Chapter 16 : Phenotypic and Genotypic Antiviral Susceptibility Testing

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Phenotypic and Genotypic Antiviral Susceptibility Testing, Page 1 of 2

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Where the use of antibiotics goes back to the discovery of penicillin by Alexander Fleming in 1928, application of antiviral treatment was not achieved until the early 1960s with the use of the nucleoside analogue idoxuridine for treatment of herpetic keratitis (1) and methisazone for treatment of smallpox, variola, and cowpox. The first major advances in antiviral treatment were obtained for herpes viruses with the discovery of another nucleoside analogue, acyclovir, by the Burroughs Wellcome Company in the early 1980s. Despite these advances, the real wave of antiviral drug discovery was the result of the HIV epidemic, and started with the development of azidothymidine (AZT) as the first antiretroviral for AIDS patients (2). Nowadays a wide spectrum of antiviral agents are used for a variety of infections. However, similarly to bacteria, development of resistance is an important complication when using antiviral agents. In addition, many viral pathogens have an RNA genome and use RNA polymerases that lack proofread activity for their replication. Therefore, mutations will be introduced into the viral genome in every replication cycle and as a consequence an altered susceptibility or even resistance to an antiviral agent may develop. These resistant variants are easily selected under pressure of an antiviral treatment as shown by the rapid development of resistance when using AZT (3, 4). The viral reverse transcriptase incorporates this thymidine analogue into the viral genome, inhibiting proper replication. Resistant viruses rapidly evolve by acquiring resistance-associated mutations (RAM) in the gene encoding for the enzyme. With HIV being a retrovirus, these mutations are also incorporated in the host DNA and therefore the resistant viral genome is stored in the DNA of the patient and will emerge upon reintroducing the drug.

Citation: van der Beek M, Claas E. 2016. Phenotypic and Genotypic Antiviral Susceptibility Testing, p 201-227. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch16
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Flow chart for diagnosis and treatment in case of failure of antiviral therapy of DNA virus infections in immunocompromised patients. Global approach to diagnosis and treatment in case of persistent DNA virus infections in immunosuppressed patients.Assessment of viral response may include the viral load after treatment and the decrease in viral load in response to the given treatment.In case of severe symptomatic disease.Assessment of immunological recovery may include total and virus-specific T-cell counts and the possibility to decrease the use of immunosuppressive medication. Details may differ per virus ( ).

Citation: van der Beek M, Claas E. 2016. Phenotypic and Genotypic Antiviral Susceptibility Testing, p 201-227. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch16
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1. Davidson SI. 1962. 5-Iodo-2-deoxy-uridine in herpetic keratitis. Lancet 2:13261327.[PubMed]
2. Richman DD, Fischl MA, Grieco MH, Gottlieb MS, Volberding PA, Laskin OL, Leedom JM, Groopman JE, Mildvan D, Hirsch MS, Jackson GG, Durack DT, Nusinoff-Lehrman S. 1987. The toxicity of azidothymidine (AZT) in the treatment of patients with AIDS and AIDS-related complex. A double-blind, placebo-controlled trial. N Engl J Med 317:192197.[PubMed]
3. Larder BA, Darby G, Richman DD. 1989. HIV with reduced sensitivity to zidovudine (AZT) isolated during prolonged therapy. Science 243:17311734.
4. Bach MC. 1989. Failure of zidovudine to maintain remission in patients with AIDS. N Engl J Med 320:594595.[PubMed]
5. Zumla A, Memish ZA, Maeurer M, Bates M, Mwaba P, J Al-Tawfiq A, Denning DW, Hayden FG, Hui DS. 2014. Emerging novel and antimicrobial-resistant respiratory tract infections: new drug development and therapeutic options. Lancet Infect Dis 14:1136–1149.
6. Hilgenfeld R. 2014. From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J 281:40854096[PubMed]
7. Debing Y, Jochmans D, Neyts J. 2013. Intervention strategies for emerging viruses: use of antivirals. Curr OpinVirol. 3:217–224.
8. Reed LJ, Muench H. 1938. A simple method for estimating fifty percent end-points. Am J Hyg 27:493497.
9. van der Beek MT, Claas EC, van der Blij-de Brouwer CS, Morfin F, Rusman LG, Kroes AC, Vossen AC. 2013. Rapid susceptibility testing for herpes simplex virus type 1 using real-time PCR. J Clin Virol 56:1924.[PubMed]
10. Wolters LM, Niesters HG, Hansen BE, van der Ende ME, Kroon FP, Richter C, Brinkman K, Meenhorst PL, de Man RA. 2002. Development of hepatitis B virus resistance for lamivudine in chronic hepatitis B patients co-infected with the human immunodeficiency virus in a Dutch cohort. J ClinVirol 24:173–181.
11. Stuyver L, Wyseur A, Rombout A, Louwagie J, Scarcez T, Verhofstede C, Rimland D, Schinazi RF, Rossau R. 1997. Line probe assay for rapid detection of drug-selected mutations in the human immunodeficiency virus type 1 reverse transcriptase gene. Antimicrob Agents Chemother 41:284291.[PubMed]
12. Liu CM, Driebe EM, Schupp J, Kelley E, Nguyen JT, McSharry JJ, Weng Q, Engelthaler DM, Keim PS. 2010. Rapid quantification of single-nucleotide mutations in mixed influenza A viral populations using allele-specific mixture analysis. J Virol Methods 163:109–115.
13. Lataillade M, Chiarella J, Yang R, Schnittman S, Wirtz V, Uy J, Seekins D, Krystal M, Mancini M, McGrath D, Simen B, Egholm M, Kozal M. 2010. Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study. PLoS One 5:e10952.[PubMed]
14. Dudley DM, Chin EN, Bimber BN, Sanabani SS, Tarosso LF, Costa PR, Sauer MM, Kallas EG, O'Connor DH. 2012. Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance. PLoS One 7:e36494.
