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Chapter 112 : Susceptibility Test Methods: Viruses*

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Susceptibility Test Methods: Viruses*, Page 1 of 2

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Abstract:

This chapter describes the phenotypic and genotypic methods that are being used to perform viral susceptibility tests and situations when testing should be considered. The phenotypic method section consists of classic methods that are still in use, such as plaque assays. Newer methods such as recombinant virus assays (RVAs) that use both a molecular and phenotypic approach are also described. The genotypic methods section describes the various sequencing platforms and reverse-hybridization assays that are commonly used. There is a paucity of FDA-approved/cleared kits available. Therefore, other kits/reagents including research-use only (RUO) and laboratory-developed tests (LDTs) using analyte-specific reagents (ASRs) are also included in the discussion. Descriptions of the genotypic assays include the reported mutations associated with antiviral resistance for selected viruses. Finally, there is a discussion of the knowledge-based expert systems available for the clinical interpretation of sequence data. This document should be useful if a clinical diagnostic laboratory chooses to develop an LDT antiviral genotypic assay.

Citation: Huang D, Bankowski M. 2015. Susceptibility Test Methods: Viruses*, p 1913-1931. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch112
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FIGURE 1

Example of a PRA (i.e., phenotypic test) used for determining acyclovir resistance in HSV-1. The reduction in the number of plaques is shown for an acyclovir-sensitive HSV-1 tested in duplicate starting with uninfected cells in the first two wells (1A/1B). Increasing acyclovir concentration is added downward to duplicate wells beginning with 2A/2B to 3A/3B and continuing from the top, right downward (1C/1D to 3C/3D) of the 12-well microtiter plate. The lowest number of plaques appears in wells 3C/3D where the highest concentration of acyclovir is added. doi:10.1128/9781555817381.ch112.f1

Citation: Huang D, Bankowski M. 2015. Susceptibility Test Methods: Viruses*, p 1913-1931. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch112
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Image of FIGURE 2
FIGURE 2

General protocol for sequence-based genotypic assays of plasma samples. The individual steps that are performed in sequence-based genotypic assays are shown. Above the first line are components that are accomplished as a result of specified protocol instructions and machinery. After completion of the block, the subsequent steps are performed with subjective input from the operator within a software program that will accept the chromatograms generated by the sequencer. The operator then chooses the portion of the reference sequence containing the unknown mutations for use in the software of their choice. This is followed by alignment and editing of the sequences to identify these mutations in the patient samples. The most commonly used consensus sequences of HIV-1 strains are either HIV-1 strain HXB2 or HIV-1 consensus B. If the operator is using an in-house genotyping assay for other viruses, the reference sequence used should be based upon the literature or “common practice.” doi:10.1128/9781555817381.ch112.f2

Citation: Huang D, Bankowski M. 2015. Susceptibility Test Methods: Viruses*, p 1913-1931. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch112
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References

