1. Deep sequence analysis of HIV adaptation following vertical transmission reveals the impact of immune pressure on the evolution of HIV
- Author
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Abha Chopra, Simon Mallal, Joseph A. Conrad, Silvana Gaudieri, Mark A. Pilkinton, Jennifer Currenti, Mina John, Francine Noel, Michaela Lucas, Spyros A. Kalams, Wyatt J. McDonnell, Eric Alves, Rita M. Smith, Elizabeth McKinnon, Shay Leary, and Louise Barnett
- Subjects
RNA viruses ,Male ,Adaptation, Biological ,Artificial Gene Amplification and Extension ,HIV Infections ,Pathology and Laboratory Medicine ,Polymerase Chain Reaction ,Epitope ,White Blood Cells ,Immunodeficiency Viruses ,Animal Cells ,Medicine and Health Sciences ,Cell Cycle and Cell Division ,Biology (General) ,Child ,Immune Response ,0303 health sciences ,Transmission (medicine) ,T Cells ,030302 biochemistry & molecular biology ,High-Throughput Nucleotide Sequencing ,Viral Load ,Middle Aged ,3. Good health ,Medical Microbiology ,Cell Processes ,Viral Pathogens ,Child, Preschool ,Viruses ,Female ,Pathogens ,Cellular Types ,Viral load ,Research Article ,Adult ,Evolutionary Processes ,QH301-705.5 ,Immune Cells ,Immunology ,Viral quasispecies ,Human leukocyte antigen ,Biology ,Research and Analysis Methods ,Microbiology ,Virus ,Evolution, Molecular ,03 medical and health sciences ,Immune system ,Evolutionary Adaptation ,Virology ,Retroviruses ,Genetics ,Humans ,Molecular Biology Techniques ,Microbial Pathogens ,Molecular Biology ,030304 developmental biology ,Evolutionary Biology ,Blood Cells ,Lentivirus ,Organisms ,Biology and Life Sciences ,HIV ,Infant ,Cell Biology ,RC581-607 ,Viral Replication ,Infectious Disease Transmission, Vertical ,Viral replication ,HIV-1 ,Parasitology ,Immunologic diseases. Allergy ,Viral Transmission and Infection - Abstract
Human immunodeficiency virus (HIV) can adapt to an individual’s T cell immune response via genomic mutations that affect antigen recognition and impact disease outcome. These viral adaptations are specific to the host’s human leucocyte antigen (HLA) alleles, as these molecules determine which peptides are presented to T cells. As HLA molecules are highly polymorphic at the population level, horizontal transmission events are most commonly between HLA-mismatched donor/recipient pairs, representing new immune selection environments for the transmitted virus. In this study, we utilised a deep sequencing approach to determine the HIV quasispecies in 26 mother-to-child transmission pairs where the potential for founder viruses to be pre-adapted is high due to the pairs being haplo-identical at HLA loci. This scenario allowed the assessment of specific HIV adaptations following transmission in either a non-selective immune environment, due to recipient HLA mismatched to original selecting HLA, or a selective immune environment, mediated by matched donor/recipient HLA. We show that the pattern of reversion or fixation of HIV adaptations following transmission provides insight into the replicative cost, and likely compensatory networks, associated with specific adaptations in vivo. Furthermore, although transmitted viruses were commonly heavily pre-adapted to the child’s HLA genotype, we found evidence of de novo post-transmission adaptation, representing new epitopes targeted by the child’s T cell response. High-resolution analysis of HIV adaptation is relevant when considering vaccine and cure strategies for individuals exposed to adapted viruses via transmission or reactivated from reservoirs., Author summary Highly mutable pathogens utilise genetic variations within T cell epitopes as a mechanism of immune escape (viral adaptation). The diversity of the human leucocyte antigen (HLA) molecules that present viral targets to T cells in human populations partially protects against rapid population-level accumulation of human immunodeficiency virus (HIV) adaptations through horizontal transmissions. In contrast, vertical transmissions occur between haplo-identical mother/child pairs, and potentially include adaptive changes through father-mother-child transmission, representing a pathway to complete pre-adaptation to HLA alleles in child hosts over only two transmission events. We utilised next-generation sequencing to examine HIV evolution in the unique setting of vertical HIV transmission. We predict the in vivo replicative cost and immune benefit of specific HIV adaptations that could be used to inform vaccine design and cure strategies to combat viral immune adaptation.
- Published
- 2019