Clinicians, health officials and researchers are interested in the spread of particular variants of HIV in space and time. New technology to make this easy and visually attractive is being developed and EUCOHIV is part of this development.
Starting from HIV typing and subtyping tools (i.e. the Rega subtyping tool), strains can be phylogenetically characterized automatically, both individual strains and batches of strains. When these strains have a known geographic origin and time of sampling, such a strain or set of strains can be phylogenetically displayed on geographical maps, and movies through time can illustrate the spread of clades. Tracking such strains with particular characteristics, such as risk group or tropism, can even provide color coded insight into how these characteristics relate to geographic or phylogenetic spread.
The aim of this GeoCladeTool is to provide on the fly visualization of some of these characteristics, with the possibility to request more sophisticated displays through the website or to be downloaded or sent by email. All of this will be interactive, searching and scrolling within a phylogenetic tree, over geographical maps, and in the time-lapse movie will be possible. We are confident that such a tool will make submission of data very attractive.
We are aware that such analyses can be highly sensitive, you can rest assured that we will abide with all ethical and privacy regulations that will protect your patient.
Your GeoCladeTool team
Check out our previous work:
de Oliveira T, Deforche K, Cassol S, Salminen M, Paraskevis D, Seebregts C, Snoeck J, van Rensburg EJ, Wensing AM, van de Vijver DA, Boucher CA, Camacho R, Vandamme AM. An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics. 2005 Oct 1;21(19):3797-800.
Alcantara LC, Cassol S, Libin P, Deforche K, Pybus OG, Van Ranst M, Galvão-Castro B, Vandamme AM, de Oliveira T. A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W634-42. Epub 2009 May 29.
Abecasis AB, Wang Y, Libin P, Imbrechts S, de Oliveira T, Camacho RJ, Vandamme A-M. Comparative performance of the REGA Subtyping tool version 2 versus version 1. Infections, Genetics and Evolution. 2010 Apr;10(3):380-5. Epub 2009 Oct 12.
Faria NR, Suchard MA, Abecasis A, Sousa JD, Ndembi N, Bonfim I, Camacho RJ, Vandamme AM, Lemey P. Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon. Infect Genet Evol. 2012 Mar;12(2):453-60. Epub 2011 May 4.
Faria NR, Hodges-Mameletzis I, Silva JC, Rodés B, Erasmus S, Paolucci S, Ruelle J, Pieniazek D, Taveira N, Treviño A, Gonçalves MF, Jallow S, Xu L, Camacho RJ, Soriano V, Goubau P, Sousa JD, Vandamme AM, Suchard MA, Lemey P. The phylogeographic footprint of colonial history in the global dispersal of human immunodeficiency virus type group A. J Gen Virol. 2012 Apr;93(Pt 4):889-99. Epub 2011 Dec 21.