Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

@article{Worobey2008DirectEO,
  title={Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960},
  author={Michael Worobey and Marlea Gemmel and Dirk E Teuwen and Tamara S. Haselkorn and Kevin J. Kunstman and Michael Bunce and Jean Jacques Muyembe and Jean-Marie M. Kabongo and Raphael Mbona Kalengayi and Eric A. Van Marck and Marcus Thomas Pius Gilbert and Steven Wolinsky},
  journal={Nature},
  year={2008},
  volume={455},
  pages={661-664}
}
Human immunodeficiency virus type 1 (HIV-1) sequences that pre-date the recognition of AIDS are critical to defining the time of origin and the timescale of virus evolution. A viral sequence from 1959 (ZR59) is the oldest known HIV-1 infection. Other historically documented sequences, important calibration points to convert evolutionary distance into time, are lacking, however; ZR59 is the only one sampled before 1976. Here we report the amplification and characterization of viral sequences… 
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References

SHOWING 1-10 OF 40 REFERENCES
An African HIV-1 sequence from 1959 and implications for the origin of the epidemic
TLDR
Multiple phylogenetic analyses not only authenticate this case as the oldest known HIV-1 infection, but also place its viral sequence near the ancestral node of subtypes B and D in the major group, indicating that these HIV- 1 subtypes, and perhaps all major-group viruses, may have evolved from a single introduction into the African population not long before 1959.
Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution.
  • K. Yusim, M. Peeters, +6 authors B. Korber
  • Biology, Medicine
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences
  • 2001
TLDR
New phylogenetic analysis of an extremely diverse set of human immunodeficiency virus envelope sequences from the Democratic Republic of the Congo suggests an increase in the exponential growth rate of the infected population through time.
Dating the common ancestor of SIVcpz and HIV‐1 group M and the origin of HIV‐1 subtypes by using a new method to uncover clock‐like molecular evolution
  • M. Salemi, K. Strimmer, +5 authors A. Vandamme
  • Biology, Medicine
    FASEB journal : official publication of the Federation of American Societies for Experimental Biology
  • 2001
TLDR
A new method of molecular clock analysis, called Site Stripping for Clock Detection (SSCD), which allows selection of nucleotide sites evolving at an equal rate in different lineages, and is able to date exactly the ‘known’ origin of the infection of HIV‐1 group M.
The Molecular Population Genetics of HIV-1 Group O
TLDR
The population genetics and epidemic history of HIV-1 group O is inferred from viral gene sequence data and the effect of variable evolutionary rates and recombination is evaluated, showing that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome.
The origins of acquired immune deficiency syndrome viruses: where and when?
TLDR
The inferred geographical origin of HIV-1 and the timing of the cross-species transmission are inconsistent with the suggestion that oral polio vaccines, putatively contaminated with viruses from chimpanzees in eastern equatorial Africa in the late 1950s, could be responsible for the origin of acquired immune deficiency syndrome.
High-Resolution Molecular Epidemiology and Evolutionary History of HIV-1 Subtypes in Albania
TLDR
It is suggested that a significant correlation exists between HIV-1 exponential spread and the socio-political changes occurred during the Balkan wars, and the actual number of infections in Albania is at least two orders of magnitude higher than previously thought.
Unprecedented Degree of Human Immunodeficiency Virus Type 1 (HIV-1) Group M Genetic Diversity in the Democratic Republic of Congo Suggests that the HIV-1 Pandemic Originated in Central Africa
TLDR
The high number of HIV-1 subtypes cocirculating, the high intrasubtype diversity, and the high numbers of possible recombinant viruses as well as different unclassified strains are all in agreement with an old and mature epidemic in the DRC, suggesting that this region is the epicenter of HIV -1 group M.
Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1
TLDR
By sequence analysis of endemic SIVcpz strains, this work could trace the origins of pandemic and nonpandemic HIV-1 to distinct, geographically isolated chimpanzee communities and establish P. t.
Timing the ancestor of the HIV-1 pandemic strains.
TLDR
Using a comprehensive full-length envelope sequence alignment, the date of the last common ancestor of the main group of HIV-1 is estimated to be 1931 (1915-41).
The emergence of HIV/AIDS in the Americas and beyond
TLDR
Using HIV-1 gene sequences recovered from archival samples from some of the earliest known Haitian AIDS patients, it is found that subtype B likely moved from Africa to Haiti in or around 1966 and then spread there for some years before successfully dispersing elsewhere.
...
1
2
3
4
...