Вопросы вирусологии. 2020; 65: 126-131
СТАТЬЯ ОТОЗВАНА: Высокопродуктивное секвенирование в диагностике и профилактике инфекции простого герпеса (Herpesviridae, Alphaherpesvirinae, Simplexvirus, Human alphaherpesvirus 1)
https://doi.org/10.36233/0507-4088-2020-65-3-126-131Аннотация
Вирусы простого герпеса (ВПГ) 1-го (ВПГ-1) и 2-го (ВПГ-2) типа относятся к числу наиболее распространённых в человеческой популяции. Клинические проявления простого герпеса широко варьируют, что обусловливает необходимость разработки надёжных молекулярных методов для своевременной диагностики герпесвирусной инфекции, а также для обнаружения мутаций в генах, отвечающих за лекарственную устойчивость. Применение ПЦР часто неспособно идентифицировать изоляты ВПГ с заменами нуклеотидов в участке связывания праймеров. Полногеномное секвенирование по Сэнгеру выявляет мутации в основном на консенсусном уровне, они накапливаются уже на продвинутой стадии вирусной инфекции. Высокопродуктивное секвенирование (секвенирование следующего поколения) имеет явные преимущества как в ранней диагностике герпесвирусной инфекции, так и в идентификации вариантов ВПГ.
Список литературы
1. WHO. Fact sheet. Herpes simplex virus. Available at: https://www.who.int/news-room/fact-sheets/detail/herpes-simplex-virus
2. Looker K.J., Magaret A.S., Turner K.M.E., Vickerman P., Gottlieb S.L., Newman L.M. Global estimates of prevalent and incident herpes simplex virus type 2 infections in 2012. PloS One. 2015; 10(1): el14989. DOI: http://doi.org/10.1371/journal.pone.0114989
3. Corey L., Wald A., Celum C.L., Quinn T.C. The effects of herpes simplex virus-2 on HIV-l acquisition and transmission: a review of two overlapping epidemics. J. Acquir. Immune Defic. Syndr. 2004; 35(5): 435-45. DOI: http://doi.org/10.1097/00126334-200404150-00001
4. Knipe D.M., Howley P. Fields Virology. New York: Lippincott Williams & Wilkins; 2013.
5. Behjati S., Tarpey P.S. What is next generation sequencing? Arch. Dis. Child. Educ. Pract. Ed. 2013; 98(6): 236-8. DOI: http://doi.org/10.1136/archdischild-2013-304340
6. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 2004; 68(4): 669- 85. DOI: http://doi.org/10.1128/MMBR.68.4.669-685.2004
7. Deurenberg R.H., Bathoorn E., Chlebowicz M.A., Couto N., Ferdous M., Garcia-Cobos S., et al. Application of next generation sequencing in clinical microbiology and infection prevention. J. Biotechnol. 2017; 243: 16-24. DOI: http://doi.org/10.1016/j.jbiotec.2016.12.022
8. Buchman T.G., Simpson T., Nosal C., Roizman B., Nahmias A.J. The structure of herpes simplex virus DNA and its application to molecular epidemiology. Ann. NY Acad. Sci. 1980; 354: 279-90. DOI: http://doi.org/10.1111/j.1749-6632.1980.tb27972.x
9. Szpara M.L., Gatherer D., Ochoa A., Greenbaum B., Dolan A., Bowden R.J., et al. Evolution and diversity in human herpes simplex virus genomes. J. Virol. 2014; 88(2): 1209-27. DOI: http://doi.org/10.1128/JVI.01987-13
10. Renzette N., Gibson L., Bhattacharjee В., Fisher D., Schleiss M.R., Jensen J.D., et al. Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection. PLoS Genet. 2013; 9(9): e1003735. DOI: http://doi.org/10.1371/journal.pgen.1003735
11. Sanjuán R., Domingo-Calap P. Mechanisms of viral mutation. Cell. Mol. Life Sci. 2016; 73(23): 4433-48. DOI: http://doi.org/10.1007/s00018-016-2299-6
12. Drake J.W., Hwang C.B.C. On the mutation rate of herpes simplex virus type I. Genetics. 2005; 170(2): 969-70. DOI: http://doi.org/10.1534/genetics.104.040410
13. Szpara M.L., Tafuri Y.R., Parsons L., Shamim S.R., Verstrepen K.J., Legendre M., et al. A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses. PLoS Pathog. 2011; 7(10): 1-23. DOI: http://doi.org/10.1371/journal.ppat.1002282