/content/book/10.1128/9781555817381.mcm11.ch112
1. Arts EJ,, Hazuda DJ. 2012. HIV-1 antiretroviral drug therapy. Cold Spring Harb Perspect Med 2:a007161. 10.1101/cshperspect.a007161
2. Wyles DL. 2013. Antiviral resistance and the future landscape of hepatitis C virus infection therapy. J Infect Dis 207(Suppl 1):S33S39.
3. Fox AN,, Jacobson IM. 2012. Recent successes and noteworthy future prospects in the treatment of chronic hepatitis C. Clin Infect Dis 55(Suppl 1):S16S24.
4. Bean B,, Fletcher C,, Englund J,, Lehrman SN,, Ellis MN. 1987. Progressive mucocutaneous herpes simplex infection due to acyclovir-resistant virus in an immunocompromised patient: correlation of viral susceptibilities and plasma levels with response to therapy. Diagn Microbiol Infect Dis 7:199204.
5. Belshe RB,, Burk B,, Newman F,, Cerruti RL,, Sim IS. 1989. Resistance of influenza A virus to amantadine and rimantadine: results of one decade of surveillance. J Infect Dis 159:430435.
6. Belshe RB,, Smith MH,, Hall CB,, Betts R,, Hay AJ. 1988. Genetic basis of resistance to rimantadine emerging during treatment of influenza virus infection. J Virol 62:15081512.
7. Berkowitz FE,, Levin MJ. 1985. Use of an enzyme-linked immunosorbent assay performed directly on fixed infected cell monolayers for evaluating drugs against varicella-zoster virus. Antimicrob Agents Chemother 28:207210.
8. Biron KK. 1991. Ganciclovir-resistant human cytomegalovirus clinical isolates; resistance mechanisms and in vitro susceptibility to antiviral agents. Transplant Proc 23(Suppl 3):162167.
9. Englund JA,, Zimmerman ME,, Swierkosz EM,, Goodman JL,, Scholl DR,, Balfour HHJr. 1990. Herpes simplex virus resistant to acyclovir. A study in a tertiary care center. Ann Intern Med 112:416422.
10. Lok AS. 2007. Navigating the maze of hepatitis B treatments. Gastroenterology 132:15861594.
11. Shafer RW. 2002. Genotypic testing for human immunodeficiency virus type 1 drug resistance. Clin Microbiol Rev 15:247277.
12. DeGruttola V,, Dix L,, D’Aquila R,, Holder D,, Phillips A,, Ait-Khaled M,, Baxter J,, Clevenbergh P,, Hammer S,, Harrigan R,, Katzenstein D,, Lanier R,, Miller M,, Para M,, Yerly S,, Zolopa A,, Murray J,, Patick A,, Miller V,, Castillo S,, Pedneault L,, Mellors J. 2000. The relation between baseline HIV drug resistance and response to antiretroviral therapy: re-analysis of retrospective and prospective studies using a standardized data analysis plan. Antivir Ther 5:4148.
13. Burd EM. 2010. Validation of laboratory-developed molecular assays for infectious diseases. Clin Microbiol Rev 23:550576.
14. Thursz M,, Yee L,, Khakoo S. 2011. Understanding the host genetics of chronic hepatitis B and C. Semin Liver Dis 31:115127.
15. Lampertico P,, Viganò M,, Cheroni C,, Facchetti F,, Invernizzi F,, Valveri V,, Soffredini R,, Abrignani S,, De Francesco R,, Colombo M. 2013. IL28B polymorphisms predict interferon-related hepatitis B surface antigen seroclearance in genotype D hepatitis B e antigen-negative patients with chronic hepatitis B. Hepatology 57:890896.
16. Holzinger ER,, Ritchie MD. 2012. Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies. Pharmacogenomics 13:213222.
17. Rodríguez-Torres M. 2013. Focus on drug interactions: the challenge of treating hepatitis C virus infection with direct-acting antiviral drugs in the HIV-positive patient. Curr Opin Infect Dis 26:5057.
18. Taylor LE,, Swan T,, Mayer KH. 2012. HIV coinfection with hepatitis C virus: evolving epidemiology and treatment paradigms. Clin Infect Dis 55(Suppl 1):S33S42.
19. Yee HS,, Chang MF,, Pocha C,, Lim J,, Ross D,, Morgan TR,, Monto A, Department of Veterans Affairs Hepatitis C Resource Center Program, National Hepatitis C Program Office. 2012. Update on the management and treatment of hepatitis C virus infection: recommendations from the Department of Veterans Affairs Hepatitis C Resource Center Program and the National Hepatitis C Program Office. Am J Gastroenterology 107:669689; quiz 690.
20. Bangsberg DR,, Hecht FM,, Charlebois ED,, Zolopa AR,, Holodniy M,, Sheiner L,, Bamberger JD,, Chesney MA,, Moss A. 2000. Adherence to protease inhibitors, HIV-1 viral load, and development of drug resistance in an indigent population. AIDS 14:357366.
21. Cingolani A,, Antinori A,, Rizzo MG,, Murri R,, Ammassari A,, Baldini F,, Di Giambenedetto S,, Cauda R,, De Luca A. 2002. Usefulness of monitoring HIV drug resistance and adherence in individuals failing highly active antiretroviral therapy: a randomized study (ARGENTA). AIDS 16:369379.
22. Genberg BL,, Wilson IB,, Bangsberg DR,, Arnsten J,, Goggin K,, Remien RH,, Simoni J,, Gross R,, Reynolds N,, Rosen M,, Liu H, MACH14 Investigators. 2012. Patterns of antiretroviral therapy adherence and impact on HIV RNA among patients in North America. AIDS 26:14151423.
23. Biron KK,, Elion GB. 1980. In vitro susceptibility of varicella-zoster virus to acyclovir. Antimicrob Agents Chemother 18:443447.
24. Biron KK,, Stanat SC,, Sorrell JB,, Fyfe JA,, Keller PM,, Lambe CU,, Nelson DJ. 1985. Metabolic activation of the nucleoside analog 9-[(2-hydroxy-1-(hydroxymethyl)ethoxy]methyl)guanine in human diploid fibroblasts infected with human cytomegalovirus. Proc Natl Acad Sci USA 82:24732477.
25. Hayden FG,, Cote KM,, Douglas RGJr. 1980. Plaque inhibition assay for drug susceptibility testing of influenza viruses. Antimicrob Agents Chemother 17:865870.
26. McLaren C,, Ellis MN,, Hunter GA. 1983. A colorimetric assay for the measurement of the sensitivity of herpes simplex viruses to antiviral agents. Antiviral Res 3:223234.
27. Rabalais GP,, Levin MJ,, Berkowitz FE. 1987. Rapid herpes simplex virus susceptibility testing using an enzyme-linked immunosorbent assay performed in situ on fixed virus-infected monolayers. Antimicrob Agents Chemother 31:946948.
28. Safrin S,, Palacios E,, Leahy BJ. 1996. Comparative evaluation of microplate enzyme-linked immunosorbent assay versus plaque reduction assay for antiviral susceptibility testing of herpes simplex virus isolates. Antimicrob Agents Chemother 40:10171019.
29. Safrin S,, Phan L,, Elbeik T. 1995. A comparative evaluation of three methods of antiviral susceptibility testing of clinical herpes simplex virus isolates. Clin Diagn Virol 4:8191.
