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Journal of Virology, June 2001, p. 5604-5613, Vol. 75, No. 12
0022-538X/01/$04.00+0   DOI: 10.1128/JVI.75.12.5604-5613.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Augmentation of Human Immunodeficiency Virus Type 1 Subtype E (CRF01_AE) Multiple-Drug Resistance by Insertion of a Foreign 11-Amino-Acid Fragment into the Reverse Transcriptase

Hironori Sato,1,* Yasuhiro Tomita,1 Kazuyoshi Ebisawa,2 Atsuko Hachiya,3 Kayo Shibamura,1 Teiichiro Shiino,1 Rongge Yang,1 Masashi Tatsumi,4 Kazuo Gushi,5 Hideaki Umeyama,2 Shinichi Oka,3 Yutaka Takebe,1 and Yoshiyuki Nagai1

AIDS Research Center, National Institute of Infectious Diseases,1 Department of Biomolecular Design, School of Pharmaceutical Sciences, Kitasato University,2 AIDS Clinical Center, International Medical Center of Japan,3 and Department of Veterinary Science, National Institute of Infectious Diseases,4 Tokyo, and Naha Prefectural Hospital, Okinawa,5 Japan

Received 22 January 2001/Accepted 16 March 2001

A human immunodeficiency virus type 1 (HIV-1) subtype E (CRF01_AE) variant (99JP-NH3-II) possessing an in-frame 33-nucleotide insertion mutation in the beta 3-beta 4 loop coding region of the reverse transcriptase (RT) gene was isolated from a patient who had not responded to nucleoside analogue RT inhibitors. This virus exhibited an extremely high level of multiple nucleoside analog resistance (MNR). Neighbor-joining tree analysis of the pol sequences indicated that the 99JP-NH3-II variant had originated from the swarm of drug-sensitive predecessors in the patient. Population-based sequence analyses of 82 independently cloned RT segments from the patient suggested that the variants with the insertion, three or four 3'-azido-3'-deoxythymidine resistance mutations, and a T69I mutation in combination had strong selective advantages during chemotherapy. Consistently, in vitro mutagenesis of a drug-sensitive predecessor virus clone demonstrated that this mutation set functions cooperatively to confer a high level of MNR without deleterious effects on viral replication capability. Homology modeling of the parental RT and its MNR mutant showed that extension of the beta 3-beta 4 loop by an insertion caused reductions in the distances between the loop and the other subdomains, narrowing the template-primer binding cleft and deoxynucleoside triphosphate-binding pocket in a highly flexible manner. The origin of the insert is elusive, as every effort to find a homologue has been unsuccessful. Taken together, these data suggest that (i) HIV-1 tolerates in vivo insertions as long as 33 nucleotides into the highly conserved enzyme gene to survive multiple anti-HIV-1 inhibitors and (ii) the insertion mutation augments multiple-drug resistance, possibly by reducing the biochemical inaccuracy of substrate-enzyme interactions in the active center.

* Corresponding author. Mailing address: Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo 162-8640, Japan. Phone: (81)-3-52851111. Fax: (81)-3-52851129. E-mail: hirosato{at}nih.go.jp.

Journal of Virology, June 2001, p. 5604-5613, Vol. 75, No. 12
0022-538X/01/$04.00+0   DOI: 10.1128/JVI.75.12.5604-5613.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


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Copyright © 2001 by the American Society for Microbiology. All rights reserved.