14. Pandey U., Bell A.S., Renner D.W., Kennedy D.A., Shreve J.T., Cairns C.L., et al. DNA from dust: comparative genomics of large DNA viruses in field surveillance samples. mSphere. 2016; 1(5): e00132-16. DOI: http://doi.org/10.1128/mSphere.00132-16
15. Pandey U., Renner D.W., Thompson R.L., Szpara M.L., Sawtell N.M. Inferred father-to-son transmission of herpes simplex virus results in near-perfect preservation of viral genome identity and in vivo phenotypes. Sci. Rep. 2017; 7(1): 13666. DOI: http://doi.org/10.1038/s41598-017-13936-6
16. Morfin F., Thouvenot D. Herpes simplex virus resistance to antiviral drugs. J. Clin. Virol. 2003; 26(1): 29-37. DOI: http://doi.org/10.1016/s1386-6532(02)00263-9
17. Fujii H., Kakiuchi S., Tsuji M., Nishimura H., Yoshikawa T., Yamada S., et al. Application of next-generation sequencing to detect acyclovir-resistant herpes simplex virus type 1 variants at low frequency in thymidine kinase gene of the isolates recovered from patients with hematopoietic stem cell transplantation. J. Virol. Methods. 2018; 251: 123-8. DOI: http://doi.org/10.1016/j.jviromet.2017.10.019
18. Somasekar S., Lee D., Rule J., Naccache S.N., Stone M., Busch M.P., el al. Viral surveillance in serum samples from patients with acute liver failure by metagenomic next-generation sequencing. Clin. Infect. Dis. 2017; 65(9): 1477-85. DOI: http://doi.org/10.1093/cid/cix596
19. Mercier-Darty M., Boutolleau D., Lepeule R., Rodriguez C., Burrel S. Utility of ultra-deep sequencing for detection of varicella-zoster virus antiviral resistance mutations. Antiviral Res. 2018; 151: 20-3. DOI: http://doi.org/10.1016/j.antiviral.2018.01.008
20. Houldcroft C.J., Bryant J.M., Depledge D.P., Margetts B.K., Simmonds J., Nicolaou S., et al. Detection of low frequency multi-drug resistance and novel putative maribavir resistance in immunocompromised pediatric patients with cytomegalovirus. Front. Microbiol. 2016; 7: 1317. DOI: http://doi.org/10.3389/fmicb.2016.01317
21. Bowden R., Sakaoka H., Donnelly P., Ward R. High recombination rate in herpes simplex virus tyре 1 natural populations suggests significant co-infection. Infect. Genet. Evol. 2004; 4(2): 115-23. DOI: http://doi.org/10.1016/j.meegid.2004.01.009
22. Lee S.W., Markham P.F., Coppo M.J., Legione A.R., Markham J.F., Noormohammadi A.H., et al. Attenuated vaccines can recombine to form virulent field viruses. Science. 2012; 37(6091): 188. DOI: http://doi.org/10.1126/science.1217134
23. Lee K., Kolb A.W., Sverchkov Y., Cuellar J.A., Craven M., Brandt C.R. Recombination analysis of herpes simplex virus 1 reveals a bias toward GC content and the inverted repeat regions. J. Virol. 2015; 89(14): 7214-23. DOI: http://doi.org/10.1128/JVI.00880-15
24. Kolb A.W., Lee K., Larsen I., Craven M., Brandt C.R. Quantitative trait locus based virulence determinant mapping of the HSV-1 genome in murine ocular infection: genes involved in viral regulatory and innate immune networks contribute to virulence. PLoS Pathog. 2016; 12(3): e1005499. DOI: http://doi.org/10.1371/journal.ppat.1005499
25. Koelle D.M., Norberg P., Fitzgibbon M.P., Russell R.M., Greninger A.L., Huang M.L., et al. Worldwide circulation of HSV-2 x HSV- 1 recombinant strains. Sci. Rep. 2017; 7: 44084. DOI: http://doi.org/10.1038/srep44084
26. Javier R.T., Sedarati F., Stevens J.G. Two avirulent herpes simplex viruses generate lethal recombinants in vivo. Science. 1986; 234(4777): 746-8. DOI: http://doi.org/10.1126/science.3022376
27. Lassalle F., Depledge D.P., Reeves M.B., Brown A.C., Christiansen M.T., Tutill H.J., et al. Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes. Virus Evol. 2016; 2(1): vew017. DOI: http://doi.org/10.1093/ve/vew017
28. Kriesel J.D., Bhatia A., Thomas A. Cold sore susceptibility gene-1 genotypes affect the expression of herpes labialis in unrelated human subjects. Hum. Genome Var. 2014; 1: 14024. DOI: http://doi.org/10.1038/hgv.2014.24