30. Centers for Disease Control and Prevention. 1999. Neuraminidase inhibitors for treatment of influenza A and B infections. MMWR Recomm Rep 48:19.
31. Wetherall NT,, Trivedi T,, Zeller J,, Hodges-Savola C,, McKimm-Breschkin JL,, Zambon M,, Hayden FG. 2003. Evaluation of neuraminidase enzyme assays using different substrates to measure susceptibility of influenza virus clinical isolates to neuraminidase inhibitors: report of the neuraminidase inhibitor susceptibility network. J Clin Microbiol 41:742750.
32. Chou S. 2010. Recombinant phenotyping of cytomegalovirus UL97 kinase sequence variants for ganciclovir resistance. Antimicrob Agents Chemother 54:23712378.
33. Wainberg MA,, Zaharatos GJ,, Brenner BG. 2011. Development of antiretroviral drug resistance. N Engl J Med 365:637646.
34. Nakauchi M,, Ujike M,, Obuchi M,, Takashita E,, Takayama I,, Ejima M,, Oba K,, Konomi N,, Odagiri T,, Tashiro M,, Kageyama T; Influenza Virus Surveillance Group of Japan. 2011. Rapid discrimination of oseltamivir-resistant 275Y and -susceptible 275H substitutions in the neuraminidase gene of pandemic influenza A/H1N1 2009 virus by duplex one-step RT-PCR assay. J Med Virol 83:11211127.
35. Sanger F,, Nicklen S,, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:54635467.
36. Delwart EL,, Pan H,, Sheppard HW,, Wolpert D,, Neumann AU,, Korber B,, Mullins JI. 1997. Slower evolution of human immunodeficiency virus type 1 quasispecies during progression to AIDS. J Virol 71:74987508.
37. Huang DD,, Eshleman SH,, Brambilla DJ,, Palumbo PE,, Bremer JW. 2003. Evaluation of the editing process in human immunodeficiency virus type 1 genotyping. J Clin Microbiol 41:32653272.
38. Metzker ML. 2010. Sequencing technologies–the next generation. Nat Rev Genet 11:3146.
39. Jabara CB,, Jones CD,, Roach J,, Anderson JA,, Swanstrom R. 2011. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci USA 108:2016620171.
40. Hussain M,, Fung S,, Libbrecht E,, Sablon E,, Cursaro C,, Andreone P,, Lok AS. 2006. Sensitive line probe assay that simultaneously detects mutations conveying resistance to lamivudine and adefovir. J Clin Microbiol 44:10941097.
41. Hindiyeh M,, Ram D,, Mandelboim M,, Meningher T,, Hirsh S,, Robinov J,, Levy V,, Orzitzer S,, Azar R,, Grossman Z,, Mendelson E. 2010. Rapid detection of influenza A pandemic (H1N1) 2009 virus neuraminidase resistance mutation H275Y by real-time reverse transcriptase PCR. J Clin Microbiol 48:18841887.
42. Duan S,, Boltz DA,, Li J,, Oshansky CM,, Marjuki H,, Barman S,, Webby RJ,, Webster RG,, Govorkova EA. 2011. Novel genotyping and quantitative analysis of neuraminidase inhibitor resistance-associated mutations in influenza a viruses by single-nucleotide polymorphism analysis. Antimicrob Agents Chemother 55:47184727.
43. Boivin G,, Chou S,, Quirk MR,, Erice A,, Jordan MC. 1996. Detection of ganciclovir resistance mutations quantitation of cytomegalovirus (CMV) DNA in leukocytes of patients with fatal disseminated CMV disease. J Infect Dis 173:523528.
44. Spector SA,, Hsia K,, Wolf D,, Shinkai M,, Smith I. 1995. Molecular detection of human cytomegalovirus and determination of genotypic ganciclovir resistance in clinical specimens. Clin Infect Dis 21(Suppl 2):S170S173.
45. Wolf DG,, Smith IL,, Lee DJ,, Freeman WR,, Flores-Aguilar M,, Spector SA. 1995. Mutations in human cytomegalovirus UL97 gene confer clinical resistance to ganciclovir and can be detected directly in patient plasma. J Clin Invest 95:257263.
46. Kotton CN,, Kumar D,, Caliendo AM,, Asberg A,, Chou S,, Danziger-Isakov L,, Humar A, Transplantation Society International CMV Consensus Group. 2013. Updated international consensus guidelines on the management of cytomegalovirus in solid-organ transplantation. Transplantation 96:333360.
47. Erice A. 1999. Resistance of human cytomegalovirus to antiviral drugs. Clin Microbiol Rev 12:286297.
48. Baldanti F,, Underwood MR,, Stanat SC,, Biron KK,, Chou S,, Sarasini A,, Silini E,, Gerna G. 1996. Single amino acid changes in the DNA polymerase confer foscarnet resistance and slow-growth phenotype, while mutations in the UL97-encoded phosphotransferase confer ganciclovir resistance in three double-resistant human cytomegalovirus strains recovered from patients with AIDS. J Virol 70:13901395.
49. Chou S,, Guentzel S,, Michels KR,, Miner RC,, Drew WL. 1995. Frequency of UL97 phosphotransferase mutations related to ganciclovir resistance in clinical cytomegalovirus isolates. J Infect Dis 172:239242.
50. Erice A,, Gil-Roda C,, Pérez JL,, Balfour HHJr,, 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.
51. 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.
52. Lurain NS,, Chou S. 2010. Antiviral drug resistance of human cytomegalovirus. Clin Microbiol Rev 23:689712.
53. Hantz S,, Michel D,, Fillet AM,, Guigonis V,, Champier G,, Mazeron MC,, Bensman A,, Denis F,, Mertens T,, Dehee A,, Alain S. 2005. Early selection of a new UL97 mutant with a severe defect of ganciclovir phosphorylation after valaciclovir prophylaxis and short-term ganciclovir therapy in a renal transplant recipient. Antimicrob Agents Chemother 49:15801583.
54. Iwasenko JM,, Scott GM,, Naing Z,, Glanville AR,, Rawlinson WD. 2011. Diversity of antiviral-resistant human cytomegalovirus in heart and lung transplant recipients. Transpl Infect Dis 13:145153.
55. Lurain NS,, Weinberg A,, Crumpacker CS,, Chou S, Adult AIDS Clinical Trials Group–CMV Laboratories. 2001. Sequencing of cytomegalovirus UL97 gene for genotypic antiviral resistance testing. Antimicrob Agents Chemother 45:27752780.
56. Chou S,, Ercolani RJ,, Marousek G,, Bowlin TL. 2013. Cytomegalovirus UL97 kinase catalytic domain mutations that confer multidrug resistance. Antimicrob Agents Chemother 57:33753379.
57. Lurain NS,, Thompson KD,, Holmes EW,, Read GS. 1992. Point mutations in the DNA polymerase gene of human cytomegalovirus that result in resistance to antiviral agents. J Virol 66:71467152.
58. Storch GA. 2000. Essentials of Diagnostic Virology. Churchill Livingstone, New York, NY.
59. Piret J,, Boivin G. 2011. Resistance of herpes simplex viruses to nucleoside analogues: mechanisms, prevalence, and management. Antimicrob Agents Chemother 55:459472.
