Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

References

• Worobey M, Santiago ML, Keele BF, Ndjango JB, Joy JB, Labama BL, Dhed’A BD, Rambaut A, Sharp PM, Shaw GM, Hahn BH. Origin of AIDS: contaminated polio vaccine theory refuted. Nature 2004; 428: 820.
   Google Scholar
• Gilbert MT, Rambaut A, Wlasiuk G, Spira TJ, Pitchenik AE, Worobey M. The emergence of HIV/AIDS in the Americas and beyond. Proc Natl Acad Sci USA 2007; 104: 18566–18570.
   PubMed Web of Science ®Google Scholar
• Hon CC, Lam TY, Shi ZL, Drummond AJ, Yip CW, Zeng F, Lam PY, Leung FC. Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus. J Virol 2008; 82: 1819–1826.
   PubMed Web of Science ®Google Scholar
• Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. The genomic and epidemiological dynamics of human influenza A virus. Nature 2008; 453: 615–619.
   PubMed Web of Science ®Google Scholar
• Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, Gregory V, Gust ID, Hampson AW, Hay AJ, Hurt AC, de Jong JC, Kelso A, Klimov AI, Kageyama T, Komadina N, Lapedes AS, Lin YP, Mosterin A, Obuchi M, Odagiri T, Osterhaus AD, Rimmelzwaan GF, Shaw MW, Skepner E, Stohr K, Tashiro M, Fouchier RA, Smith DJ. The global circulation of seasonal influenza A (H3N2) viruses. Science 2008; 320: 340–346.
   PubMed Web of Science ®Google Scholar
• Tippmann HF. Analysis for free: comparing programs for sequence analysis. Brief Bioinform 2004; 5: 82–87.
   PubMed Web of Science ®Google Scholar
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25: 4876–4882.
   PubMed Web of Science ®Google Scholar
• Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. Multiple sequence alignment with Clustal X. Trends Biochem Sci 1998; 23: 403–405.
   PubMed Web of Science ®Google Scholar
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947–2948.
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatic 2004; 5: 113.
   PubMed Web of Science ®Google Scholar
• Zhou DX, Tang JW, Chu IM, Cheung JL, Tang NL, Tam JS, Chan PK. J Med Virol 2006; 78: 574–581.
   Google Scholar
• Page RDM, Holmes EC. Molecular Evolution: A Phylogenetic Approach. Pp 172–227. Oxford: Wiley-Blackwell, 1998.
   Google Scholar
• Eck RV, Dayhoff MO. Atlas of Protein Sequence and Structure. Pp 162–168. Silver Spring, MD: National Biomedical Research Foundation, 1966.
   Google Scholar
• Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406–425.
   PubMed Web of Science ®Google Scholar
• Palumbi SR. Rates of molecular evolution and the fraction of nucleotide positions free to vary. J Mol Evol 1989; 29: 180–187.
   Google Scholar
• Whelan S, Lio P, Goldman N. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet 2001; 17: 262–272.
   PubMed Web of Science ®Google Scholar
• Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN, Ed. Mammalian Protein Metabolism. Pp 21–132. New York: Academic Press, 1969.
   Google Scholar
• Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16: 111–120.
   PubMed Web of Science ®Google Scholar
• Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368–376.
   PubMed Web of Science ®Google Scholar
• Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985; 22: 160–174.
   PubMed Web of Science ®Google Scholar
• Lanave C, Preparata G, Saccone C, Serio G. A new method for calculating evolutionary substitution rates. J Mol Evol 1984; 20: 86–93.
   PubMed Web of Science ®Google Scholar
• Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. In Lectures on Mathematics in the Life Sciences. Pp 57–86. New York: American Mathematical Society, 1986.
   Google Scholar
• Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998; 14: 817–818.
   PubMed Web of Science ®Google Scholar
• Posada D. ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res 2006; 34(Web Server issue): W700–W703.
   Google Scholar
• Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 2001; 294: 2310–2314.
