Журнал микробиологии, эпидемиологии и иммунобиологии. 2020; 97: 511-517
Генетическая вариабельность SARS-CoV-2 в биологических образцах от пациентов г. Москвы
Сперанская А. С., Каптелова В. В., Самойлов А. Е., Бухарина А. Ю., Шипулина О. Ю., Корнеенко Е. В., Акимкин В. Г.
https://doi.org/10.36233/0372-9311-2020-97-6-1Аннотация
Список литературы
1. Tang X., Wu C., Li X., Song Y., Yao X., Wu X., et al. On the origin and continuing evolution of SARS-CoV-2. Natl. Sci. Rev. 2020; 7(6): 1012–23. https://doi.org/10.1093/nsr/nwaa036
2. Komissarov A.B., Safina K.R., Garushyants S.K., Fadeev A.V., Sergeeva M.V., Ivanova A.A., et al. Genomic epidemiology of the early stages of SARS-CoV-2 outbreak in Russia. medRxiv. Preprint. 2020. https://doi.org/10.1101/2020.07.14.20150979
3. Sýkorová E., Fajkus J., Mezníková M., Lim K.Y., Neplechová K., Blattner F.R., et al. Minisatellite telomeres occur in the family Alliaceae but are lost in Allium. Am. J. Bot. 2006; 93(6): 814–23. https://doi.org/10.3732/ajb.93.6.814
4. Nyayanit D., Yadav P.D., Kharde R., Shete-Aich A. Quasispecies analysis of the SARS-CoV-2 from representative clinical samples: A preliminary analysis. Indian J. Med. Res. 2020; 152(1): 105. https://doi.org/10.4103/ijmr.ijmr_2251_20
5. Jary A., Leducq V., Malet I., Marot S., Klement-Frutos E., Teyssou E., et al. Evolution of viral quasispecies during SARSCoV-2 infection. Clin. Microbiol. Infect. 2020; 26(11): 1560. e1-1560.e4. https://doi.org/10.1016/j.cmi.2020.07.032
6. Chaudhry M.Z., Eschke K., Grashoff M., Abassi L., Kim Y., Brunotte L., et al. SARS-CoV-2 quasispecies mediate rapid virus evolution and adaptation. bioRxiv. Preprint. 2020. https://doi.org/10.1101/2020.08.10.241414
7. Xu D., Zhang Z., Wang F.S. SARS-associated coronavirus quasispecies in individual patients. N. Engl. J. Med. 2004; 350(13): 1366–7. https://doi.org/10.1056/nejmc032421
8. Park D., Huh H.J., Kim Y.J., Son D.S., Jeon H.J., Im E.H., et al. Analysis of intrapatient heterogeneity uncovers the microevolution of Middle East respiratory syndrome coronavirus. Mol. Case Stud. 2016; 2(6): a001214. https://doi.org/10.1101/mcs.a001214
9. Kuipers J., Batavia A.A., Jablonski K.P., Bayer F., Borgsmüller N., Dondi A., et al. Within-patient genetic diversity of SARS-CoV-2. bioRxiv. Preprint. 2020. https://doi.org/10.1101/2020.10.12.335919
10. McElroy K., Zagordi O., Bull R., Luciani F., Beerenwinkel N. Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias. BMC Genomics. 2013; 14(1): 501. https://doi.org/10.1186/1471-2164-14-501
11. Fahnøe U., Pedersen A.G., Dräger C., Orton R.J., Blome S., Höper D., et al. Creation of functional viruses from non-functional cDNA clones obtained from an RNA virus population by the use of ancestral reconstruction. PLoS One. 2015; 10(10): e0140912. https://doi.org/10.1371/journal.pone.0140912
12. Kireev D.E., Lopatukhin A.E., Murzakova A.V., Pimkina E.V., Speranskaya A.S., Neverov A.D., et al. Evaluating the accuracy and sensitivity of detecting minority HIV-1 populations by Illumina next-generation sequencing. J. Virol. Methods. 2018; 261: 40–5. https://doi.org/10.1016/j.jviromet.2018.08.001
13. Лаповок И.А., Лопатухин А.Э., Киреев Д.Е. Двойная ВИЧ-инфекция: эпидемиология, клиническая значимость и диагностика. Инфекционные болезни. 2019; 17(2): 81–7. [Lapovok I.A., Lopatukhin A.E., Kireev D.E. Dual HIV infection: epidemiology, clinical significance, and diagnosis. Infektsionnye bolezni. 2019; 17(2): 81–7. (in Russ.)] https://doi.org/10.20953/1729-9225-2019-2-81-87
