HIV sequence databases

Abstract

Two important databases are often used in HIV genetic research, the HIV Sequence Database in Los Alamos, which collects all sequences and focuses on annotation and data analysis, and the HIV RT/Protease Sequence Database in Stanford, which collects sequences associated with the development of viral resistance against anti-retroviral drugs and focuses on analysis of those sequences. The types of data and services these two databases offer, the tools they provide, and the way they are set up and operated are described in detail.

Figure 1. Primate lentivirus tree

This phylogenetic tree illustrates the basic relationships of different primate lentiviruses, and is based on a pol gene alignment. The human HIV-1s and HIV-2s are the most closely related to SIVs found in chimpanzee and sooty mangabey. The HIV M, N, and O groups are noted, and representative sequences from different HIV-1 M group subtypes are included, each subtype is a set of genetically associated viruses. The map on the left shows the region where chimpanzees carrying SIVs have primarily been found, although this search is being extended through non-invasive methods to test wild chimpanzee populations.

Figure 2. Vaccine constructs

A subset of the SIV and SHIV (combined SIV-HIV) constructs that are being used for SIV vaccine trials, which are often complex products of molecular engineering, are shown. Each different color or pattern represents a different clone that has contributed. A more complete listing is available at the database.