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

@article{Salemi2001DatingTC,
  title={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},
  author={Marco Salemi and Korbinian Strimmer and William W. Hall and Margaret Duffy and Eric Delaporte and Souleymane Mboup and Martine Peeters and Anne-Mieke Vandamme},
  journal={The FASEB Journal},
  year={2001},
  volume={15},
  pages={276 - 278}
}
Attempts to estimate the time of origin of human immunodeficiency virus (HIV)‐1 by using phylogenetic analysis are seriously flawed because of the unequal evolutionary rates among different viral lineages. Here, we report 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. The method was validated on a dataset of patients all infected with hepatitis C virus in 1977… Expand
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References

SHOWING 1-10 OF 38 REFERENCES
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). Expand
Dating the origin of HIV-1 subtypes
TLDR
Zhu et al. suggest that subtypes B and D have evolved from a single introduction “not long before 1959”, and that HIV-1 group M viruses probably shared a common ancestor “in the 1940s or the early 1950s”. Expand
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. Expand
Genetic diversity of the envelope glycoprotein from human immunodeficiency virus type 1 isolates of African origin
TLDR
The data presented in this study confirm the existence of several genetic subtypes within the global HIV epidemic and broaden the genetic variability previously observed for envelope subtypes. Expand
Rates and dates of divergence between AIDS virus nucleotide sequences.
TLDR
The analysis suggests that the AIDS virus had existed in central Africa before 1960 and spread to North America before the mid 1970s, and the result is consistent with the view that AIDS spread from Haiti to the United States. Expand
Different population dynamics of human T cell lymphotropic virus type II in intravenous drug users compared with endemically infected tribes.
TLDR
Molecular clock analysis showed that HTLV-II has two different evolutionary rates with the molecular clock for the virus in IDUs ticking 150-350 times faster than the one in endemically infected tribes, and a sharp increase in the population size of the virus among IDUs during the last decades probably caused by the worldwide increase in intravenous drug use. Expand
Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes
TLDR
The genome of a new SIVcpz strain is sequenced and the subspecies identity of all known SIV cpz-infected chimpanzees is determined, by mitochondrial DNA analysis, and it is found that two chimpanzee subspecies in Africa harbour SIVCPz and that their respective viruses form two highly divergent (but subspecies-specific) phylogenetic lineages. Expand
Near-full-length genome sequencing of divergent African HIV type 1 subtype F viruses leads to the identification of a new HIV type 1 subtype designated K.
TLDR
The equidistance of subtype K to the other subtypes of HIV-1 suggests that this subtype existed as long as the others, the lower distance between B and D, and between F1 and F2 suggest a more recent subdivision for these latter strains. Expand
Evolution of influenza virus genes.
TLDR
Comparisons of nucleotide sequences of the eight different influenza A virus segments (genes) were compared to demonstrate the presence of molecular clocks in the viral genes; they accumulated both silent and amino acid-changing substitutions at approximately constant rates with respect to time during evolution. Expand
Long-Term Evolution of the Hypervariable Region of Hepatitis C Virus in a Common-Source-Infected Cohort
TLDR
The long-term evolution of the hepatitis C virus hypervariable region (HVR) and flanking regions of the E1 and E2 envelope proteins have been studied in a cohort of women infected from a common source of anti-D immunoglobulin, indicating that this region can evolve in multiple directions from the same point. Expand
...
1
2
3
4
...