60. Gaudreau A,, Hill E,, Balfour HHJr,, Erice A,, Boivin G. 1998. Phenotypic and genotypic characterization of acyclovir-resistant herpes simplex viruses from immunocompromised patients. J Infect Dis 178:297303.
61. 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.
62. 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.
63. Grant RM,, Kuritzkes DR,, Johnson VA,, Mellors JW,, Sullivan JL,, Swanstrom R,, D’Aquila RT,, Van Gorder M,, Holodniy M,, Lloyd RMJr,, Reid C,, Morgan GF,, Winslow DL. 2003. Accuracy of the TRUGENE HIV-1 genotyping kit. J Clin Microbiol 41:15861593.
64. 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.
65. Erali M,, Page S,, Reimer LG,, Hillyard DR. 2001. Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods. J Clin Microbiol 39:21572165.
66. Mracna M,, Becker-Pergola G,, Dileanis J,, Guay LA,, Cunningham S,, Jackson JB,, Eshleman SH. 2001. Performance of Applied Biosystems ViroSeq HIV-1 Genotyping System for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda. J Clin Microbiol 39:43234327.
67. Tural C,, Ruiz L,, Holtzer C,, Schapiro J,, Viciana P,, González J,, Domingo P,, Boucher C,, Rey-Joly C,, Clotet B, Havana Study Group. 2002. Clinical utility of HIV-1 genotyping and expert advice: the Havana trial. AIDS 16:209218.
68. 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.
69. Beddows S,, Galpin S,, Kazmi SH,, Ashraf A,, Johargy A,, Frater AJ,, White N,, Braganza R,, Clarke J,, McClure M,, Weber JN. 2003. Performance of two commercially available sequence-based HIV-1 genotyping systems for the detection of drug resistance against HIV type 1 group M subtypes. J Med Virol 70:337342.
70. Eshleman SH,, Hackett JJr,, 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 42:27112717.
71. Kantor R,, Katzenstein DA,, Efron B,, Carvalho AP,, Wynhoven B,, Cane P,, Clarke J,, Sirivichayakul S,, Soares MA,, Snoeck J,, Pillay C,, Rudich H,, Rodrigues R,, Holguin A,, Ariyoshi K,, Bouzas MB,, Cahn P,, Sugiura W,, Soriano V,, Brigido LF,, Grossman Z,, Morris L,, Vandamme AM,, Tanuri A,, Phanuphak P,, Weber JN,, Pillay D,, Harrigan PR,, Camacho R,, Schapiro JM,, Shafer RW. 2005. Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration. PLoS Med 2:e112.
72. Hirsch MS,, Brun-Vézinet F,, D’Aquila RT,, Hammer SM,, Johnson VA,, Kuritzkes DR,, Loveday C,, Mellors JW,, Clotet B,, Conway B,, Demeter LM,, Vella S,, Jacobsen DM,, Richman DD. 2000. Antiretroviral drug resistance testing in adult HIV-1 infection: recommendations of an International AIDS Society-USA Panel. JAMA 283:24172426.
73. Hirsch MS,, Conway B,, D’Aquila RT,, Johnson VA,, Brun-Vézinet F,, Clotet B,, Demeter LM,, Hammer SM,, Jacobsen DM,, Kuritzkes DR,, Loveday C,, Mellors JW,, Vella S,, Richman DD. 1998. Antiretroviral drug resistance testing in adults with HIV infection: implications for clinical management. International AIDS Society—USA Panel. JAMA 279:19841991.
74. Thompson MA,, Aberg JA,, Hoy JF,, Telenti A,, Benson C,, Cahn P,, Eron JJ,, Gunthard HF,, Hammer SM,, Reiss P,, Richman DD,, Rizzardini G,, Thomas DL,, Jacobsen DM,, Volberding PA. 2012. Antiretroviral treatment of adult HIV infection: 2012 recommendations of the International Antiviral Society-USA panel. JAMA 308:387402.
75. Wittkop L,, Günthard HF,, de Wolf F,, Dunn D,, Cozzi-Lepri A,, de Luca A,, Kucherer C,, Obel N,, von Wyl V,, Masquelier B,, Stephan C,, Torti C,, Antinori A,, García F,, Judd A,, Porter K,, Thiébaut R,, Castro H,, van Sighem AI,, Colin C,, Kjaer J,, Lundgren JD,, Paredes R,, Pozniak A,, Clotet B,, Phillips A,, Pillay D,, Chenê G; Euro-Coord – CHAIN Study Group. 2011. Effect of transmitted drug resistance on virological and immunological response to initial combination antiretroviral therapy for HIV (EuroCoord-CHAIN joint project): a European multicohort study. Lancet Infect Dis 11:363371.
76. Lu J,, Deeks SG,, Hoh R,, Beatty G,, Kuritzkes BA,, Martin JN,, Kuritzkes DR. 2006. Rapid emergence of enfuvirtide resistance in HIV-1-infected patients: results of a clonal analysis. J Acquir Immune Defic Syndr 43:6064.
77. Lin NH,, Kuritzkes DR. 2009. Tropism testing in the clinical management of HIV-1 infection. Curr Opin HIV AIDS 4:481487.
78. Garrido C,, Roulet V,, Chueca N,, Poveda E,, Aguilera A,, Skrabal K,, Zahonero N,, Carlos S,, Garcia F,, Faudon JL,, Soriano V,, de Mendoza C. 2008. Evaluation of eight different bioinformatics tools to predict viral tropism in different human immunodeficiency virus type 1 subtypes. J Clin Microbiol 46:887891.
79. Seclén E,, Garrido C,, González Mdel M,, González-Lahoz J,, de Mendoza C,, Soriano V,, Poveda E. 2010. High sensitivity of specific genotypic tools for detection of X4 variants in antiretroviral-experienced patients suitable to be treated with CCR5 antagonists. J Antimicrob Chemother 65:14861492.
80. Jensen MA,, Coetzer M,, van ’t Wout AB,, Morris L,, Mullins JI. 2006. A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences. J Virol 80:46984704.
81. Lengauer T,, Sander O,, Sierra S,, Thielen A,, Kaiser R. 2007. Bioinformatics prediction of HIV coreceptor usage. Nat Biotechnol 25:14071410.
82. Sánchez V,, Masía M,, Robledano C,, Padilla S,, Lumbreras B,, Poveda E,, De Mendoza C,, Soriano V,, Gutiérrez F. 2011. A highly sensitive and specific model for predicting HIV-1 tropism in treatment-experienced patients combining interpretation of V3 loop sequences and clinical parameters. J Acquir Immune Defic Syndr 56:5158.
83. Swenson LC,, Mo T,, Dong WW,, Zhong X,, Woods CK,, Jensen MA,, Thielen A,, Chapman D,, Lewis M,, James I,, Heera J,, Valdez H,, Harrigan PR. 2011. Deep sequencing to infer HIV-1 coreceptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis 203:237245.
84. Delwart EL,, Sheppard HW,, Walker BD,, Goudsmit J,, Mullins JI. 1994. Human immunodeficiency virus type 1 evolution in vivo tracked by DNA heteroduplex mobility assays. J Virol 68:66726683.
85. Valsamakis A. 2007. Molecular testing in the diagnosis and management of chronic hepatitis B. Clin Microbiol Rev 20:426439.
86. Lok AS,, Zoulim F,, Locarnini S,, Bartholomeusz A,, Ghany MG,, Pawlotsky JM,, Liaw YF,, Mizokami M,, Kuiken C. 2007. Antiviral drug-resistant HBV: standardization of nomenclature and assays and recommendations for management. Hepatology 46:254265.