14. Falchi A., Arena C., Andreoletti L., Jacques J., Leveque N., Blanchon T., et al. Dual infections by influenza A/H3N2 and B viruses and by influenza A/H3N2 and A/H1N1 viruses during winter 2007, Corsica Island, France. J. Clin. Virol. 2008; 41(2): 148–51. https://doi.org/10.1016/j.jcv.2007.11.003
15. Semple M.G., Cowell A., Dove W., Greensill J., McNamara P.S., Halfhide C., et al. Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis. J. Infect. Dis. 2005; 191(3): 382–6. https://doi.org/10.1086/426457
16. van der Kuyl A.C., Cornelissen M. Identifying HIV-1 dual infections. Retrovirology. 2007; 4: 67. https://doi.org/10.1186/1742-4690-4-67
17. Weinberg A., Bloch K.C., Li S., Tang Y.W., Palmer M., Tyler K.L. Dual infections of the central nervous system with Epstein‐Barr virus. J. Infect. Dis. 2005; 191(2): 234–7. https://doi.org/10.1086/426402
18. Hashim H.O., Mohammed M.K., Mousa M.J., Abdulameer H.H., Alhassnawi A.T., Hassan S.A., et al. Unexpected co-infection with different strains of SARS-CoV-2 in patients with COVID-19. Preprints.org. 2020. Preprint. https://doi.org/10.20944/preprints202009.0375.v1
19. Liu S., Shen J., Fang S., Li K., Liu J., Yang L., et al. Genetic spectrum and distinct evolution patterns of SARS-CoV-2. Front. Microbiol. 2020; 11: 593548. https://doi.org/10.3389/fmicb.2020.593548
20. Gudbjartsson D.F., Helgason A., Jonsson H., Magnusson O.T., Melsted P., Norddahl G.L., et al. Spread of SARS-CoV-2 in the Icelandic population. N. Engl. J. Med. 2020; 382(24): 2302–15. https://doi.org/10.1056/nejmoa2006100
21. Samoilov A., Kaptelova V.V., Bukharina A.Y., Shipulina O.Y., Korneenko E.V., Lukyanov A.V. et al. Change of dominant strain during dual SARS-CoV-2 infection: preprint. medRxiv. Preprint. 2020. https://doi.org/10.1101/2020.11.29.20238402
22. Ilmjärv S., Abdul F., Acosta-Gutiérrez S., Estarellas C., Galdadas I., Casimir M., et al. Epidemiologically most successful SARS-CoV-2 variant: concurrent mutations in RNA-dependent RNA polymerase and spike protein. medRxiv. Preprint. 2020. https://doi.org/10.1101/2020.08.23.20180281
23. Speranskaya A., Kaptelova V., Valdokhina A., Bulanenko V., Samoilov A., Korneenko E., et al. SCV-2000bp: a primer panel for SARS-CoV-2 full-genome sequencing. bioRxiv. Preprint. 2020. https://doi.org/10.1101/2020.08.04.234880
24. Kaptelova V.V., Speranskaya A.S. Protocol for SCV-2000bp: a primer panel for SARS-CoV-2 full-genome sequencing v1. https://dx.doi.org/10.17504/protocols.io.bn77mhrn
25. Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–20. https://doi.org/10.1093/bioinformatics/btu170
26. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011; 17(1): 10. https://doi.org/10.14806/ej.17.1.200
27. Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 2012; 9(4): 357–9. https://doi.org/10.1038/nmeth.1923
28. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16): 2078–9. https://doi.org/10.1093/bioinformatics/btp352
29. Quinlan A.R., Hall I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6): 841–2. https://doi.org/10.1093/bioinformatics/btq033
30. Romano M., Ruggiero A., Squeglia F., Maga G., Berisio R. A structural view of SARS-CoV-2 RNA replication machinery: RNA synthesis, proofreading and final capping. Cells. 2020; 9(5): 1267. https://doi.org/10.3390/cells9051267
31. Zhao Z., Li H., Wu X., Zhong Y., Zhang K., Zhang Y.P., et al. Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol. Biol. 2004; 4: 21. https://doi.org/10.1186/1471-2148-4-21
Journal of microbiology, epidemiology and immunobiology. 2020; 97: 511-517
Genetic variability of SARS-CoV-2 in biological samples from patients in Moscow
Speranskaya A. S., Kaptelova V. V., Samoilov A. E., Bukharina A. Yu., Shipulina O. Yu., Korneenko E. V., Akimkin V. G.
