ࡱ > o q n ~2 bjbj $v ̟ ̟ ~* S S S S o L ! I I I I I I I S! U! U! U! U! U! U! f" % U! I I I I M U! q I I j! q q q Q I I q I S! q q q u\ S g
q ! 0 ! q % q % q q q I I I d S S :
Table S1. Comparison of evolutionary rates estimated for the HIV-1 pol gene
ManuscriptMean Rate [lower ad upper highest posterior density intervals]SubtypeSalemi et al. PLoS One 2008 ADDIN EN.CITE Salemi200843434317Salemi, M.de Oliveira, T.Ciccozzi, M.Rezza, G.Goodenow, M. M.Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA. salemi@pathology.ufl.eduHigh-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in AlbaniaPLoS OnePLoS Onee1390312008/01/03AlbaniaEvolution, MolecularGeographyHIV Infections/ virologyHIV-1/classification/ geneticsHumansLikelihood FunctionsMolecular EpidemiologyPhylogeny20081932-6203 (Electronic)18167549214810210.1371/journal.pone.0001390 [doi]Nlmeng[1]1.4 x 10-3 (strict clock) [0.28 - 2.6]Subtype AHue et al. J Virology 2009 ADDIN EN.CITE Hue200939393917Hue, S.Gifford, R. J.Dunn, D.Fernhill, E.Pillay, D.UCL/MRC Centre for Medical Molecular Virology, University College London, Windeyer Building, 46 Cleveland Street, London W1T 4JF, United Kingdom. stephane.hue@ucl.ac.ukDemonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-naive individualsJ VirolJ Virol2645-548362009/01/23Cluster AnalysisDrug Resistance, ViralGreat BritainHIV Infections/ transmission/ virologyHIV-1/ drug effects/ genetics/isolation & purificationHumansMaleMolecular Sequence DataPhylogenySequence Analysis, DNApol Gene Products, Human Immunodeficiency Virus/genetics2009Mar1098-5514 (Electronic)
1098-5514 (Linking)191582382648277JVI.01556-08 [pii]
10.1128/JVI.01556-08 [doi]Nlmeng[2]2.6 x 10-3 (strict clock) [1.9 3.3]Subtype BHue et al. PNAS 2005 ADDIN EN.CITE Hue200540404017Hue, S.Pillay, D.Clewley, J. P.Pybus, O. G.Centre for Virology, Division of Infection and Immunity, University College London, 46 Cleveland Street, London W1T 4JF, UK.Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groupsProc Natl Acad Sci U S AProc Natl Acad Sci U S A4425-9102122005/03/16Disease OutbreaksEvolution, MolecularGenes, polGreat Britain/epidemiologyHIV Infections/epidemiology/ transmission/ virologyHIV-1/classification/ genetics/isolation & purificationHumansMaleMolecular Sequence DataPhylogenyRisk FactorsTime Factors2005Mar 220027-8424 (Print)
0027-8424 (Linking)157675755554920407534102 [pii]
10.1073/pnas.0407534102 [doi]Nlmeng[3]2.55 x 10-3 (strict clock) [1.7 - 3.5]Subtype BDalai et el. AIDS 2009 ADDIN EN.CITE Dalai200942424217Dalai, S. C.de Oliveira, T.Harkins, G. W.Kassaye, S. G.Lint, J.Manasa, J.Johnston, E.Katzenstein, D.Stanford University School of Medicine, Stanford University Medical Center, Stanford, CA 94305, USA. sdalai@stanford.eduEvolution and molecular epidemiology of subtype C HIV-1 in ZimbabweAIDSAIDS2523-3223182009/09/232009Nov 271473-5571 (Electronic)
1473-5571 (Linking)1977069310.1097/QAD.0b013e3283320ef3 [doi]Nlmeng[4]2.16 x 10-3 (strict clock) [1.8 - 2.5]
2.19 x 10-3 (relax clock) [1.7 - 2.5]Subtype CBello et al. AIDS 2008 ADDIN EN.CITE Bello200816161617Bello, G.Passaes, C. P.Guimaraes, M. L.Lorete, R. S.Matos Almeida, S. E.Medeiros, R. M.Alencastro, P. R.Morgado, M. G.Laboratorio de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil. gbello@ioc.fiocruz.brOrigin and evolutionary history of HIV-1 subtype C in BrazilAIDSAIDS1993-200022152008/08/30Bayes TheoremBrazil/epidemiologyDisease OutbreaksEvolution, MolecularFounder EffectHIV Infections/epidemiology/ virologyHIV-1/ classification/genetics/isolation & purificationHumansPhylogenyTime Factorsenv Gene Products, Human Immunodeficiency Virus/geneticspol Gene Products, Human Immunodeficiency Virus/genetics2008Oct 11473-5571 (Electronic)
1473-5571 (Linking)1875392810.1097/QAD.0b013e328315e0aa [doi]Nlmeng[5]1.5 x 10-3 (strict clock) [1.0 - 2.0]
1.6 x 10-3 (relax clock) [1.0 2.0]Subtype CTee et al. J. Virology 2008 ADDIN EN.CITE ADDIN EN.CITE.DATA [6]1.8 x 10-3 (strict clock) [1.4 2.3]Subtype CDe Oliveira et al, (this manuscript)1.64 x 10-3 (strict clock) [1.18 - 2.09]
1.81 x 10-3 (relax clock) [1.27 - 2.37]Subtype C
Footnote: All rates were estimated for the region between 2,253 and 3,251 nucleotides (HXB2 coordinates), and extending no more than 500 nucleotides beyond this range in either direction.
References
ADDIN EN.REFLIST 1. Salemi M, de Oliveira T, Ciccozzi M, Rezza G, Goodenow MM (2008) High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania. PLoS One 3: e1390.
2. Hue S, Gifford RJ, Dunn D, Fernhill E, Pillay D (2009) Demonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-naive individuals. J Virol 83: 2645-2654.
3. Hue S, Pillay D, Clewley JP, Pybus OG (2005) Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A 102: 4425-4429.
4. Dalai SC, de Oliveira T, Harkins GW, Kassaye SG, Lint J, et al. (2009) Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe. AIDS 23: 2523-2532.
5. Bello G, Passaes CP, Guimaraes ML, Lorete RS, Matos Almeida SE, et al. (2008) Origin and evolutionary history of HIV-1 subtype C in Brazil. AIDS 22: 1993-2000.
6. Tee KK, Pybus OG, Li XJ, Han X, Shang H, et al. (2008) Temporal and spatial dynamics of human immunodeficiency virus type 1 circulating recombinant forms 08_BC and 07_BC in Asia. J Virol 82: 9206-9215.
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