29. Thompson R.L., Williams R.W., Kotb M., Sawtell N.M. A forward phenotypically driven unbiased genetic analysis of host genes that moderate herpes simplex virus virulence and stromal keratitis in mice. PLoS One. 2014; 9(3): e92342. DOI: http://doi.org/10.1371/journal.pone.0092342
30. Shipley M.M., Renner D.W., Ott M., Bloom D.C., Koelle D.M., Johnston C., et al Genome-wide surveillance of genital herpes simplex virus type 1 from multiple anatomic over time. J. Infect. Dis. 2018; 218(4): 595-605. DOI: http://doi.org/10.1093/infdis/jiy216
31. Kleinstein S.E., Shea P.R., Allen A.S., Koelle D.M., Wald A., Goldstein D.B. Genome-wide association study (GWAS) of human host factors influencing viral severity of herpes simplex virus type 2 (HSV-2). Genes Immun. 2018; 20(2): 112-20. DOI: http://doi.org/10.1038/s41435-018-0013-4
32. Johnston C., Koelle D.M., Wald A. Current status and prospects for development of an HSV vaccine. Vaccine. 2014; 32(14): 1553-60. DOI: http://doi.org/10.1016/j.vaccine.2013.08.066
33. Newman R.M., Lamers S.L., Weiner B., Ray S.C., Colgrove R.C., Diaz F., et al. Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2. J. Virol. 2015; 89(16): 8219-32. DOI: http://doi.org/10.1128/JVI.01303-15
34. Johnston С., Magaret A., Roychoudhury P., Greninger A.L., Reeves D., Schiffer J., et al. Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: a nested cross-sectional viral genotyping study. PLoS Med. 2017; 14(12): e1002475. DOI: http://doi.org/10.1371/journal.pmed.1002475
35. Anderson T.P., Werno A.M., Beynon K.A., Murdoch D.R. Failure to genotype herpes simplex virus by real-time PCR assay and melting curve analysis due to sequence variation within probe binding sites. J. Clin. Microbiol. 2003; 41(5): 2135-7. DOI: http://doi.org/10.1128/jcm.41.5.2135-2137.2003
36. Wald A., Corey L. Persistence in the population: epidemiology, transmission. In: Arvin A., Campadelli-Fiume G., Mocarski E., Moore P.S., Roizman B., Whitley R., et al. Human Herpesviruses: Biology, Therapy, and Immunoprophylaxis. Cambridge: Cambridge University Press; 2007.
37. Sataoka H., Saheki Y., Uzuki K., Nakakita T., Saito H., Sekine K., et al. Two outbreaks of herpes simplex virus type 1 nosocomial infection among newborns. J. Clin. Microbiol. 1986; 24(1): 36-40.
38. Gutiérrez S., Michalakis Y., Blanc S. Virus population bottlenecks during within-host progression and host-to-host transmission. Curr. Opin. Virol. 2012; 2(5): 546-55. DOI: http://doi.org/10.1016/j.coviro.2012.08.001
39. Nakamura K., Oshima T., Morimoto T., Ikeda S., Yoshikawa H., Shiwa Y., et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. 2011; 39(13): e90. DOI: http://doi.org/10.1093/nar/gkr344
40. Greninger A.L., Roychoudhury P., Xie H., Casto A., Cent A., Pepper G., et al. Ultrasensitive capture of human herpes simplex virus genomes directly from clinical samples reveals extraordinarily limited evolution in cell culture. mSphere. 2018; 3(3): e00283-18. DOI: http://doi.org/10.1128/mSphereDirect.00283-18
41. Guan H., Shen A., Lv X., Yang X., Ren H., Zhao Y., et al. Detection of virus in CSF from the cases with meningoencephalitis by next-generation sequencing. J. Neurovirol. 2016; 22(2): 240-5. DOI: http://doi.org/10.1007/s13365-015-0390-7
42. Naccache S.N., Federman S., Veeeraraghavan N., Zaharia M., Lee D., Samayoa E., et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 2014; 24(7): 1180-92. DOI: http://doi.org/10.1101/gr.171934.113
43. Oliver G.R., Hart S.N., Klee E.W. Bioinformatics for clinical next generation sequencing. Clin. Chem. 2015; 61(1): 124-35. DOI: http://doi.org/10.1373/clinchem.2014.224360
