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Science 19 November 1993:
Vol. 262. no. 5137, pp. 1257 - 1261
DOI: 10.1126/science.8235655
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Articles

Science, Vol 262, Issue 5137, 1257-1261
Copyright © 1993 by American Association for the Advancement of Science

articles

Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes

EL Delwart, EG Shpaer, J Louwagie, FE McCutchan, M Grez, H Rubsamen-Waigmann, and JI Mullins

Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305-5402.

The genetic diversity of human immunodeficiency virus (HIV) is a major concern thought to impact on immunologic escape and eventual vaccine efficacy. Here, simple and rapid methods are described for the detection and estimation of genetic divergence between HIV strains on the basis of the observation that DNA heteroduplexes formed between related sequences have a reduced mobility in polyacrylamide gels proportional to their degree of divergence. Reliable phylogenetic subtypes were assigned for HIV-1 strains from around the world. Relationships between viruses were closest when derived from the same or epidemiologically linked individuals. When derived from epidemiologically unlinked individuals, the relationships between viruses in a given geographic region correlated with the length of time HIV-1 had been detected in the population and the number of strains initiating widespread infection. Heteroduplex mobility analysis thus provides a tool to expedite epidemiological investigations by assisting in the classification of HIV and is readily applicable to the screening and characterization of other infectious agents and cellular genes.


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J. Virol. 75, 4936-4940
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One-Tube Real-Time Isothermal Amplification Assay To Identify and Distinguish Human Immunodeficiency Virus Type 1 Subtypes A, B, and C and Circulating Recombinant Forms AE and AG.
M. P. de Baar, E. C. Timmermans, M. Bakker, E. de Rooij, B. van Gemen, and J. Goudsmit (2001)
J. Clin. Microbiol. 39, 1895-1902
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Route of Simian Immunodeficiency Virus Inoculation Determines the Complexity but Not the Identity of Viral Variant Populations That Infect Rhesus Macaques.
J. L. Greenier, C. J. Miller, D. Lu, P. J. Dailey, F. X. Lü, K. J. Kunstman, S. M. Wolinsky, and M. L. Marthas (2001)
J. Virol. 75, 3753-3765
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Perinatal Transmission of Major, Minor, and Multiple Maternal Human Immunodeficiency Virus Type 1 Variants In Utero and Intrapartum.
R. E. Dickover, E. M. Garratty, S. Plaeger, and Y. J. Bryson (2001)
J. Virol. 75, 2194-2203
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Evaluation of PCR-Generated Chimeras, Mutations, and Heteroduplexes with 16S rRNA Gene-Based Cloning.
X. Qiu, L. Wu, H. Huang, P. E. McDonel, A. V. Palumbo, J. M. Tiedje, and J. Zhou (2001)
Appl. Envir. Microbiol. 67, 880-887
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Cellular Immune Responses and Viral Diversity in Individuals Treated during Acute and Early HIV-1 Infection.
M. Altfeld, E. S. Rosenberg, R. Shankarappa, J. S. Mukherjee, F. M. Hecht, R. L. Eldridge, M. M. Addo, S. H. Poon, M. N. Phillips, G. K. Robbins, et al. (2001)
J. Exp. Med. 193, 169-180
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Simple, Sensitive, and Specific Detection of Human Immunodeficiency Virus Type 1 Subtype B DNA in Dried Blood Samples for Diagnosis in Infants in the Field.
I. A. Beck, K. D. Drennan, A. J. Melvin, K. M. Mohan, A. M. Herz, J. Alarcón, J. Piscoya, C. Velázquez, and L. M. Frenkel (2001)
J. Clin. Microbiol. 39, 29-33
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Unprecedented Degree of Human Immunodeficiency Virus Type 1 (HIV-1) Group M Genetic Diversity in the Democratic Republic of Congo Suggests that the HIV-1 Pandemic Originated in Central Africa.
N. Vidal, M. Peeters, C. Mulanga-Kabeya, N. Nzilambi, D. Robertson, W. Ilunga, H. Sema, K. Tshimanga, B. Bongo, and E. Delaporte (2000)
J. Virol. 74, 10498-10507
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A Dual Infection/Competition Assay Shows a Correlation between Ex Vivo Human Immunodeficiency Virus Type 1 Fitness and Disease Progression.
M. E. Quiñones-Mateu, S. C. Ball, A. J. Marozsan, V. S. Torre, J. L. Albright, G. Vanham, G. van der Groen, R. L. Colebunders, and E. J. Arts (2000)
J. Virol. 74, 9222-9233
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A Double-Blind, Adjuvant-Controlled Trial of Human Immunodeficiency Virus Type 1 (HIV-1) Immunogen (Remune) Monotherapy in Asymptomatic, HIV-1-Infected Thai Subjects with CD4-Cell Counts of >300.
V. Churdboonchart, C. Sakondhavat, S. Kulpradist, B. I. Na Ayudthya, V. Chandeying, S. Rugpao, C. Boonshuyar, W. Sukeepaisarncharoen, W. Sirawaraporn, D. J. Carlo, et al. (2000)
Clin. Vaccine Immunol. 7, 728-733
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HIV-1 genotypes in peripheral blood monocytes.
T. Zhu (2000)
J. Leukoc. Biol. 68, 338-344
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Failure of Routine HIV-1 Tests in a Case Involving Transmission With Preseroconversion Blood Components During the Infectious Window Period.
A. E. Ling, K. E. Robbins, T. M. Brown, V. Dunmire, S. Y. S. Thoe, S.-Y. Wong, Y. S. Leo, D. Teo, J. Gallarda, B. Phelps, et al. (2000)
JAMA 284, 210-214
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Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis.
J. Dunbar, L. O. Ticknor, and C. R. Kuske (2000)
Appl. Envir. Microbiol. 66, 2943-2950
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Position and degree of mismatches and the mobility of DNA heteroduplexes.
D. A. Upchurch, R. Shankarappa, and J. I. Mullins (2000)
Nucleic Acids Res. 28, e69
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Phylogenetic Analyses Indicate an Atypical Nurse-to-Patient Transmission of Human Immunodeficiency Virus Type 1.
C. P. Goujon, V. M. Schneider, J. Grofti, J. Montigny, V. Jeantils, P. Astagneau, W. Rozenbaum, F. Lot, C. Frocrain-Herchkovitch, N. Delphin, et al. (2000)
J. Virol. 74, 2525-2532
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Simplified Hepatitis C Virus Genotyping by Heteroduplex Mobility Analysis.
P. A. White, X. Zhai, I. Carter, Y. Zhao, and W. D. Rawlinson (2000)
J. Clin. Microbiol. 38, 477-482
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High Rate of Recombination throughout the Human Immunodeficiency Virus Type 1 Genome.
A. E. Jetzt, H. Yu, G. J. Klarmann, Y. Ron, B. D. Preston, and J. P. Dougherty (2000)
J. Virol. 74, 1234-1240
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Simplified Strategy for Detection of Recombinant Human Immunodeficiency Virus Type 1 Group M Isolates by gag/env Heteroduplex Mobility Assay.