2016
DOI: 10.1128/jvi.00441-16
|View full text |Cite
|
Sign up to set email alerts
|

Deep Sequencing of the HIV-1 env Gene Reveals Discrete X4 Lineages and Linkage Disequilibrium between X4 and R5 Viruses in the V1/V2 and V3 Variable Regions

Abstract: HIV-1 requires the CD4 receptor and a coreceptor (CCR5 [R5 phenotype] or CXCR4 [X4 phenotype]) to enter cells. Coreceptor tropism can be assessed by either phenotypic or genotypic analysis, the latter using bioinformatics algorithms to predict tropism based on the env V3 sequence. We used the Primer ID sequencing strategy with the MiSeq sequencing platform to reveal the structure of viral populations in the V1/V2 and C2/V3 regions of the HIV-1 env gene in 30 late-stage and 6 early-stage subjects. We also used … Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
3
1
1

Citation Types

3
30
0

Year Published

2018
2018
2023
2023

Publication Types

Select...
7
1

Relationship

2
6

Authors

Journals

citations
Cited by 32 publications
(33 citation statements)
references
References 55 publications
3
30
0
Order By: Relevance
“…This diversity is primarily attributed to the absence of a proofreading mechanism in the HIV reverse transcriptase enzyme, as well as high levels of viremia and recombination (van Zyl et al, 2018). Other factors that contribute to this diversity include: host immune response (APOBEC enzyme hypermutations) (Bruner et al, 2016), length of infection (accumulation of mutations and depletion of CD4 T cell targets) (Arrildt et al, 2015;Zhou et al, 2016), viral compartmentalization (Yukl and Wong, 2015;van Zyl et al, 2018;Miller et al, 2019), and selection for viral quasispecies that are able to evade killing by host immune mechanisms (Phillips et al, 1991;Wei et al, 2003;Kearney et al, 2009;van Zyl et al, 2018).…”
Section: The Hiv Reservoir: Spectrum Of Viral Expression Diversity mentioning
confidence: 99%
“…This diversity is primarily attributed to the absence of a proofreading mechanism in the HIV reverse transcriptase enzyme, as well as high levels of viremia and recombination (van Zyl et al, 2018). Other factors that contribute to this diversity include: host immune response (APOBEC enzyme hypermutations) (Bruner et al, 2016), length of infection (accumulation of mutations and depletion of CD4 T cell targets) (Arrildt et al, 2015;Zhou et al, 2016), viral compartmentalization (Yukl and Wong, 2015;van Zyl et al, 2018;Miller et al, 2019), and selection for viral quasispecies that are able to evade killing by host immune mechanisms (Phillips et al, 1991;Wei et al, 2003;Kearney et al, 2009;van Zyl et al, 2018).…”
Section: The Hiv Reservoir: Spectrum Of Viral Expression Diversity mentioning
confidence: 99%
“…, we include an example of such an analysis taken from Zhou et al. showing the persistence of R5 viruses at high levels in the blood even when X4 viruses are present (although we do not know what the ratio of these variants might be in tissues or how much different tissues contribute to plasma viremia). The more accurate characterization of the three entry phenotypes of HIV‐1 puts R5 T cell‐tropic viruses at the center of the HIV‐1 story, gives a better definition beyond “neurotropic” to the types of viruses that are found in the CNS, explains why they may have evolved there, and places both X4 T cell‐tropic viruses and M‐tropic viruses as usually minor evolutionary variants that are rarely transmitted and appear when CD4+/CCR5+ T cells are depleted.…”
Section: Introductionmentioning
confidence: 99%
“…For comparison, a group of three “early‐stage subjects” are included showing limited diversity associated with the transmission of a single variant and R5‐predicted phenotypes. Taken from Zhou et al . with permission.…”
Section: Introductionmentioning
confidence: 99%
“…HIV diversity is also influenced by a large population size and high recombination rate [ 1 4 ]. Other factors that contribute to the high genetic diversity of HIV are host APOBEC-mediated substitutions [ 5 , 6 ] and changes in the population of susceptible cells over the duration of infection [ 7 , 8 ] and across different anatomical compartments, such as the brain [ 9 11 ]. HIV evolution is driven, in large part, by the selection of expressed variants that carry mutations allowing escape from cell killing or virus neutralization by host immune responses [ 12 15 ].…”
Section: Introductionmentioning
confidence: 99%