Michael Worobey

..K. Taubenberger, J. Virol. 76:7860-7862, 2002), can also be explained by laboratory contamination or other experimental errors. Many putative examples of evolutionary stasis in influenza A virus appear to be due to laboratory artifacts...

..The recovery of viral gene sequences from decades-old paraffin-embedded tissues opens the door to a detailed palaeovirological investigation of the evolutionary history of HIV-1 that is not accessible by other methods...

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..Our findings recommend that the extraction methodology adopted should be chosen carefully. Here we provide a quick reference table that can be used to determine appropriate protocols for particular aims...

..Our results suggest either that SIV is a surprisingly young lentiviral lineage or that SIV and, perhaps, HIV dating estimates are seriously compromised by unaccounted-for biases...

..We also compared the quality of inference between Bayesian and maximum likelihood time-free inference models and found them to be qualitatively similar...

..We also suggest that accurate tMRCA estimates from large computationally difficult sequence alignments may be obtained by implementing our novel method of bootstrapping smaller randomly subsampled alignments...

..Our phylogeographic approach establishes that SIV is ancient and at least 32,000 years old. Our conservative calibration point and analyses of gene sequence saturation and dating bias suggest it may be much older...

..This is clearly undesirable when dealing with rare species or otherwise important specimens, such as type specimens...

..Our results suggest that HIV-1 circulated cryptically in the United States for approximately 12 years before the recognition of AIDS in 1981...

..The discovery of PSFVaye indicates that primate foamy virus might be more broadly distributed than previously thought...

..This study substantially weakens the theory of ancient SIV infection followed by codivergence with its primate hosts...

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..These findings suggest an ancient marine origin of retroviruses and have important implications in understanding foamy virus biology...

..Moreover, co-infection experiments should be performed to confirm whether recombination can occur...

..This suggests that so long as these regions maintain sufficient O-linked glycosylation, they are free to evolve rapidly without loss of function as pathogenicity factors...

..In the light of this evidence, we suggest that the systematic screening of FFPE collections may in the future provide valuable insights into the past...

..8 and 11.8 Ma. The discovery of MELV in weasel genomes extends the host range of lentiviruses to the Caniformia (order Carnivora) and provides important insights into the prehistoric diversity of lentiviruses...

..These observations provide genetic data supportive of sexual reproduction in Giardia...

..Therefore, our data imply that recombination between R5 and X4 HIV-1 variants occurs in vivo...

..The single-strain lineages C to G and the 96FR12034 lineage identified here should be considered only as putative groups until related strains are identified that confirm circulation of these viruses in the human population...

..In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome...

..Our findings are discussed with respect to potential zoonotic events that may result from increased levels of human encroachlment into wild habitats...

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