HIV-1 Incidence and Infection Time Estimator

HIITE designates the infection stage as either being chronic or incident, and approximates the infection time of those incident subjects. Users can directly upload a single fasta file (number of sequences > 4) onto HITTE for instantaneous processing and output execution. HIITE takes two types of input: i) full envelope gene sequences and ii) envelope gene segment of HXB2 7134-7499 (check “HXB2 7134-7499” option). Check the “Align” command if input sequences need to be aligned. Alignment is done using a context dependent align algorithm. HIITE’s output includes the stage of infection (chronic or incident) along with the Hamming distance distribution plot, diversity, genome similarity index GSI, and variance. For incident infection cases, estimated days post infection with 95% prediction intervals are provided.

The application is deployed here

Example:

Input

Fasta File

Output

Infection Stage with Time Since Infection

    Incident: 51.5 [0.0 – 132.7] days

Hamming Distance Distribution

Whole

Single Lineage

Statistics

Single Lineage Diversity	0.104
Single Lineage GSI	0.852
Single Lineage Variance	0.091
Diversity	0.62
GSI	0.48
Variance	7.365

Reference:

S. Y. Park, T. M. T. Love, S. Kapoor, and H. Y. Lee, HIITE: HIV-1 Incidence and Infection Time Estimator - Bioinformatics

Release Notes:

HIITE release supports python 2.7 only. HITTE requires the following third-party python modules:

1. Scikit-learn (>=0.18.1)
2. Numpy (>=1.8.2)
3. Scipy (>=0.13.3)
4. Biopython (>=1.68)