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Paul Dan CRISTEA, Rodica Aurora TUDUCEBio-Medical Engineering Center, “Politehnica” University of BucharestSpl. Independentei 313, 060042 Bucharest, Romania{pcristea, trodica}@dsp.pub.ro

Genomic Signal Analysis of HIV-1 Clade F Protease and Reverse

Transcriptase Variability

Genomic Signal Analysis of HIV-1 Clade F Protease and Reverse

Transcriptase Variability

XVI International AIDS ConferenceToronto Canada • August 13 - 18 août 2006XVI Congrès international sur le sidaLate Breaker Track AThursday, 17 August 2006, Session Time: 16:15 - 17:45Room: SR 7, Abstract number: THLB0308

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DNA structureDNA structureDNA structureDNA structure5' end

3' end

OP

O

O- O

OCH2

OP

O

O- O

OCH2

OP

O

O- O

OCH2

OP

O

O- O

OCH2

5' end

3' end

O

OO

CH2

O-

PO

O

OO

CH2

O-

PO

O

OO

CH2

O-

PO

O

OO

CH2

O-

PO

NN

O

H NH

H HO

H

H

N

N

NN

NH

N N

O

OH

H

CH3H

NHH

AT

GC

H

H N

H

N

NN

N H

NN

O

O H

H

CH3

AT

N

NN

N

N N

O

NHH O

H

H

N

N

NN

NH

G C

H

H

H

5' t

o 3

' dir

ecti

on

5' t

o 3

' dir

ecti

on

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Conversion of symbolic sequences Conversion of symbolic sequences Conversion of symbolic sequences Conversion of symbolic sequences

C (cytosine) . T (thymine)

A (adenine)G (guanine)

R (purines)

S (strong link) W (weak link)

M (amino)

K (keto)

Y (pyrimidines)

Nucleotide classesNucleotide classesNucleotide classesNucleotide classes

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Mapping of nucleotide classes Mapping of nucleotide classes ( ( IUPAC symbolsIUPAC symbols ) )

Mapping of nucleotide classes Mapping of nucleotide classes ( ( IUPAC symbolsIUPAC symbols ) )

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Cumulated phase - sum of the phases from the first to the current element in a sequence.

Cumulated and Unwrapped PhasesCumulated and Unwrapped PhasesCumulated and Unwrapped PhasesCumulated and Unwrapped Phases

Unwrapped phase - corrected phase of elements in a sequence, so that the absolute value of the difference between the phase of an element in the sequence and the phase of its preceding element is kept smaller than .

Positive transitions: AG, GC, CT, TA Negative transitions: AT, TC, CG, GA Neutral transitions: AA, TT, CC, GG, AC, CA, GT, TG

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Homo sapiensHomo sapiens chr 1, all contigs (phase 3, length 228507674 bp)chr 1, all contigs (phase 3, length 228507674 bp)

Homo sapiensHomo sapiens chr 1, all contigs (phase 3, length 228507674 bp)chr 1, all contigs (phase 3, length 228507674 bp)

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EscherichiaEscherichia colicoli K12K12EscherichiaEscherichia colicoli K12K12

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Human immunodeficiency virusHuman immunodeficiency virus 1 NC 001802 1 NC 001802Human immunodeficiency virusHuman immunodeficiency virus 1 NC 001802 1 NC 001802

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• Variations of nucleotides (SNPs) tend to compensate each other.

• A genomic sequence satisfies more structural restrictions than a "plain text", and resembles more to a "poem", which obeys rules of symmetry giving "rhythm" and "rhyme".

• The recurrence of patterned structures in nucleotide sequences results in mathematical rules satisfied by genomic signals.

Study of HIV VariabilityStudy of HIV VariabilityStudy of HIV VariabilityStudy of HIV Variability

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• In HIV virus only SNPs type mutations are significant, while cross-over type mutations do not occur.

• SNPs resulting in drug resistance are located in well defined positions in each gene.

• Samples were classified in three groups from the point of view of their resistance to current antiretroviral compounds: sensitive (S), resistant (R) and multiresistant (M).

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•Sequences from Clade F HIV-1 isolates from Romanian patients have been genotyped in the laboratory of the National Institute of Infectious Diseases “Prof. Dr. Matei Bals” of Bucharest.

•The analyzed segment has 1302 base pairs, aligning with the standard sequence of HIV-1 (accession NC001802 in GenBank) over the interval 1799..2430 bp.

•This segment is currently used for the standard identification and assessment of HIV-1 strains, and comprises the protease (PR) gene and two thirds of the reverse transcriptase (RT) gene.

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Unwrapped phase for PR of three multiple drug resistant isolates of HIV-1, subtype F

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Variations of the unwrapped phase signals with respect to the MaxFlat reference

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Digital derivatives of the variations with respect to the maximum flat reference

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Protease inhibitors• HIV mutations in patients starting the antiretroviral

therapy occur primarily at the level of the final enzyme product, preventing the blocking of the PR catalytic site under the effect of the drug.

• In multiple drug resistant patients, significant changes also occur at the level of PR gene RNA secondary structure.

• The changes consists in the replacement of large loops and bulges by smaller closed-loop structures. This result reveals a more complex mechanism of both drug action and drug-resistance development process.

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RNA secondary structureRNA secondary structure

PR_S_518_2003 PR_S_800_2003 PR_S_623_2003

PR_R_398_2003 PR_R_435_2003 PR_R_464_2003

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PR_M_382_2003 PR_M_519_2003 PR_M_505_2003

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Phylogenetic Neighbor- Joining Tree of 28 instances of multiresistant HIV-1, Subtype F built using the PR genomic signal of length 297 bp

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AcknowledgmentAcknowledgment AcknowledgmentAcknowledgment

The data referring to the F subtype HIV strains isolated in Romania have been provided by Dr. Dan Otelea from the National Institute of Infectious Diseases “Prof.Dr.Matei Bals”.

The project has been partially supported by grants from the Ministry of Education and Research of Romania in the framework of the RELANSIN and CNCSIS Programmes.