Abstract
SARS-CoV-2 infection kabi RNK genomiga ega viruslar global epidemiyalar va pandemiyalarning asosiy etiologik omillaridan biri hisoblanadi. Ushbu viruslarni tezkor va aniq aniqlashda real vaqt rejimidagi revers transkripsion polimeraza zanjir reaksiyasi (real-time RT-PCR) eng ishonchli molekulyar diagnostika usullaridan biri bo‘lib, uning sezgirligi va spetsifikligi ko‘p jihatdan virus RNKsini yuqori sifatda ajratib olishga bog‘liq. Mazkur sharh maqolada SARS-CoV-2 misolida virus RNKsini ajratib olishning asosiy yondashuvlari, jumladan TRIzol asosidagi organik ekstraksiya, silika spin-kolonka va magnit boncuklarga asoslangan usullar tizimli ravishda tahlil qilindi. Shuningdek, klinik namunalarni to‘g‘ri yig‘ish, transport qilish va saqlash sharoitlari, RNase kontaminatsiyasi va PCR inhibitorlarining ta’siri, RT-qPCR uchun RNK sifatiga qo‘yiladigan talablar, resurslari cheklangan laboratoriyalar uchun iqtisodiy samarali ekstraksiya usullari hamda SARS-CoV-2 diagnostikasidagi amaliy qo‘llanish jihatlari yoritildi. Bundan tashqari, ajratib olingan virus RNKsining genomik monitoring, mutatsiyalarni aniqlash, yangi avlod sekvensiyalash (NGS), diagnostik test tizimlari va ilmiy tadqiqotlarda tutgan o‘rni muhokama qilindi. Maqolada yuqori sifatli RNK olish imkonini beruvchi sodda, tezkor, arzon va avtomatlashtirishga mos texnologiyalarni rivojlantirish kelajakdagi epidemiyalar va pandemiyalarga tayyorgarlik ko‘rishda muhim ahamiyatga ega ekanligi ta’kidlangan.References
1. Agarwal A., Fernando S.M., Honarmand K., et al. Risk of dispersion or aerosol generation and infection transmission with nasopharyngeal and oropharyngeal swabs for detection of COVID-19: A systematic review. BMJ Open. 2021;11:e040616.
2. Ahmed W., Bertsch P.M., Bivins A., et al. Effects of storage temperature on SARS-CoV-2 RNA quantification in wastewater solids. Science of the Total Environment. 2020;745:141089.
3. Ali Z., Rahman M., Hossain M., et al. Advances in magnetic bead-based nucleic acid extraction technologies for molecular diagnostics. Analytical Biochemistry. 2024;686:115615.
4. Barron M.D., Choi J., Zhan T., et al. Automated extraction and detection of SARS-CoV-2 from saliva specimens for high-throughput diagnostics. Journal of Molecular Diagnostics. 2020;22(12):1491–1498.
5. Baseler L., Chertow D.S., Johnson K.M., Feldmann H., Morens D.M. The pathogenesis of Ebola virus disease. Annual Review of Pathology: Mechanisms of Disease. 2017;12:387–418.
6. Basso D., Aita A., Navaglia F., et al. Salivary SARS-CoV-2 antigen rapid detection: A prospective cohort study. Clinical Chimica Acta. 2021;517:54–59.
7. Bivins A., North D., Ahmad A., et al. Wastewater-based epidemiology: global collaborative to maximize contributions in the fight against COVID-19. Environmental Science & Technology. 2022;56(3):1494–1504.
8. Boom R., Sol C.J.A., Salimans M.M.M., Jansen C.L., Wertheim-van Dillen P.M.E., van der Noordaa J. Rapid and simple method for purification of nucleic acids. Journal of Clinical Microbiology. 1990;28(3):495–503.
9. Bourgarel M., et al. Recovery of arboviral RNA from arthropod vectors and formalin-fixed tissues. Viruses. 2020;12(9):1014.
10. Bragança, M. V. F., et al. (2015). NS1 recombinant proteins are efficiently produced in Pichia pastoris and have great potential for use in diagnostic kits for dengue virus infections. Diagnostic Microbiology and Infectious Disease, 83(4), 363–371.
11. Bruce E.A., Huang M.L., Perchetti G.A., et al. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step. PLoS Biology. 2020;18(10):e3000896.
12. Butler-Laporte G., Lawandi A., Schiller I., et al. Comparison of saliva and nasopharyngeal swab nucleic acid amplification testing for detection of SARS-CoV-2: A systematic review and meta-analysis. JAMA Internal Medicine. 2021;181(3):353–360.
