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Protease polymorphisms in HIV-1 subtype CRF01_AE represent selection by antiretroviral therapy and host immune pressure

Manosuthi, Weerawata,b; Butler, David Ma; Pérez-Santiago, Josuéa; Poon, Art FYa; Pillai, Satish Kc; Mehta, Sanjay Ra; Pacold, Mary Ea; Richman, Douglas Da,d; Pond, Sergei Kosakovskya; Smith, Davey Ma,d

doi: 10.1097/QAD.0b013e3283350eef
Clinical Science: Concise Communications

Background: Most of our knowledge about how antiretrovirals and host immune responses influence the HIV-1 protease gene is derived from studies of subtype B virus. We investigated the effect of protease resistance-associated mutations (PRAMs) and population-based HLA haplotype frequencies on polymorphisms found in CRF01_AE pro.

Methods: We used all CRF01_AE protease sequences retrieved from the LANL database and obtained regional HLA frequencies from the dbMHC database. Polymorphisms and major PRAMs in the sequences were identified using the Stanford Resistance Database, and we performed phylogenetic and selection analyses using HyPhy. HLA binding affinities were estimated using the Immune Epitope Database and Analysis.

Results: Overall, 99% of CRF01_AE sequences had at least 1 polymorphism and 10% had at least 1 major PRAM. Three polymorphisms (L10 V, K20RMI and I62 V) were associated with the presence of a major PRAM (P < 0.05). Compared to the subtype B consensus, six additional polymorphisms (I13 V, E35D, M36I, R41K, H69K, L89M) were identified in the CRF01_AE consensus; all but L89M were located within epitopes recognized by HLA class I alleles. Of the predominant HLA haplotypes in the Asian regions of CRF01_AE origin, 80% were positively associated with the observed polymorphisms, and estimated HLA binding affinity was estimated to decrease 19–40 fold with the observed polymorphisms at positions 35, 36 and 41.

Conclusion: Polymorphisms in CRF01_AE protease gene were common, and polymorphisms at residues 10, 20 and 62 most likely represent selection by use of protease inhibitors, whereas R41K and H69K were more likely attributable to recognition of epitopes by the HLA haplotypes of the host population.

aUniversity of California San Diego, La Jolla, California, USA

bBamrasnaradura Infectious Diseases Institute, Nonthaburi, Thailand

cUniversity of California San Francisco, San Francisco, USA

dVeterans Affairs San Diego Healthcare System, San Diego, California, USA.

Received 27 June, 2009

Revised 28 October, 2009

Accepted 6 November, 2009

Correspondence to Weerawat Manosuthi, MD, Department of Medicine, Bamrasnaradura Infectious Diseases Institute, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand. Tel: 66 2 5903408; fax: 66 2 5903411; e-mail:

© 2010 Lippincott Williams & Wilkins, Inc.