15. Weller S, Blum MR, Doucette M, Burnette T, Cederberg DM, de Miranda P, Smiley ML. 1993. Pharmacokinetics of the acyclovir pro-drug valaciclovir after escalating single- and multiple-dose administration to normal volunteers. Clin Pharmacol Ther 54:595605.[PubMed]
16. Glenny AM, Fernandez Mauleffinch LM, Pavitt S, Walsh T. 2009. Interventions for the prevention and treatment of herpes simplex virus in patients being treated for cancer. Cochrane Database Syst Rev (1):CD006706.[PubMed]
17. Brown F, Banken L, Saywell K, Arum I. 1999. Pharmacokinetics of valganciclovir and ganciclovir following multiple oral dosages of valganciclovir in HIV- and CMV-seropositive volunteers. Clin Pharmacokinet 37:167176.[PubMed]
18. Hodson EM, Barclay PG, Craig JC, Jones C, Kable K, Strippoli GF, Vimalachandra D, Webster AC. 2005. Antiviral medications for preventing cytomegalovirus disease in solid organ transplant recipients. Cochrane Database Syst Rev (4):CD003774.[PubMed]
19. Matthews T, Boehme R. 1988. Antiviral activity and mechanism of action of ganciclovir. Rev Infect Dis 10(Suppl 3):S490S494.[PubMed]
20. Strippoli GF, Hodson EM, Jones CJ, Craig JC. 2006. Pre-emptive treatment for cytomegalovirus viraemia to prevent cytomegalovirus disease in solid organ transplant recipients. Cochrane Database Syst Rev (1):CD005133.[PubMed]
21. Zhang LF, Wang YT, Tian JH, Yang KH, Wang JQ. 2011. Preemptive versus prophylactic protocol to prevent cytomegalovirus infection after renal transplantation: a meta-analysis and systematic review of randomized controlled trials. Transpl Infect Dis 13:622632.
22. Winston DJ, Saliba F, Blumberg E, Abouljoud M, Garcia-Diaz JB, Goss JA, Clough L, Avery R, Limaye AP, Ericzon BG, Navasa M, Troisi RI, Chen H, Villano SA, Uknis ME 1263–301 Clinical Study Group. 2012. Efficacy and safety of maribavir dosed at 100 mg orally twice daily for the prevention of cytomegalovirus disease in liver transplant recipients: a randomized, double-blind, multicenter controlled trial. Am J Transplant 12:30213030.
23. Marty, FM, Ljungman P, Papanicolaou GA, Winston DJ, Chemaly RF, Strasfeld L, Young JA, Rodriguez T, Maertens J, Schmitt M, Einsele H, Ferrant A, Lipton JH, Villano SA, Chen H, Boeckh M. 2011. Maribavir prophylaxis for prevention of cytomegalovirus disease in recipients of allogeneic stem-cell transplants: a phase 3, double-blind, placebo-controlled, randomised trial. Lancet Infect Dis 11:284–292.
24. Winston DJ, Young JA, Pullarkat V, Papanicolaou GA, Vij R, Vance E, Alangaden GJ, Chemaly RF, Petersen F, Chao N, Klein J, Sprague K, Villano SA, Boeckh M. 2008. Maribavir prophylaxis for prevention of cytomegalovirus infection in allogeneic stem cell transplant recipients: a multicenter, randomized, double-blind, placebo-controlled, dose-ranging study. Blood 111:5403–5410.
25. Marty FM, Boeckh M. 2011. Maribavir and human cytomegalovirus-what happened in the clinical trials and why might the drug have failed? Curr OpinVirol 1:555–562.
26. Cole NL, Balfour HH Jr. 1986. Varicella-Zoster virus does not become more resistant to acyclovir during therapy. J Infect Dis 153:605608.[PubMed]
27. Danve-Szatanek C, Aymard M, Thouvenot D, Morfin F, Agius G, Bertin I, Billaudel S, Chanzy B, Coste-Burel M, Finkielsztejn L, Fleury H, Hadou T, Henquell C, Lafeuille H, Lafon ME, Le Faou A, Legrand MC, Maille L, Mengelle C, Morand P, Morinet F, Nicand E, Omar S, Picard B, Pozzetto B, Puel J, Raoult D, Scieux C, Segondy M, Seigneurin JM, Teyssou R, Zandotti C. 2004. Surveillance network for herpes simplex virus resistance to antiviral drugs: 3-year follow-up. J Clin Microbiol 42:242249.[PubMed]
28. Ozaki T, Nishimura N, Kajita Y, Ida M, Shiraki K. 1998. Susceptibilities to aciclovir in viral isolates from children with varicella. Arch Dis Child 78:95.[PubMed]
29. Stránská R, Schuurman R, Nienhuis E, Goedegebuure IW, Polman M, Weel JF, Wertheim-Van Dillen PM, Berkhout RJ, van Loon AM. 2005. Survey of acyclovir-resistant herpes simplex virus in the Netherlands: prevalence and characterization. J Clin Virol 32:718.[PubMed]
30. Piret J, Boivin G. 2011. Resistance of herpes simplex viruses to nucleoside analogues: mechanisms, prevalence, and management. Antimicrob Agents Chemother 55:459472.[PubMed]
31. van der Beek MT. 2012. Doctoral thesis. Herpesvirus infections in immunocompromised patients: treatment, treatment failure and antiviral resistance, Leiden University. ISBN/EAN: 978-90-9026850-7
32. Clinical and Laboratory Standards Institute. Antiviral Susceptibility Testing: Herpes Simplex Virus by Plaque Reduction Assay; Approved Standard M33-A. 2004. CLSI, Wayne, PA.
