Natural Selection During Subtype C HIV-1 Transmission Open Access
Deymier, Martin (2015)
Abstract
HIV-1, the causative agent of AIDS, kills approximately 1.6 million people per year globally. The majority of infected persons live in sub-Saharan Africa, where disease burden is greatest. A major roadblock to the development of an effective vaccine is the extraordinary genetic diversity of HIV, both around the world as well as within a single infected individual. However, during transmission of HIV between individuals, a strong genetic bottleneck occurs, wherein from a large diverse population of viruses present in a chronically infected person, only a single genetic variant establishes infection in the naïve host. Identifying the viral characteristics of these transmitted/founder (TF) variants may provide a useful common target for any future vaccine. We and others have strived to define common genetic and phenotypic characteristics of these TF virus variants, although few traits have so far been confirmed. Work from our lab established that a genetic bottleneck occurs during transmission, and confirmed that there is a transmission selection bias for consensus amino acid residues. This selection bias suggests that consensus amino acid residues lead to virus variants with increased transmission fitness. In order to further investigate the phenotypic characteristics of HIV TF variants, we have examined the populations of full-length genome HIV from six linked heterosexual transmission pairs near the time of transmission. We confirmed that TF variants had more consensus-like genomes across all viral genes. However, following the generation of full-length infectious molecular clones, we did not observe a selection for variants with increased infectivity, in vitro replicative capacity, or inherent resistance to IFNα. Our findings indicate that although selection for more consensus-like variants suggests a selection of virus with increased transmission fitness, this fitness is not associated with in vitro measurements of virus replication. Continued efforts to describe these uniquely derived full-length genome TF viruses in comparison to their non-transmitted counterparts will offer additional insight into viral requirements of transmission and may provide potential common targets for an effective vaccine.
Table of Contents
CHAPTER I : INTRODUCTION 1
CHAPTER II : PARTICLE INFECTIVITY OF HIV-1 FULL-LENGTH GENOME INFECTIOUS MOLECULAR CLONES IN A SUBTYPE C HETEROSEXUAL TRANSMISSION PAIR FOLLOWING HIGH FIDELITY AMPLIFICATION AND UNBIASED CLONING 21
ABSTRACT 22
INTRODUCTION 23
RESULTS 26
DISCUSSION 33
MATERIALS AND METHODS 36
TABLE 1 - CHARACTERISTICS OF THE SAMPLES FROM THE SUBTYPE C HIV-1 TRANSMISSION PAIR. 43
TABLE 2 - DNA PRIMERS USED IN THE STUDY. 44
FIGURE 1 - HIGHLIGHTER AND PHYLOGENETIC ANALYSIS OF HIV-1 NEAR FULL-LENGTH SINGLE GENOME AMPLICONS FROM A HETEROSEXUAL EPIDEMIOLOGICALLY-LINKED TRANSMISSION PAIR. 45
FIGURE 2 - DIAGRAM FOR THE FULL-LENGTH GENOME CLONING STRATEGY. (A) FIRST, THE LTR OF THE TF WAS AMPLIFIED FROM GENOMIC DNA AND CLONED USING THE IN-FUSION SYSTEM. 46
FIGURE 3 - PARTICLE INFECTIVITIES OF HIV FULL-LENGTH GENOME INFECTIOUS MOLECULAR CLONES FROM A LINKED HETEROSEXUAL TRANSMISSION PAIR. 48
FIGURE 4 - PARTICLE INFECTIVITIES OF TWO VIRAL VARIANTS WITH THE CHIMERIC R AND ORIGINAL AMPLICON R SEQUENCES. 49
REFERENCES 50
CHAPTER III : HETEROSEXUAL TRANSMISSION OF SUBTYPE C HIV-1 SELECTS CONSENSUS-LIKE VARIANTS WITHOUT INCREASED REPLICATIVE CAPACITY OR INTERFERON-α RESISTANCE 55
ABSTRACT 56
INTRODUCTION 58
RESULTS 61
DISCUSSION 70
MATERIALS AND METHODS 78
TABLE 1 - TRANSMISSION PAIR CHARACTERISTICS 87
FIGURE 1 - HIV-1 FULL-LENGTH GENOME PHYLOGENETIC ANALYSIS OF SIX EPIDEMIOLOGICALLY-LINKED HETEROSEXUAL TRANSMISSION PAIRS. 89
FIGURE 2 - TRANSMISSION SELECTS FOR MORE CONSENSUS-LIKE TF VARIANTS. 90
FIGURE 3 - PARTICLE INFECTIVITY OF TF AND NT INFECTIOUS MOLECULAR CLONES. 91
FIGURE 4 - TF VARIANTS ARE MORE SENSITIVE TO NEUTRALIZATION BY DONOR PLASMA THAN NT VIRUSES 92
FIGURE 5 - IN VITRO REPLICATION OF TF AND NT VIRUSES IN PBMC. 94
FIGURE 6 - INTERFERON-α RESISTANCE OF TF AND NT VIRUSES. 95
SUPPLEMENTAL FIGURE 1 - PARTICLE INFECTIVITY FROM 293T AND PBMC DERIVED VIRUS. 97
SUPPLEMENTAL FIGURE 2 - PARTICLE INFECTIVITY CORRELATES WITH REPLICATIVE CAPACITY. 98
SUPPLEMENTAL FIGURE 3 - REPLICATION OF TF AND NT VIRUSES IN MONOCYTE DERIVED DENDRITIC CELLS. 99
SUPPLEMENTAL FIGURE 4 - TF AND NT RESISTANCE TO IFN-α. 100
SUPPLEMENTAL FIGURE 5 - REPLICATION OF TF AND 6-MONTH CONSENSUS INFECTIOUS MOLECULAR CLONES. 102
REFERENCES 103
CHAPTER IV : DISCUSSION 113
REFERENCES 123
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