   PubMed Web of Science ®Google Scholar
• Gilks WR, Richardson S, Spiegelhalter DJ. Markov Chain Monte Carlo in Practice. Pp 4–7. London: Chapman & Hall/CRC, 1996.
   Google Scholar
• Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of state calculations by fast computing machines. J Chem Phys 1953; 21: 1087–1091.
   Web of Science ®Google Scholar
• Hastings WK. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 1970; 57: 97–109.
   Web of Science ®Google Scholar
• Tierney L. Markov chains for exploring posterior distributions. Ann Statist 1994; 22: 1701–1728.
   Web of Science ®Google Scholar
• Alfaro ME, Zoller S, Lutzoni F. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol 2003; 20: 255–266.
   PubMed Web of Science ®Google Scholar
• Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783–791.
   PubMed Web of Science ®Google Scholar
• Efron B. Bootstrap Methods: another look at the jackknife. Ann Stat 1979; 7: 1–26.
   Web of Science ®Google Scholar
• Metzler DE. Biochemistry: The Chemical Reactions of Living Cells. Vol. 1. Pp 236–237. San Diego: Academic Press, 2001.
   Google Scholar
• Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, Luo SW, Li PH, Zhang LJ, Guan YJ, Butt KM, Wong KL, Chan KW, Lim W, Shortridge KF, Yuen KY, Peiris JS, Poon LL. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science 2003; 302: 276–278.
   PubMed Web of Science ®Google Scholar
• Tang JW, Cheung JL, Chu IM, Sung JJ, Peiris M, Chan PK. The large 386-nt deletion in SARS-associated coronavirus: evidence for quasispecies? J Infect Dis 2006; 194: 808–813.
   Google Scholar
• Muller HJ. Some genetic aspects of sex. Am Nat 1932; 66: 118–138.
   Google Scholar
• Felsenstein J. The evolutionary advantage of recombination. Genetics 1974; 78: 737–756.
   PubMed Web of Science ®Google Scholar
• Jenkins GM, Rambaut A, Pybus OG, Holmes EC. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol 2002; 54: 156–165.
   PubMed Web of Science ®Google Scholar
• Yang Z, Bielawski JP. Statistical methods for detecting molecular adaptation. Trends Ecol Evol 2000; 15: 496–503.
   PubMed Web of Science ®Google Scholar
• Suzuki Y. Natural selection on the influenza virus genome. Mol Biol Evol 2006; 23: 1902–1911.
   Google Scholar
• Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986; 3: 418–426.
   PubMed Web of Science ®Google Scholar
• Goldman N, Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 1994; 11: 725–736.
   PubMed Web of Science ®Google Scholar
• Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007; 24: 1586–1591.
   PubMed Web of Science ®Google Scholar
• Pond SL, Frost SD, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005; 21: 676–679.
   PubMed Web of Science ®Google Scholar
• Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24: 1596–1599.
   PubMed Web of Science ®Google Scholar
• Yang Z, Nielsen R, Goldman N, Pedersen AM. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 2000; 155: 431–449.
   PubMed Web of Science ®Google Scholar
• Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 1998; 15: 568–573.
   PubMed Web of Science ®Google Scholar
• Shackelton LA, Parrish CR, Truyen U, Holmes EC. High rate of viral evolution associated with the emergence of carnivore parvovirus. Proc Natl Acad Sci USA 2005; 102: 379–384.
   PubMed Web of Science ®Google Scholar
• Lam TT, Hon CC, Pybus OG, Kosakovsky Pond SL, Wong RT, Yip CW, Zeng F, Leung FC. Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia. PLoS Pathog 2008; 4: e1000130.
   Google Scholar
• Yang Z, Nielsen R. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol 1998; 46: 409–418.
   PubMed Web of Science ®Google Scholar
• McCutchan FE. Understanding the genetic diversity of HIV-1. AIDS 2000; 14(Suppl 3): S31–S44.
