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Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960
Paper by Michael Worobey Presentation by Mary O’Connor
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Goal of Paper Define the time of most recent common ancestor (TMRCA) for the HIV-1 M group by conducting a “comparative evolutionary genetic study of the pre-AIDS epidemic HIV-1 group M viruses” Illuminate the timescale of the HIV-1 virus’s evolution Instrumental pre-AIDS sequences used: DRC60 (dating from 1960, Kinshasa) ZR59 (dating from 1959, Kinshasa)
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Definition of Terms Pandemic Relaxed Molecular Clock (unconstrained)
BMCMC 95% Highest Probability Distribution (HPD) Uncorrected Pairwise Distance Blinded Assay Reference Sequence BEAST Coalescent Tree Prior
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Background: General Information
HIV = Human Immunodeficiency Virus Member of the Lentivirus family (slowly replicating retroviruses associated with long-term illnesses) Symptoms: Severe flu-like symptoms, contraction of various illnesses Transmitted as single stranded RNA through bodily fluids
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Background: General Information
Eventually causes AIDS and failure of immune system 34 million people infected with HIV by 2011 1.8 million people died of AIDS in 2010 68% of HIV cases and 66% of deaths occur in sub-Saharan Africa Nearly 30 million people have died of AIDS since it was first recognized in 1981.
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Background: Origins AIDS first seen in US in 1981 when people started dying of rare diseases Earliest documented case of HIV was in DRC in 1959 HIV-1 originated in chimpanzees in west Africa as SIVcpz Transferred to humans in the early 20th century, likely through predation SIV may mutate into HIV if it is rapidly transmitted from person to person. This gives it time to mutate before any one immune system can suppress it.
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Background: Phylogeny
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Background: Geography of HIV M Group Subtypes
This graphic describes the distribution of HIV-1 M group subtypes throughout the world.
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Discussion of Methods Screened 27 Bouin’s-fixed paraffin-embedded tissue blocks from Kinshasa with PCR and reverse transcription and found one containing HIV-1 RNA (DRC60). Note: Researchers started with pre-sequences ZR59. Viral sequence was extracted with special procedure specific for degraded sequences. Fragments were amplified through PCR with primers that are known to correspond to sections of the gag, pol, and env gene regions.
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Discussion of Methods PCR products for ZR59, DRC60, and three modern control sequences were cloned and sequenced. Blinded Assay conducted: A second lab successful identified and sequenced the same DRC60 gene regions with nearly the same results (1.4% uncorrected pairwise distance).
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Discussion of Methods Sequences were phylogenetically analyzed with an unconstrained BMCMC method (relaxed molecular clock).
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Discussion of Methods Validated time of origin of DRC60 and ZR59 by treating the origin date as unknown and calculating the rate of evolution based on the tree that had already been generated. Uncorrected Pairwise distance between DRC60 and ZR59 in env region calculated to be 11.7% (Greater than 99.2% of within-subtype comparisons)
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Discussion of Methods Estimated TMRCE of HIV-1 M group with BEAST using a relaxed molecular clock.
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Estimation of TMRCA Calibrated substitution rates at many data points to account for relaxed molecular clock Inclusion of older sequences (DRC60 and ZR59) improved estimations for the TMRCA for M group
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Best-fit model assumed a constant population size of the virus
Estimation of TMRCA Best-fit model assumed a constant population size of the virus
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Summary and Analysis of Results
Significant genetic difference between ZR59 and DRC60 proves that the “diversification of HIV-1 in west-central Africa occurred in the early twentieth century, long before the recognition of the AIDS pandemic” HIV-1 group M experienced a long period of slow growth in first half of twentieth century. Close timing of the growth of big cities such as Kinshasa with the TMRCA implies that cities helped the initial establishment and spread of HIV-1
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Limitations of Study Potentially damaged/ modified sequences from the Bouin’s fixative solution. Lack of information before 1976.
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Future Work Are there differences in transmission, virulence, and treatment? How quickly is HIV evolving and how do we prepare for the emergence of new subgroups or even new clades? Should we be studying the SIV strains that got transmitted to humans? Why did certain ones carry over to humans? Archival banks of Bouin’s-fixed paraffin embedded tissue specimens
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References
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