33. Chou S, Waldemer RH, Senters AE, Michels KS, Kemble GW, Miner RC, Drew WL. 2002. Cytomegalovirus UL97 phosphotransferase mutations that affect susceptibility to ganciclovir. J Infect Dis 185:162169.[PubMed]
34. Erice A, Gil-Roda C, Pérez JL, Balfour HH Jr, Sannerud KJ, Hanson MN, Boivin G, Chou S. 1997. Antiviral susceptibilities and analysis of UL97 and DNA polymerase sequences of clinical cytomegalovirus isolates from immunocompromised patients. J Infect Dis 175:10871092.[PubMed]
35. Jabs, DA, Martin BK, Forman MS, Dunn JP, Davis JL, Weinberg DV, Biron KK, Baldanti F. 2001. Mutations conferring ganciclovir resistance in a cohort of patients with acquired immunodeficiency syndrome and cytomegalovirus retinitis. J Infect Dis 183:333–337.
36. Lurain NS, Bhorade SM, Pursell KJ, Avery RK, Yeldandi VV, Isada CM, Robert ES, Kohn DJ, Arens MQ, Garrity ER, Taege AJ, Mullen MG, Todd KM, Bremer JW, Yen-Lieberman B. 2002. Analysis and characterization of antiviral drug-resistant cytomegalovirus isolates from solid organ transplant recipients. J Infect Dis 186:760768.[PubMed]
37. Myhre HA, Haug Dorenberg D, Kristiansen KI, Rollag H, Leivestad T, Asberg A, Hartmann A. 2011. Incidence and outcomes of ganciclovir-resistant cytomegalovirus infections in 1244 kidney transplant recipients. Transplantation 92:217223.[PubMed]
38. Smith IL, Cherrington JM, Jiles RE, Fuller MD, Freeman WR, Spector SA. 1997. High-level resistance of cytomegalovirus to ganciclovir is associated with alterations in both the UL97 and DNA polymerase genes. J Infect Dis 176:6977.[PubMed]
39. Göhring K, Mikeler E, Jahn G, Rohde F, Hamprecht K. 2008. Rapid semiquantitative real-time PCR for the detection of human cytomegalovirus UL97 mutations conferring ganciclovir resistance. Antivir Ther 13:461466.[PubMed]
40. Liu JB, Zhang Z. 2008. Development of SYBR Green I-based real-time PCR assay for detection of drug resistance mutations in cytomegalovirus. J Virol Methods 149:129135.[PubMed]
41. Yeo AC, Chan KP, Kumarasinghe G, Yap HK. 2005. Rapid detection of codon 460 mutations in the UL97 gene of ganciclovir-resistant cytomegalovirus clinical isolates by real-time PCR using molecular beacons. Mol Cell Probes 19:389393.[PubMed]
42. Posthuma CC, van der Beek MT, van der Blij-de Brouwer CS, van der Heiden PL, Marijt EW, Spaan WJ, Claas EC, Nederstigt C, Vossen AC, Snijder EJ, Kroes AC. 2011. Mass spectrometry-based comparative sequencing to detect ganciclovir resistance in the UL97 gene of human cytomegalovirus. J Clin Virol 51:2530.[PubMed]
43. Görzer I, Guelly C, Trajanoski S, Puchhammer-Stöckl E. 2010. Deep sequencing reveals highly complex dynamics of human cytomegalovirus genotypes in transplant patients over time. J Virol 84:71957203.[PubMed]
44. Burrel S, Deback C, Agut H, Boutolleau D. 2010. Genotypic characterization of UL23 thymidine kinase and UL30 DNA polymerase of clinical isolates of herpes simplex virus: natural polymorphism and mutations associated with resistance to antivirals. Antimicrob Agents Chemother 54:48334842.[PubMed]
45. Chibo D, Druce J, Sasadeusz J, Birch C. 2004. Molecular analysis of clinical isolates of acyclovir resistant herpes simplex virus. Antiviral Res 61:8391.[PubMed]
46. Andrei G, Snoeck R, De Clercq E, Esnouf R, Fiten P, Opdenakker G. 2000. Resistance of herpes simplex virus type 1 against different phosphonylmethoxyalkyl derivatives of purines and pyrimidines due to specific mutations in the viral DNA polymerase gene. J Gen Virol 81:639648.[PubMed]
47. Andrei G, Balzarini J, Fiten P, De Clercq E, Opdenakker G, Snoeck R. 2005. Characterization of herpes simplex virus type 1 thymidine kinase mutants selected under a single round of high-dose brivudin. J Virol 79:58635869.[PubMed]
48. Andrei G, Fiten P, Goubau P, van Landuyt H, Gordts B, Selleslag D, De Clercq E, Opdenakker G, Snoeck R. 2007. Dual infection with polyomavirus BK and acyclovir-resistant herpes simplex virus successfully treated with cidofovir in a bone marrow transplant recipient. Transpl Infect Dis 9:126131.[PubMed]
49. Andrei G, Snoeck R. 2013. Herpes simplex virus drug-resistance: new mutations and insights. Curr Opin Infect Dis 26:551560.[PubMed]
50. Bestman-Smith J, Schmit I, Papadopoulou B, Boivin G. 2001. Highly reliable heterologous system for evaluating resistance of clinical herpes simplex virus isolates to nucleoside analogues. J Virol 75:31053110.[PubMed]
51. Bestman-Smith J, Boivin G. 2003. Drug resistance patterns of recombinant herpes simplex virus DNA polymerase mutants generated with a set of overlapping cosmids and plasmids. J Virol 77:78207829.[PubMed]
52. Bohn K, Zell R, Schacke M, Wutzler P, Sauerbrei A. 2011. Gene polymorphism of thymidine kinase and DNA polymerase in clinical strains of herpes simplex virus. Antivir Ther 16:989997.[PubMed]
53. Burrel S, Bonnafous P, Hubacek P, Agut H, Boutolleau D. 2012. Impact of novel mutations of herpes simplex virus 1 and 2 thymidine kinases on acyclovir phosphorylation activity. Antiviral Res 96:386–390.
54. Burrel S, Boutolleau D, Azar G,, Doan S,, Deback C, Cochereau I, Agut H, Gabison EE. 2013. Phenotypic and genotypic characterization of acyclovir-resistant corneal HSV-1 isolates from immunocompetent patients with recurrent herpetic keratitis. J Clin Virol 58:321–324.