87. Janssen HL,, van Zonneveld M,, Senturk H,, Zeuzem S,, Akarca US,, Cakaloglu Y,, Simon C,, So TM,, Gerken G,, de Man RA,, Niesters HG,, Zondervan P,, Hansen B,, Schalm SW, HBV 99-01 Study Group, Rotterdam Foundation for Liver Research. 2005. Pegylated interferon alfa-2b alone or in combination with lamivudine for HBeAg-positive chronic hepatitis B: a randomised trial. Lancet 365:123129.
88. Sonneveld MJ,, Janssen HL. 2011. Chronic hepatitis B: peginterferon or nucleos(t)ide analogues? Liver Int 31(Suppl 1):7884.
89. Kessler HH,, Stelzl E,, Marth E,, Stauber RE. 2003. Detection of mutations in the hepatitis B virus polymerase gene. Clin Chem 49:989992.
90. Bartholomeusz A,, Schaefer S. 2004. Hepatitis B virus genotypes: comparison of genotyping methods. Rev Med Virol 14:316.
91. Shaw T,, Bartholomeusz A,, Locarnini S. 2006. HBV drug resistance: mechanisms, detection and interpretation. J Hepatol 44:593606.
92. Yuen LK,, Ayres A,, Littlejohn M,, Colledge D,, Edgely A,, Maskill WJ,, Locarnini SA,, Bartholomeusz A. 2007. SeqHepB: A sequence analysis program and relational database system for chronic hepatitis B. Antiviral Res 75:6474.
93. Niesters HG,, Zoulim F,, Pichoud C,, Buti M,, Shapiro F,, D’Heuvaert N,, Celis L,, Doutreloigne J,, Sablon E. 2010. Validation of the INNO-LiPA HBV DR assay (version 2) in monitoring hepatitis B virus-infected patients receiving nucleoside analog treatment. Antimicrob Agents Chemother 54:12831289.
94. Lok AS,, Zoulim F,, Locarnini S,, Mangia A,, Niro G,, Decraemer H,, Maertens G,, Hulstaert F,, De Vreese K,, Sablon E. 2002. Monitoring drug resistance in chronic hepatitis B virus (HBV)-infected patients during lamivudine therapy: evaluation of performance of INNO-LiPA HBV DR assay. J Clin Microbiol 40:37293734.
95. Osiowy C,, Giles E. 2003. Evaluation of the INNO-LiPA HBV genotyping assay for determination of hepatitis B virus genotype. J Clin Microbiol 41:54735477.
96. Ghany MG,, Kim HY,, Stoddard A,, Wright EC,, Seeff LB,, Lok AS, HALT-C Trial Group. 2011. Predicting clinical outcomes using baseline and follow-up laboratory data from the hepatitis C long-term treatment against cirrhosis trial. Hepatology 54:15271537.
97. Ghany MG,, Nelson DR,, Strader DB,, Thomas DL,, Seeff LB. 2011. An update on treatment of genotype 1 chronic hepatitis C virus infection: 2011 practice guideline by the American Association for the Study of Liver Diseases. Hepatology 54:14331444.
98. Wyles DL. 2012. Beyond telaprevir and boceprevir: resistance and new agents for hepatitis C virus infection. Top Antivir Med 20:139145.
99. Scheel TK,, Rice CM. 2013. Understanding the hepatitis C virus life cycle paves the way for highly effective therapies. Nat Med 19:837849.
100. Vallet S,, Larrat S,, Laperche S,, Le Guillou-Guillemette H,, Legrand-Abravanel F,, Bouchardeau F,, Pivert A,, Henquell C,, Mirand A,, André-Garnier E,, Giordanengo V,, Lagathu G,, Thibault V,, Scholtes C,, Schvoerer E,, Gaudy-Graffin C,, Maylin S,, Trimoulet P,, Brochot E,, Hantz S,, Gozlan J,, Roque-Afonso AM,, Soussan P,, Plantier JC,, Charpentier C,, Chevaliez S,, Colson P,, Mackiewicz V,, Aguilera L,, Rosec S,, Gouriou S,, Magnat N,, Lunel-Fabiani F,, Izopet J,, Morand P,, Payan C,, Pawlotsky JM. 2013. Multicenter quality control of hepatitis C virus protease inhibitor resistance genotyping. J Clin Microbiol 51:14281433.
101. Svarovskaia ES,, Martin R,, McHutchison JG,, Miller MD,, Mo H. 2012. Abundant drug-resistant NS3 mutants detected by deep sequencing in hepatitis C virus-infected patients undergoing NS3 protease inhibitor monotherapy. J Clin Microbiol 50:32673274.
102. Ninomiya M,, Ueno Y,, Funayama R,, Nagashima T,, Nishida Y,, Kondo Y,, Inoue J,, Kakazu E,, Kimura O,, Nakayama K,, Shimosegawa T. 2012. Use of illumina deep sequencing technology to differentiate hepatitis C virus variants. J Clin Microbiol 50:857866.
103. Fiore AE,, Fry A,, Shay D,, Gubareva L,, Bresee JS,, Uyeki TM. 2011. Antiviral agents for the treatment and chemoprophylaxis of influenza—recommendations of the Advisory Committee on Immunization Practices (ACIP). MMWR Recomm Rep 60:124.
104. Bright RA,, Medina MJ,, Xu X,, Perez-Oronoz G,, Wallis TR,, Davis XM,, Povinelli L,, Cox NJ,, Klimov AI. 2005. Incidence of adamantane resistance among influenza A (H3N2) viruses isolated worldwide from 1994 to 2005: a cause for concern. Lancet 366:11751181.
105. Centers for Disease Control and Prevention (CDC). 2009. Update: drug susceptibility of swine-origin influenza A (H1N1) viruses, April 2009. MMWR Morb Mortal Wkly Rep 58:433435.
106. Deyde VM,, Okomo-Adhiambo M,, Sheu TG,, Wallis TR,, Fry A,, Dharan N,, Klimov AI,, Gubareva LV. 2009. Pyrosequencing as a tool to detect molecular markers of resistance to neuraminidase inhibitors in seasonal influenza A viruses. Antiviral Res 81:1624.
107. Deyde VM,, Xu X,, Bright RA,, Shaw M,, Smith CB,, Zhang Y,, Shu Y,, Gubareva LV,, Cox NJ,, Klimov AI. 2007. Surveillance of resistance to adamantanes among influenza A(H3N2) and A(H1N1) viruses isolated worldwide. J Infect Dis 196:249257.
108. World Health Organization. 2012. Pyrosequencing Protocol for the Detection of the Substitution at Residue 275 in the Neuraminidase of 2009 Pandemic H1N1 Viruses Using the PyroMark™ Q96 ID Platform. http://www.who.int/influ enza/gisrs_laboratory/antiviral_susceptibility/pyrosequen cing_na275_q96.pdf?ua=1.
109. Hanna GJ,, D’Aquila RT. 2001. Clinical use of genotypic and phenotypic drug resistance testing to monitor antiretroviral chemotherapy. Clin Infect Dis 32:774782.
110. Sing T,, Low AJ,, Beerenwinkel N,, Sander O,, Cheung PK,, Domingues FS,, Buch J,, Daumer M,, Kaiser R,, Lengauer T,, Harrigan PR. 2007. Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther 12:10971106.
111. Shafer RW,, Jung DR,, Betts BJ. 2000. Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries. Nat Med 6:12901292.
112. Shafer RW. 2006. Rationale and uses of a public HIV drug-resistance database. J Infect Dis 194(Suppl 1):S51S58.
113. Rhee SY,, Gonzales MJ,, Kantor R,, Betts BJ,, Ravela J,, Shafer RW. 2003. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 31:298303.
