HerpesDRG: a comprehensive resource for human herpesvirus antiviral drug resistance genotyping | BMC Bioinformatics

Limaye AP. Ganciclovir-resistant cytomegalovirus in organ transplant recipients. Clin Infect Dis. 2002;35(7):866–72.Article 
CAS 
PubMed 

Google Scholar 
Ariza-Heredia EJ, Nesher L, Chemaly RF. Cytomegalovirus diseases after hematopoietic stem cell transplantation: a mini-review. Cancer Lett. 2014;342(1):1–8.Article 
CAS 
PubMed 

Google Scholar 
Emery V. Investigation of CMV disease in immunocompromised patients. J Clin Pathol. 2001;54(2):84–8.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Lee DH, Zuckerman RA, AST Infectious Diseases Community of Practice. Herpes simplex virus infections in solid organ transplantation: guidelines from the American Society of Transplantation Infectious Diseases Community of Practice. Clin Transplant. 2019;33(9):e13526.Article 
PubMed 

Google Scholar 
Bacon TH, Levin MJ, Leary JJ, Sarisky RT, Sutton D. Herpes simplex virus resistance to acyclovir and penciclovir after two decades of antiviral therapy. Clin Microbiol Rev. 2003;16(1):114–28.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kakiuchi S, Tsuji M, Nishimura H, Yoshikawa T, Wang L, Takayama-Ito M, et al. Association of the emergence of acyclovir-resistant herpes simplex virus type 1 with prognosis in hematopoietic stem cell transplantation patients. J Infect Dis. 2017;215(6):865–73.Article 
CAS 
PubMed 

Google Scholar 
Komatsu TE, Pikis A, Naeger LK, Harrington PR. Resistance of human cytomegalovirus to ganciclovir/valganciclovir: a comprehensive review of putative resistance pathways. Antiviral Res. 2014;1(101):12–25.Article 

Google Scholar 
Patel SJ, Kuten SA, Knight RJ, Hong DM, Gaber AO. Resolution of mild ganciclovir-resistant cytomegalovirus disease with reduced-dose cidofovir and CMV-hyperimmune globulin. J Transplant. 2014;2014: 342319.Article 
PubMed 
PubMed Central 

Google Scholar 
Lurain NS, Chou S. Antiviral drug resistance of human cytomegalovirus. Clin Microbiol Rev. 2010;23(4):689–712.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kotton CN, Kumar D, Caliendo AM, Huprikar S, Chou S, Danziger-Isakov L, et al. The third international consensus guidelines on the management of cytomegalovirus in solid-organ transplantation. Transplantation. 2018;102(6):900–31.Article 
PubMed 

Google Scholar 
Danve C, Morfin F, Thouvenot D, Aymard M. A screening dye-uptake assay to evaluate in vitro susceptibility of herpes simplex virus isolates to acyclovir. J Virol Methods. 2002;105(2):207–17.Article 
CAS 
PubMed 

Google Scholar 
Chou S, Van Wechel LC, Lichy HM, Marousek GI. Phenotyping of cytomegalovirus drug resistance mutations by using recombinant viruses incorporating a reporter gene. Antimicrob Agents Chemother. 2005;49(7):2710–5.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sauerbrei A, Taut J, Zell R, Wutzler P. Resistance testing of clinical varicella-zoster virus strains. Antiviral Res. 2011;90(3):242–7.Article 
CAS 
PubMed 

Google Scholar 
Paolucci S, Campanini G, Cassaniti I, Tebaldi A, Novazzi F, Fratini A, et al. Emergence of Letermovir-resistant HCMV UL56 mutant during rescue treatment in a liver transplant recipient with ganciclovir-resistant infection HCMV: a case report. BMC Infect Dis. 2021;21(1):994.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
van der Beek MT, Vermont CL, Bredius RGM, Marijt EWA, van der Blij-de Brouwer CS, Kroes ACM, et al. Persistence and antiviral resistance of varicella zoster virus in hematological patients. Clin Infect Dis. 2013;56(3):335–43.Article 
PubMed 

Google Scholar 
Sauerbrei A, Bohn-Wippert K, Kaspar M, Krumbholz A, Karrasch M, Zell R. Database on natural polymorphisms and resistance-related non-synonymous mutations in thymidine kinase and DNA polymerase genes of herpes simplex virus types 1 and 2. J Antimicrob Chemother. 2016;71(1):6–16.Article 
CAS 
PubMed 

Google Scholar 
Chou S. Advances in the genotypic diagnosis of cytomegalovirus antiviral drug resistance. Antiviral Res. 2020;1(176): 104711.Article 

Google Scholar 
Razonable RR, Inoue N, Pinninti SG, Boppana SB, Lazzarotto T, Gabrielli L, et al. Clinical diagnostic testing for human cytomegalovirus infections. J Infect Dis. 2020;221(Supplement_1):S74-85.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chevillotte M, von Einem J, Meier BM, Lin FM, Kestler HA, Mertens T. A new tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes. Antiviral Res. 2010;85(2):318–27.Article 
CAS 
PubMed 

