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Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression

Abrahams, Melissa-Rose; Treurnicht, Florette K.; Ngandu, Nobubelo K.; Goodier, Sarah A.; Marais, Jinny C.; Bredell, Helba; Thebus, Ruwayhida; de Assis Rosa, Debra; Mlisana, Koleka; Seoighe, Cathal; Karim, Salim Abdool; Gray, Clive M.; Williamson, Carolyn

doi: 10.1097/QAD.0b013e32835cab64
Basic Science

Objective(s): There is limited information on full-length genome sequences and the early evolution of transmitted HIV-1 subtype C viruses, which constitute the majority of viruses spread in Africa. The purpose of this study was to characterize the earliest changes across the genome of subtype C viruses following transmission, to better understand early control of viremia.

Design: We derived the near full-length genome sequence responsible for clinical infection from five HIV subtype C-infected individuals with different disease progression profiles and tracked adaptation to immune responses in the first 6 months of infection.

Methods: Near full-length genomes were generated by single genome amplification and direct sequencing. Sequences were analyzed for amino acid mutations associated with cytotoxic T lymphocyte (CTL) or antibody-mediated immune pressure, and for reversion.

Results: Fifty-five sequence changes associated with adaptation to the new host were identified, with 38% attributed to CTL pressure, 35% to antibody pressure, 16% to reversions and the remainder were unclassified. Mutations in CTL epitopes were most frequent in the first 5 weeks of infection, with the frequency declining over time with the decline in viral load. CTL escape predominantly occurred in nef, followed by pol and env. Shuffling/toggling of mutations was identified in 81% of CTL epitopes, with only 7% reaching fixation within the 6-month period.

Conclusion: There was rapid virus adaptation following transmission, predominantly driven by CTL pressure, with most changes occurring during high viremia. Rapid escape and complex escape pathways provide further challenges for vaccine protection.

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aDivision of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town

bAIDS Research Unit: Immunology, National Institute of Communicable Diseases, Johannesburg

cCentre for the AIDS Program of Research in South Africa

dDepartment of Medical Microbiology, University of KwaZulu Natal, Durban, South Africa

eSchool of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland.

Correspondence to Carolyn Williamson, Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Services, Observatory 7925, South Africa. Tel: +27 21 406 6683; fax: +27 21 406 6682; e-mail:

Received 17 July, 2012

Revised 5 November, 2012

Accepted 15 November, 2012

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Copyright © 2013 Wolters Kluwer Health, Inc.