2022 / 01

Следующая статья
DOI: 10.47183/mes.2022.003

МЕТОД

Разработка ПЦР-теста для выявления генетических вариантов альфа, бета, гамма, дельта вируса SARS-CoV-2

Г. А. Шипулин, Ю. А. Савочкина, А. К. Шуряева, Е. Е. Шивлягина, А. О. Носова, Е. Е. Давыдова, А. Р. Лупарев, Т. В. Малова, С. М. Юдин
Информация об авторах

Центр стратегического планирования и управления медико-биологическими рисками здоровью Федерального медико-биологического агентства, г. Москва, Россия

Для корреспонденции: Анна Константиновна Шуряева
ул. Погодинская, д. 10, стр. 1, 119121, г. Москва; ur.zmpsc@aveayruhsa

Информация о статье

Вклад авторов: Г. А. Шипулин, Ю. А. Савочкина, Е. Е. Давыдова, С. М. Юдин — планирование эксперимента; Г. А. Шипулин, Ю. А. Савочкина, С. М. Юдин — анализ литературы; А. К. Шуряева, Е. Е. Шивлягина, А. О. Носова, А. Р. Лупарев, Т. В. Малова — постановка эксперимента и интерпретация результатов; Ю. А. Савочкина, Е. Е. Шивлягина, А. О. Носова — разработка набора реагентов; А. Р. Лупарев — статистический анализ; Г. А. Шипулин, А. К. Шуряева — написание и редактирование рукописи; Е. Е. Давыдова, С. М. Юдин — редактирование рукописи.

Соблюдение этических стандартов: исследование проведено в соответствии с требованиями Хельсинской декларации и ГОСТ Р ИСО 14155-2014.

Статья получена: 15.12.2021 Статья принята к печати: 13.01.2022 Опубликовано online: 09.02.2022
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  1. Bogoch II, Watts A, Thomas-Bachli A, Huber C, Kraemer MUG, Khan K, et al. Pneumonia of unknown aetiology in Wuhan, China: potential for international spread via commercial air travel. J Travel Med. 2020; 27 (2): 1–3.
  2. Hui DS, I Azhar E, Madani TA, Ntoumi F, Kock R, Dar O, et al. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China. Int J Infect Dis. 2020; 91: 264–6.
  3. Rothan HA, Byrareddy SN. The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. J Autoimmun. 2020 May; 109:102433.
  4. Sánchez CM, Gebauer F, Suñé C, Mendez A, Dopazo J, Enjuanes L.Genetic evolution and tropism of transmissible gastroenteritis coronaviruses. Virology. 1992 Sep; 190 (1): 92–105.
  5. GISAID EpiFlu™ Database. Available from: http://www.GISAID. org.
  6. World Health Organization. Available from: https://www.who.int.
  7. Lauring AS, Hodcroft EB. Genetic variants of SARS-CoV-2 — What do they mean? JAMA. 2021; 325: 529–31.
  8. CDC 2021. Emerging SARS-CoV-2 variants. Available from: https://www.cdc.gov/coronavirus/2019-ncov/more/science-andresearch/scientific-brief-emerging-variants.html.
  9. Grubaugh ND, Hodcroft EB, Fauver JR, Phelan AL, Cevik M. Public health actions to control new SARS-CoV-2 variants. Cell. 2021;184 (5): 1127–32.
  10. Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. MedRxiv. 2020; 12.21.20248640.
  11. Nelson G, Buzko O, Spilman PR, Niazi K, Rabizadeh S, Soon-Shiong PR. Molecular dynamic simulation reveals E484K mutation enhances spike RBD-ACE2 affinity and the combination of E484K, K417N and N501Y mutations (501Y. V2 variant) induces conformational change greater than N501Y mutant alone, potentially resulting in an escape mutant. bioRxiv. 2021.01.13.426558.
  12. National Institute of Infectious Diseases of JAPAN Brief report 12.01.2021. Available from: https://www.niid.go.jp/niid/images/ epi/corona/covid19-33-en-210112.pdf.
  13. Cherian S, Potdar V, Jadhav S, Yadav P, Gupta N, Das M, et al. Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. Microorganisms. 2021; 9 (7): 1542.
  14. Lacobucci G. Covid-19: New UK variant may be linked to increased death rate, early data indicate. BMJ. 2021; 372: n230.
  15. Santos JC, Passos GA. The high infectivity of SARS-CoV-2 B.1.1.7 is associated with increased interaction force between Spike-ACE2 caused by the viral N501Y mutation. bioRxiv. 2020.12.29.424708.
  16. Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, et al. Estimated transmissibility and impact of SARSCoV-2 lineage B.1.1.7 in England. Science. 2021; 372 (6538): eabg3055.
  17. Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021; 593 (7857): 142–6.
  18. Wibmer CK, Ayres F, Hermanus T, Madzivhandila M, Kgagudi P, Oosthuysen B, et al. SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma. Nat Med. 2021; 27: 622–5.
  19. Garcia-Beltran WF, Lam EC, St Denis K, Nitido AD, Garcia ZH, Hauser BM, et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell. 2021; 184 (9): 2372–2383.e9.
  20. Kissler S, Fauver JR, Mack C, Tai C, Breban MI, et al. Densely sampled viral trajectories suggest longer duration of acute infection with B.1.1.7 variant relative to non-B.1.1.7 SARS-CoV-2. Harvard University’s DASH repository 2021. medRxiv. 2021.
  21. Callaway E, Mallapaty S. Novavax offers first evidence that COVID vaccines protect people against variants. Nature. 2021; 590: 17.
  22. Greaney AJ, Loes AN, Crawford KHD, Starr TN, Malone KD, Chu HY, et al. Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies. Cell Host Microbe. 2021; 29 (3): 463–476.e6.
  23. Wu K, Werner AP, Moliva JI, Koch M, Choi A, et al. mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants. BioRxiv. 2021. 01.25.427948.
  24. Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID's innovative contribution to global health. Global challenges (Hoboken, NJ). 2017; 1: 33–46.
  25. Starr TN, Greaney AJ, Hilton SK, Ellis D, Crawford KHD, Dingens AS. et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell. 2020; 182 (5): 1295–1310.e20.
  26. You Y, Moreira BG, Behlke MA, Owczarzy R. Design of LNA probes that improve mismatch discrimination. Nucleic Acids Res. 2006; 34 (8): e60.
  27. European Centre for Disease Prevention and Control, WHO Regional Office for Europe. Methods for the detection and identification of SARS-CoV-2 variants. 3 March 2021. ECDC and WHO Regional Office for Europe: Stockholm and Copenhagen. 2021.
  28. Van Pelt-Verkuil E, van Belkum A, Hays JP. Principles and Technical Aspects of PCR Amplification. Springer Science & Business Media. 2008; 330 p.
  29. Yuryev A. Methods in Molecular Biology: PCR Primer Design. Humana Press. 2007; 432 p.
  30. Kibbe WA. OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res. 2007. Available from: http:// biotools.nubic.northwestern.edu/OligoCalc.html.
  31. Integrated DNA Technologies. OligoAnalyzer Tool. Available from: https://www.idtdna.com/pages/tools/oligoanalyzer.
  32. The mfold Web Server (Hosted by The RNA Institute, College of Arts and Sciences). Available from: http://unafold.rna.albany.edu/?q=mfold/DNA-Folding-Form.