https://doi.org/10.36233/0372-9311-2020-97-6-1Abstract
References
1. Tang X., Wu C., Li X., Song Y., Yao X., Wu X., et al. On the origin and continuing evolution of SARS-CoV-2. Natl. Sci. Rev. 2020; 7(6): 1012–23. https://doi.org/10.1093/nsr/nwaa036
2. Komissarov A.B., Safina K.R., Garushyants S.K., Fadeev A.V., Sergeeva M.V., Ivanova A.A., et al. Genomic epidemiology of the early stages of SARS-CoV-2 outbreak in Russia. medRxiv. Preprint. 2020. https://doi.org/10.1101/2020.07.14.20150979
3. Sýkorová E., Fajkus J., Mezníková M., Lim K.Y., Neplechová K., Blattner F.R., et al. Minisatellite telomeres occur in the family Alliaceae but are lost in Allium. Am. J. Bot. 2006; 93(6): 814–23. https://doi.org/10.3732/ajb.93.6.814
4. Nyayanit D., Yadav P.D., Kharde R., Shete-Aich A. Quasispecies analysis of the SARS-CoV-2 from representative clinical samples: A preliminary analysis. Indian J. Med. Res. 2020; 152(1): 105. https://doi.org/10.4103/ijmr.ijmr_2251_20
5. Jary A., Leducq V., Malet I., Marot S., Klement-Frutos E., Teyssou E., et al. Evolution of viral quasispecies during SARSCoV-2 infection. Clin. Microbiol. Infect. 2020; 26(11): 1560. e1-1560.e4. https://doi.org/10.1016/j.cmi.2020.07.032
6. Chaudhry M.Z., Eschke K., Grashoff M., Abassi L., Kim Y., Brunotte L., et al. SARS-CoV-2 quasispecies mediate rapid virus evolution and adaptation. bioRxiv. Preprint. 2020. https://doi.org/10.1101/2020.08.10.241414
7. Xu D., Zhang Z., Wang F.S. SARS-associated coronavirus quasispecies in individual patients. N. Engl. J. Med. 2004; 350(13): 1366–7. https://doi.org/10.1056/nejmc032421
8. Park D., Huh H.J., Kim Y.J., Son D.S., Jeon H.J., Im E.H., et al. Analysis of intrapatient heterogeneity uncovers the microevolution of Middle East respiratory syndrome coronavirus. Mol. Case Stud. 2016; 2(6): a001214. https://doi.org/10.1101/mcs.a001214
9. Kuipers J., Batavia A.A., Jablonski K.P., Bayer F., Borgsmüller N., Dondi A., et al. Within-patient genetic diversity of SARS-CoV-2. bioRxiv. Preprint. 2020. https://doi.org/10.1101/2020.10.12.335919
10. McElroy K., Zagordi O., Bull R., Luciani F., Beerenwinkel N. Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias. BMC Genomics. 2013; 14(1): 501. https://doi.org/10.1186/1471-2164-14-501
11. Fahnøe U., Pedersen A.G., Dräger C., Orton R.J., Blome S., Höper D., et al. Creation of functional viruses from non-functional cDNA clones obtained from an RNA virus population by the use of ancestral reconstruction. PLoS One. 2015; 10(10): e0140912. https://doi.org/10.1371/journal.pone.0140912
12. Kireev D.E., Lopatukhin A.E., Murzakova A.V., Pimkina E.V., Speranskaya A.S., Neverov A.D., et al. Evaluating the accuracy and sensitivity of detecting minority HIV-1 populations by Illumina next-generation sequencing. J. Virol. Methods. 2018; 261: 40–5. https://doi.org/10.1016/j.jviromet.2018.08.001
13. Lapovok I.A., Lopatukhin A.E., Kireev D.E. Dvoinaya VICh-infektsiya: epidemiologiya, klinicheskaya znachimost' i diagnostika. Infektsionnye bolezni. 2019; 17(2): 81–7. [Lapovok I.A., Lopatukhin A.E., Kireev D.E. Dual HIV infection: epidemiology, clinical significance, and diagnosis. Infektsionnye bolezni. 2019; 17(2): 81–7. (in Russ.)] https://doi.org/10.20953/1729-9225-2019-2-81-87
