FDA; 2020. Available from: https://www.fda.gov/media/136873/download
- Lohse S, Pfuhl T, Berko-Gottel B, et al. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people. Lancet Infect Dis. 2020;20(11):P1231–P1232.
- Garg J, Singh V, Pandey P, et al. Evaluation of sample pooling for diagnosis of COVID-19 by Real time PCR- A resource saving combat strategy. J Med Virol. 2021;93(3):1526–1531.
- Pooled Sample Testing and Screening Testing for COVID-19: FDA; 2020. Available from: https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/pooled-sample-testing-and-screening-testing-covid-19
- Tahamtan A, Ardebili A. Real-time RT-PCR in COVID-19 detection: issues affecting the results. Expert Rev Mol Diagn. 2020 May;20(5):453–454.
- Habibzadeh P, Sajadi MM, Emami A, et al. Rate of re-positive RT-PCR test among patients recovered from COVID-19. Biochem Med (Zagreb). 2020;30(3):030401.
- Quan P-L, Sauzade M, Brouzes E. A technology review. Sensors. 2018;18(4):1271.
- Salipante SJ, Jerome KR. Digital PCR-an emerging technology with broad applications in microbiology. Clin Chem. 2020;66(1):117–123.
- Hindson CM, Chevillet JR, Briggs HA, et al. Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat Methods. 2013;10(10):1003–1005.
- Svec D, Tichopad A, Novosadova V, et al. How good is a PCR efficiency estimate: recommendations for precise and robust qPCR efficiency assessments. Biomol Detect Quantif. 2015;3:9–16.
- Dingle TC, Sedlak RH, Cook L, et al. Tolerance of droplet-digital PCR vs real-time quantitative PCR to inhibitory substances. Clin Chem. 2013;59(11):1670–1672.
- Hoffman NG, Cook L, Atienza EE, et al. Marked variability of BK virus load measurement using quantitative real-time PCR among commonly used assays. J Clin Microbiol. 2008;46(8):2671–2680.
- Whale AS, Huggett JF, Tzonev S. Fundamentals of multiplexing with digital PCR. Biomol Detect Quantif. 2016;10:15–23.
- Kuypers J, Jerome KR. Applications of digital PCR for clinical microbiology. J Clin Microbiol. 2017;55(6):1621–1628.
- Suo T, Liu X, Feng J, et al. ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens. Emerg Microbes Infect. 2020;9(1):1259–1268.
- Falzone L, Musso N, Gattuso G, et al. Sensitivity assessment of droplet digital PCR for SARS-CoV-2 detection. Int J Mol Med. 2020;46(3):957–964.
- Liu X, Feng J, Zhang Q, et al. Analytical comparisons of SARS-COV-2 detection by qRT-PCR and ddPCR with multiple primer/probe sets. Emerg Microbes Infect. 2020;9(1):1175–1179.
- Alteri C, Cento V, Antonello M, et al. Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients. PLoS One. 2020;15(9):e0236311.
- Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. Lab Chip. 2012;12(14):2469–2486.
- Notomi T, Okayama H, Masubuchi H, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28(12):E63.
- Kellner MJ, Ross JJ, Schnabl J, et al. A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing. bioRxiv. 2020. DOI:https://doi.org/10.1101/2020.06.23.166397
- Mori Y, Nagamine K, Tomita N, et al. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Biophys Res Commun. 2001;289(1):150–154.
- Yan C, Cui J, Huang L, et al. Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay. Clin Microbiol Infect. 2020;26(6):773–779.
- Shirato K, Yano T, Senba S, et al. Detection of Middle East respiratory syndrome coronavirus using reverse transcription loop-mediated isothermal amplification (RT-LAMP). Virol J. 2014;11:139.
- Hong TC, Mai QL, Cuong DV, et al. Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus. J Clin Microbiol. 2004;42(5):1956–1961.
- Kacian DL, Fultz TJ. inventors; Gen-Probe Inc, assignee. Kits for nucleic acid sequence amplification methods. United States patent US5888779A. 1999. Available from: https://patentimages.storage.googleapis.com/02/21/aa/e06896e20b88c1/US5888779.pdf
- Ali MM, Li F, Zhang Z, et al. Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. Chem Soc Rev. 2014;43(10):3324–3341.