   Google Scholar
• Piyasirisilp S, McCutchan FE, Carr JK, Sanders-Buell E, Liu W, Chen J, Wagner R, Wolf H, Shao Y, Lai S, Beyrer C, Yu XF. A recent outbreak of human immunodeficiency virus type 1 infection in southern China was initiated by two highly homogeneous, geographically separated strains, circulating recombinant form AE and a novel BC recombinant. J Virol 2000; 74: 11286–11295.
   PubMed Web of Science ®Google Scholar
• Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y. Evolution and ecology of influenza A viruses. Microbiol Rev 1992; 56: 152–179.
   PubMedGoogle Scholar
• World Health Organization Confirmed Human Cases of Avian Influenza A (H5N1). Available at: http://www.who.int/csr/disease/avian_influenza/country/en. Accessed on 11 March 2010.
   Google Scholar
• Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 1999; 73: 152–160.
   PubMed Web of Science ®Google Scholar
• Salminen MO, Carr JK, Burke DS, McCutchan FE. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses 1995; 11: 1423–1425.
   PubMed Web of Science ®Google Scholar
• Bromham L, Penny D. The modern molecular clock. Nat Rev Genet 2003; 4: 216–224.
   PubMed Web of Science ®Google Scholar
• Pybus OG. Model selection and the molecular clock. PLoS Bio 2006; 4: e151.
   Google Scholar
• Nerome K, Kanegae Y, Yoshioka Y, Itamura S, Ishida M, Gojobori T, Oya A. Evolutionary pathways of N2 neuraminidases of swine and human influenza A viruses: origin of the neuraminidase genes of two reassortants (H1N2) isolated from pigs. J Gen Virol 1991; 72(Pt 3): 693–698.
   Google Scholar
• Rambaut A. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 2000; 16: 395–399.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 2002; 161: 1307–1320.
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Larget B, Swofford D. A compound poisson process for relaxing the molecular clock. Genetics 2000; 154: 1879–1892.
   PubMed Web of Science ®Google Scholar
• Sanderson MJ. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol 2002; 19: 101–109.
   PubMed Web of Science ®Google Scholar
• Thorne JL, Kishino H, Painter IS. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 1998; 15: 1647–1657.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol 2006; 4: e88.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Pybus OG, Rambaut A. Inference of viral evolutionary rates from molecular sequences. Adv Parasitol 2003; 54: 331–358.
   Google Scholar
• Korber B, Muldoon M, Theiler J, Gao F, Gupta R, Lapedes A, Hahn BH, Wolinsky S, Bhattacharya T. Timing the ancestor of the HIV-1 pandemic strains. Science 2000; 288: 1789–1796.
   PubMed Web of Science ®Google Scholar
• Rutschmann F. Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Divers Distrib 2006; 12: 35–48.
   Web of Science ®Google Scholar
• Welch JJ, Bromham L. Molecular dating when rates vary. Trends Ecol Evol (Amst) 2005; 20: 320–327.
   PubMed Web of Science ®Google Scholar
• Kumar S. Molecular clocks: four decades of evolution. Nat Rev Genet 2005; 6: 654–662.
   PubMed Web of Science ®Google Scholar
• Ho SY, Phillips MJ, Drummond AJ, Cooper AD. Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Mol Biol Evol 2005; 22: 1355–1363.
   PubMed Web of Science ®Google Scholar
• Yoder AD, Yang Z. Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol 2000; 17: 1081–1090.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007; 7: 214.
   PubMed Web of Science ®Google Scholar
• Newton MA, Raftery AE. Approximate Bayesian inference with the weighted likelihood bootstrap. J Roy Stat Soc SerB 1994; 56: 3–48.
   Google Scholar
• Drummond AJ, Strimmer K. PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 2001; 17: 662–663.