44. Parsons L.R., Tafuri Y.R., Shreve J.T., Bowen C.D., Shipley M.M., Enquist L.W., et al. Rapid genome assembly and comparison decode intrastrain variation in human alphaherpesviruses. mBio. 2015; 6(2): e02213-14. DOI: http://doi.org/10.1128/mBio.02213-14
45. Wan Y., Renner D.W., Albert I., Szpara M.L. VirAmp: a galaxy-based viral genome assembly pipeline. Gigascience. 2015; 4: 19. DOI: http://doi.org/10.1186/s13742-015-0060-y
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Problems of Virology. 2020; 65: 126-131
RETRACTED: High-throughput sequencing in diagnostics and prevention of herpes simplex virus infection (Herpesviridae, Alphaherpesvirinae, Simplexvirus, Human alphaherpesvirus 1)
https://doi.org/10.36233/0507-4088-2020-65-3-126-131Abstract
Herpes simplex viruses types 1 (HSV-1) and 2 (HSV-2) are among the most common viruses in the human population. The clinical manifestations of HSV infection vary widely, which necessitates reliable molecular methods for the timely diagnosis of herpes virus infection, as well as for detection of mutations in the genes responsible for drug resistance. PCR is often unable to detect HSV isolates with nucleotide substitutions at the primer binding site. Sanger sequencing of the whole genome reveals mutations mainly at the consensus level, which accumulate at advanced stages of viral infection. High-throughput sequencing (HTS, next generation sequencing) offers an obvious advantage both in early diagnosis of herpes virus infection and identification of HSV variants.
References
1. WHO. Fact sheet. Herpes simplex virus. Available at: https://www.who.int/news-room/fact-sheets/detail/herpes-simplex-virus
2. Looker K.J., Magaret A.S., Turner K.M.E., Vickerman P., Gottlieb S.L., Newman L.M. Global estimates of prevalent and incident herpes simplex virus type 2 infections in 2012. PloS One. 2015; 10(1): el14989. DOI: http://doi.org/10.1371/journal.pone.0114989
3. Corey L., Wald A., Celum C.L., Quinn T.C. The effects of herpes simplex virus-2 on HIV-l acquisition and transmission: a review of two overlapping epidemics. J. Acquir. Immune Defic. Syndr. 2004; 35(5): 435-45. DOI: http://doi.org/10.1097/00126334-200404150-00001
4. Knipe D.M., Howley P. Fields Virology. New York: Lippincott Williams & Wilkins; 2013.
5. Behjati S., Tarpey P.S. What is next generation sequencing? Arch. Dis. Child. Educ. Pract. Ed. 2013; 98(6): 236-8. DOI: http://doi.org/10.1136/archdischild-2013-304340
6. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 2004; 68(4): 669- 85. DOI: http://doi.org/10.1128/MMBR.68.4.669-685.2004
7. Deurenberg R.H., Bathoorn E., Chlebowicz M.A., Couto N., Ferdous M., Garcia-Cobos S., et al. Application of next generation sequencing in clinical microbiology and infection prevention. J. Biotechnol. 2017; 243: 16-24. DOI: http://doi.org/10.1016/j.jbiotec.2016.12.022
8. Buchman T.G., Simpson T., Nosal C., Roizman B., Nahmias A.J. The structure of herpes simplex virus DNA and its application to molecular epidemiology. Ann. NY Acad. Sci. 1980; 354: 279-90. DOI: http://doi.org/10.1111/j.1749-6632.1980.tb27972.x
9. Szpara M.L., Gatherer D., Ochoa A., Greenbaum B., Dolan A., Bowden R.J., et al. Evolution and diversity in human herpes simplex virus genomes. J. Virol. 2014; 88(2): 1209-27. DOI: http://doi.org/10.1128/JVI.01987-13
10. Renzette N., Gibson L., Bhattacharjee V., Fisher D., Schleiss M.R., Jensen J.D., et al. Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection. PLoS Genet. 2013; 9(9): e1003735. DOI: http://doi.org/10.1371/journal.pgen.1003735
11. Sanjuán R., Domingo-Calap P. Mechanisms of viral mutation. Cell. Mol. Life Sci. 2016; 73(23): 4433-48. DOI: http://doi.org/10.1007/s00018-016-2299-6
12. Drake J.W., Hwang C.B.C. On the mutation rate of herpes simplex virus type I. Genetics. 2005; 170(2): 969-70. DOI: http://doi.org/10.1534/genetics.104.040410
