Introduction

lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages.

Quick start

Installation

lineagespot is distributed as a Bioconductor package and requires R (version “4.1”), which can be installed on any operating system from CRAN, and Bioconductor (version “3.14”).

To install lineagespot package enter the following commands in your R session:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("lineagespot")

## Check that you have a valid Bioconductor installation
BiocManager::valid()

Raw data analysis

Example fastq files are provided through zenodo. For the pre processing steps of them, the bioinformatics analysis pipeline is provided here.

Running lineagespot

Once lineagespot is successfully installed, it can be loaded as follow:

library(lineagespot)

lineagespot can be run by calling one function that implements the overall pipeline:

results <- lineagespot(vcf_folder = system.file("extdata", "vcf-files", 
                                                package = "lineagespot"),

                      gff3_path = system.file("extdata", 
                                              "NC_045512.2_annot.gff3", 
                                              package = "lineagespot"),

                      ref_folder = system.file("extdata", "ref", 
                                               package = "lineagespot"))

Explore the results

The function returns three tables:

An overall variant table containing all variants included in the input VCF files, along with the related information (gene, location etc.)

# overall table
head(results$variants.table)
#>          CHROM   POS                         ID    REF    ALT    DP AD_ref
#>         <char> <num>                     <char> <char> <char> <int>  <num>
#> 1: NC_045512.2   328   NC_045512.2;328;ACA;ACCA    ACA   ACCA    36     34
#> 2: NC_045512.2   355        NC_045512.2;355;C;T      C      T    42     41
#> 3: NC_045512.2   366        NC_045512.2;366;C;T      C      T    42     28
#> 4: NC_045512.2   401 NC_045512.2;401;CTTAA;CTAA  CTTAA   CTAA    37     35
#> 5: NC_045512.2   406     NC_045512.2;406;AGA;AA    AGA     AA    35     34
#> 6: NC_045512.2   421        NC_045512.2;421;C;A      C      A    35     34
#>    AD_alt Gene_Name  Nt_alt AA_alt         AF codon_num                sample
#>     <num>    <char>  <char> <char>      <num>     <num>                <char>
#> 1:      1     ORF1a  64dupC  Q22fs 0.02777778        21 SampleA_freebayes_ann
#> 2:      1     ORF1a   90C>T   G30G 0.02380952        30 SampleA_freebayes_ann
#> 3:     14     ORF1a  101C>T   S34F 0.33333333        34 SampleA_freebayes_ann
#> 4:      2     ORF1a 138delT  D48fs 0.05405405        46 SampleA_freebayes_ann
#> 5:      1     ORF1a 142delG  D48fs 0.02857143        47 SampleA_freebayes_ann
#> 6:      1     ORF1a  156C>A   G52G 0.02857143        52 SampleA_freebayes_ann

A table with the identified overlaps/hits between the variant table and the given lineage reports.

# lineages' hits
head(results$lineage.hits)
#>    Gene_Name AA_alt                sample    DP AD_alt        AF lineage
#>       <char> <char>                <char> <num>  <num>     <num>  <char>
#> 1:         M   I82T SampleC_freebayes_ann  3984   2770 0.6952811    AY.1
#> 2:         N   D63G SampleC_freebayes_ann  2180    787 0.3610092    AY.1
#> 3:         N  R203M SampleC_freebayes_ann  4147   4125 0.9946950    AY.1
#> 4:         N  G215C SampleC_freebayes_ann  4477   2574 0.5749386    AY.1
#> 5:         N  D377Y SampleC_freebayes_ann  4271   1623 0.3800047    AY.1
#> 6:     ORF1a A1306S SampleC_freebayes_ann  2202   1267 0.5753860    AY.1

A lineage report table where metrics for the abundance of each lineage are computed. To this end, the mean AF (allele frequence) of the variants per lineage, the mean AF of the unique variants per lineage and the non-zero min. AF of the lineage’s unique variants are computed. Moreover given a AF threshold the number of variants in each sample is computed along with the resulting proportion (Number of variants to the number of lineage rules).