55. Burrel S, Aime C, Hermet L, Ait-Arkoub Z, Agut H, Boutolleau D. 2013. Surveillance of herpes simplex virus resistance to antivirals: a 4-year survey. Antiviral Res 100:365–372.
56. Duan R, de Vries RD, Osterhaus AD, Remeijer L, Verjans GM. 2008. Acyclovir-resistant corneal HSV-1 isolates from patients with herpetic keratitis. J Infect Dis 198:659663.[PubMed]
57. Duan R, de Vries RD, van Dun JM, van Loenen FB, Osterhaus AD, Remeijer L, Verjans GM. 2009. Acyclovir susceptibility and genetic characteristics of sequential herpes simplex virus type 1 corneal isolates from patients with recurrent herpetic keratitis. J Infect Dis 200:14021414.[PubMed]
58. Frobert E, Ooka T, Cortay JC, Lina B, Thouvenot D, Morfin F. 2005. Herpes simplex virus thymidine kinase mutations associated with resistance to acyclovir: a site-directed mutagenesis study. Antimicrob Agents Chemother 49:10551059.[PubMed]
59. Frobert E, Ooka T, Cortay JC, Lina B, Thouvenot D, Morfin F. 2007. Resistance of herpes simplex virus type 1 to acyclovir: thymidine kinase gene mutagenesis study. Antiviral Res 73:147150.[PubMed]
60. Frobert E, Cortay JC, Ooka T, Najioullah F, Thouvenot D, Lina B, Morfin F. 2008. Genotypic detection of acyclovir-resistant HSV-1: characterization of 67 ACV-sensitive and 14 ACV-resistant viruses. Antiviral Res 79:2836.[PubMed]
61. Gaudreau A, Hill E, Balfour HH Jr, Erice A, Boivin G. 1998. Phenotypic and genotypic characterization of acyclovir-resistant herpes simplex viruses from immunocompromised patients. J Infect Dis 178:297303.[PubMed]
62. Gibbs JS, Chiou HC, Bastow KF, Cheng YC, Coen DM. 1988. Identification of amino acids in herpes simplex virus DNA polymerase involved in substrate and drug recognition. Proc Natl Acad Sci USA 85:66726676.[PubMed]
63. Harris W, Collins P, Fenton RJ, Snowden W, Sowa M, Darby G. 2003. Phenotypic and genotypic characterization of clinical isolates of herpes simplex virus resistant to aciclovir. J Gen Virol 84:13931401.[PubMed]
64. Horsburgh BC, Chen SH, Hu A, Mulamba GB, Burns WH, Coen DM. 1998. Recurrent acyclovir-resistant herpes simplex in an immunocompromised patient: can strain differences compensate for loss of thymidine kinase in pathogenesis? J Infect Dis 178:618625.[PubMed]
65. Hwang YT, Smith JF, Gao L,, and Hwang CB. 1998. Mutations in the Exo III motif of the herpes simplex virus DNA polymerase gene can confer altered drug sensitivities. Virology 246:298–305.
66. Kakiuchi S, Nonoyama S, Wakamatsu H, Kogawa K, Wang L, Kinoshita-Yamaguchi H, Takayama-Ito M, Lim CK, Inoue N, Mizuguchi M, Igarashi T,, and Saijo M. 2013. Neonatal herpes encephalitis caused by a virologically confirmed acyclovir-resistant herpes simplex virus 1 strain. J Clin Microbiol 51:356–359.
67. Knopf CW. 1987. The herpes simplex virus type 1 DNA polymerase gene: site of phosphonoacetic acid resistance mutation in strain Angelotti is highly conserved. J Gen Virol 68:14291433.[PubMed]
68. Kudo E, Shiota H, Naito T, Satake K, Itakura M. 1998. Polymorphisms of thymidine kinase gene in herpes simplex virus type 1: analysis of clinical isolates from herpetic keratitis patients and laboratory strains. J Med Virol 56:151158.[PubMed]
69. Kussmann-Gerber S, Kuonen O, Folkers G, Pilger BD, Scapozza L. 1998. Drug resistance of herpes simplex virus type 1—structural considerations at the molecular level of the thymidine kinase. Eur J Biochem 255:472481.[PubMed]
70. Larder BA, Kemp SD, Darby G. 1987. Related functional domains in virus DNA polymerases. EMBO J 6:169175.[PubMed]
71. Malartre N, Boulieu R, Falah N, Cortay JC, Lina B, Morfin F, Frobert E. 2012. Effects of mutations on herpes simplex virus 1 thymidine kinase functionality: an in vitro assay based on detection of monophosphate forms of acyclovir and thymidine using HPLC/DAD. Antiviral Res 95:224228.
72. Morfin F, Souillet G, Bilger K, Ooka T, Aymard M, Thouvenot D. 2000. Genetic characterization of thymidine kinase from acyclovir-resistant and -susceptible herpes simplex virus type 1 isolated from bone marrow transplant recipients. J Infect Dis 182:290293.[PubMed]
73. Pan D, Kaye SB, Hopkins M, Kirwan R, Hart IJ, Coen DM. 2014. Common and new acyclovir resistant herpes simplex virus-1 mutants causing bilateral recurrent herpetic keratitis in an immunocompetent patient. J Infect Dis 209:345–349.
