Estimating the in-vivo HIV template switching and recombination rate

  title={Estimating the in-vivo HIV template switching and recombination rate},
  author={Deborah Cromer and Andrew J. Grimm and Timothy E. Schlub and Johnson Mak and Miles P. Davenport},
Background:HIV recombination has been estimated in vitro using a variety of approaches, and shows a high rate of template switching per reverse transcription event. In-vivo studies of recombination generally measure the accumulation of recombinant strains over time, and thus do not directly estimate a comparable template switching rate. Method:To examine whether the estimated in-vitro template switching rate is representative of the rate that occurs during HIV infection in vivo, we adopted a… 

Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection

A computational tool is developed to track recombination in patients, identify recombination hot spots, and show contribution of recombination to antibody escape, which provides insight into molecular mechanisms by which viral recombination contributes to HIV-1 persistence and immunopathogenesis.

HIV-1–Specific Immunodominant T-Cell Responses Drive the Dynamics of HIV-1 Recombination Following Superinfection

A recombination structure analysis of the gag, pol, and nef genes from longitudinal samples of patient LNA819 showed that Pol-LY10, Pol-RY9, and Nef-GL9 were the immunodominant epitopes and vaccines targeting antigens that are less likely to escape immune pressure by recombination and/or mutation are likely to be of benefit to patients with HIV-1.

A step forward understanding HIV-1 diversity

Surprisingly, it appears that despite the error-prone nature of the viral polymerase, the bulk of mutations found in patients are indeed due to the effect of a cellular restriction factor, and a confirmation of the estimates previously made using tissue culture studies is obtained.

Modeling HIV multiple infection.

Recombination in the rabies virus and other lyssaviruses.

  • A. DeviatkinA. Lukashev
  • Biology
    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
  • 2018

Mechanisms and Factors That Drive Extensive Human Immunodeficiency Virus Type-1 Hypervariability: An Overview.

In this review, recent advances in HIV-1 research are summarized and valuable insights are provided that may guide the development of effective therapeutic and preventive strategies against HIV- 1 infection in the near future are summarized.

HIV and SIV Evolution

This chapter provides a brief overview of the evolution of human and simian immunodeficiency viruses.

Genetically barcoded SIV reveals the emergence of escape mutations in multiple viral lineages during immune escape

Assessing the survival of barcoded viral lineages during selection provides a direct and quantitative measure of the stringency of the underlying genetic bottleneck, making it possible to predict the ability of the virus to escape selective forces induced by host immune responses as well as during therapeutic interventions.



Accurately Measuring Recombination between Closely Related HIV-1 Genomes

A HIV-1 marker system is developed by making a small number of codon modifications in gag which allow recombination to be measured over various lengths between closely related viral genomes, and it is shown that recombination does not occur randomly within the HIV genome.

Human Immunodeficiency Virus Type 1 Recombination: Rate, Fidelity, and Putative Hot Spots

DNA sequence analysis of crossover junctions indicated that homologous recombination during viral replication was not particularly mutagenic, indicating that there are other factors or conditions not yet reproduced in cell-free systems which contribute to fidelity during retroviral recombination.

High Rate of Recombination throughout the Human Immunodeficiency Virus Type 1 Genome

The results obtained indicate that HIV-1 undergoes approximately two to three recombination events per genome per replication cycle, implying that both HIV-2 RNAs are typically utilized during reverse transcription and that recombination is an important aspect of HIV- 1 replication.

Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination

It is suggested that the majority of intra- or intersubtype A/D HIV-1 recombinants, generated with each round of infection, are not replication-competent and do not survive in the multiple-cycle system.

Identification of a major restriction in HIV-1 intersubtype recombination.

The discovery of a major restriction in HIV-1 intersubtype recombination is presented and the hypothesis that mismatched sequences in the DIS region alter the formation of heterozygous virions is supported, thereby lowering the observable recombination rate.

Comparison of the Genetic Recombination Rates of Human Immunodeficiency Virus Type 1 in Macrophages and T Cells

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) exhibits a high level of genetic variation generated by frequent mutation and genetic recombination during reverse transcription. We have measured

Identifying Recombination Hot Spots in the HIV-1 Genome

This is the first study to identify the location of recombination hot spots between two similar viral genomes with great statistical power and under conditions that closely reflect natural recombination events among HIV-1 quasispecies.

Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection

The effective recombination rate and the average selection coefficient are estimated to be on the order of 1% per genome per generation (10−5 per base per generation) and 0.5%, respectively.

Sequence determinants of breakpoint location during HIV-1 intersubtype recombination

Experimental recombination was more frequent than expected on the basis of simulated recombination, and local sequence determinants for recombination between divergent HIV-1 isolates are defined for the first time.

Analysis, quantification, and evolutionary consequences of HIV-1 in vitro recombination.

In three of the four viral combinations studied, a steady increase in the proportion of recombinant genomes was observed over time, and this rise coincided with the progressive loss of one of the parental strains, resulting in less diverse viral populations.