13. Szpara M.L., Tafuri Y.R., Parsons L., Shamim S.R., Verstrepen K.J., Legendre M., et al. A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses. PLoS Pathog. 2011; 7(10): 1-23. DOI: http://doi.org/10.1371/journal.ppat.1002282
14. Pandey U., Bell A.S., Renner D.W., Kennedy D.A., Shreve J.T., Cairns C.L., et al. DNA from dust: comparative genomics of large DNA viruses in field surveillance samples. mSphere. 2016; 1(5): e00132-16. DOI: http://doi.org/10.1128/mSphere.00132-16
15. Pandey U., Renner D.W., Thompson R.L., Szpara M.L., Sawtell N.M. Inferred father-to-son transmission of herpes simplex virus results in near-perfect preservation of viral genome identity and in vivo phenotypes. Sci. Rep. 2017; 7(1): 13666. DOI: http://doi.org/10.1038/s41598-017-13936-6
16. Morfin F., Thouvenot D. Herpes simplex virus resistance to antiviral drugs. J. Clin. Virol. 2003; 26(1): 29-37. DOI: http://doi.org/10.1016/s1386-6532(02)00263-9
17. Fujii H., Kakiuchi S., Tsuji M., Nishimura H., Yoshikawa T., Yamada S., et al. Application of next-generation sequencing to detect acyclovir-resistant herpes simplex virus type 1 variants at low frequency in thymidine kinase gene of the isolates recovered from patients with hematopoietic stem cell transplantation. J. Virol. Methods. 2018; 251: 123-8. DOI: http://doi.org/10.1016/j.jviromet.2017.10.019
18. Somasekar S., Lee D., Rule J., Naccache S.N., Stone M., Busch M.P., el al. Viral surveillance in serum samples from patients with acute liver failure by metagenomic next-generation sequencing. Clin. Infect. Dis. 2017; 65(9): 1477-85. DOI: http://doi.org/10.1093/cid/cix596
19. Mercier-Darty M., Boutolleau D., Lepeule R., Rodriguez C., Burrel S. Utility of ultra-deep sequencing for detection of varicella-zoster virus antiviral resistance mutations. Antiviral Res. 2018; 151: 20-3. DOI: http://doi.org/10.1016/j.antiviral.2018.01.008
20. Houldcroft C.J., Bryant J.M., Depledge D.P., Margetts B.K., Simmonds J., Nicolaou S., et al. Detection of low frequency multi-drug resistance and novel putative maribavir resistance in immunocompromised pediatric patients with cytomegalovirus. Front. Microbiol. 2016; 7: 1317. DOI: http://doi.org/10.3389/fmicb.2016.01317
21. Bowden R., Sakaoka H., Donnelly P., Ward R. High recombination rate in herpes simplex virus tyre 1 natural populations suggests significant co-infection. Infect. Genet. Evol. 2004; 4(2): 115-23. DOI: http://doi.org/10.1016/j.meegid.2004.01.009
22. Lee S.W., Markham P.F., Coppo M.J., Legione A.R., Markham J.F., Noormohammadi A.H., et al. Attenuated vaccines can recombine to form virulent field viruses. Science. 2012; 37(6091): 188. DOI: http://doi.org/10.1126/science.1217134
23. Lee K., Kolb A.W., Sverchkov Y., Cuellar J.A., Craven M., Brandt C.R. Recombination analysis of herpes simplex virus 1 reveals a bias toward GC content and the inverted repeat regions. J. Virol. 2015; 89(14): 7214-23. DOI: http://doi.org/10.1128/JVI.00880-15
24. Kolb A.W., Lee K., Larsen I., Craven M., Brandt C.R. Quantitative trait locus based virulence determinant mapping of the HSV-1 genome in murine ocular infection: genes involved in viral regulatory and innate immune networks contribute to virulence. PLoS Pathog. 2016; 12(3): e1005499. DOI: http://doi.org/10.1371/journal.ppat.1005499
25. Koelle D.M., Norberg P., Fitzgibbon M.P., Russell R.M., Greninger A.L., Huang M.L., et al. Worldwide circulation of HSV-2 x HSV- 1 recombinant strains. Sci. Rep. 2017; 7: 44084. DOI: http://doi.org/10.1038/srep44084
26. Javier R.T., Sedarati F., Stevens J.G. Two avirulent herpes simplex viruses generate lethal recombinants in vivo. Science. 1986; 234(4777): 746-8. DOI: http://doi.org/10.1126/science.3022376