74. Saijo M, Suzutani T, De Clercq E, Niikura M, Maeda A, Morikawa S, Kurane I. 2002. Genotypic and phenotypic characterization of the thymidine kinase of ACV-resistant HSV-1 derived from an acyclovir-sensitive herpes simplex virus type 1 strain. Antiviral Res 56:253262.[PubMed]
75. Saijo M, Suzutani T, Morikawa S, Kurane I. 2005. Genotypic characterization of the DNA polymerase and sensitivity to antiviral compounds of foscarnet-resistant herpes simplex virus type 1 (HSV-1) derived from a foscarnet-sensitive HSV-1 strain. Antimicrob Agents Chemother 49:606611.[PubMed]
76. Sauerbrei A, Deinhardt S, Zell R, Wutzler P. 2010. Phenotypic and genotypic characterization of acyclovir-resistant clinical isolates of herpes simplex virus. Antiviral Res 86:246252.[PubMed]
77. Sauerbrei A, Bohn K, Heim A, Hofmann J, Weissbrich B, Schnitzler P, Hoffmann D, Zell R, Jahn G, Wutzler P, Hamprecht K. 2011. Novel resistance-associated mutations of thymidine kinase and DNA polymerase genes of herpes simplex virus type 1 and type 2. Antivir Ther 16:12971308.[PubMed]
78. Sauerbrei A, Liermann K, Bohn K, Henke A, Zell R, Gronowitz S, Wutzler P. 2012. Significance of amino acid substitutions in the thymidine kinase gene of herpes simplex virus type 1 for resistance. Antiviral Res 96:105–107.
79. Schmit I, Boivin G. 1999. Characterization of the DNA polymerase and thymidine kinase genesof herpes simplex virus isolates from AIDS patients in whom acyclovirand foscarnet therapy sequentially failed. J Infect Dis 180:487490.[PubMed]
80. Sergerie Y, Boivin G. 2008. Hydroxyurea enhances the activity of acyclovir and cidofovir against herpes simplex virus type 1 resistant strains harboring mutations in the thymidine kinase and/or the DNA polymerase genes. Antiviral Res 77:77–80.
81. Stránská R, van Loon AM, Polman M, Beersma MF, Bredius RG, Lankester AC, Meijer E, Schuurman R. 2004. Genotypic and phenotypic characterization of acyclovir-resistant herpes simplex viruses isolated from haematopoietic stem cell transplant recipients. Antivir Ther 9:565575.[PubMed]
82. Suzutani T, Saijo M, Nagamine M, Ogasawara M, Azuma M. 2000. Rapid phenotypic characterization method for herpes simplex virus and Varicella-Zoster virus thymidine kinases to screen for acyclovir-resistant viral infection. J Clin Microbiol 38:18391844.[PubMed]
83. Suzutani T, Ishioka K, De Clercq E, Ishibashi K, Kaneko H, Kira T, Hashimoto K, Ogasawara M, Ohtani K, Wakamiya N, Saijo M. 2003. Differential mutation patterns in thymidine kinase and DNA polymerase genes of herpes simplex virus type 1 clones passaged in the presence of acyclovir or penciclovir. Antimicrob Agents Chemother 47:17071713.[PubMed]
84. van Velzen M, van Loenen FB, Meesters RJ, de Graaf M, Remeijer L, Luider TM, Osterhaus AD, Verjans GM. 2012. Latent acyclovir-resistant herpes simplex virus type 1 in trigeminal ganglia of immunocompetent individuals. J Infect Dis 205:1539–1543.
85. van Velzen M, van Loenen FB, Meesters RJ, de Graaf M, Remeijer L, Luider TM, Osterhaus AD, Verjans GM. 2013. Acyclovir-resistant herpes simplex virus type 1 in intra-ocular fluid samples of herpetic uveitis patients. J Clin Virol 57:215–221.
86. Wang LX, Takayama-Ito M, Kinoshita-Yamaguchi H, Kakiuchi S, Suzutani T, Nakamichi K, Lim CK, Kurane I, Saijo M. 2013. Characterization of DNA polymerase-associated acyclovir-resistant herpes simplex virus type 1: mutations, sensitivity to antiviral compounds, neurovirulence, and in-vivo sensitivity to treatment. Jpn J Infect Dis 66:404–410.
87. Wang Y, Wang Q, Zhu Q, Zhou R, Liu J, Peng T. 2011. Identification and characterization of acyclovir-resistant clinical HSV-1 isolates from children. J Clin Virol 52:107–112.
88. Danve C, Morfin F, Thouvenot D, Aymard M. 2002. A screening dye-uptake assay to evaluate in vitro susceptibility of herpes simplex virus isolates to acyclovir. J Virol Methods 105:207–217.
89. Stránská R, Schuurman R, Scholl DR, Jollick JA, Shaw CJ, Loef C, Polman M, van Loon AM. 2004. ELVIRA HSV, a yield reduction assay for rapid herpes simplex virus susceptibility testing. Antimicrob Agents Chemother 48:23312333.[PubMed]
90. Tardif KD, Jorgensen S, Langer J, Prichard M, Schlaber RG. 2014. Simultaneous titration and phenotypic antiviral drug susceptibility testing for herpes simplex virus 1 and 2. J Clin Virol 61:382386.
91. Stránská R, van Loon AM, Polman M, Schuurman R. 2002. Application of real-time PCR for determination of antiviral drug susceptibility of herpes simplex virus. Antimicrob Agents Chemother 46:29432947.[PubMed]
92. Thi TN, Deback C, Malet I, Bonnafous P, Ait-Arkoub Z, Agut H. 2006. Rapid determination of antiviral drug susceptibility of herpes simplex virus types 1 and 2 by real-time PCR. Antiviral Res 69:152157.[PubMed]
93. Brink AA, van Gelder M, Wolffs PF, Bruggeman CA, van Loo IH. 2011. Compartmentalization of acyclovir-resistant varicella zoster virus: implications for sampling in molecular diagnostics. Clin Infect Dis 52:982–987.