13. Che X.Y., Qiu L.W., Pan Y.X., et al. Sensitive and specific enzyme-linked immunosorbent assay using recombinant nucleocapsid protein for serodiagnosis of SARS-associated coronavirus infection. Journal of Clinical Microbiology. 2004;42(6):2629–2635.
14. Cook N., Knight A., Richards G.P. Persistence and elimination of human norovirus in food and on food contact surfaces: A critical review. Journal of Food Protection. 2019;82(7):1230–1255.
15. Corman V.M., Landt O., Kaiser M., et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance. 2020;25(3):2000045.
16. Cui X., Li X., Li J., et al. Host ribosomal RNA depletion strategies for enhanced viral metagenomic sequencing and RNA detection. Frontiers in Microbiology. 2022;13:845452.
17. Curtis K.A., Rudolph D.L., Owen S.M. Rapid preservation and extraction of viral nucleic acids using the RNASound card. Journal of Virological Methods. 2018;252:55–61.
18. Czumbel L.M., Kiss S., Farkas N., et al. Saliva as a candidate for COVID-19 diagnostic testing: A meta-analysis. Frontiers in Medicine. 2020;7:465.
19. Dharmayanti N.L.P.I., et al. Genetic characterization of H5N1 avian influenza viruses isolated from humans in Indonesia, 2008–2015. Virus Genes. 2018;54(3):315–324.
20. Di Carlo P., Chiacchiaretta P., D’Antonio F., et al. Environmental surveillance of SARS-CoV-2 on high-touch surfaces in public spaces in Central Italy. International Journal of Environmental Research and Public Health. 2022;19(4):2234.
21. Duffy S. Why are RNA virus mutation rates so damn high? PLoS Biology. 2018;16(8):e3000003.
22. Fabre A.L., Colotte M., Luis A., Tuffet S., Bonnet J. An efficient method for long-term room temperature storage of RNA. European Journal of Human Genetics. 2014;22(3):379–385.
23. Fleige S., Pfaffl M.W. RNA integrity and the effect on the real-time qRT-PCR performance. Molecular Aspects of Medicine. 2006;27(2-3):126–139.
24. Fumian T.M., Leite J.P.G., Miagostovich M.P. Improved RNA extraction strategies for detection of foodborne viruses in fruits and vegetables. Food and Environmental Virology. 2022;14(3):215–227.
25. Gaillard C., Strauss F. Ethanol precipitation of DNA with linear polyacrylamide as carrier. Nucleic Acids Research. 1990;18(2):378.
26. Goldfarb D.M., Tilley P., Al-Rawahi G.N., et al. Self-collected saline gargle samples as an alternative to health care worker-collected nasopharyngeal swabs for COVID-19 diagnosis in outpatients. Journal of Clinical Microbiology. 2021;59(4):e02427-20.
27. Hadfield J., Megill C., Bell S.M., et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34(23):4121–4123.
28. Harvey A.P., Fuhrmeister E.R., Cantrell M.E., et al. Longitudinal monitoring of SARS-CoV-2 RNA on high-touch surfaces in a community setting. Environmental Science & Technology Letters. 2021;8(2):168–175.
29. Hasan M.R., Mirza F., Al-Hail H., et al. Detection of SARS-CoV-2 RNA by direct TRIzol-based extraction from clinical specimens. Journal of Virological Methods. 2021;295:114209.
30. Huang, J. H., Wey, J. J., Sun, Y. C., Chin, C., Chien, L. J., Wu, Y. C., & King, C. C. (2001). Development of a monoclonal antibody-based antigen capture ELISA for detection of Dengue virus NS1 protein. Journal of Medical Virology, 65(3), 553–560.
31. International Committee on Taxonomy of Viruses. Virus Taxonomy: 2024 Release. Available at: https://ictv.global.
32. Kevill J.L., Pellett C., Farkas K., et al. A comparison of precipitation and filtration-based SARS-CoV-2 recovery methods and RNA extraction kits for wastewater-based epidemiology. Science of the Total Environment. 2022;808:151916.
33. Kim Y., Yoon S.H., Kim H.J., et al. Recent advances in RNA extraction and purification technologies for viral diagnostics. Biosensors. 2022;12(11):987.
34. Kozak R.A., et al. Improved concentration and extraction strategies for low viral load plasma specimens. Journal of Virological Methods. 2021;294:114177.
35. Krammer F. SARS-CoV-2 vaccines in development. Nature. 2020;586:516–527.
36. Kuhn J.H., Adachi T., Adhikari N.K.J., et al. New filovirus disease classification and nomenclature. Nature Reviews Microbiology. 2019;17(5):261–263.
