HerpesDRG: a comprehensive resource for human herpesvirus antiviral drug resistance genotyping.
Aciclovir
Amenamevir
CMV
Database
Drug-resistance
Ganciclovir
Herpes
Letermovir
VZV
Journal
BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194
Informations de publication
Date de publication:
27 Aug 2024
27 Aug 2024
Historique:
received:
14
04
2024
accepted:
29
07
2024
medline:
28
8
2024
pubmed:
28
8
2024
entrez:
27
8
2024
Statut:
epublish
Résumé
The prevention and treatment of many herpesvirus associated diseases is based on the utilization of antiviral therapies, however therapeutic success is limited by the development of drug resistance. Currently no single database cataloguing resistance mutations exists, which hampers the use of sequence data for patient management. We therefore developed HerpesDRG, a drug resistance mutation database that incorporates all the known resistance genes and current treatment options, built from a systematic review of available genotype to phenotype literature. The database is released along with an R package that provides a simple approach to resistance variant annotation and clinical implication analysis from common sanger and next generation sequencing data. This represents the first openly available and community maintainable database of drug resistance mutations for the human herpesviruses (HHV), developed for the community of researchers and clinicians tackling HHV drug resistance.
Identifiants
pubmed: 39192205
doi: 10.1186/s12859-024-05885-5
pii: 10.1186/s12859-024-05885-5
doi:
Substances chimiques
Antiviral Agents
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
279Subventions
Organisme : Medical Research Council
ID : MR/N013867/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 204870/Z/16/Z
Pays : United Kingdom
Informations de copyright
© 2024. The Author(s).
Références
Limaye AP. Ganciclovir-resistant cytomegalovirus in organ transplant recipients. Clin Infect Dis. 2002;35(7):866–72.
doi: 10.1086/342385
pubmed: 12228824
Ariza-Heredia EJ, Nesher L, Chemaly RF. Cytomegalovirus diseases after hematopoietic stem cell transplantation: a mini-review. Cancer Lett. 2014;342(1):1–8.
doi: 10.1016/j.canlet.2013.09.004
pubmed: 24041869
Emery V. Investigation of CMV disease in immunocompromised patients. J Clin Pathol. 2001;54(2):84–8.
doi: 10.1136/jcp.54.2.84
pubmed: 11215290
pmcid: 1731357
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.
doi: 10.1111/ctr.13526
pubmed: 30859647
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.
doi: 10.1128/CMR.16.1.114-128.2003
pubmed: 12525428
pmcid: 145299
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.
doi: 10.1093/infdis/jix042
pubmed: 28453848
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.
doi: 10.1016/j.antiviral.2013.10.011
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.
doi: 10.1155/2014/342319
pubmed: 24991428
pmcid: 4058803
Lurain NS, Chou S. Antiviral drug resistance of human cytomegalovirus. Clin Microbiol Rev. 2010;23(4):689–712.
doi: 10.1128/CMR.00009-10
pubmed: 20930070
pmcid: 2952978
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.
doi: 10.1097/TP.0000000000002191
pubmed: 29596116
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.
doi: 10.1016/S0166-0934(02)00103-9
pubmed: 12270654
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.
doi: 10.1128/AAC.49.7.2710-2715.2005
pubmed: 15980340
pmcid: 1168698
Sauerbrei A, Taut J, Zell R, Wutzler P. Resistance testing of clinical varicella-zoster virus strains. Antiviral Res. 2011;90(3):242–7.
doi: 10.1016/j.antiviral.2011.04.005
pubmed: 21539861
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.
doi: 10.1186/s12879-021-06694-4
pubmed: 34556034
pmcid: 8461837
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.
doi: 10.1093/cid/cis879
pubmed: 23074321
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.
doi: 10.1093/jac/dkv285
pubmed: 26433780
Chou S. Advances in the genotypic diagnosis of cytomegalovirus antiviral drug resistance. Antiviral Res. 2020;1(176): 104711.
doi: 10.1016/j.antiviral.2020.104711
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.
doi: 10.1093/infdis/jiz601
pubmed: 32134488
pmcid: 7057790
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.
doi: 10.1016/j.antiviral.2009.10.004
pubmed: 19853628
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.
doi: 10.1093/nar/gks1022
pubmed: 23125365
Shafer RW. Rationale and uses of a public HIV drug-resistance database. J Infect Dis. 2006;194(Suppl 1):S51–8.
doi: 10.1086/505356
pubmed: 16921473
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.
doi: 10.1128/jcm.00429-23
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.
doi: 10.1186/1471-2156-14-6
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.
doi: 10.1016/j.jcv.2016.04.017
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.
doi: 10.1016/j.antiviral.2019.104647
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.
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.
doi: 10.1111/1346-8138.13948
pubmed: 28681394
pmcid: 5697646
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.
doi: 10.1128/AAC.01623-15
pubmed: 26259791
pmcid: 4576131
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.
doi: 10.1128/AAC.00214-16
pubmed: 27044553
pmcid: 4879386
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.
doi: 10.1128/JVI.77.14.7820-7829.2003
pubmed: 12829822
pmcid: 161916
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80.
doi: 10.1093/molbev/mst010
pubmed: 23329690
pmcid: 3603318
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.
doi: 10.1099/mgen.0.000056
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.
doi: 10.1101/gr.129684.111
pubmed: 22300766
pmcid: 3290792
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.
doi: 10.1093/bioinformatics/btu168
pubmed: 24681907
pmcid: 4080743
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=shiny
Pedersen 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.pdf
Lazaro 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