- Dahl F, Baner J, Gullberg M, et al. Circle-to-circle amplification for precise and sensitive DNA analysis. Proc Natl Acad Sci USA. 2004;101(13):4548–4553.
- Tian B, Gao F, Fock J, et al. Homogeneous circle-to-circle amplification for real-time optomagnetic detection of SARS-CoV-2 RdRp coding sequence. Biosens Bioelectron. 2020;165:112356.
- Ishino Y, Shinagawa H, Makino K, et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987;169(12):5429–5433.
- Hille F, Charpentier E. CRISPR-Cas: biology, mechanisms and relevance. Philos Trans R Soc Lond B Biol Sci. 2016;371(1707):20150496.
- Pickar-Oliver A, Gersbach CA. The next generation of CRISPR-Cas technologies and applications. Nat Rev Mol Cell Biol. 2019;20(8):490–507.
- Gootenberg JS, Abudayyeh OO, Lee JW, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017;356(6336):438–442.
- Chen JS, Ma E, Harrington LB, et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018;360(6387):436–439.
- Myhrvold C, Freije CA, Gootenberg JS, et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science. 2018;360(6387):444–448.
- Kellner MJ, Koob JG, Gootenberg JS, et al. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat Protoc. 2019;14(10):2986–3012.
- Zhang F, Abudayyeh OO, Gootenberg JS. A protocol for detection of COVID-19 using CRISPR diagnostics (v.20200321); 2020. Available from: https://www.broadinstitute.org/files/publications/special/COVID-19%20detection%20(updated).pdf
- Patchsung M, Jantarug K, Pattama A, et al. Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA. Nat Biomed Eng. 2020;4(12):1140–1149.
- Joung J, Ladha A, Saito M, et al. Detection of SARS-CoV-2 with SHERLOCK one-pot testing. N Engl J Med. 2020;383(15):1492–1494.
- Broughton JP, Deng X, Yu G, et al. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol. 2020;38(7):870–874.
- Fozouni P, Son S, Díaz de León Derby M, et al. Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone. medRxiv. 2020. DOI:https://doi.org/10.1101/2020.09.28.20201947
- Vora GJ, Meador CE, Stenger DA, et al. Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl Environ Microbiol. 2004;70(5):3047–3054.
- Chen Q, Li J, Deng Z, et al. Comprehensive detection and identification of seven animal coronaviruses and human respiratory coronavirus 229E with a microarray hybridization assay. Intervirology. 2010;53(2):95–104.
- Shi R, Ma W, Wu Q, et al. Design and application of 60mer oligonucleotide microarray in SARS coronavirus detection. Chin Sci Bull. 2003;48(12):1165–1169.
- Guo X, Geng P, Wang Q, et al. Development of a single nucleotide polymorphism DNA microarray for the detection and genotyping of the SARS coronavirus. J Microbiol Biotechnol. 2014;24(10):1445–1454.
- Hardick J, Metzgar D, Risen L, et al. Initial performance evaluation of a spotted array Mobile Analysis Platform (MAP) for the detection of influenza A/B, RSV, and MERS coronavirus. Diagn Microbiol Infect Dis. 2018;91(3):245–247.
- de Souza Luna LK, Heiser V, Regamey N, et al. Generic detection of coronaviruses and differentiation at the prototype strain level by reverse transcription-PCR and nonfluorescent low-density microarray. J Clin Microbiol. 2007;45(3):1049–1052.
- Pachetti M, Marini B, Benedetti F, et al. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med. 2020;18(1):179.
- Benedetti F, Snyder GA, Giovanetti M, et al. Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1. J Transl Med. 2020;18(1):329.
- Habibzadeh P, Honarvar B, Silawi M, et al. Association between rs2303861 polymorphism in CD82 gene and non-alcoholic fatty liver disease: a preliminary case-control study. Croat Med J. 2019;60(4):361–368.
- Habibzadeh P, Inaloo S, Silawi M, et al. A novel TTC19 mutation in a patient with neurological, psychological, and gastrointestinal impairment. Front Neurol. 2019;10:944.
