Amanda N. Wavrin Week 3

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Useful Links

Previous HIV Virus Knowledge

The be honest, my previous knowledge of the HIV virus is limited. I know that HIV is a virus and that it is sexually transmitted. I also know that there is no cure for HIV and that it is extremely difficult to treat. The evolution of the HIV virus is a hot topic and I know much research has been conducted revolving around its evolution. I do know that its origins are said to be in Africa and it is prevelent in Africa to this day.

Three questions about HIV that I would like to have answered are:

  1. What is the origin of the HIV viurs? Do we know its evolution?
  2. What are the effects of the HIV virus on the human body? What are the symptoms?
  3. What is the human immune system's response to the HIV virus once infected?

Using PubMed

  • Begin by going to
  • Search dUTPase
  • Clicking on the first article brings up a page with an abstract for the article
  • By clicking on the hyperlink available for the author(s) it will conduct a search on PubMed for that author
  • The screen shots shown for this page on PubMed today are different than those shown in the Bioinformatics for Dummies book used in lab.
  • PubMed Screen Shot
  • As seen on the screen above, there are no drop down boxes such an a "display" or "show" box
  • Search by author name using the name Abergel
  • Restrict your search results by adding dUTPase next to Abergel
  • If large colored rectangle appear above the title, a journal offers free access to the full text for that paper
  • You can aslo search PubMed using fields
  • By clicking the drop down button next to the Display, you can click on MEDLINE
  • In your search, if you follow each term by the code that identifies its field (in brackets) it will modify your search
  • You can also limit your search by chosing the Advanced search link

Scholarly Review About the HIV Virus

  • When searching HIV Virus on Google Scholar I got different results than when using PubMed. The Advanced Search option on Google Scholar was not very helpful. I did not get the same papers when I searched both sites but both resulted in interesting articles.
  • When searching ISI Web of Knowledge I searched HIV Virus and specified articles from 2000-present. Once again I got different results from when I searched Google Scholar and PubMed. ISI appeared nicely organized.

Terms and Definitions

  • Seroconversion- The change of a serologic test from negative to positive, indicating the development of antibodies in response to infection or immunisation.
  • Phyletic- Denoting the evolution of sequential changes in a line of descent by which one species is transformed into a new species.
  • Cohort- A cohort is a group of animals of the same species, indentified by a common characteristic, which are studied over a period of time as part of a scietific or medical investigation.
  • Epitopes- 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.
  • Epidemiology- The study of the distribution and determinants of health related states and events in populations and the control of health problems.
  • Hypervariable Region- The regions of the immunoglobulin molecule that contain most of the residues involved in the antibody binding site.
  • Virology- The study of viruses and viral diseases.
  • CD4 T cell- A form of T-lymphocyte with CD4 receptor on the cell surpface that recognizes antigens of a virus-infected cell.
  • Viral Load- The number of viral particles (usually HIV) in a sample of blood plasma.
  • PCR- Polymerase chain reaction. The first practical system for invitro amplification of DNA.

Dictionary used:

Outline: Patterns of HIV-1 evolution in individuals with differeing rates if CD4 T call decline


  • HIV-1 has high mutation and replication rates, which allows them to adapt to a rapidly changing host environment
  • The patterns of HIV-1 evolution was studied in 15 different individuals. These individuals were selected for their differences in the CDT4 T cell decline. The 15 subjects fell into three groups: rapid progressors, moderate progressors, and non progressors
  • In a stable environmant, the "best fit" virus will be predominate. This has been observed in other systems.
  • An unstable host environment could have several different effects on the virus pool
    • Diversity could be reduced to the few surviving variants
    • Or, if only the most numerous viral variants were targeted, there would be a significant reduction in viral numbers but not in the genetic diversity

Previous Studies

  • Previous studies looked at smaller groups of infected subjects
  • They used techniques that did not directly examin sequence patterns
  • Analyzed a smaller number of time points per subject


  • Study Population
    • 15 individuals were chosen who were known injection drug users participating in the ALIVE (AIDS Linked to Intravenous Experiences) study
    • The participants had different levels of CD4 T cells: put into 1 of 3 categories- rapid, moderate, and non progressors
    • Every six months blood was obtained for studies
  • Sequencing of HIV-1
    • Nested PCR was used on a region of the env gene from PBMC
    • External env primers and nested primers were used
  • Plasma Viral Load
    • Determined by reverse transcription
  • Generation of Phylogenetic Trees
    • Trees constructed by using MEGA computer software
    • Taxon labels were used to show the time at which the strain was isolated and the amount of identical replicates used
    • They sare colored ti indicate the time at which they were observed
  • Correlation Analysis
    • Analyzed the correlation between genetic diversity and CD4 T cell count a year later
    • Also analyzed the correlation between mutational divergence and CD4 T cell count after a year
  • Determination of dS/dN Raios
    • Starin differences were classified as synonymous or nonsynonymous
    • The Jukes-Cantor correction was used for multiple hits
    • The resulting dS, dN, and dS/dN values were averaged
  • Examination of Source of Greater Initial Visit Diversity in Subjects 9 and 15
    • 9 and 15 had high genetic variation
    • These individuals may have been infected with two different viruses
    • Exclusion of number 15 did not change the dS/dN analysis conclusion
  • Comparison of the Rate of Change of Divergence and Diversity
    • The slope of the regression line of the ratio of divergence/diversity over time for each subject was found


  • CD4 T cell decline was variable among the subjects
  • Non progressor group had low viral loads
  • The viral load data did not distinguish betwen the moderate and rapid progressor groups
  • V3 is an important site of host-virus interaction and was the region that sequence analysis was focused on
  • Diversity and divergence were negatively correlated with the CD4 T cell count over a year
  • The greater the diversity and divergence of a subject's virus, the more likely they were to have a greater CD4 T cell decline over the next year
  • Mylogenetic trees showed no evidence of the predominance of a single strain


  • Both genetic diversity and divergence were higher in individuals with a greater CD4 T cell decline
  • Synonymous substitution rates were comparable in all three subject groups
  • Nonsynonymous rates in progressors were three times those in non progressors
  • Viral strains for non progressors selected against amino acid changes
  • Viral strains from progressors selected for amino acid change
  • McDonald's study found greater genetic diversity in slow progressors then in rapid progressors
  • Wolinksy observed less diversity in subjects with rapidly declining CD4 T cell counts
  • Virus' from 80% of Markham's rapid progressors showed high diversity and divergence
  • In general, the observed relationship between an increase in genetic diversity/divergence and the decline of CD4 T cells in these subjects was consistent with the model of Nowak
  • The importance of this work is that is it working towards finding a way to stop the HIV virus. The goal would be to beat/stop the genetic mutations and diversity of the virus.

Figures and Tables

  • Fig. 1- Shows the CD4 T cell trajectory, diversity, and divergence over time for the subjects in each of the three groups
  • Table 1- Shows a summary of the data on the 15 seroconverters
  • Fig. 2- Shows the mean slope of the genetic diversity/divergence in the different progressor groups
  • Fig. 3- Is a phylogenetic tree of evolution from subject 4
  • Fig. 4- Are phylogenetic trees of four other randomly selected subjects (subjects 5, 7, 8, 14)