cmvdrg

overview

cmvdrg is a R package to enable antiviral drug resistance genotyping, with Human Cytomegalovirus sequencing data. Accepted inputs are FASTA (whole genomes & fragments) which will be mapped to RefSeq NC_006273.2. NGS variant data assembled to NC_006273.2 is accepted in VCF >= ver4.0 & Varscan2 tab formats.

Database

Contains the relationships between:

• Mutation
• Drug susceptibility, values are EC50 fold changes to susceptible strains. “Susceptible” or “Resistant” are present if data is anecdotal.
• The method for Resistance Phenotyping, including where possible strain information used in marker transfer. i.e. AD169, TOWNE.
• Publication reference, DOI, web address & review paper reference if used.
• Where a co-mutation susceptibility profile is available for a known drug, this is included.
• Administrative information, last update to row & whether it is used in calculations or not. i.e. A “Active”" is included, where there is ambiguity the status field is “U” Unused, or “R” to Review

Web service

A user-friendly Shiny Applications has been bundled with this package. The same application is available over the internet here http://cmv-resistance.ucl.ac.uk/cmvdrg/ where the terms of use are contained.

Installation

You can install the current version from GitHub with:

# install.packages("devtools")
devtools::install_github("ucl-pathgenomics/cmvdrg")

Dependencies for FASTA file handling are MAFFT and SNP-Sites available preferably via conda. snp-sites >= 2.3 has been tested.

conda config --add channels bioconda
conda install snp-sites
conda install mafft

Usage

library("cmvdrg")

#----- call resistant variants
my_sample = system.file("testdata", "A10.vcf", package = "cmvdrg")

data = call_resistance(infile = my_sample, all_mutations = F,inc_anecdotal = F)

data[ , c("change", "freq", "Ganciclovir", "Maribavir", "Foscarnet", "ref_doi")]
#>       change   freq Ganciclovir Maribavir Foscarnet
#> 1 UL54_D588N   5.2%           2                 2.8
#> 2 UL54_D588N   5.2%         3.8                   9
#> 3 UL97_C592G 10.77%           3                    
#> 4 UL97_C592G 10.77%           3                    
#> 5 UL97_C592G 10.77%           3                    
#> 6 UL97_H411Y  1.69%                    18          
#> 7 UL97_H411Y  1.69%         0.5        12          
#> 8 UL97_T409M 37.13%                    90          
#> 9 UL97_T409M 37.13%         0.9        81          
#>                                           ref_doi
#> 1                  doi: 10.1016/j.jcv.2011.01.004
#> 2   https://doi.org/10.1016/S1386-6532(01)00160-3
#> 3                            10.1128/AAC.00186-10
#> 4       https://dx.doi.org/10.1128%2FAAC.01259-10
#> 5 https://doi.org/10.1016/j.antiviral.2019.104616
#> 6 https://doi.org/10.1016/j.antiviral.2019.104616
#> 7                       DOI: 10.1128/JVI.01787-07
#> 8 https://doi.org/10.1016/j.antiviral.2019.104616
#> 9                  https://doi.org/10.1086/518514


#----- call all variants
mutations_all = call_resistance(infile = my_sample, all_mutations = T)

#to view all mutations in resistance genes we can filter
mutations_res = mutations_all[mutations_all$GENEID %in% c("UL54", "UL97", "UL27", "UL51", "UL56", "UL89"),]


# are there any non-synonymous (DNA variants that result in a change of amino acid) variants in resistance genes
mutations_res_nonsyn = mutations_res[mutations_res$CONSEQUENCE == "nonsynonymous",]


# here the top 3 mutations are nonsynonymous, with no identified resistance effect.
head(mutations_res_nonsyn[,c(1,8,21,32:40)])
#>           change   freq   CONSEQUENCE Ganciclovir Cidofovir Foscarnet
#> 996    UL51_T47M 99.88% nonsynonymous        <NA>      <NA>      <NA>
#> 1002 UL54_A1108T 99.05% nonsynonymous        <NA>      <NA>      <NA>
#> 1004  UL54_A692V   100% nonsynonymous        <NA>      <NA>      <NA>
#> 1007  UL54_D588N   5.2% nonsynonymous           2       1.3       2.8
#> 1008  UL54_D588N   5.2% nonsynonymous         3.8       2.7         9
#> 1018  UL54_L897S 99.82% nonsynonymous        <NA>      <NA>      <NA>
#>      Brincidofovir Letermovir Tomeglovir GW275175 Maribavir Cyclopropavir
#> 996             NA       <NA>         NA       NA      <NA>            NA
#> 1002            NA       <NA>         NA       NA      <NA>            NA
#> 1004            NA       <NA>         NA       NA      <NA>            NA
#> 1007            NA                    NA       NA                      NA
#> 1008            NA                    NA       NA                      NA
#> 1018            NA       <NA>         NA       NA      <NA>            NA

other functionality

#----- visualise variants
plot_lollipop(data, "UL97")

#----- Generate a clinical overview of strain sensetivity
#clin_table = make_clin_table(data)

#-----view the full database
db = cmvdrg_data()
head(db$aa_change)
#> [1] "D301N" "C304S" "N408D" "N408K" "N408S" "N410K"


#----- run the shiny application
# runShinyCMV()

Getting help

If you encounter a clear bug, please file an issue with a minimal reproducible example on the GitHub Issues page. For questions and other discussions feel free to contact. Oscar Charles - maintainer