Balance between transmitted HLA preadapted and nonassociated polymorphisms is a major determinant of HIV-1 disease progression

J Exp Med. 2016 Sep 19;213(10):2049-63. doi: 10.1084/jem.20151984. Epub 2016 Aug 22.


HIV-1 adapts to a new host through mutations that facilitate immune escape. Here, we evaluate the impact on viral control and disease progression of transmitted polymorphisms that were either preadapted to or nonassociated with the new host's HLA. In a cohort of 169 Zambian heterosexual transmission pairs, we found that almost one-third of possible HLA-linked target sites in the transmitted virus Gag protein are already adapted, and that this transmitted preadaptation significantly reduced early immune recognition of epitopes. Transmitted preadapted and nonassociated polymorphisms showed opposing effects on set-point VL and the balance between the two was significantly associated with higher set-point VLs in a multivariable model including other risk factors. Transmitted preadaptation was also significantly associated with faster CD4 decline (<350 cells/µl) and this association was stronger after accounting for nonassociated polymorphisms, which were linked with slower CD4 decline. Overall, the relative ratio of the two classes of polymorphisms was found to be the major determinant of CD4 decline in a multivariable model including other risk factors. This study reveals that, even before an immune response is mounted in the new host, the balance of these opposing factors can significantly influence the outcome of HIV-1 infection.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adaptation, Physiological / immunology*
  • Alleles
  • CD4-Positive T-Lymphocytes / immunology
  • Disease Progression*
  • Epitopes / immunology
  • Female
  • HIV Infections / genetics*
  • HIV Infections / immunology
  • HIV Infections / pathology*
  • Histocompatibility Antigens Class I / genetics*
  • Humans
  • Immunity
  • Male
  • Models, Biological
  • Multivariate Analysis
  • Polymorphism, Genetic*
  • T-Lymphocytes, Cytotoxic / immunology
  • Viral Load / immunology
  • gag Gene Products, Human Immunodeficiency Virus


  • Epitopes
  • Histocompatibility Antigens Class I
  • gag Gene Products, Human Immunodeficiency Virus

Associated data

  • GENBANK/FJ606137
  • GENBANK/FJ606433
  • GENBANK/JQ219842
  • GENBANK/KM048382
  • GENBANK/KM048989
  • GENBANK/KP715728
  • GENBANK/KP715844
  • GENBANK/KU043117
  • GENBANK/KU043162