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

1. Gottlieb SL, Johnston C. Future prospects for new vaccines against sexually transmitted infections. Curr Opin Infect Dis. 2017;30:77–86. doi: 10.1097/QCO.0000000000000343 27922851

2. Johnston C, Gottlieb SL, Wald A. Status of vaccine research and development of vaccines for herpes simplex virus. Vaccine. 2016;34:2948–52. doi: 10.1016/j.vaccine.2015.12.076 26973067

3. Belshe RB, Heineman TC, Bernstein DI, Bellamy AR, Ewell M, van der Most R, et al. Correlate of immune protection against HSV-1 genital disease in vaccinated women. J Infect Dis. 2014;209:828–36. doi: 10.1093/infdis/jit651 24285844

4. Belshe RB, Leone PA, Bernstein DI, Wald A, Levin MJ, Stapleton JT, et al. Efficacy results of a trial of a herpes simplex vaccine. N Engl J Med. 2012;366:34–43. doi: 10.1056/NEJMoa1103151 22216840

5. Cairns TM, Huang Z-Y, Gallagher JR, Lin Y, Lou H, Whitbeck JC, et al. patient-specific neutralizing antibody responses to herpes simplex virus are attributed to epitopes on gD, gB, or both and can be type specific. J Virol. 2015;89:9213–31. doi: 10.1128/JVI.01213-15 26109729

6. Cairns TM, Huang ZY, Whitbeck JC, Ponce de Leon M, Lou H, Wald A, et al. Dissection of the antibody response against herpes simplex virus glycoproteins in naturally infected humans. J Virol. 2014;88:12612–22. doi: 10.1128/JVI.01930-14 25142599

7. Laing KJ, Magaret AS, Mueller DE, Zhao L, Johnston C, De Rosa SC, et al. Diversity in CD8(+) T cell function and epitope breadth among persons with genital herpes. J Clin Immunol. 2010;30:703–22. doi: 10.1007/s10875-010-9441-2 20635156

8. Jing L, Laing KJ, Dong L, Russell RM, Barlow RS, Haas JG, et al. Extensive CD4 and CD8 T cell cross-reactivity between alphaherpesviruses. J Immunol. 2016;196:2205–18. doi: 10.4049/jimmunol.1502366 26810224

9. Zhu J, Peng T, Johnston C, Phasouk K, Kask AS, Klock A, et al. Immune surveillance by CD8aa+ skin-resident T cells in human herpes virus infection. Nature. 2013;497:494–7. doi: 10.1038/nature12110 23657257

10. Dropulic LK, Garabedian D, Oestreich M, Pietz HL, Wang K, Koelle DM, et al. Phase I study of the safety of a replication-defective herpes simplex virus-2 vaccine, HSV529, in adults with or without HSV infection. 42nd Annual International Herpesvirus Workshop; 2017 Jul 29–Aug 2; Ghent, Belgium.

11. Andtbacka RH, Kaufman HL, Collichio F, Amatruda T, Senzer N, Chesney J, et al. Talimogene laherparepvec improves durable response rate in patients with advanced melanoma. J Clin Oncol. 2015;33:2780–8. doi: 10.1200/JCO.2014.58.3377 26014293

12. Redd AD, Collinson-Streng A, Martens C, Ricklefs S, Mullis CE, Manucci J, et al. Identification of HIV superinfection in seroconcordant couples in Rakai, Uganda, by use of next-generation deep sequencing. J Clin Microbiol. 2011;49:2859–67. doi: 10.1128/JCM.00804-11 21697329

13. Lakeman AD, Nahmias AJ, Whitley RJ. Analysis of DNA from recurrent genital herpes simplex virus isolates by restriction endonuclease digestion. Sex Transm Dis. 1986;13:61–6. 3012807

14. Maitland NJ, Smith IW, Peutherer JF, Robertson DH, Jones KW. Restriction endonuclease analysis of DNA from genital isolates of herpes simplex virus type 2. Infect Immun. 1982;38:834–42. 6295948