27. Lassalle F., Depledge D.P., Reeves M.B., Brown A.C., Christiansen M.T., Tutill H.J., et al. Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes. Virus Evol. 2016; 2(1): vew017. DOI: http://doi.org/10.1093/ve/vew017
28. Kriesel J.D., Bhatia A., Thomas A. Cold sore susceptibility gene-1 genotypes affect the expression of herpes labialis in unrelated human subjects. Hum. Genome Var. 2014; 1: 14024. DOI: http://doi.org/10.1038/hgv.2014.24
29. Thompson R.L., Williams R.W., Kotb M., Sawtell N.M. A forward phenotypically driven unbiased genetic analysis of host genes that moderate herpes simplex virus virulence and stromal keratitis in mice. PLoS One. 2014; 9(3): e92342. DOI: http://doi.org/10.1371/journal.pone.0092342
30. Shipley M.M., Renner D.W., Ott M., Bloom D.C., Koelle D.M., Johnston C., et al Genome-wide surveillance of genital herpes simplex virus type 1 from multiple anatomic over time. J. Infect. Dis. 2018; 218(4): 595-605. DOI: http://doi.org/10.1093/infdis/jiy216
31. Kleinstein S.E., Shea P.R., Allen A.S., Koelle D.M., Wald A., Goldstein D.B. Genome-wide association study (GWAS) of human host factors influencing viral severity of herpes simplex virus type 2 (HSV-2). Genes Immun. 2018; 20(2): 112-20. DOI: http://doi.org/10.1038/s41435-018-0013-4
32. Johnston C., Koelle D.M., Wald A. Current status and prospects for development of an HSV vaccine. Vaccine. 2014; 32(14): 1553-60. DOI: http://doi.org/10.1016/j.vaccine.2013.08.066
33. Newman R.M., Lamers S.L., Weiner B., Ray S.C., Colgrove R.C., Diaz F., et al. Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2. J. Virol. 2015; 89(16): 8219-32. DOI: http://doi.org/10.1128/JVI.01303-15
34. Johnston S., Magaret A., Roychoudhury P., Greninger A.L., Reeves D., Schiffer J., et al. Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: a nested cross-sectional viral genotyping study. PLoS Med. 2017; 14(12): e1002475. DOI: http://doi.org/10.1371/journal.pmed.1002475
35. Anderson T.P., Werno A.M., Beynon K.A., Murdoch D.R. Failure to genotype herpes simplex virus by real-time PCR assay and melting curve analysis due to sequence variation within probe binding sites. J. Clin. Microbiol. 2003; 41(5): 2135-7. DOI: http://doi.org/10.1128/jcm.41.5.2135-2137.2003
36. Wald A., Corey L. Persistence in the population: epidemiology, transmission. In: Arvin A., Campadelli-Fiume G., Mocarski E., Moore P.S., Roizman B., Whitley R., et al. Human Herpesviruses: Biology, Therapy, and Immunoprophylaxis. Cambridge: Cambridge University Press; 2007.
37. Sataoka H., Saheki Y., Uzuki K., Nakakita T., Saito H., Sekine K., et al. Two outbreaks of herpes simplex virus type 1 nosocomial infection among newborns. J. Clin. Microbiol. 1986; 24(1): 36-40.
38. Gutiérrez S., Michalakis Y., Blanc S. Virus population bottlenecks during within-host progression and host-to-host transmission. Curr. Opin. Virol. 2012; 2(5): 546-55. DOI: http://doi.org/10.1016/j.coviro.2012.08.001
39. Nakamura K., Oshima T., Morimoto T., Ikeda S., Yoshikawa H., Shiwa Y., et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. 2011; 39(13): e90. DOI: http://doi.org/10.1093/nar/gkr344
40. Greninger A.L., Roychoudhury P., Xie H., Casto A., Cent A., Pepper G., et al. Ultrasensitive capture of human herpes simplex virus genomes directly from clinical samples reveals extraordinarily limited evolution in cell culture. mSphere. 2018; 3(3): e00283-18. DOI: http://doi.org/10.1128/mSphereDirect.00283-18
41. Guan H., Shen A., Lv X., Yang X., Ren H., Zhao Y., et al. Detection of virus in CSF from the cases with meningoencephalitis by next-generation sequencing. J. Neurovirol. 2016; 22(2): 240-5. DOI: http://doi.org/10.1007/s13365-015-0390-7
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