Analysis of HIV Evolution

1
Analysis of HIV Evolution

• Bobak Seddighzadeh
• and
• Kristoffer Chin
• Department of Biology
• Loyola Marymount University
• Bio 398-01
• February 23, 2010

2
Outline

• Background
• Question
• Methods
• Results
• Discussion
• References

3
Function of the HIV Virus

•  HIV is a retrovirus that affects immune cells,
  specifically T cells.
• Retroviruses contain reverse transcriptase also
  known as RNA-dependent DNA polymerase.
• Reverse transcriptase synthesizes single stranded
  RNA into a c-DNA molecule.
• Since viruses cannot synthesize their own
  proteins, they require a host cell to carry out
  its replication process.
• HIV infects the host cell. It then injects its
  genome from its capsid and uses reverse
  transcriptase to create a c-DNA template that it
  then incorperates into the host cells DNA. The
  host cell transcribes and translates proteins
  that assemble into more copies of the virus.
• Virus can have either the lytic or lysogenic life
  cycle

4
Markham Study of HIV Virus

• Evolution is the change in the allele frequency
  in a population over a period of time
• More specific to HIV, the population refers to
  all the HIV viruses in an affected individual,
  and the allele refers to each variant of the HIV
  env gene.
• Different individuals in the population vary in
  heritable traits that can be passed onto
  offspring that may or may not give them a
  selective advantage.
• Markham et al. (1998) Study
• Nucleotide sequences of the env region were used
  to study evolution
• The viruses were classified into groups according
  to rate of CD4 T cell decline progressors and
  non-progressors
• Progressors had increased rates of diversity and
  divergence in comparison to non-progressors and
  ultimately higher rates of CD4 T cell decline.
• We wanted to know why a disparity exists in the
  rate of evolution amongst variants

5
Differences in Nucletide Sequences?

• More specifically our question was what is or
  are the nucleotide sequences in the env region of
  the V3 domain that are responsible for the
  increased genetic diversity, divergence, and rate
  of CD4 T cell decline amongst rapid progressors
  and non-progressors
• My partner and I predict that the increased rate
  of CD4 decline, genetic divergence and diversity
  are directly related to two possible mechanism
  A) HIV-1 variants termed rapid progressors
  selected for a structural mechanism that does not
  protect the genetic material against mutations as
  effectively B) or HIV-1 variants termed rapid
  progressors selected for a mechanism that induces
  mutations on its own DNA. We also predict that
  both these mechanism are related to nucleotide
  differences found in the env region of the V3
  domain.

6
Methods Selection of Subjects, ClustalW,
ClustDist, Counting Nucleotide Differences

• Selection
• Subjects and visits highest rate of CD4 T Cell
  decline
• Clones Largest Max distance, for more variation
• ClustalW
• Analysis and comparison of S
• Analysis and comparison of Unrooted trees of
  subjects
• ClustDist
• Analysis of Max Distance of Nucleotide sequence
  differences
• Counting nucleotide differences
• Analysis of specific nucleotide differences from
  Non and Rapid Progressors using Excel

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ResultsNon and Rapid Progressors Subjects,
Visits, and Clone Selection
Non Progressors Subject Visit Clones Max Distance
2 1, 3, 4 (1,5) (4,5) (3,8) (3) (11) (14)
12 3, 4, 5 (1,3) (1,2) (5,6) (3) (6) (9)
13 2, 3, 5 (1,2) (3,6) (3,6) (1) (3) (4)
Rapid Progressors Subject Visit Clones Max Distance
4 2, 3, 4 (5, 13) (2,16) (1,4) (16) (14) (15)
10 4, 5, 6 (5,8) (3,10) (4,7) (13) (12) (20)
11 2, 3, 4 (1,6) (2,5) (6,8) (3) (7) (7)
8
Results Unrooted tree of selected Rapid
Progressors
of Clones S Theta Min Distance Max Distance
18 100 29 4 51
9
Results Unrooted tree of selected Non Progressors
of Clones S Theta Min Distance Max Distance
18 71 20 1 47
10
Results Unrooted tree of selected Rapid and Non
Progressors
of Clones S Theta Min Distance Max Distance
36 142 34 1 52
11
Results Samples of differences of Nucleotide
Sequence in Non and Rapid Progressors
S4V4-4 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATTATAATAGTACAGCTG S4V4-4 AATAAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAATAAGAAGGATA--- S4V4-4 CCTATAGGACCCGGCAGAGCATTTTATACAACAGG--------CAGAATAGGCAATATAAGGCAA S4V4-4 GCTCATTGTAACATTATTGAAACAAAATGGAATAACACTTTAAAACTGATAGTTGACAAA S4V4-4 TTAAGAGAACAGTTTGG-----GAATAAAACAATAATCTTTAATCAATCCTCA
S10V4-5 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S10V4-5 AATGAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGGATA--- S10V4-5 CATATGGGACCAGGCAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGGCAA S10V4-5 GCACATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAA S10V4-5 TTAAGAGAACAATTTAG-----GAATAAAACAATAATCTTTAAGCAATCCTCA
S2V1-1 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATA--- S2V1-1 CATATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAA S2V1-1 GCATATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAA S2V1-1 TTGAGAGAACACTTTGG-----GAATAAAACAATAGTCTTTAATCACTCCTCA
S13V3-3 GAGATAGTAATTAGATCCGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V3-3 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATA--- S13V3-3 AATATAGGACCAGGTAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAA S13V3-3 GCATATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTACAAAA S13V3-3 TTAAGAGAACAATTTAG----------GAATGCTACAATAGTCTTTAATCACTCATCA
12
Past Studies in the Nucleotide Sequences in HIV