114. Vandenbroucke I,, Van Marck H,, Mostmans W,, Van Eygen V,, Rondelez E,, Thys K,, Van Baelen K,, Fransen K,, Vaira D,, Kabeya K,, De Wit S,, Florence E,, Moutschen M,, Vandekerckhove L,, Verhofstede C,, Stuyver LJ. 2010. HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays. AIDS Res Ther 7:4.
115. Bunnik EM,, Swenson LC,, Edo-Matas D,, Huang W,, Dong W,, Frantzell A,, Petropoulos CJ,, Coakley E,, Schuitemaker H,, Harrigan PR,, van ’t Wout AB. 2011. Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing. PLoS Pathog 7:e1002106. 10.1371/jour nal.ppat.1002106
116. Gonzalez-Serna A,, McGovern RA,, Harrigan PR,, Vidal F,, Poon AF,, Ferrando-Martinez S,, Abad MA,, Genebat M,, Leal M,, Ruiz-Mateos E. 2012. Correlation of the virological response to short-term maraviroc monotherapy with standard and deep-sequencing-based genotypic tropism prediction methods. Antimicrob Agents Chemother 56:12021207.
117. Besse B,, Coste-Burel M,, Bourgeois N,, Feray C,, Imbert-Marcille BM,, André-Garnier E. 2012. Genotyping and resistance profile of hepatitis C (HCV) genotypes 1-6 by sequencing the NS3 protease region using a single optimized sensitive method. J Virol Methods 185:94100.
118. Clinical and Laboratory Standards Institute. 2004. Antiviral Susceptibility Testing: Herpes Simplex Virus by Plaque Reduction Assay; Approved Standard. CLSI document M33-A. Clinical and Laboratory Standards Institute,Wayne, PA.
119. Landry ML,, Stanat S,, Biron K,, Brambilla D,, Britt W,, Jokela J,, Chou S,, Drew WL,, Erice A,, Gilliam B,, Lurain N,, Manischewitz J,, Miner R,, Nokta M,, Reichelderfer P,, Spector S,, Weinberg A,, Yen-Lieberman B,, Crumpacker C. 2000. A standardized plaque reduction assay for determination of drug susceptibilities of cytomegalovirus clinical isolates. Antimicrob Agents Chemother 44:688692.
120. Lurain NS,, Weinberg A,, Crumpacker CS,, Chou S; Adult AIDS Clinical Trials Group–CMV Laboratories. 2001. Sequencing of cytomegalovirus UL97 gene for genotypic antiviral resistance testing. Antimicrob Agents Chemother 45:27752780.
121. Bacon TH,, Levin MJ,, Leary JJ,, Sarisky RT,, Sutton D. 2003. Herpes simplex virus resistance to acyclovir and penciclovir after two decades of antiviral therapy. Clin Microbiol Rev 16:114128.
122. Coen DM. 1996. Antiviral drug resistance in herpes simplex virus. Adv Exp Med Biol 394:4957.
123. 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.
124. Morfin F,, Thouvenot D. 2003. Herpes simplex virus resistance to antiviral drugs. J Clin Virol 26:2937.
125. Reyes M,, Shaik NS,, Graber JM,, Nisenbaum R,, Wetherall NT,, Fukuda K,, Reeves WC, Task Force on Herpes Simplex Virus Resistence. 2003. Acyclovir-resistant genital herpes among persons attending sexually transmitted disease and human immunodeficiency virus clinics. Arch Intern Med 163:7680.
126. Safrin S,, Phan L. 1993. In vitro activity of penciclovir against clinical isolates of acyclovir-resistant and foscarnet-resistant herpes simplex virus. Antimicrob Agents Chemother 37:22412243.
127. Sauerbrei A,, Deinhardt S,, Zell R,, Wutzler P. 2010. Testing of herpes simplex virus for resistance to antiviral drugs. Virulence 1:555557.
128. Sauerbrei A,, Vödisch S,, Bohn K,, Schacke M,, Gronowitz S. 2013. Screening of herpes simplex virus type 1 isolates for acyclovir resistance using DiviTum(R) assay. J Virol Methods 188:7072.
129. 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.
130. Gilbert C,, Bestman-Smith J,, Boivin G. 2002. Resistance of herpesviruses to antiviral drugs: clinical impacts and molecular mechanisms. Drug Resist Updat 5:88114.
131. 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.
132. Leary JJ,, Wittrock R,, Sarisky RT,, Weinberg A,, Levin MJ. 2002. Susceptibilities of herpes simplex viruses to penciclovir and acyclovir in eight cell lines. Antimicrob Agents Chemother 46:762768.
133. Sarisky RT,, Quail MR,, Clark PE,, Nguyen TT,, Halsey WS,, Wittrock RJ,, O’Leary Bartus J,, Van Horn MM,, Sathe GM,, Van Horn S,, Kelly MD,, Bacon TH,, Leary JJ. 2001. Characterization of herpes simplex viruses selected in culture for resistance to penciclovir or acyclovir. J Virol 75:17611769.
134. 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.
135. 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.
136. Gubareva LV,, Matrosovich MN,, Brenner MK,, Bethell RC,, Webster RG. 1998. Evidence for zanamivir resistance in an immunocompromised child infected with influenza B virus. J Infect Dis 178:12571262.
137. Abed Y,, Baz M,, Boivin G. 2006. Impact of neuraminidase mutations conferring influenza resistance to neuraminidase inhibitors in the N1 and N2 genetic backgrounds. Antivir Ther 11:971976.
138. Collins PJ,, Haire LF,, Lin YP,, Liu J,, Russell RJ,, Walker PA,, Martin SR,, Daniels RS,, Gregory V,, Skehel JJ,, Gamblin SJ,, Hay AJ. 2009. Structural basis for oseltamivir resistance of influenza viruses. Vaccine 27:63176323.
139. Hurt AC,, Holien JK,, Barr IG. 2009. In vitro generation of neuraminidase inhibitor resistance in A(H5N1) influenza viruses. Antimicrob Agents Chemother 53:44334440.
140. Kiso M,, Mitamura K,, Sakai-Tagawa Y,, Shiraishi K,, Kawakami C,, Kimura K,, Hayden FG,, Sugaya N,, Kawaoka Y. 2004. Resistant influenza A viruses in children treated with oseltamivir: descriptive study. Lancet 364:759765.
141. Le QM,, Kiso M,, Someya K,, Sakai YT,, Nguyen TH,, Nguyen KH,, Pham ND,, Ngyen HH,, Yamada S,, Muramoto Y,, Horimoto T,, Takada A,, Goto H,, Suzuki T,, Suzuki Y,, Kawaoka Y. 2005. Avian flu: isolation of drug-resistant H5N1 virus. Nature 437:1108.
142. McKimm-Breschkin J,, Trivedi T,, Hampson A,, Hay A,, Klimov A,, Tashiro M,, Hayden F,, Zambon M. 2003. Neuraminidase sequence analysis and susceptibilities of influenza virus clinical isolates to zanamivir and oseltamivir. Antimicrob Agents Chemother 47:22642272.
143. Allen MI,, Deslauriers M,, Andrews CW,, Tipples GA,, Walters KA,, Tyrrell DL,, Brown N,, Condreay LD. 1998. Identification and characterization of mutations in hepatitis B virus resistant to lamivudine. Lamivudine Clinical Investigation Group. Hepatology 27:16701677.
144. Choe WH,, Hong SP,, Kim BK,, Ko SY,, Jung YK,, Kim JH,, Yeon JE,, Byun KS,, Kim KH,, Ji SI,, Kim SO,, Lee CH,, Kwon SY. 2009. Evolution of hepatitis B virus mutation during entecavir rescue therapy in patients with antiviral resistance to lamivudine and adefovir. Antivir Ther 14:985993.
