THE WORLD-HEALTH-ORGANIZATION GLOBAL PROGRAM ON AIDS PROPOSAL FOR STANDARDIZATION OF HIV SEQUENCE NOMENCLATURE

The World Health Organization Global Programme on AIDS (WHO/GPA) is co nducting a large-scale collaborative study of human immunodeficiency v irus type 1 (HIV-1) variation, based in four potential vaccine-trial s ite countries: Brazil, Rwanda, Thailand, and Uganda.(1) Through the co urse of this study, it was crucial to keep track of certain attributes of the samples from which the viral nucleotide sequences were derived (e.g., country of origin and viral culture characterization), so that meaningful sequence comparisons could be made. Here we describe a sys tem developed in the context of the WHO/GPA study that summarizes such critical attributes by representing them as standardized characters d irectly incorporated into sequence names. This nomenclature allows lin kage of clinical, phenotypic, and geographic information with molecula r data. We propose that other investigators involved in human immunode ficiency virus (HIV) nucleotide sequencing efforts adopt a similar sta ndardized sequence nomenclature to facilitate cross-study sequence com parison. HIV sequence data are being generated at an ever-increasing r ate; directly coupled to this increase is our deepening understanding of biological parameters that influence or result from sequence variab ility. A standardized sequence nomenclature that includes relevant bio logical information would enable researchers to better utilize the gro wing body of sequence data, and enhance their ability to interpret the biological implications of their own data through facilitating compar isons with previously published work.