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Nearly 30 years since its discovery, the human immunodeficiency virus (HIV) continues to prove a difficult virus to pin down because it mutates so rapidly—a trait which, so far, has made an effective vaccine for this often-deadly condition impossible to develop.
That might change, thanks in part to new Microsoft tools that are being used to construct maps of the mutating virus, which may in turn help identify prospective vaccine candidates.
HIV mutates at such a high rate that the virus is distinct for each individual patient. The level of viral variation in one HIV patient is comparable to the worldwide level of variation during the course of an influenza epidemic.
The PhyloD Viewer draws proteins as circles to reveal mutation patterns that could aid in HIV vaccine design.
A first step in overcoming this challenge is to identify consistent patterns in viral adaptation. Tools such as PhyloD, PhyloD Viewer, and Phylo Detective can be used to identify and visualize HIV covariation and adaptation. By identifying patterns and constraints in HIV evolution, scientists are able to focus on HIV's weaknesses, with the goal of designing a vaccine that will be resistant to HIV mutation. The arcs in the circle pictured above, developed with the PhyloD Viewer, represent how HIV in a single patient is connected to itself as parts of it mutate.
This research delivered a statistical approach that could help further research into HIV mutation. It also led to the observation that patterns of HIV evolution are broadly predictable based on host immunogenetic profiles. In other words, we found a promising consistency in the way that HIV adapts to the human immune response, which could pave the way for vaccine design.
It's worth noting that this work is built on the Microsoft Biology Foundation, which provides consistent file formats, statistical packages, and resources to farm out computations to clusters of machines—permitting scientists to focus on the science of modeling the virus and identifying its vulnerabilities.
—Jonathan Carlson, Researcher for Microsoft Research, eScience