145. Das K,, Xiong X,, Yang H,, Westland CE,, Gibbs CS,, Sarafianos SG,, Arnold E. 2001. Molecular modeling and biochemical characterization reveal the mechanism of hepatitis B virus polymerase resistance to lamivudine (3TC) and emtricitabine (FTC). J Virol 75:47714779.
146. Delaney WEIV,, Yang H,, Westland CE,, Das K,, Arnold E,, Gibbs CS,, Miller MD,, Xiong S. 2003. The hepatitis B virus polymerase mutation rtV173L is selected during lamivudine therapy and enhances viral replication in vitro. J Virol 77:1183311841.
147. Ono SK,, Kato N,, Shiratori Y,, Kato J,, Goto T,, Schinazi RF,, Carrilho FJ,, Omata M. 2001. The polymerase L528M mutation cooperates with nucleotide binding-site mutations, increasing hepatitis B virus replication and drug resistance. J Clin Invest 107:449455.
148. Warner N,, Locarnini S. 2008. The antiviral drug selected hepatitis B virus rtA181T/sW172* mutant has a dominant negative secretion defect and alters the typical profile of viral rebound. Hepatology 48:8898.
149. Warner N,, Locarnini S,, Kuiper M,, Bartholomeusz A,, Ayres A,, Yuen L,, Shaw T. 2007. The L80I substitution in the reverse transcriptase domain of the hepatitis B virus polymerase is associated with lamivudine resistance and enhanced viral replication in vitro. Antimicrob Agents Chemother 51:22852292.
150. Santantonio T,, Fasano M,, Durantel S,, Barraud L,, Heichen M,, Guastadisegni A,, Pastore G,, Zoulim F. 2009. Adefovir dipivoxil resistance patterns in patients with lamivudine-resistant chronic hepatitis B. Antivir Ther 14:557565.
151. Tenney DJ,, Levine SM,, Rose RE,, Walsh AW,, Weinheimer SP,, Discotto L,, Plym M,, Pokornowski K,, Yu CF,, Angus P,, Ayres A,, Bartholomeusz A,, Sievert W,, Thompson G,, Warner N,, Locarnini S,, Colonno RJ. 2004. Clinical emergence of entecavir-resistant hepatitis B virus requires additional substitutions in virus already resistant to lamivudine. Antimicrob Agents Chemother 48:34983507.
152. Tenney DJ,, Rose RE,, Baldick CJ,, Levine SM,, Pokornowski KA,, Walsh AW,, Fang J,, Yu CF,, Zhang S,, Mazzucco CE,, Eggers B,, Hsu M,, Plym MJ,, Poundstone P,, Yang J,, Colonno RJ. 2007. Two-year assessment of entecavir resistance in lamivudine-refractory hepatitis B virus patients reveals different clinical outcomes depending on the resistance substitutions present. Antimicrob Agents Chemother 51:902911.
153. 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.
154. Westland CE,, Yang H,, Delaney WEt,, Wulfsohn M,, Lama N,, Gibbs CS,, Miller MD,, Fry J,, Brosgart CL,, Schiff ER,, Xiong S. 2005. Activity of adefovir dipivoxil against all patterns of lamivudine-resistant hepatitis B viruses in patients. J Viral Hepat 12:6773.
155. Angus P,, Vaughan R,, Xiong S,, Yang H,, Delaney W,, Gibbs C,, Brosgart C,, Colledge D,, Edwards R,, Ayres A,, Bartholomeusz A,, Locarnini S. 2003. Resistance to adefovir dipivoxil therapy associated with the selection of a novel mutation in the HBV polymerase. Gastroenterology 125:292297.
156. Borroto-Esoda K,, Miller MD,, Arterburn S. 2007. Pooled analysis of amino acid changes in the HBV polymerase in patients from four major adefovir dipivoxil clinical trials. J Hepatol 47:492498.
157. Fung SK,, Chae HB,, Fontana RJ,, Conjeevaram H,, Marrero J,, Oberhelman K,, Hussain M,, Lok AS. 2006. Virologic response and resistance to adefovir in patients with chronic hepatitis B. J Hepatol 44:283290.
158. Hadziyannis SJ,, Tassopoulos NC,, Heathcote EJ,, Chang TT,, Kitis G,, Rizzetto M,, Marcellin P,, Lim SG,, Goodman Z,, Ma J,, Brosgart CL,, Borroto-Esoda K,, Arterburn S,, Chuck SL, Adefovir Dipivoxil 438 Study Group. 2006. Long-term therapy with adefovir dipivoxil for HBeAg-negative chronic hepatitis B for up to 5 years. Gastroenterology 131:17431751.
159. Villet S,, Pichoud C,, Billioud G,, Barraud L,, Durantel S,, Trépo C,, Zoulim F. 2008. Impact of hepatitis B virus rtA181V/T mutants on hepatitis B treatment failure. J Hepatol 48:747755.
160. Yang H,, Westland C,, Xiong S,, Delaney WE4th. 2004. In vitro antiviral susceptibility of full-length clinical hepatitis B virus isolates cloned with a novel expression vector. Antiviral Res 61:2736.
161. Yeh CT,, Chien RN,, Chu CM,, Liaw YF. 2000. Clearance of the original hepatitis B virus YMDD-motif mutants with emergence of distinct lamivudine-resistant mutants during prolonged lamivudine therapy. Hepatology 31:13181326.
162. Zoulim F,, Locarnini S. 2009. Hepatitis B virus resistance to nucleos(t)ide analogues. Gastroenterology 137:15931608.e1–2.
163. Persing DH (ed). 2011. Molecular Microbiology: Diagnostic Principles and Practice, 2nd ed. ASM Press, Washington, DC.
164. Barbotte L,, Ahmed-Belkacem A,, Chevaliez S,, Soulier A,, Hezode C,, Wajcman H,, Bartels DJ,, Zhou Y,, Ardzinski A,, Mani N,, Rao BG,, George S,, Kwong A,, Pawlotsky JM. 2010. Characterization of V36C, a novel amino acid substitution conferring hepatitis C virus (HCV) resistance to telaprevir, a potent peptidomimetic inhibitor of HCV protease. Antimicrob Agents Chemother 54:26812683.
165. Curry S,, Qiu P,, Tong X. 2008. Analysis of HCV resistance mutations during combination therapy with protease inhibitor boceprevir and PEG-IFN alpha-2b using TaqMan mismatch amplification mutation assay. J Virol Methods 153:156162.
166. Ogert RA,, Howe JA,, Vierling JM,, Kwo PY,, Lawitz EJ,, McCone J,, Schiff ER,, Pound D,, Davis MN,, Gordon SC,, Ravendhran N,, Rossaro L,, Jacobson IM,, Ralston R,, Chaudhri E,, Qiu P,, Pedicone LD,, Brass CA,, Albrecht JK,, Barnard RJ,, Hazuda DJ,, Howe AY. 2013. Resistance-associated amino acid variants associated with boceprevir plus pegylated interferon-α2b and ribavirin in patients with chronic hepatitis C in the SPRINT-1 trial. Antivir Ther 18:387397.
167. Shang L,, Lin K,, Yin Z. 2014. Resistance mutations against HCV protease inhibitors and antiviral drug design. Curr Pharm Des 20:694703.
168. Verbinnen T,, Van Marck H,, Vandenbroucke I,, Vijgen L,, Claes M,, Lin TI,, Simmen K,, Neyts J,, Fanning G,, Lenz O. 2010. Tracking the evolution of multiple in vitro hepatitis C virus replicon variants under protease inhibitor selection pressure by 454 deep sequencing. J Virol 84:1112411133.
