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Journal of Virology, December 1998, p. 10234-10241, Vol. 72, No. 12
0022-538X/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

An Isolate of Human Immunodeficiency Virus Type 1 Originally Classified as Subtype I Represents a Complex Mosaic Comprising Three Different Group M Subtypes (A, G, and I)

Feng Gao,1 David L. Robertson,2 Catherine D. Carruthers,1 Yingying Li,1 Elizabeth Bailes,3 Leondios G. Kostrikis,4 Mika O. Salminen,5 Frederic Bibollet-Ruche,1 Martine Peeters,6 David D. Ho,4 George M. Shaw,1,7 Paul M. Sharp,3 and Beatrice H. Hahn1,*

Department of Medicine and Microbiology,1 Howard Hughes Medical Institute,7 University of Alabama at Birmingham, Birmingham, Alabama 35294; Laboratory of Structural and Genetic Information, CNRS-EP 91, Marseilles 13402,2 and Laboratoire Retrovirus, ORSTOM, Montpellier,6 France; Division of Genetics, Queens Medical Centre, University of Nottingham, Nottingham, United Kingdom3; Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 100164; and Department of Infectious Diseases, National Public Health Institute, Helsinki 00300, Finland5

Received 26 May 1998/Accepted 18 August 1998

Full-length reference clones and sequences are currently available for eight human immunodeficiency virus type 1 (HIV-1) group M subtypes (A through H), but none have been reported for subtypes I and J, which have only been identified in a few individuals. Phylogenetic information for subtype I, in particular, is limited since only about 400 bp of env gene sequences have been determined for just two epidemiologically linked viruses infecting a couple who were heterosexual intravenous drug users from Cyprus. To characterize subtype I in greater detail, we employed long-range PCR to clone a full-length provirus (94CY032.3) from an isolate obtained from one of the individuals originally reported to be infected with this subtype. Phylogenetic analysis of C2-V3 env gene sequences confirmed that 94CY032.3 was closely related to sequences previously classified as subtype I. However, analysis of the remainder of its genome revealed various regions in which 94CY032.3 was significantly clustered with either subtype A or subtype G. Only sequences located in vpr and nef, as well as the middle portions of pol and env, formed independent lineages roughly equidistant from all other known subtypes. Since these latter regions most likely have a common origin, we classify them all as subtype I. These results thus indicate that the originally reported prototypic subtype I isolate 94CY032 represents a triple recombinant (A/G/I) with at least 11 points of recombination crossover. We also screened HIV-1 recombinants with regions of uncertain subtype assignment for the presence of subtype I sequences. This analysis revealed that two of the earliest mosaics from Africa, Z321B (A/G/?) and MAL (A/D/?), contain short segments of sequence which clustered closely with the subtype I domains of 94CY032.3. Since Z321 was isolated in 1976, subtype I as well as subtypes A and G must have existed in Central Africa prior to that date. The discovery of subtype I in HIV-1 hybrids from widely distant geographic locations also suggests a more widespread distribution of this virus subtype, or at least segments of it, than previously recognized.

* Corresponding author. Mailing address: Department of Medicine and Microbiology, University of Alabama at Birmingham, 701 S. 19th St., LHRB 613, Birmingham, AL 35294. Phone: (205) 934-0412. Fax: (205) 934-1580. E-mail: bhahn{at}cordelia.dom.uab.edu.

Journal of Virology, December 1998, p. 10234-10241, Vol. 72, No. 12
0022-538X/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.


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