Jmenzago Week 3

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The purpose of this assignment was to better understand the evolutionary behavior of the HIV-1 virus and its relationship to CD4 T cell decline to progress towards the development of a singular, indiscriminate treatment for the variety of HIV strains in a host.


  1. seroconversion - The change of a serologic test from negative to positive, indicating the development of antibodies in response to infection or immunization. (Biology Online, 2020)
  2. virology - the study of viruses and viral diseases. (Biology Online, 2020)
  3. mononuclear - Having a single nucleus. (Biology Online, 2020)
  4. viral load - The number of viral particles (usually hIV) in a sample of blood plasma. HIV viral load is increasingly employed as a surrogate marker for disease progression. It is measured by pCR and bDNA tests and is expressed in number of HIV copies or equivalents per milliliter. (Biology Online, 2020)
  5. synonymous mutation - alternate name for silent mutation, where a nucleotide substitution does not result in an amino acid substitution in the translation product (Oxford Dictionary of Biochemistry and Molecular Biology, 2008)
  6. nonsynonymous mutation - a nucleotide substitution in a protein-coding gene that results in an amino acid substitution in the translation product (Oxford Dictionary of Biochemistry and Molecular Biology, 2008)
  7. seronegative - Giving a negative result in a test of blood serum, e.g. for the presence of a virus. (Lexico, 2020)
  8. epidemiology - The study of the distribution and determinants of health-related states and events in populations and the control of health problems, the study of epidemic disease. (Biology Online, 2020)
  9. chemostats - a device for the continuous culture of bacteria (and other) cells, where growth occurs in an aerated fermenter vessel and its rate is controlled by the rate of addition of fresh nutrients from a reservoir (Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
  10. epitope - That part of an antigenic molecule to which the t-cell receptor responds, a site on a large molecule against which an antibody will be produced and to which it will bind. (Biology Online, 2020)

Article Outline

General Information

  • The study hopes to better understand viral genetic divergence and diversity to treat HIV more effectively. Current treatment at the time of the study's publication is focused on targeting the most prominent strain of HIV in a host, but this does not eliminate the multitude of other less prominent strains. By developing treatment aimed at reducing viral diversity, treatment should be more effective because one drug could indiscriminately attack all HIV strains.
  • Previous studies used small sample sizes, made some conclusions about genetic evolution without examining sequence patterns, and only studied a limited amount of time points.
  • This study overcame the limitations of previous studies by frequently analyzing HIV-1 evolution in 15 subjects over a course of 4 years after seroconversion.
  • This study found that genetic diversity is associated with CD4 T cell decline, and that there are different selection patterns in rapid progressors vs nonprogressors.


  • 15 participants from ALIVE in Baltimore, Maryland
    • Participants underwent seroconversion and were monitored from the point of treatment every 6 months for 4 years
    • Participants categorized into three groups
      • Rapid progressors - CD4 T cell levels declined to less than 200 within 2 years
      • Moderate progressors - CD4 T cell levels declined to 200-650 during 4 year period
      • Nonprogressors - CD4 T cell levels above 650 throughout study period
  • Nested PCR was used to amplify HIV-1 env gene sequence
  • Reverse transcription-PCR was used to determine plasma viral load
  • Phylogenetic trees were generated for the strain from each participant
    • The clones of sequences observed during each visit make up the tree
    • Intermediates were associated with their earliest-observed dependent sequence
  • Correlation analysis was used to determine the relationship between genetic diversity or mutational divergence and CD4 T cell count after 1 year
  • Determination of dS/dN ratios
    • the consensus sequences of each subject were compared to each subsequently observed strain and classified as either synonymous or nonsynonymous
    • The dS, dN, and ratio values were averaged for all strains at a visit to remove bias from unequal sample sizes
    • median value was used for the average since the values showed a skewed distribution
    • Summary data formed basis of all other analysis
  • Subjects 9 and 15 were tested for the presence of two different viruses due to high genetic variation observed from first visit
    • Phylogenetic trees were constructed to compare the clones from their first visit to those of 150-200 randomly selected clones from other participants
  • Rate of change for divergence and diversity was compared
    • regression line of divergence/diversity over time was fit for each individual and summarized with the slope


