HIV-phyloTSI

Estimate time since infection (TSI) from HIV deep-sequencing data. Amplicon-based and capture-based sequencing are supported. This code requires sequencing reads for each sample to be mapped using shiver, and the resulting BAM files batched and processed by phyloscanner. We recommend batching 5-100 samples per phyloscanner run to avoid excessive runtimes for large datasets, and using the GTR+F+R6 (FreeRate) substitution model. Example input files are provided in ExampleInputs.

Installation using conda:

1. Clone this repository and cd to its location: git clone git@github.com:BDI-pathogens/HIV-phyloTSI.git; cd HIV-phyloTSI
2. Create the conda environment: conda env create -f hivphylotsi.yml
3. Activate it: conda activate hivphylosti
   • Alternatively, you can manually install the requirements: python3, pandas v0.25.3 and scikit-learn v0.22.
4. Test run using example input data: ./HIVPhyloTSI.py -d Model -p ExampleInputs/testpatstats.csv -m ExampleInputs/testmaf.csv -o test.csv

A csv file test.csv is created with TSI estimates for data in ExampleInputs/. The input and output data are described in more detail below.

Input:

Two CSV files:

1. PatStats: patStats.csv from phyloscanner, where host.id refers to individual samples (do not merge multiple timepoints); and

2. MAF: a csv file of minor allele frequencies (MAF), where rows match the host.id values in your PatStats file, and columns are labelled by position relative to HXB2. MAF is calculated from the shiver BaseFreqs_WithHXB2.csv, or from any pileup of reads, at each HXB2 position as follows:

        MAF = 1-max(A+C+G+T)/(A+C+G+T)
   

where A, C, G and T are counts of each base (ignoring gaps and Ns).

Output:

A CSV file is produced that contains the aggregated values for gag, pol, gp120 and gp41 regions for MAF at codon position 1/2 and codon position 3, largest.subgraph.rtt from phyloscanner (LRTT), number of tips and whether the sample looks like a dual infection. A binary indicator for amplicon-based sequencing is also added (is_mrc). The final columns are predictions from the model, as follows:

Square root TSI values (intermediate output):

• RF_pred_sqrt - prediction of square-root transformed TSI
• RF_std - standard error on the above, calculated as standard deviation of the full range of predictions from the 1000 decision trees in the forest
• RF_cc025 and RF_cc975 - the 95% limits of the above distribution, ie the 2.5th and 97.5th percentile of predictions from the 1000 decision trees
• RF_pred_MAE - the prediction error, calculated as the mean in square-root-space of the prediction from the error model

Linearised TSI values (final output):

• RF_pred_linear - linearised TSI estimate ( model prediction in years ) - calculated as RF_pred_sqrt^2
• RF_pred_min_linear and RF_pred_max_linear - limits of the prediction interval in linear TSI (ie the predicted seroconversion interval), calculated as 2 standard deviations of the error model above and below the point estimate.