- Habibzadeh P, Silawi M, Dastsooz H, et al. Clinical and molecular characterization of a patient with mitochondrial Neurogastrointestinal Encephalomyopathy. BMC Gastroenterol. 2020;20(1):142.
- Muhamad Rizal NS, Neoh HM, Ramli R, et al. Advantages and limitations of 16S rRNA next-generation sequencing for pathogen identification in the diagnostic microbiology laboratory: perspectives from a middle-income country. Diagnostics (Basel). 2020;10(10):816.
- Habibzadeh P, Tabatabaei Z, Inaloo S, et al. Case report: expanding the genetic and phenotypic spectrum of autosomal recessive spastic ataxia of Charlevoix-Saguenay. Front Genet. 2020;11:585136.
- GISAID; 2020 [updated 2021 Jan 16]. Available from: https://www.gisaid.org/
- Hayes S, Mahony J, Nauta A, et al. Metagenomic approaches to assess bacteriophages in various environmental niches. Viruses. 2017;9(6):127.
- Nooij S, Schmitz D, Vennema H, et al. Overview of virus metagenomic classification methods and their biological applications. Front Microbiol. 2018;9:749.
- Quince C, Walker AW, Simpson JT, et al. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol. 2017;35(9):833–844.
- Babiker A, Bradley HL, Stittleburg VD, et al. Metagenomic sequencing to detect respiratory viruses in persons under investigation for COVID-19. J Clin Microbiol. 2020. DOI:https://doi.org/10.1128/JCM.02142-20
- Hillmann B, Al-Ghalith GA, Shields-Cutler RR, et al. Evaluating the Information content of shallow shotgun metagenomics. mSystems. 2018. DOI:https://doi.org/10.1128/mSystems.00069-18
- Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet. 2019;20(6):341–355.
- Kiselev D, Matsvay A, Abramov I, et al. Current trends in diagnostics of viral infections of unknown etiology. Viruses. 2020;12(2):211.
- Detection and characterization of respiratory viruses, including SARS-CoV-2, using Illumina RNA Prep with Enrichment: Illumina; 2020 [cited 2020]. Available from: https://emea.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/illumina-rna-enrichment-coronavirus-app-note-470-2020-005/illumina-rna-enrichment-coronavirus-app-note-470-2020-005.pdf
- Bloom JS, Jones EM, Gasperini M, et al. Swab-Seq: a high-throughput platform for massively scaled up SARS-CoV-2 testing. medRxiv. 2020. DOI:https://doi.org/10.1101/2020.08.04.20167874
- Bohn MK, Mancini N, Loh TP, et al. IFCC Interim guidelines on molecular testing of SARS-CoV-2 Infection. Clin Chem Lab Med. 2020;58(12):1993–2000.
- Habibzadeh F, Habibzadeh P, Yadollahie M, et al. On the information hidden in a classifier distribution. Sci Rep. 2021;11(1):917.
- Vandenberg O, Martiny D, Rochas O, et al. Considerations for diagnostic COVID-19 tests. Nat Rev Microbiol. 2020. DOI:https://doi.org/10.1038/s41579-020-00461-z
- Lieberman JA, Pepper G, Naccache SN, et al. Comparison of commercially available and laboratory-developed assays for in vitro detection of SARS-CoV-2 in clinical laboratories. J Clin Microbiol. 2020. DOI:https://doi.org/10.1128/JCM.00821-20
- Bwire GM, Majigo MV, Njiro BJ, et al. Detection profile of SARS-CoV-2 using RT-PCR in different types of clinical specimens: a systematic review and meta-analysis. J Med Virol. 2021;93(2):719–725.
- Mutant coronavirus in the United Kingdom sets off alarms, but its importance remains unclear: Science magazine; 2020. Available from: https://www.sciencemag.org/news/2020/12/mutant-coronavirus-united-kingdom-sets-alarms-its-importance-remains-unclear
- Daughton CG. Wastewater surveillance for population-wide Covid-19: the present and future. Sci Total Environ. 2020;736:139631.
- Medema G, Heijnen L, Elsinga G, et al. Presence of SARS-coronavirus-2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the epidemic in The Netherlands. Environ Sci Technol Lett. 2020;7(7):511–516.