# lineagespot report
head(results$lineage.report)
#>    lineage                sample     meanAF meanAF_uniq minAF_uniq_nonzero
#>     <char>                <char>      <num>       <num>              <num>
#> 1:    AY.1 SampleA_freebayes_ann 0.08333333   0.0000000                 NA
#> 2:    AY.1 SampleB_freebayes_ann 0.08333333   0.0000000                 NA
#> 3:    AY.1 SampleC_freebayes_ann 0.43162568   0.0000000                 NA
#> 4:    AY.2 SampleA_freebayes_ann 0.07692308   0.0000000                 NA
#> 5:    AY.2 SampleB_freebayes_ann 0.07692308   0.0000000                 NA
#> 6:    AY.2 SampleC_freebayes_ann 0.33117826   0.1198191          0.1594335
#>        N lineage N. rules lineage prop.
#>    <int>            <int>         <num>
#> 1:     1               31    0.03225806
#> 2:     1               31    0.03225806
#> 3:     6               31    0.19354839
#> 4:     1               29    0.03448276
#> 5:     1               29    0.03448276
#> 6:     4               29    0.13793103

Session info

Here is the output of sessionInfo() on the system on which this document was compiled running pandoc 3.2.1:

#> R version 4.4.1 (2024-06-14)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] lineagespot_1.11.0 RefManageR_1.4.0   BiocStyle_2.35.0  
#> 
#> loaded via a namespace (and not attached):
#>  [1] KEGGREST_1.45.1             SummarizedExperiment_1.35.5
#>  [3] rjson_0.2.23                xfun_0.48                  
#>  [5] bslib_0.8.0                 Biobase_2.67.0             
#>  [7] lattice_0.22-6              vctrs_0.6.5                
#>  [9] tools_4.4.1                 bitops_1.0-9               
#> [11] generics_0.1.3              curl_5.2.3                 
#> [13] stats4_4.4.1                parallel_4.4.1             
#> [15] AnnotationDbi_1.69.0        RSQLite_2.3.7              
#> [17] blob_1.2.4                  Matrix_1.7-1               
#> [19] BSgenome_1.75.0             data.table_1.16.2          
#> [21] S4Vectors_0.43.2            lifecycle_1.0.4            
#> [23] GenomeInfoDbData_1.2.13     compiler_4.4.1             
#> [25] stringr_1.5.1               Rsamtools_2.21.2           
#> [27] Biostrings_2.75.0           codetools_0.2-20           
#> [29] GenomeInfoDb_1.41.2         htmltools_0.5.8.1          
#> [31] sys_3.4.3                   buildtools_1.0.0           
#> [33] sass_0.4.9                  RCurl_1.98-1.16            
#> [35] yaml_2.3.10                 crayon_1.5.3               
#> [37] jquerylib_0.1.4             BiocParallel_1.41.0        
#> [39] cachem_1.1.0                DelayedArray_0.33.1        
#> [41] abind_1.4-8                 digest_0.6.37              
#> [43] stringi_1.8.4               restfulr_0.0.15            
#> [45] VariantAnnotation_1.51.2    maketools_1.3.1            
#> [47] bibtex_0.5.1                fastmap_1.2.0              
#> [49] grid_4.4.1                  cli_3.6.3                  
#> [51] SparseArray_1.5.45          magrittr_2.0.3             
#> [53] S4Arrays_1.5.11             GenomicFeatures_1.57.1     
#> [55] XML_3.99-0.17               UCSC.utils_1.1.0           
#> [57] backports_1.5.0             bit64_4.5.2                
#> [59] lubridate_1.9.3             timechange_0.3.0           
#> [61] rmarkdown_2.28              XVector_0.45.0             
#> [63] httr_1.4.7                  matrixStats_1.4.1          
#> [65] bit_4.5.0                   png_0.1-8                  
#> [67] memoise_2.0.1               evaluate_1.0.1             
#> [69] knitr_1.48                  BiocIO_1.17.0              
#> [71] GenomicRanges_1.57.2        IRanges_2.39.2             
#> [73] rtracklayer_1.65.0          rlang_1.1.4                
#> [75] Rcpp_1.0.13                 glue_1.8.0                 
#> [77] DBI_1.2.3                   BiocManager_1.30.25        
#> [79] xml2_1.3.6                  BiocGenerics_0.53.0        
#> [81] jsonlite_1.8.9              R6_2.5.1                   
#> [83] plyr_1.8.9                  GenomicAlignments_1.41.0   
#> [85] MatrixGenerics_1.17.1       zlibbioc_1.51.2