• Hill and Hernandez found a certain loop in the
  gene sequence in Rapid progressors that in the
  beginning of infection and showed up again in the
  end.
• They also found that lack of immunity shows
  diverse forms, but there is a significant
  domination once there is a fit form of the
  disease
• Found significant diversification in the
  beginning of the infection and slowly lowered.
• Specific Changes in the V3 region alter phenotype
  that correlated to disease progression

13
Past Studies in the Nucleotide Sequences in HIV

• Usage of CCR4 is related to high sequence
  conservation in contrast theCXCR4 tropic viruses
  that spread sequence space over larger regions.
• The location of the sequences in the space can be
  used toimprove the accuracy of the prediciton of
  the coreceptror usage.
• Bozek found that patients with high CD4 T cell
  counts  had highly conservessequences in
  comparison to patients that had low CD4 T cell
  counts.

14
Interpretation of Differences found in Nucleotide
Sequences

• 10 nucleotide sequence difference were found in
  the comparison of the non and rapid progressor
  subjects that were chosen
• These 10 differences shows that there were some
  common sequences that may be necessary to the
  rapid decline of T Cells that is caused by the
  HIV virus
• The 10 differences may not seem a lot, but the
  unrooted tree of both Non and Rpaid progressors
  shows a strong diversity in visits 13 and 11, 12
  and 11.
• The other branches of the trees shows close
  relation among the other visitors which can be
  interpreted that there is no significant changes
  in the nucelotide sequences in non and rapid
  progressors
• Markham found a lot more diversity in the rapid
  progressors, it is possible that the clones that
  we chose was not as effective
• We were more concerned with nucleotide
  differences, and we did not evenconsider the
  sequence space. This may provide insight as to
  why thereare not significant nucleotide
  differences amongst progressors
  andnon-progressors yet they functionalally
  different.

15
Translation of Sequences and Nucleotide Spaces

• In future studies, we believe that a translation
  of the nucleotide sequences will show light to
  the results we found
• There may be no specific change that is found in
  the nucleotide sequence, but it is quite possible
  with the amino acids
• Hill an Hernandez found differences in the amino
  acids as finding more Basic than acidic
• Analyzing the Nucleotide spacing found in the V3
  region as analyzed by Bozek

16
References

• Borrego P, Marcelino JM, Rocha C, Doroana M,
  Antunes F, Maltez F, Gomes P, Novo C, Barroso H,
  and Taveira N. The role of the humoral immune
  response in the molecular evolution of the
  envelope C2, V3 and C3 regions in chronically
  HIV-2 infected patients. Retrovirology 2008 Sep
  8 5 78.
• Hill MD and Hernandez W. Nucleotide and amino
  acid mutations in human immunodeficiency virus
  corresponding to CD4 decline. Arch Virol 2006
  Jun 151(6) 1149-58.
• Templeton AR, Reichert RA, Weisstein AE, Yu XF,
  and Markham RB. Selection in context patterns of
  natural selection in the glycoprotein 120 region
  of human immunodeficiency virus 1 within infected
  individuals. Genetics 2004 Aug 167(4) 1547-61.
• Bozek K, Thielen A, Sierra S, Kaiser R, and
  Lengauer T. V3 loop sequence space analysis
  suggests different evolutionary patterns of CCR5-
  and CXCR4-tropic HIV. PLoS One 2009 Oct 9 4(10)
  e7387.