- Giri AK, Rana DR. Charting the challenges behind the testing of COVID-19 in developing countries: Nepal as a case study. Biosaf Health. 2020;2(2):53–56.
- Abdullahi IN, Emeribe AU, Akande AO, et al. Roles and challenges of coordinated public health laboratory response against COVID-19 pandemic in Africa. J Infect Dev Ctries. 2020;14(7):691–695.
- COVID-19 Public Health Emergency of International Concern (PHEIC) global research and innovation forum towards a research roadmap: WHO; 2020 [cited 2020 Oct 30]. Available from: https://www.who.int/publications/m/item/covid-19-public-health-emergency-of-international-concern-(pheic)-global-research-and-innovation-forum
- Dinnes J, Deeks JJ, Adriano A, et al. Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev. 2020;(8):CD013705.
- Zhang W, Du RH, Li B, et al. Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes. Emerg Microbes Infect. 2020;9(1):386–389.
- Rolando JC, Jue E, Barlow JT, et al. Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and non-specific amplification. Nucleic Acids Res. 2020;48(7):e42.
- Wolfel R, Corman VM, Guggemos W, et al. Virological assessment of hospitalized patients with COVID-2019. Nature. 2020;581(7809):465–469.
- Hindson BJ, Ness KD, Masquelier DA, et al. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem. 2011;83(22):8604–8610.
- Regan JF, Kamitaki N, Legler T, et al. A rapid molecular approach for chromosomal phasing. PLoS One. 2015;10(3):e0118270.
- Regan JF, Kamitaki N, Legler T, et al. First NGS-based COVID-19 diagnostic. Nat Biotechnol. 2020;38(7):777.
- Butler DJ, Mozsary C, Meydan C, et al. Shotgun transcriptome and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. bioRxiv. 2020. DOI:https://doi.org/10.1101/2020.04.20.048066
- Wu M, Chen Y, Xia H, et al. Transcriptional and proteomic insights into the host response in fatal COVID-19 cases. Proc Natl Acad Sci USA. 2020;117(45):28336–28343.
- Xiong Y, Liu Y, Cao L, et al. Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Emerg Microbes Infect. 2020;9(1):761–770.
- Miranda JP, Osorio J, Videla M, et al. Analytical and clinical validation for RT-qPCR detection of SARS-CoV-2 without RNA extraction. Front Med. 2020;7:567572.
- Fomsgaard AS, Rosenstierne MW. An alternative workflow for molecular detection of SARS-CoV-2 – escape from the NA extraction kit-shortage, Copenhagen, Denmark. Euro Surveill. 2020;25(14):2000398.
- Munir S, Ahmed S, Ibrahim M, et al. A spellbinding interplay between biological barcoding and nanotechnology. Front Bioeng Biotechnol. 2020;8:883.
- Chen L, Liang J. An overview of functional nanoparticles as novel emerging antiviral therapeutic agents. Mater Sci Eng C Mater Biol Appl. 2020;112:110924.
- Cheong J, Yu H, Lee CY, et al. Fast detection of SARS-CoV-2 RNA via the integration of plasmonic thermocycling and fluorescence detection in a portable device. Nat Biomed Eng. 2020;4(12):1159–1167.
- Perez JM, Josephson L, Weissleder R. Use of magnetic nanoparticles as nanosensors to probe for molecular interactions. Chembiochem. 2004;5(3):261–264.
- Ganganboina AB, Chowdhury AD, Khoris IM, et al. Hollow magnetic-fluorescent nanoparticles for dual-modality virus detection. Biosens Bioelectron. 2020;170:112680.
- Zhou R, Li Y, Dong T, et al. A sequence-specific plasmonic loop-mediated isothermal amplification assay with orthogonal color readouts enabled by CRISPR Cas12a. Chem Commun (Camb). 2020;56(24):3536–3538.
- Ramdas K, Darzi A, Jain S. 'Test, re-test, re-test': using inaccurate tests to greatly increase the accuracy of COVID-19 testing. Nat Med. 2020;26(6):810–811.
- Venkatesan P. COVID-19 diagnostics-not at the expense of other diseases. Lancet Microbe. 2020;1(2):e64.