37. Kumar S., Verma A., Singh P., et al. One-pot synthesis and surface functionalization of silica-coated magnetic nanoparticles for nucleic acid purification. ACS Applied Nano Materials. 2023;6(9):8124–8135.
38. Lauring A.S., Andino R. Quasispecies theory and the behavior of RNA viruses. PLoS Pathogens. 2010;6(7):e1001005.
39. Lewandowski K., Xu Y., Pullan S.T., et al. Metagenomic nanopore sequencing of influenza virus direct from clinical respiratory samples. Journal of Clinical Microbiology. 2019;58(1):e00963-19.
40. Li D., Baert L., Uyttendaele M. Inactivation and detection of foodborne viruses in fresh produce. Comprehensive Reviews in Food Science and Food Safety. 2021;20(2):1587–1616.
41. Mahony J.B., Petrich A., Smieja M. Molecular diagnosis of respiratory virus infections. Critical Reviews in Clinical Laboratory Sciences. 2011;48(5-6):217–249.
42. Mardian Y., Kosasih H., Karyana M., Neal A., Lau C.Y. Review of current COVID-19 diagnostics and opportunities for further development. Frontiers in Medicine. 2021;8:615099.
43. Marzinotto S., Bonotto C., Cattelan A.M., et al. Optimization of SARS-CoV-2 RNA extraction from highly viscous respiratory specimens during the Omicron wave. Journal of Clinical Virology. 2022;155:105246.
44. Medema G., Heijnen L., Elsinga G., Italiaander R., Brouwer A. Presence of SARS-CoV-2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the epidemic in the Netherlands. Environmental Science & Technology Letters. 2020;7(7):511–516.
45. Miller R.R., Johnson G., Patel S., et al. Simultaneous extraction of viral RNA and bacterial DNA from clinical specimens for multiplex molecular diagnostics. Microbiology Spectrum. 2023;11(2):e04567-22.
46. Mitra R., et al. Development of a simple field-deployable RNA extraction device for viral diagnostics. ACS Sensors. 2021;6(8):2981–2990.
47. Nagy E., Kovács A., Tóth K., et al. Polyplex-based carrier RNA systems for enhanced viral RNA extraction. Biomacromolecules. 2023;24(7):3124–3134.
48. Naqvi A.A.T., Fatima K., Mohammad T., et al. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies. Heliyon. 2020;6(6):e04269.
49. National Center for Biotechnology Information. Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome. RefSeq: NC_045512.2.
50. Nicosia A., Tagliabracci A., Cingolani M., et al. Regeneration and reuse of silica spin columns for nucleic acid purification in molecular diagnostics. Scientific Reports. 2022;12:14856.
51. Oberacker P., Stepper P., Bond D.M., et al. Bio-On-Magnetic-Beads (BOMB): open platform for high-throughput nucleic acid extraction and manipulation. PLoS Biology. 2019;17(1):e3000107.
52. Oude Munnink B.B., Nieuwenhuijse D.F., Stein M., et al. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making. Nature Medicine. 2021;27:1405–1410.
53. Pan Y., Zhang D., Yang P., Poon L.L.M., Wang Q. Viral load of SARS-CoV-2 in clinical samples. The Lancet Infectious Diseases. 2020;20(4):411–412.
54. Parrish N.M., Fisher R., Steadman A., et al. An improved method for capture, inactivation, and purification of SARS-CoV-2 RNA using silica-coated magnetic nanoparticles (MAVRICS). mBio. 2020;11(6):e02403-20.
55. Pecson B.M., Darby E., Haas C.N., et al. Reproducibility and sensitivity of 36 methods to quantify SARS-CoV-2 genetic signal in raw wastewater. Environmental Science: Water Research & Technology. 2021;7:504–520.
56. Puthavathana P., Auewarakul P., Charoenying P.C., et al. Molecular characterization of the complete genome of human influenza H5N1 virus isolates from Thailand. Journal of General Virology. 2005;86(2):423–433.
57. Pérez-Rodríguez F.J., et al. Comparative evaluation of nucleic acid extraction methods for enterovirus and poliovirus detection in stool samples. Food and Environmental Virology. 2022;14(4):341–350.
58. QIAGEN. QIAamp Viral RNA Mini Handbook. Hilden, Germany: QIAGEN; 2024.
59. Quick J., Loman N.J., Duraffour S., et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016;530:228–232.
60. Rio D.C., Ares M. Jr., Hannon G.J., Nilsen T.W. Purification of RNA using TRIzol (TRI reagent). Cold Spring Harbor Protocols. 2010;2010(6):pdb.prot5439.
