Samantha M. Hurndon

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Journal Club Entry: Patterns of HIV-1 evolution in individuals with differing rates of CD4T cell decline.


  1. epitopes - antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells.
  2. Viral variant -a viral form or version that varies from other forms of the same thing or from a standard.
  3. Cohort study: A cohort is a group of people who share a common characteristic or experience within a defined period (e.g. all people used in this study were injection drug users)
  4. Seroconversion: used to determine detectable specific antibodies to microorganisms in the blood serum due to infection/immunization.
  5. irologic: relating to virology; a branch of science that deals with viruses.
  6. Rapid progressors: attained a level fewer than 200 CD4 T cells within 2 years of seroconverson
  7. Moderate progressors: CD4 T cells declined to 200-650 within the 4 year period.
  8. nonprgressors: maintained CD4 T cells above 650
  9. Stratification: arrangement or formation in layers or strata
  10. Recombination (biology), the process by which genetic material is broken and joined to other genetic material
  11. Inherent Bias: an inability to measure accuarately and directly what one would wish to measure, meaning that indirect measurements are used which might be subject to unknown distortions.


  • High mutation and replication rates of the HIV-1 viruses permit rapid adaption to changes in the host environment.
  • In stable environments the “best fit” virus would dominate, causing successive mutations that would not be represented largely in the gene pool.
  • On the other hand, an unstable host environment could have a range of effects, genetically, on the composition of the virus pool.
  • Instability could be triggered by a dynamic host immune response. (Specifically in HIV-1, coreceptors that exhibit difference.)
  • By analyzing patterns of diversity during the evolution of HIV-1, one can determine the type and efficiency of selection forces that influence the evolution of the virus, a well as how those viruses are adapting to the forces.
  • Pervious studies that were done did not use enough subjects. They also did not use direct examination of sequences patterns.
  • 15 subjects were followed after seroconversion with frequent check up intervals for up to 4 years.
  • Different patterns of selection was seen with nonprogressors, moderately and rapidly progressing subject.
  • Higher level of genetic diversity is seen to be inversely related with CD4 T cell decline.


  1. The study population
    • 15 subjects were used. All subjects selected were intravenous drug users.
    • cohort study where participants were pulled from were all infected or at risk injection users. Blood was obtained from them for virologic/immunologic studies.
    • followed from moment of seroconversion. Attained different levels of CD4 T cells. The subjects were placed into three groups (Rapid, Moderate and nonprogressors)
  2. Sequencing of HIV-1 env Genes
    • Nested PCR was used for genetic sequencing.
    • Sequences analyzed can be seen though GenBank
  3. Plasma Viral Load.
    • Determined by reverse transcription-PCR
  4. Generation of phylogenetic trees:
    • Used the MEGA computer package, correcting for base composition and transition/transversion bias.
    • The time at which each strain was isolated and number of identical replicates can be found on the taxon labels
    • taxons; color labeled for point in time that they were observed.
  5. Correlation Analysis
    • This is the correlation of genetic diversity (mutational divergence) and CD4 T cell count for one year later.
  6. Determination of dS/dN Ratios
    • The difference for the two strains were classified as synonymous or nonsynonymous.
    • Then they adjusted the number of sites where the mutations occurred to correct inherent bias towards nonynonymous changes shown by random mutations. (Jukes-Cantor correction)
    • An average over all strains observed from the dS and dN was taken. Lastly a median value was used for the average.
  7. Examination of Source of Greater Initial Visit Diversity in Subjects 9 and 15
    • These two subjects had high genetic variation.
    • May have been infected with two different viruses. They grouped as monophyletic viruses.
    • Found that these subjects were HIV-1 seronegative 7 months before the first visit.
  8. Comparison of the Rate of Change of Divergence and Diversity


  1. Figure 1
    • This shows all 15 subjects and their CD4 T cell trajectory, diversity and divergence. This was looked at from the point of the first seropositive visit.
    • Median annual changes ranged. (Some were increased and some decreased)
    • Results shown:
      • Rapid progressors:
        • CD4 T cells declined quickly. Diversity and Divergence increased.
      • Moderate progressors:
        • Decline in CD4 T cells for the most part. And like rapid progressors and increase was seen with diversity and divergence.
      • Nonprogressors
        • CD4 T cells increase. Diversity and divergence seem to stay at the bottom of the graphs indicating the there was no increase or much decrease, rather they stayed relatively on the low side.
  2. Table 1
    • This shows the annual changes in nucleotide diversity in CD4. This is the data from the experiment.
    • The rapid progressors showed a large rate of increase in divergence.
    • Non progressors showed low viral loads.
  3. Figure 2
    • This compares the different progressor groups by mean slope per year.
    • In figure A you can see that non-progressors had the lowest mean slope on intravisit genetic diversity. Moderate is slightly higher and Rapid progressors are much higher with larger error bars. This indicates that the data spread for the rapid progressors is much larger than non and moderate.
      • In figure B the mean slope per year of nucleotides mutated from seroconversion virus is the Y-axis, comparing the progressors. Like figure A, non progressors is the lowest and rapid is the highest. The Moderate progressors on B is much closer to the Rapid than nonprogressors.
  4. Figure 3
    • This shows the phylogenetic tree from subject 9.
    • What is seen here is limited progression. Which is seen along the single branch.
  5. Figure 4:
    • This figure shows the phylogenetic of viral evolution from 4,5,7 and 8.
      • There is no deep branching, indicating that the differences are not too significant.
      • Subject seven seemed to have clones that varied the most.
    • Other key points in the results:
    • For the majority of the subjects there was no evidence of predominance of a single strain that covered an extended period of time.
    • Selection against amino acid change from viral strains of the non progressors was seen.


  • purpose of this study: to look at the differences in the levels of CDT 4 cells and the effects that it has on mutation rates and the types of mutations that give the best adaptation to the host environment
  • It was concluded that higher levels of genetic diversity and divergence in an individual is associated with greater declines in CD4 T cells
  • Another study agreed with the results found from this study.
  • nonsynonymous mutations were observed in rapid and moderate progressors.
  • nonpregressors may have immune response that is more effect.

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Bioinformatics Individual Journal Entries

Week 2: Aipotu Evolution

Week 3: HIV Evolution

Week 3: Journal Club

Week 4: Group project

Week 5: Group project

Week 6: DNA Glycosylase Exercise

Week 7: Journal Club

Week 8: Amino Acids Tools

Week9: Amino Acid Sequences/Presentation

Week 10: DNA Microarray Introduction

Samantha M. Hurndon Week 11: Week 11: DNA Microarray Journal Club

Samantha M. Hurndon Week 12: DNA Microarray project

Samanhta M. Hurndon Week 14: Final Project

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