Time since Infection - Intrapatient HIV evolution

Estimate time since infection from NGS diversity

Introduction

This page implements the method to estimate the date of infection from NGS diversity data as presented in Puller et al, biorxiv, 10.1101/129387.
The estimates are based on whole genome diversity data from the eleven patients studied here with well characterized date of infection. Those data are used to estimate the rate at which intra-host diversity increases over time, which in turn is used to estimate the date of infection from diversity measurements.

Input

Input diversity

HXB2 coordinates: to

Minor variant cutoff:

Results

Point estimate of duration of infection: years

Interquartile range of duration of infection: years

Mean absolute error: years

Conversion formula

For batch analysis, please use the formula below to convert diversity measurements in the specified region into estimates of the time since infection:

ETI = + x diversity

Diversity relative to training data

The grey dots in the graph show the diversity of samples used to train the estimator. They are recalculated from the raw data specifically for the cutoff and region specified above. The red dot indicates the input diversity.

Distribution

The histogram shows the distribution of fit residuals centered on the estimated time of infection for the parameters above. This distribution is merely meant to give an impression of the variability assuming that the diversity estimate is based on data of similar depth and quality as training data. Negative estimates are omitted.

Make a new estimate:

Enter HXB2 coordinates and diversity

Enter diversity (average hamming distance), the cutoff used to to call minor variants, and the start and end of the region across which diversity is calculated.

Diversity:
Minor variant cutoff:
Region start (HXB2):
Region end (HXB2):
Codon position:

Note: "Codon position" applies only when the entire region is within one gene!

HXB2 coordinates of major landmarks

gene	start	end
gag	790	2292
p17	790	1185
p24	1186	1878
pol	2085	5096
PR	2253	2549
RT	2550	3869
env	6225	8795
nef	8797	9417