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Application for funding a Central EEC Service in AIDS-Research

Objective

To coordinate the HIV sequencing work at the European level and to perform the nucleotide sequence determination in the most time and cost efficient way, the EC established the Centralized Facility (CF) for HIV Genome Analysis at the Georg-Speyer-Haus in Frankfurt (Germany) in December 1990. Here, sequencing is done by modern techniques, an automated laser fluorescence machine (A.L.F.) and experienced personel which are prerequisites for efficient sequencing. The material, especially the sequencing primers, which have first to be designed from consensus sequences of HIV, can then be shared for all projects to be sequenced at the CF, a fact that serves a lot of time and money. Also, the data evaluation is centralized at the CF and the applicants receive the final sequence data by electronic mail or on floppy disk.
The extreme variability of the human immunodeficiency virus (HIV) is the major obstacle in the development of an effective vaccine or a therapy. The continuous mutations introduced into the viral genomes during their replication cycles very rapidly lead to new variants which can escape the neutralization mechanisms imposed either naturally by the immune system of the host or artificially through a vaccine or a therapeutic drug. To understand these mechanisms of escape at the genetic level, to correlate viral phenotypes with genotypes and to establish the actual epidemiological patterns by correlating the genetic variants with their geographic distribution requires considerable sequence information. To perform this work in the most time and cost efficient way, the European Community (EC) established the Centralized Facility (CF) for HIV Genome Analysis where sequencing is done on an automated laser fluorescence machine (ALF). European acquired immune deficiency syndrome (AIDS) researchers send their HIV deoxyribonucleic acid (DNA) to be sequenced to the CF.

More than 100 kilobases (kb) of evaluated sequence data have been produced by the CF which corresponds to 300 to 400 kb of actual sequencing work. The data were generated for 9 projects from 4 European countries. A set of 135 fluorescent primers is available for HIV-1, 25 for HIV-2 and 13 for various cloning vectors. Most of the HIV primers were derived from an HIV consensus sequence and can be used for the majority of the variants. The other primers have been adjusted for individual clones or HIV subtypes. In addition, the introduction of fluoro-dATP as labelling agent and the technique of solid phase sequencing for the ALF improved the length of the readable sequence per gel run up to 700 base pairs (bp) per lane.
The extreme variability of the human immunodeficiency virus HIV is the major obstacle in the development of an effective vaccine or a therapy. The continuous mutations introduced into the viral genomes during their replication cycles very rapidly lead to new variants which can escape the neutralisation mechanisms imposed either naturally by the immune system of the host or artificially through a vaccine or a therapeutic drug. To understand these mechanisms of escape at the genetic level, to correlate viral phenotypes with genotypes and to establish the actual epidemiological patterns by correlating the genetic variants with their geographic distribution obviously requires a lot of sequence information.

Coordinator

Chemotherapeutisches Forschungsinstitut
Address
Georg-speyer-haus Paul-ehrlich-straße 42-44
60596 Frankfurt Am Main
Germany