14. Falchi A., Arena C., Andreoletti L., Jacques J., Leveque N., Blanchon T., et al. Dual infections by influenza A/H3N2 and B viruses and by influenza A/H3N2 and A/H1N1 viruses during winter 2007, Corsica Island, France. J. Clin. Virol. 2008; 41(2): 148–51. https://doi.org/10.1016/j.jcv.2007.11.003
15. Semple M.G., Cowell A., Dove W., Greensill J., McNamara P.S., Halfhide C., et al. Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis. J. Infect. Dis. 2005; 191(3): 382–6. https://doi.org/10.1086/426457
16. van der Kuyl A.C., Cornelissen M. Identifying HIV-1 dual infections. Retrovirology. 2007; 4: 67. https://doi.org/10.1186/1742-4690-4-67
17. Weinberg A., Bloch K.C., Li S., Tang Y.W., Palmer M., Tyler K.L. Dual infections of the central nervous system with Epstein‐Barr virus. J. Infect. Dis. 2005; 191(2): 234–7. https://doi.org/10.1086/426402
18. Hashim H.O., Mohammed M.K., Mousa M.J., Abdulameer H.H., Alhassnawi A.T., Hassan S.A., et al. Unexpected co-infection with different strains of SARS-CoV-2 in patients with COVID-19. Preprints.org. 2020. Preprint. https://doi.org/10.20944/preprints202009.0375.v1
19. Liu S., Shen J., Fang S., Li K., Liu J., Yang L., et al. Genetic spectrum and distinct evolution patterns of SARS-CoV-2. Front. Microbiol. 2020; 11: 593548. https://doi.org/10.3389/fmicb.2020.593548
20. Gudbjartsson D.F., Helgason A., Jonsson H., Magnusson O.T., Melsted P., Norddahl G.L., et al. Spread of SARS-CoV-2 in the Icelandic population. N. Engl. J. Med. 2020; 382(24): 2302–15. https://doi.org/10.1056/nejmoa2006100
21. Samoilov A., Kaptelova V.V., Bukharina A.Y., Shipulina O.Y., Korneenko E.V., Lukyanov A.V. et al. Change of dominant strain during dual SARS-CoV-2 infection: preprint. medRxiv. Preprint. 2020. https://doi.org/10.1101/2020.11.29.20238402
22. Ilmjärv S., Abdul F., Acosta-Gutiérrez S., Estarellas C., Galdadas I., Casimir M., et al. Epidemiologically most successful SARS-CoV-2 variant: concurrent mutations in RNA-dependent RNA polymerase and spike protein. medRxiv. Preprint. 2020. https://doi.org/10.1101/2020.08.23.20180281
23. Speranskaya A., Kaptelova V., Valdokhina A., Bulanenko V., Samoilov A., Korneenko E., et al. SCV-2000bp: a primer panel for SARS-CoV-2 full-genome sequencing. bioRxiv. Preprint. 2020. https://doi.org/10.1101/2020.08.04.234880
24. Kaptelova V.V., Speranskaya A.S. Protocol for SCV-2000bp: a primer panel for SARS-CoV-2 full-genome sequencing v1. https://dx.doi.org/10.17504/protocols.io.bn77mhrn
25. Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–20. https://doi.org/10.1093/bioinformatics/btu170
26. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011; 17(1): 10. https://doi.org/10.14806/ej.17.1.200
27. Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 2012; 9(4): 357–9. https://doi.org/10.1038/nmeth.1923
28. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16): 2078–9. https://doi.org/10.1093/bioinformatics/btp352
29. Quinlan A.R., Hall I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6): 841–2. https://doi.org/10.1093/bioinformatics/btq033
30. Romano M., Ruggiero A., Squeglia F., Maga G., Berisio R. A structural view of SARS-CoV-2 RNA replication machinery: RNA synthesis, proofreading and final capping. Cells. 2020; 9(5): 1267. https://doi.org/10.3390/cells9051267
31. Zhao Z., Li H., Wu X., Zhong Y., Zhang K., Zhang Y.P., et al. Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol. Biol. 2004; 4: 21. https://doi.org/10.1186/1471-2148-4-21
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