Results shown in Figures and Tables

  • Figure 1
    • Plots of CD4 T cell trajectory, diversity, and divergence for each subject over the course of the study
    • There was no noticeable pattern for CD4 T cell count decline
      • Non-progressors generally maintained CD4 T cell levels about 400 counts above the plotted divergence and diversity levels
        • Subject 2 had an increase of about 300 T cell counts in the final year of the study, closing the gap of diversity value and subject CD4 T cell counts to less than 100
  • Table 1
    • A summary of the data collected on the 15 subjects
    • Annual rate of CD4 T cell decline
      • All rapid progressors had an annual rate greater than 100 cell/year
      • All nonprogressors had an increase (>55 cells/year) in CD4 T cell counts
      • Subject 7 had a rate of 392 cells/year (more than all rapid progressors except for Subject 4), but was still classified as a moderate progressor because the subject's cell level never fell below 200
        • Had initial CD4 T cell count of 1,072 (highest of all subjects)
    • 3 of the 6 rapid progressors had slopes of change above 2.00 (Subjects 1, 4, and 10), no subjects of other progression had slopes above 2.00
    • Median dS/dN ratios for progressors suggest an advantage for nonsynonymous mutations
      • The value of the ratio should be 1 if mutation is truly random
      • Rapid and moderate progressors had a median value of 0.4, meaning that the rate of nonsynonymous mutations per potential site of nonsynonymous mutation (dN) was higher than that of the rate of synonymous mutations per potential site of synonymous mutation (dS)
        • Statistically significant for both rapid progressors (P=0.01) and moderate progressors (P=0.001)
  • Figure 2
    • Comparison between the slope/year of diversity in different progressor groups and the slope/year of divergence in different progressor groups
    • Divergence and diversity increased in all three progressor categories over time
      • Increase of was progressively greater per year from nonprogressor to moderate progressor to rapid progressor
  • Figure 3
    • Shows the phylogenetic tree of the HIV strain from Subject 9
    • Trees for 10 of the 15 subjects, including this one, show no evidence that one strain of HIV is dominant over an extended period of time.
      • In this figure, viruses from visit 4 are close to those from visit 1, viruses from visit 5 are spread throughout the tree, and viruses from visit 8 come from those in visit 6, despite viruses in visit 6 and 7 emerging from clones from visit 5.
  • Figure 4
    • Shows the phylogenetic trees of 4 of the 15 subjects
      • Subject 9 is not one of these four
    • Evolution is not sustained along a single branch in any of the four subjects


  • McDonald et al. also found that greater genetic divergence is seen in rapid progressors, however, unlike this study, they observed that the intravisit diversity was lower in rapid progressors than in slow progressors at their second visit.
    • Conclusions could have been different because the subjects in McDonald et al. were not followed from seroconversion and monitored at fewer time points.
  • Wolinsky et al. observed less genetic diversity in the two most rapid progressors than subjects with slower progression.
    • These two could be exceptions that were affected by a single rapidly replicating virus because they failed to develop an effective immune response to their infection.
  • The results of this study are most consistent with that of Nowak, who proposed that increasing viral genetic diversity is associated with CD4 T cell decline.
  • This study suggests that rapid progression of CD4 T cell decline in those infected with HIV-1 is a result of high levels of viral genetic diversity, and that this could be a result of an ineffective immune response that is not broad enough to defend against the multitude of viral variants.
  • Future research could analyze the natural immune system response to genetically diverse viruses and, if there is an efficient model there, use it to develop an indiscriminate treatment. Future research could also further study nonprogressors to better understand why they do not have rapid CD4 T cell decline like other hosts.

Caveat Emptor

Overall, the study was a progressive step towards understanding how HIV-1 evolves in hosts to develop effective treatment against it. However, I would say that the paper has some shortcomings with regard to the sample population. While Markham et al. noted that previous studies were limited by their small sample sizes, 15 subjects in most biological studies is not an adequate sample size for confident results. Also, there were inconsistencies in the number of observations for the subjects, which could skew results. The subject observed the least was observed 3 times, and the subject observed the most was observed 9 times in the 4 year period. They accounted for this by comparing the averages of the median values, but I do not have enough knowledge about statistical analysis to say if this is enough to make up for the disparity of observations.

Scientific Conclusion

This study sought to better understand the genetic evolution of HIV-1 env gene and its relationship to CD4 T cell decline with the hopes of developing an indiscriminate treatment against a variety of HIV-1 strains. Results suggested that hosts with HIV-1 strains that have high genetic diversity and divergence also exhibit high rates of CD4 T cell decline. Future research should explore if there are any natural immune responses to genetically diverse viruses to use them as models for developing treatment for HIV-1.


  • My homework partner for the week was Annika Dinulos
    • We communicated over text multiple times to help each other understand data presented in the paper, especially for the part we need to present in class (last 3 columns in Table 1)
  • The paper analyzed for this page was "Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline" by Markham et al.
  • I used Biology Online, Lexico, and Oxford Dictionary of Biochemistry and Molecular Biology to define new scientific terms from the paper
  • I followed the instructions on BIOL368/S20:Week 3 to create this page
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Jmenzago (talk) 23:11, 5 February 2020 (PST)



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