94. Hatchette T, Tipples GA, Peters G, Alsuwaidi A, Zhou J, Mailman TL. 2008. Foscarnet salvage therapy for acyclovir-resistant varicella zoster: report of a novel thymidine kinase mutation and review of the literature. Pediatr Infect Dis J 27:7577.[PubMed]
95. Morfin F, Frobert E, Thouvenot D. 2003. [Contribution of the laboratory in case of resistance to acyclovir of herpes simplex and varicella zoster virus]. Ann Biol Clin (Paris) 61:3340.[PubMed]
96. Sahli R, Andrei G, Estrade C, Snoeck R, Meylan PR. 2000. A rapid phenotypic assay for detection of acyclovir-resistant varicella-zoster virus with mutations in the thymidine kinase open reading frame. Antimicrob Agents Chemother 44:873878.[PubMed]
97. Saint-Léger E, Caumes E, Breton G, Douard D, Saiag P, Huraux JM, Bricaire F, Agut H, Fillet AM. 2001. Clinical and virologic characterization of acyclovir-resistant varicella-zoster viruses isolated from 11 patients with acquired immunodeficiency syndrome. Clin Infect Dis 33:20612067.[PubMed]
98. Sauerbrei A, Taut J, Zell R, Wutzler P. 2011. Resistance testing of clinical varicella-zoster virus strains. Antiviral Res. 90:242–247.
99. van der Beek MT, Vermont CL, Bredius RG, Marijt EW, van der Blij-de Brouwer CS, Kroes AC, Claas EC, Vossen AC. 2013. Persistence and antiviral resistance of varicella zoster virus in hematological patients. Clin Infect Dis 56:335343.[PubMed]
100. Andrei G, Topalis D, Fiten P, McGuigan C, Balzarini J, Opdenakker G, Snoeck R. 2012. In vitro-selected drug-resistant varicella-zoster virus mutants in the thymidine kinase and DNA polymerase genes yield novel phenotype-genotype associations and highlight differences between antiherpesvirus drugs. J Virol 86:26412652.[PubMed]
101. Boivin G, Edelman CK, Pedneault L, Talarico CL, Biron KK, Balfour HH Jr. 1994. Phenotypic and genotypic characterization of acyclovir-resistant varicella-zoster viruses isolated from persons with AIDS. J Infect Dis 170:6875.[PubMed]
102. Bryan CJ, Prichard MN, Daily S, Jefferson G, Hartline C, Cassady KA, Hilliard L, Shimamura M. 2008. Acyclovir-resistant chronic verrucous vaccine strain varicella in a patient with neuroblastoma. Pediatr Infect Dis J 27:946948.[PubMed]
103. Fillet AM, Dumont B, Caumes E, Visse B, Agut H, Bricaire F, Huraux JM. 1998. Acyclovir-resistant varicella-zoster virus: phenotypic and genetic characterization. J Med Virol 55:250254.[PubMed]
104. Ida M, Kageyama S, Sato H, Kamiyama T, Yamamura J, Kurokawa M, Morohashi M, Shiraki K. 1999. Emergence of resistance to acyclovir and penciclovir in varicella-zoster virus and genetic analysis of acyclovir-resistant variants. Antiviral Res 40:155166.[PubMed]
105. Kamiyama T, Kurokawa M, Shiraki K. 2001. Characterization of the DNA polymerase gene of varicella-zoster viruses resistant to acyclovir. J Gen Virol 82:27612765.[PubMed]
106. Kodama E, Mori S, Shigeta S. 1995. Analysis of mutations in the thymidine kinase gene of varicella zoster virus associated with resistance to 5-iodo-2′-deoxyuridine and 5-bromo-2′-deoxyuridine. Antiviral Res 27:165170.[PubMed]
107. Levin MJ, Dahl KM, Weinberg A, Giller R, Patel A, Krause PR. 2003. Development of resistance to acyclovir during chronic infection with the Oka vaccine strain of varicella-zoster virus, in an immunosuppressed child. J Infect Dis 188:954959.[PubMed]
108. Morfin F, Thouvenot D, De Turenne-Tessier M, Lina B, Aymard M, Ooka T. 1999. Phenotypic and genetic characterization of thymidine kinase from clinical strains of varicella-zoster virus resistant to acyclovir. Antimicrob Agents Chemother 43:24122416.[PubMed]
109. Ng TI, Shi Y, Huffaker HJ, Kati W, Liu Y, Chen CM, Lin Z, Maring C, Kohlbrenner WE, Molla A. 2001. Selection and characterization of varicella-zoster virus variants resistant to (R)-9-[4-hydroxy-2-(hydroxymethy)butyl]guanine. Antimicrob Agents Chemother 45:16291636.[PubMed]
110. Roberts GB, Fyfe JA, Gaillard RK, Short SA. 1991. Mutant varicella-zoster virus thymidine kinase: correlation of clinical resistance and enzyme impairment. J Virol 65:64076413.[PubMed]
111. Sawyer MH, Inchauspe G, Biron KK, Waters DJ, Straus SE, Ostrove JM. 1988. Molecular analysis of the pyrimidine deoxyribonucleoside kinase gene of wild-type and acyclovir-resistant strains of varicella-zoster virus. J Gen Virol 69:25852593.[PubMed]
112. Suzutani T, Saijo M, Nagamine M, Ogasawara M, Azuma M. 2000. Rapid phenotypic characterization method for herpes simplex virus and Varicella-Zoster virus thymidine kinases to screen for acyclovir-resistant viral infection. J Clin Microbiol 38:18391844.[PubMed]
113. Talarico CL, Phelps WC, Biron KK. 1993. Analysis of the thymidine kinase genes from acyclovir-resistant mutants of varicella-zoster virus isolated from patients with AIDS. J Virol 67:10241033.[PubMed]
114. Visse B, Dumont B, Huraux JM, Fillet AM. 1998. Single amino acid change in DNA polymerase is associated with foscarnet resistance in a varicella-zoster virus strain recovered from a patient with AIDS. J Infect Dis 178(Suppl 1):S55S57.[PubMed]
115. Arvia R, Corcioli F, Azzi A. 2013. High resolution melting analysis as a tool to detect molecular markers of antiviral resistance in influenza A viruses. J Virol Methods 189:265–270.