Google Scholar 
Hayer J, Jadeau F, Deléage G, Kay A, Zoulim F, Combet C. HBVdb: a knowledge database for Hepatitis B Virus. Nucleic Acids Res. 2013;41(D1):D566–70.Article 
CAS 
PubMed 

Google Scholar 
Shafer RW. Rationale and uses of a public HIV drug-resistance database. J Infect Dis. 2006;194(Suppl 1):S51–8.Article 
PubMed 

Google Scholar 
Streck NT, Espy MJ, Ferber MJ, Klee EW, Razonable RR, Gonzalez D, et al. Use of next-generation sequencing to detect mutations associated with antiviral drug resistance in cytomegalovirus. J Clin Microbiol. 2023;26: e0042923.Article 

Google Scholar 
Chin EL, da Silva C, Hegde M. Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations. BMC Genet. 2013;19(14):6.Article 

Google Scholar 
Garrigue I, Moulinas R, Recordon-Pinson P, Delacour ML, Essig M, Kaminski H, et al. Contribution of next generation sequencing to early detection of cytomegalovirus UL97 emerging mutants and viral subpopulations analysis in kidney transplant recipients. J Clin Virol. 2016;1(80):74–81.Article 

Google Scholar 
Guermouche H, Burrel S, Mercier-Darty M, Kofman T, Rogier O, Pawlotsky JM, et al. Characterization of the dynamics of human cytomegalovirus resistance to antiviral drugs by ultra-deep sequencing. Antiviral Res. 2020;1(173): 104647.Article 

Google Scholar 
Houldcroft CJ, Bryant JM, Depledge DP, Margetts BK, Simmonds J, Nicolaou S, et al. Detection of low frequency multi-drug resistance and novel putative maribavir resistance in immunocompromised pediatric patients with cytomegalovirus. Front Microbiol. 2016;9:7.
Google Scholar 
Venturini C, Colston JM, Charles O, Lankina A, Best T, Atkinson C, et al. Persistent low-level variants in a subset of viral genes are highly predictive of poor outcome in immunocompromised patients with cytomegalovirus infection. J Infect Dis. 2024;jiae001. https://doi.org/10.1093/infdis/jiae001.Kawashima M, Nemoto O, Honda M, Watanabe D, Nakayama J, Imafuku S, et al. Amenamevir, a novel helicase–primase inhibitor, for treatment of herpes zoster: a randomized, double-blind, valaciclovir-controlled phase 3 study. J Dermatol. 2017;44(11):1219–27.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Serris A, Pouvaret A, Loiseau C, Abid H, Burrel S, Fourgeaud J, et al. Pritelivir for recurrent aciclovir-resistant herpes simplex virus 2 infections in immunocompromised patients. J Antimicrob Chemother. 2022;dkac165. https://doi.org/10.1093/jac/dkac165.Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2018;46(Database issue):D8–13.Chou S. Rapid in vitro evolution of human cytomegalovirus ul56 mutations that confer letermovir resistance. Antimicrob Agents Chemother. 2015;59(10):6588–93.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chou S, Ercolani RJ, Lanier ER. Novel cytomegalovirus UL54 DNA polymerase gene mutations selected in vitro that confer brincidofovir resistance. Antimicrob Agents Chemother. 2016;60(6):3845–8.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bestman-Smith J, Boivin G. Drug resistance patterns of recombinant herpes simplex virus DNA polymerase mutants generated with a set of overlapping cosmids and plasmids. J Virol. 2003;77(14):7820–9.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genomics. 2016;2(4):e000056.Article 

Google Scholar 
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22(3):568–76.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Obenchain V, Lawrence M, Carey V, Gogarten S, Shannon P, Morgan M. VariantAnnotation : a bioconductor package for exploration and annotation of genetic variants. Bioinformatics. 2014;30(14):2076–8.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
R Core Team R. A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2014. Available from: http://www.R-project.org/Chang W, Cheng J, Yihui X, Jonathan M. shiny: Web Application Framework for R. R package version 1.3.2 [Internet]. Available from: https://CRAN.R-project.org/package=shinyPedersen MS, Petersen NF, Nielsen CY, Kirkby NS, Schønning K. Identification of resistance mutations in human cytomegalovirus by Oxford Nanopore sequencing [Internet]. Poster presented at: ECCMID 2022; 2022 [cited 2024 Jun 10]. Available from: https://www.rigshospitalet.dk/afdelinger-og-klinikker/diagnostisk/klinisk-mikrobiologi/forskning/Documents/2022/identification-of-resistance-mutations-in-human-cytomegalovirus-by-oxford-nanopore-sequencing.pdfLazaro F. CMV Resistance testing (UL54 and UL97). 2023 Dec 5 [cited 2024 Jun 10]; Available from: https://doi.org/10.17504/protocols.io.bp2l6xy4zlqe/v1

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