The vaccine candidates incorporate non-human primate adenovirus vectors based on technology developed by scientists at the University of Pennsylvania and licensed to GSK.
Financial terms of the agreement were not disclosed but Cobra said the work will be performed in its Oxford and Keele facilities.
"We are very pleased to have been awarded this new manufacturing contract by two such renowned organisations at the forefront of AIDS clinical research," David Thatcher, chief executive of Cobra, commented.
"It validates our manufacturing expertise with virus products and will contribute significantly to building our revenue stream over 2006 and 2007."
The contract is in support of a previously announced collaboration between IAVI and GSK to advance the development of the technology, which uses non-infectious vaccine vectors to stimulate specific immune responses directed against HIV.
The adenovirus vectors, originally isolated from non-human primates, are engineered to be non-infectious and are capable of efficiently delivering genes expressing HIV proteins to the immune system.
The IAVI-GSK collaborative research focuses on vaccines designed to elicit immune responses against variants of HIV that circulate predominantly in Africa, where in 2005 3.2m of the 5m new HIV infections surfacing globally were recorded.
The deal is a welcomed boost for Cobra, which believes its expertise in adenovirus manufacture and related process development will contribute to the production of successful HIV vaccine candidates.
Last month the British company announced the development of a new method for inserting or deleting genes in bacteria.
Its Xer-cise technology was developed over several years and enables genes to be switched in and out of bacterial chromosomal DNA cleanly and more efficiently than current methods.
Gene insertion and deletion is particularly problematic in the more novel species of bacteria of industrial interest such as Bacillus but Cobra claims Xer-cise is of generic utility and is simple to employ.
The company has said it will use its new genetic engineering method to help its customers with the accelerated development of their drugs.