116. Boivin G. 2013. Detection and management of antiviral resistance for influenza viruses. Influenza Other Respi Viruses 7(Suppl 3):1823.[PubMed]
117. Gubareva LV, Trujillo AA, Okomo-Adhiambo M, Mishin VP, Deyde VM, Sleeman K, Nguyen HT, Sheu TG, Garten RJ, Shaw MW, Fry AM, Klimov AI. 2010. Comprehensive assessment of 2009 pandemic influenza A (H1N1) virus drug susceptibility in vitro. Antivir Ther 15:11511159.[PubMed]
118. Okomo-Adhiambo M, Sheu TG, Gubareva LV. 2013. Assays for monitoring susceptibility of influenza viruses to neuraminidase inhibitors. Influenza Other Respi Viruses 7(Suppl 1):4449.[PubMed]
119. Hurt AC. 2014. The epidemiology and spread of drug resistant human influenza viruses. Curr Opin Virol 8:22–29.
120. Gooskens J, Jonges M, Claas EC, Meijer A, Kroes AC. 2009. Prolonged influenza virus infection during lymphocytopenia and frequent detection of drug-resistant viruses. J Infect Dis 199:14351441.[PubMed]
121. Okomo-Adhiambo M, Hurt AC, Gubareva LV. 2012. The chemiluminescent neuraminidase inhibition assay: a functional method for detection of influenza virus resistance to the neuraminidase inhibitors. Methods Mol Biol 865:95113.[PubMed]
122. Hurt AC, Okomo-Adhiambo M, Gubareva LV. 2012. The fluorescence neuraminidase inhibition assay: a functional method for detection of influenza virus resistance to the neuraminidase inhibitors. Methods Mol Biol 865:115125.[PubMed]
123. World Health Organization. Hepatitis B. Factsheet 204, update July 2015. http://www.who.int/mediacentre/factsheets/fs204/en/.
124. Libbrecht E, Doutreloigne J, Van De Velde H, Yuen MF, Lai CL, Shapiro F, Sablon E. 2007. Evolution of primary and compensatory lamivudine resistance mutations in chronic hepatitis B virus-infected patients during long-term lamivudine treatment, assessed by a line probe assay. J Clin Microbiol 45:3935–3941.
125. Colonno RJ, Rose R, Baldick CJ, Levine S, Pokornowski K, Yu CF, Walsh A, Fang J, Hsu M, Mazzucco C, Eggers B, Zhang S, Plym M, Klesczewski K, Tenney DJ. 2006. Entecavir resistance is rare in nucleoside naïve patients with hepatitis B. Hepatology 44:16561665.[PubMed]
126. Tenney DJ, Rose RE, Baldick CJ, Pokornowski KA, Eggers BJ, Fang J, Wichroski MJ, Xu D, Yang J, Wilber RB, Colonno RJ. 2009. Long-term monitoring shows hepatitis B virus resistance to entecavir in nucleoside-naïve patients is rare through 5 years of therapy. Hepatology 49:15031514.[PubMed]
127. Buti M, Tsai N, Petersen J, Flisiak R, Gurel S, Krastev Z, Schall RA, Flaherty JF, Martins EB, Charuworn P, Kitrinos KM, Subramanian GM, Gane E, Marcellin P. 2015. Seven-year efficacy and safety of treatment with tenofovir disoproxil fumarate for chronic hepatitis B virus infection. Dig Dis Sci 60:14571464.[PubMed]
128. Snow-Lampart A, Chappell B, Curtis M, Zhu Y, Myrick F, Schawalder J, Kitrinos K, Svarovskaia ES, Miller MD, Sorbel J, Heathcote J, Marcellin P, Borroto-Esoda K. 2011. No resistance to tenofovir disoproxil fumarate detected after up to 144 weeks of therapy in patients monoinfected with chronic hepatitis B virus. Hepatology 53:763773.[PubMed]
129. World Health Organization. Hepatitis C. Factsheet 164, update July 2015. http://www.who.int/mediacentre/factsheets/fs164/en/.
130. deLemos AS, Chung RT. 2014. Hepatitis C treatment: an incipient therapeutic revolution. Trends Mol Med 20:315–321.
131. Feeney ER, Chung RT. 2014. Antiviral treatment of hepatitis C. BMJ 349:g3308.
132. Rodríguez-Torres M. 2013. Sofosbuvir (GS-7977), a pan-genotype, direct-acting antiviral for hepatitis C virus infection. Expert Rev Anti Infect Ther 11:12691279.[PubMed]
133. Vermehren J, Sarrazin C. 2012. The role of resistance in HCV treatment. Best Pract Res Clin Gastroenterol 26:487–503.
134. Kieffer TL, George S. 2014. Resistance to hepatitis C virus protease inhibitors. Curr Opin Virol 8:16–21.
135. Poveda E, Wyles DL, Mena A, Pedreira JD, Castro-Iglesias A, Cachay E. 2014. Update on hepatitis C virus resistance to direct-acting antiviral agents. Antiviral Res 108:181–191.
136. Schneider MD, Sarrazin C. 2014. Antiviral therapy of hepatitis C in 2014: do we need resistance testing? Antiviral Res 105:64–71.
137. Nakamoto S, Kanda T, Wu S, Shirasawa H, Yokosuka O. 2014. Hepatitis C virus NS5A inhibitors and drug resistance mutations. World J Gastroenterol 20:29022912.[PubMed]
138. Reddy KR, Zeuzem S, Zoulim F, Weiland O, Horban A, Stanciu C, Villamil FG, Andreone P, George J, Dammers E, Fu M, Kurland D, Lenz O, Ouwerkerk-Mahadevan S, Verbinnen T, Scott J, Jessner W. 2015. Simeprevir versus telaprevir with peginterferon and ribavirin in previous null or partial responders with chronic hepatitis C virus genotype 1 infection (ATTAIN): a randomised, double-blind, non-inferiority phase 3 trial. Lancet Infect Dis 15:27–35.