61. Rogers A.A., Baumann R.E., Borillo G.A., et al. Evaluation of transport media and specimen transport conditions for the detection of SARS-CoV-2 by use of real-time reverse transcription-PCR. Journal of Clinical Microbiology. 2020;58(8):e00708-20.
62. Sambrook J., Russell D.W. Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2001.
63. Simon-Loriere E., Holmes E.C. Why do RNA viruses recombine? Nature Reviews Microbiology. 2011;9(8):617–626.
64. Song S.J., Amir A., Metcalf J.L., et al. Preservation methods differ in fecal microbiome stability and RNA recovery. mSystems. 2021;6(2):e01306-20.
65. Summer S., Hawkins M., Harter C., et al. Validation of viral transport media for the detection of SARS-CoV-2 by RT-PCR. Journal of Clinical Microbiology. 2021;59(11):e00586-21.
66. Tan C.W., Chia W.N., Qin X., et al. Capture-based purification of viral RNA for direct sequencing and characterization. Nature Communications. 2020;11:1350.
67. Tan S.C., Yiap B.C. DNA, RNA, and protein extraction: the past and the present. Journal of Biomedicine and Biotechnology. 2009;2009:574398.
68. Tsujimoto Y., Terada J., Kimura M., et al. Diagnostic accuracy of nasopharyngeal swab, nasal swab and saliva swab samples for the detection of SARS-CoV-2 using RT-PCR. Infection. 2021;49(3):581–589.
69. Wang L., Chen Y., Zhao X., et al. Co-extraction of viral RNA and DNA from a single clinical sample using magnetic bead-based methodology. Journal of Molecular Diagnostics. 2022;24(8):876–885.
70. Wibawa H., et al. Whole-genome analysis reveals reassortment among H5N1 avian influenza viruses circulating in West Java, Indonesia. Archives of Virology. 2020;165(6):1347–1358.
71. Wong, S. J., Boyle, R. H., Demarest, V. L., Woodmansee, A. N., Kramer, L. D., Li, H., & Drebot, M. A. (2003). Immunoassay targeting nonstructural protein 1 for early diagnosis of West Nile virus infection. Clinical and Diagnostic Laboratory Immunology, 10(4), 597–605.
72. Woolhouse M.E.J., Brierley L. Epidemiological characteristics of human-infective RNA viruses. Scientific Data. 2018;5:180017.
73. World Health Organization (WHO). Guidance on regulations for the transport of infectious substances 2023–2024. Geneva: WHO; 2023.
74. Wu, R., Hu, S., Xiao, Y., Li, Z., Shi, D., & Bi, D. (2007). Development of an indirect ELISA based on recombinant NS1 protein for detection of antibodies against H5N1 avian influenza virus. Veterinary Microbiology, 126(1–3), 173–183.
75. Wylezich C., Papa A., Beer M., Höper D. A versatile sample processing workflow for metagenomic pathogen detection. Scientific Reports. 2018;8:13108.
76. Bustin, S. A., and Nolan, T. (2004). Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. Journal of Biomolecular Techniques, 15(3), 155–166.
77. Fleige, S., and Pfaffl, M. W. (2006). RNA integrity and the effect on the real-time qRT-PCR performance. Molecular Aspects of Medicine, 27(2–3), 126–139.
78. Sidstedt, M., Rådström, P., and Hedman, J. (2020). PCR inhibition in qPCR, dPCR and MPS—mechanisms and solutions. Analytical and Bioanalytical Chemistry, 412, 2009–2023.
79. Wilson, I. G. (1997). Inhibition and facilitation of nucleic acid amplification. Applied and Environmental Microbiology, 63(10), 3741–3751.
80. Bustin, S. A., Benes, V., Garson, J. A., et al. (2009). The MIQE guidelines: Minimum information for publication of quantitative real-time PCR experiments. Clinical Chemistry, 55(4), 611–622.
81. Pan, Y., et al. (2020). Viral load of SARS-CoV-2 in clinical samples. The Lancet Infectious Diseases, 20(4), 411–412.
82. Vogels, C. B. F., et al. (2021). Multiplex qPCR discriminates variants of concern to enhance global surveillance. PLOS Biology, 19(5), e3001236.

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Copyright (c) 2026 B. Turdaliyev Dilmurodjon, B. Sayidova Ra'no, O'. Allayev Otabek, B. Xoliyorova Feruza, Sh. Ashuraliyev Humoyun (Author)