169. Abraham B,, Lastere S,, Reynes J,, Bibollet-Ruche F,, Vidal N,, Segondy M. 1999. Ganciclovir resistance and UL97 gene mutations in cytomegalovirus blood isolates from patients with AIDS treated with ganciclovir. J Clin Virol 13:141148.
170. Baldanti F,, Sarasini A,, Silini E,, Barbi M,, Lazzarin A,, Biron KK,, Gerna G. 1995. Four dually resistant human cytomegalovirus strains from AIDS patients: single mutations in UL97 and UL54 open reading frames are responsible for ganciclovir- and foscarnet-specific resistance, respectively. Scand J Infect Dis suppl 99:103104.
171. Baldanti F,, Silini E,, Sarasini A,, Talarico CL,, Stanat SC,, Biron KK,, Furione M,, Bono F,, Palu G,, Gerna G. 1995. A three-nucleotide deletion in the UL97 open reading frame is responsible for the ganciclovir resistance of a human cytomegalovirus clinical isolate. J Virol 69:796800.
172. Bowen EF,, Cherrington JM,, Lamy PD,, Griffiths PD,, Johnson MA,, Emery VC. 1999. Quantitative changes in cytomegalovirus DNAemia and genetic analysis of the UL97 and UL54 genes in AIDS patients receiving cidofovir following ganciclovir therapy. J Med Virol 58:402407.
173. Bowen EF,, Johnson MA,, Griffiths PD,, Emery VC. 1997. Development of a point mutation assay for the detection of human cytomegalovirus UL97 mutations associated with ganciclovir resistance. J Virol Methods 68:225234.
174. Chou S,, Marousek G,, Guentzel S,, Follansbee SE,, Poscher ME,, Lalezari JP,, Miner RC,, Drew WL. 1997. Evolution of mutations conferring multidrug resistance during prophylaxis and therapy for cytomegalovirus disease. J Infect Dis 176:786789.
175. Chou S,, Meichsner CL. 2000. A nine-codon deletion mutation in the cytomegalovirus UL97 phosphotransferase gene confers resistance to ganciclovir. Antimicrob Agents Chemother 44:183185.
176. Cihlar T,, Fuller MD,, Mulato AS,, Cherrington JM. 1998. A point mutation in the human cytomegalovirus DNA polymerase gene selected in vitro by cidofovir confers a slow replication phenotype in cell culture. Virology 248:382393.
177. Erice A,, Borrell N,, Li W,, Miller WJ,, Balfour HHJr. 1998. Ganciclovir susceptibilities and analysis of UL97 region in cytomegalovirus (CMV) isolates from bone marrow recipients with CMV disease after antiviral prophylaxis. J Infect Dis 178:531534.
178. Cihlar T,, Fuller MD,, Cherrington JM. 1998. Characterization of drug resistance-associated mutations in the human cytomegalovirus DNA polymerase gene by using recombinant mutant viruses generated from overlapping DNA fragments. J Virol 72:59275936.
179. Hanson MN,, Preheim LC,, Chou S,, Talarico CL,, Biron KK,, Erice A. 1995. Novel mutation in the UL97 gene of a clinical cytomegalovirus strain conferring resistance to ganciclovir. Antimicrob Agents Chemother 39:12041205.
180. Swierkosz EM,, Scholl DR,, Brown JL,, Jollick JD,, Gleaves CA. 1987. Improved DNA hybridization method for detection of acyclovir-resistant herpes simplex virus. Antimicrob Agents Chemother 31:14651469.
181. Balows A (ed). 1991. Manual of Clinical Microbiology, 5th ed. American Society for Microbiology, Washington, DC.
182. St Clair MH,, Martin JL,, Tudor-Williams G,, Bach MC,, Vavro CL,, King DM,, Kellam P,, Kemp SD,, Larder BA. 1991. Resistance to ddI and sensitivity to AZT induced by a mutation in HIV-1 reverse transcriptase. Science 253:15571559.
183. Safrin S,, Assaykeen T,, Follansbee S,, Mills J. 1990. Foscarnet therapy for acyclovir-resistant mucocutaneous herpes simplex virus infection in 26 AIDS patients: preliminary data. J Infect Dis 161:10781084.
184. Safrin S,, Crumpacker C,, Chatis P,, Davis R,, Hafner R,, Rush J,, Kessler HA,, Landry B,, Mills J. 1991. A controlled trial comparing foscarnet with vidarabine for acyclovir-resistant mucocutaneous herpes simplex in the acquired immunodeficiency syndrome. The AIDS Clinical Trials Group. N Engl J Med 325:551555.
185. Drew WL,, Miner RC,, Busch DF,, Follansbee SE,, Gullett J,, Mehalko SG,, Gordon SM,, Owen WFJr,, Matthews TR,, Buhles WC,, DeArmond B. 1991. Prevalence of resistance in patients receiving ganciclovir for serious cytomegalovirus infection. J Infect Dis 163:716719.
186. Pepin JM,, Simon F,, Dazza MC,, Brun-Vézinet F. 1992. The clinical significance of in vitro cytomegalovirus susceptibility to antiviral drugs. Res Virol 143:126128.
187. Jacobson MA,, Berger TG,, Fikrig S,, Becherer P,, Moohr JW,, Stanat SC,, Biron KK. 1990. Acyclovir-resistant varicella zoster virus infection after chronic oral acyclovir therapy in patients with the acquired immunodeficiency syndrome (AIDS). Ann Intern Med 112:187191.
188. Safrin S,, Berger TG,, Gilson I,, Wolfe PR,, Wofsy CB,, Mills J,, Biron KK. 1991. Foscarnet therapy in five patients with AIDS and acyclovir-resistant varicella-zoster virus infection. Ann Intern Med 115:1921.

Tables

Generic image for table
TABLE 1

Clinical situations where antiviral resistance testing may be indicated

Citation: Huang D, Bankowski M. 2015. Susceptibility Test Methods: Viruses*, p 1913-1931. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch112
Generic image for table
TABLE 2

Proposed guidelines for antiviral susceptibility results of herpes group and influenza A viruses

Citation: Huang D, Bankowski M. 2015. Susceptibility Test Methods: Viruses*, p 1913-1931. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch112
Generic image for table
TABLE 3

Gene targets used for antiviral resistance testing with genotypic methods

Citation: Huang D, Bankowski M. 2015. Susceptibility Test Methods: Viruses*, p 1913-1931. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch112
Generic image for table
TABLE 4

CMV UL54 and UL97 gene targets and the associated mutations conferring antiviral resistance

Citation: Huang D, Bankowski M. 2015. Susceptibility Test Methods: Viruses*, p 1913-1931. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch112
Generic image for table
TABLE 5

Bioinformatics-based sites for analysis of resistance from genotyped samples

Citation: Huang D, Bankowski M. 2015. Susceptibility Test Methods: Viruses*, p 1913-1931. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch112

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