139. Bourlière M, Bronowicki JP, de Ledinghen V, Hézode C, Zoulim F, Mathurin P, Tran A, Larrey DG, Ratziu V, Alric L, Hyland RH, Jiang D, Doehle B, Pang PS, Symonds WT, Subramanian GM, McHutchison JG, Marcellin P, Habersetzer F, Guyader D, Grangé JD, Loustaud-Ratti V, Serfaty L, Metivier S, Leroy V, Abergel A, Pol S. 2015. Ledipasvir-sofosbuvir with or without ribavirin to treat patients with HCV genotype 1 infection and cirrhosis non-responsive to previous protease-inhibitor therapy: a randomised, double-blind, phase 2 trial (SIRIUS). Lancet Infect Dis 15:397–404.
140. Krishnan P, Tripathi R, Schnell G, Reisch T, Beyer J, Irvin M, Xie W, Larsen L, Cohen D,. Podsadecki T, Pilot-Matias T, Collins C. 2015. Resistance analysis of baseline and treatment-emergent variants in hepatitis C virus genotype 1 in the AVIATOR study with paritaprevir-ritonavir, ombitasvir, and dasabuvir. Antimicrob.Agents Chemother 59:5445–5454.
141. Ross L, Boulmé R, Fisher R, Hernandez J, Florance A, Schmit JC, Williams V. 2005. A direct comparison of drug susceptibility to HIV type 1 from antiretroviral experienced subjects as assessed by the antivirogram and PhenoSense assays and by seven resistance algorithms. AIDS Res Hum Retroviruses 21:933939.[PubMed]
142. Grant RM, Kuritzkes DR, Johnson VA, Mellors JW, Sullivan JL, Swanstrom R, D'Aquila RT, Van Gorder M, Holodniy M, Lloyd RM Jr, Reid C, Morgan GF, Winslow DL. 2003. Accuracy of the TRUGENE HIV-1 genotyping kit. J Clin Microbiol 41:15861593.[PubMed]
143. Jagodzinski LL, Cooley JD, Weber M, Michael NL. 2003. Performance characteristics of human immunodeficiency virus type 1 (HIV-1) genotyping systems in sequence-based analysis of subtypes other than HIV-1 subtype B. J Clin Microbiol 41:9981003.[PubMed]
144. Eshleman SH, Hackett J Jr, Swanson P, Cunningham SP, Drews B, Brennan C, Devare SG, Zekeng L, Kaptué L, Marlowe N. 2004. Performance of the Celera Diagnostics ViroSeq HIV-1 Genotyping System for sequence-based analysis of diverse human immunodeficiency virus type 1 strains. J Clin Microbiol 42:2711–2717.
145. Cunningham S, Ank B, Lewis D, Lu W, Wantman M, Dileanis JA, Jackson JB, Palumbo P, Krogstad P, Eshleman SH. 2001. Performance of the applied biosystems ViroSeq human immunodeficiency virus type 1 (HIV-1) genotyping system for sequence-based analysis of HIV-1 in pediatric plasma samples. J Clin Microbiol 39:12541257.[PubMed]
146. Parkin N, de Mendoza C, Schuurman R, Jennings C, Bremer J, Jordan MR, Bertagnolio S. 2012. Evaluation of in-house genotyping assay performance using dried blood spot specimens in the Global World Health Organization laboratory network. Clin Infect Dis 54(Suppl 4):S273S279.
147. Aitken SC, Kliphuis A, Wallis CL, Chu ML, Fillekes Q, Barth R, Stevens W, Rinke de Wit TF, Schuurman R. 2012. Development and evaluation of an assay for HIV-1 protease and reverse transcriptase drug resistance genotyping of all major group-M subtypes. J Clin Virol 54:21–25.
148. Woods CK, Brumme CJ, Liu TF, Chui CK, Chu AL, Wynhoven B, Hall TA, Trevino C, Shafer RW, Harrigan PR. 2012. Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool. J Clin Microbiol 50:1936–1942.
149. Liu TF, Shafer RW. 2006. Web resources for HIV type 1 genotypic-resistance test interpretation. Clin.Infect.Dis. 42:1608–1618.
150. Tang MW, Liu TF, Shafer RW. 2012. The HIVdb system for HIV-1 genotypic resistance interpretation. Intervirology 55:98101.
151. Wensing AM, Calvez V, Günthard HF, Johnson VA, Paredes R, Pillay D, Shafer RW, Richman DD. 2014. 2014 Update of the drug resistance mutations in HIV-1. Top Antivir Med 22:642650.[PubMed]
152. Stelzl E, Pröll J, Bizon B, Niklas N, Danzer M, Hackl C, Stabentheiner S, Gabriel C, Kessler HH. 2011. Human immunodeficiency virus type 1 drug resistance testing: evaluation of a new ultra-deep sequencing-based protocol and comparison with the TRUGENE HIV-1 Genotyping Kit. J Virol Methods 178:94–97.
153. Avidor B, Girshengorn S, Matus N, Talio H, Achsanov S, Zeldis I, Fratty IS, Katchman E, Brosh-Nissimov T, Hassin D, Alon D, Bentwich Z, Yust I, Amit S, Forer R, Vulih Shultsman I, Turner D. 2013. Evaluation of a benchtop HIV ultradeep pyrosequencing drug resistance assay in the clinical laboratory. J Clin Microbiol 51:880–886.
154. Cozzi-Lepri A, Noguera-Julian M, Di Giallonardo F, Schuurman R, Däumer M, Aitken S, Ceccherini-Silberstein F, D'Arminio Monforte A, Geretti AM, Booth CL, Kaiser R, Michalik C, Jansen K, Masquelier B, Bellecave P, Kouyos RD, Castro E, Furrer H, Schultze A, Günthard HF, Brun-Vezinet F, Paredes R, Metzner KJ. 2015. Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing. J Antimicrob Chemother 70:930–940.
155. Ferreira GL. 2012. Global dengue epidemiology trends. Rev Inst Med Trop Sao Paulo 54(Suppl 18):S5S6.
156. World Health Organization. Dengue: Guidelines for Diagnosis, Prevention and Control—New Edition. 2009. WHO Press.
157. Van Herp M, Declerck H, Decroo T. 2015. Favipiravir—a prophylactic treatment for Ebola contacts? Lancet 385:2350.