15. Sakaoka H, Aomori T, Gouro T, Kumamoto Y. Demonstration of either endogenous recurrence or exogenous reinfection by restriction endonuclease cleavage analysis of herpes simplex virus from patients with recrudescent genital herpes. J Med Virol. 1995;46:387–96. 7595418

16. Roest RW, Maertzdorf J, Kant M, van der Meijden WI, Osterhaus ADME, Verjans GMGM. High incidence of genotypic variance between sequential herpes simplex virus type 2 isolates from HIV-1-seropositive patients with recurrent genital herpes. J Infect Dis. 2006;194:1115–8. doi: 10.1086/507683 16991086

17. Johnston C, Magaret A, Roychoudhury P, Greninger AL, Cheng A, Diem K, et al. Highly conserved intragenic HSV-2 sequences: results from next-generation sequencing of HSV-2 UL and US regions from genital swabs collected from 3 continents. Virology. 2017;510:90–8. doi: 10.1016/j.virol.2017.06.031 28711653

18. Holt KE, Baker S, Dongol S, Basnyat B, Adhikari N, Thorson S, et al. High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children. BMC Infect Dis. 2010;10:144. doi: 10.1186/1471-2334-10-144 20509974

19. Raz N, Danin-Poleg Y, Hayman RB, Bar-On Y, Linetsky A, Shmoish M, et al. Genome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3. PLoS ONE. 2014;9:e114576. doi: 10.1371/journal.pone.0114576 25526263

20. Campino S, Auburn S, Kivinen K, Zongo I, Ouedraogo J-B, Mangano V, et al. population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay. PLoS ONE. 2011;6:e20251. doi: 10.1371/journal.pone.0020251 21673999

21. Looker KJ, Magaret AS, Turner KME, Vickerman P, Gottlieb SL, Newman LM. Global estimates of prevalent and incident herpes simplex virus type 2 infections in 2012. PLoS ONE. 2015;10:e114989. doi: 10.1371/journal.pone.0114989 25608026

22. Patel P, Bush T, Mayer KH, Desai S, Henry K, Overton ET, et al. Prevalence and risk factors associated with herpes simplex virus-2 infection in a contemporary cohort of HIV-infected persons in the United States. Sex Transm Dis. 2012;39:154–60. doi: 10.1097/OLQ.0b013e318239d7fd 22249305

23. Celum C, Wald A, Hughes J, Sanchez J, Reid S, Delany-Moretlwe S, et al. Effect of aciclovir on HIV-1 acquisition in herpes simplex virus 2 seropositive women and men who have sex with men: a randomised, double-blind, placebo-controlled trial. Lancet. 2008;371:2109–19. doi: 10.1016/S0140-6736(08)60920-4 18572080

24. Celum C, Wald A, Lingappa JR, Magaret AS, Wang RS, Mugo N, et al. Acyclovir and transmission of HIV-1 from persons infected with HIV-1 and HSV-2. N Engl J Med. 2010;362:427–39. doi: 10.1056/NEJMoa0904849 20089951

25. Rinaldo A, Bacanu SA, Devlin B, Sonpar V, Wasserman L, Roeder K. Characterization of multilocus linkage disequilibrium. Genet Epidemiol. 2005;28:193–206. doi: 10.1002/gepi.20056 15637716

26. Liu G, Wang Y, Wong L. FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium. BMC Bioinformatics. 2010;11:66. doi: 10.1186/1471-2105-11-66 20113476

27. Jerome KR, Huang ML, Wald A, Selke S, Corey L. Quantitative stability of DNA after extended storage of clinical specimens as determined by real-time PCR. J Clin Microbiol. 2002;40:2609–11. doi: 10.1128/JCM.40.7.2609-2611.2002 12089286

28. LaRue BL, Ge J, King JL, Budowle B. A validation study of the Qiagen Investigator DIPplex® kit; an INDEL-based assay for human identification. Int J Legal Med. 2012;126:533–40. doi: 10.1007/s00414-012-0667-9 22249274

29. Department of Energy Joint Genome Institute. BBDuk guide. Walnut Creek (CA): Department of Energy Joint Genome Institute; 2017.

30. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77. doi: 10.1089/cmb.2012.0021 22506599

31. Angiuoli SV, Salzberg SL. Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics. 2011;27:334–42. doi: 10.1093/bioinformatics/btq665 21148543

32. R Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2017.

33. Wilm A, Aw PPK, Bertrand D, Yeo GHT, Ong SH, Wong CH, et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012;40:11189–201. doi: 10.1093/nar/gks918 23066108

34. Newman RM, Lamers SL, Weiner B, Ray SC, Colgrove RC, Diaz F, et al. Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2. J Virol. 2015;89:8219–32. doi: 10.1128/JVI.01303-15 26018166

35. Kolb AW, Larsen IV, Cuellar JA, Brandt CR. Genomic, Phylogenetic, and recombinational characterization of herpes simplex virus 2 strains. J Virol. 2015;89:6427–34. doi: 10.1128/JVI.00416-15 25855744

36. Petro CD, Weinrick B, Khajoueinejad N, Burn C, Sellers R, Jacobs WR Jr, et al. HSV-2 ΔgD elicits FcγR-effector antibodies that protect against clinical isolates. JCI Insight. 2016;1:e88529. doi: 10.1172/jci.insight.88529 27536733

37. Burrel S, Boutolleau D, Ryu D, Agut H, Merkel K, Leendertz FH, et al. Ancient recombination events between human herpes simplex viruses. Mol Biol Evol. 2017;34:1713–21. doi: 10.1093/molbev/msx113 28369565

38. Minaya MA, Jensen T, Goll J, Korom M, Datla SH, Belshe RB, et al. Molecular evolution of herpes simplex virus 2 complete genomes: comparison between primary and recurrent infections. J Virol. 2017 Nov 14. doi: 10.1128/JVI.00942-17 28931680

39. Koelle DM, Norberg P, Fitzgibbon MP, Russell RM, Greninger AL, Huang M, et al. Worldwide circulation of HSV-2 × HSV-1 recombinant strains. Sci Rep. 2017;7:44084. doi: 10.1038/srep44084 28287142

40. Ross SA, Arora N, Novak Z, Fowler KB, Britt WJ, Boppana SB. Cytomegalovirus reinfections in healthy seroimmune women. J Infect Dis. 2010;201:386–9. doi: 10.1086/649903 20039807

41. Ross SA, Novak Z, Pati S, Patro RK, Blumenthal J, Danthuluri VR, et al. mixed infection and strain diversity in congenital cytomegalovirus infection. J Infect Dis. 2011;204:1003–7. doi: 10.1093/infdis/jir457 21881114

42. Pokalyuk C, Renzette N, Irwin KK, Pfeifer SP, Gibson L, Britt WJ, et al. Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspective. Mol Ecol. 2017;26:1980–90. doi: 10.1111/mec.13953 27988973

43. Renzette N, Pokalyuk C, Gibson L, Bhattacharjee B, Schleiss MR, Hamprecht K, et al. Limits and patterns of cytomegalovirus genomic diversity in humans. Proc Natl Acad Sci U S A. 2015;112:E4120–8. doi: 10.1073/pnas.1501880112 26150505

44. Taha Y, Scott FT, Parker SP, Court DS, Quinlivan ML, Breuer J. Reactivation of 2 genetically distinct varicella-zoster viruses in the same individual. Clin Infect Dis. 2006;43:1301–3. doi: 10.1086/508539 17051496

45. Burrel S, Ait-Arkoub Z, Voujon D, Deback C, Abrao EP, Agut H, et al. Molecular characterization of herpes simplex virus 2 strains by analysis of microsatellite polymorphism. J Clin Microbiol. 2013;51:3616–23. doi: 10.1128/JCM.01714-13 23966512

46. Kolb AW, Ané C, Brandt CR. Using HSV-1 genome phylogenetics to track past human migrations. PLoS ONE. 2013;8:e76267. doi: 10.1371/journal.pone.0076267 24146849