   Google Scholar
• Lemey P, Salemi M, Wang B, Duffy M, Hall WH, Saksena NK, Vandamme AM. Site stripping based on likelihood ratio reduction is a useful tool to evaluate the impact of non-clock-like behavior on viral phylogenetic reconstructions. FEMS Immunol Med Microbiol 2003; 39: 125–132.
   Google Scholar
• Hon CC, Lam TY, Drummond A, Rambaut A, Lee YF, Yip CW, Zeng F, Lam PY, Ng PT, Leung FC. Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B. J Virol 2006; 80: 8503–8509.
   PubMed Web of Science ®Google Scholar
• Salemi M, Lamers SL, Yu S, de Oliveira T, Fitch WM, McGrath MS. Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. J Virol 2005; 79: 11343–11352.
   PubMed Web of Science ®Google Scholar
• Lemey P, Pybus OG, Rambaut A, Drummond AJ, Robertson DL, Roques P, Worobey M, Vandamme AM. The molecular population genetics of HIV-1 group O. Genetics 2004; 167: 1059–1068.
   Google Scholar
• Lam TY, Hon CC, Wang Z, Hui RK, Zeng F, Leung FC. Evolutionary analyses of European H1N2 swine influenza A virus by placing timestamps on the multiple reassortment events. Virus Res 2008; 131: 271–278.
   Google Scholar
• Slatkin M, Hudson RR. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 1991; 129: 555–562.
   PubMed Web of Science ®Google Scholar
• Rogers AR, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 1992; 9: 552–569.
   PubMed Web of Science ®Google Scholar
• Nee S, Holmes EC, Rambaut A, Harvey PH. Inferring population history from molecular phylogenies. Philos Trans R Soc Lond B Biol Sci 1995; 349: 25–31.
   Google Scholar
• Pybus OG, Rambaut A, Harvey PH. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 2000; 155: 1429–1437.
   PubMed Web of Science ®Google Scholar
• Paradis E. Testing for constant diversification rates using molecular phylogenies: a general approach based on statistical tests for goodness of fit. Mol Biol Evol 1998; 15: 476–479.
   Google Scholar
• Hue S, Pillay D, Clewley JP, Pybus OG. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci USA 2005; 102: 4425–4429.
   Google Scholar
• Salemi M, de Oliveira T, Soares MA, Pybus O, Dumans AT, Vandamme AM, Tanuri A, Cassol S, Fitch WM. Different epidemic potentials of the HIV-1B and C subtypes. J Mol Evol 2005; 60: 598–605.
   Google Scholar
• Carrington CV, Foster JE, Pybus OG, Bennett SN, Holmes EC. Invasion and maintenance of dengue virus type 2 and type 4 in the Americas. J Virol 2005; 79: 14680–14687.
   Google Scholar
• Pybus OG, Charleston MA, Gupta S, Rambaut A, Holmes EC, Harvey PH. The epidemic behavior of the hepatitis C virus. Science 2001; 292: 2323–2325.
   PubMed Web of Science ®Google Scholar
• Pybus OG, Drummond AJ, Nakano T, Robertson BH, Rambaut A. The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. Mol Biol Evol 2003; 20: 381–387.
   Web of Science ®Google Scholar
• Tanaka Y, Takahashi K, Orito E, Karino Y, Kang JH, Suzuki K, Matsui A, Hori A, Matsuda H, Sakugawa H, Asahina Y, Kitamura T, Mizokami M, Mishiro S. Molecular tracing of Japan-indigenous hepatitis E viruses. J Gen Virol 2006; 87(Pt 4): 949–954.
   Google Scholar
• de Graaf M, Osterhaus AD, Fouchier RA, Holmes EC. Evolutionary dynamics of human and avian metapneumoviruses. J Gen Virol 2008; 89(Pt 12): 2933–2942.
   Google Scholar
• Biek R, Henderson JC, Waller LA, Rupprecht CE, Real LA. A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus. Proc Natl Acad Sci USA 2007; 104: 7993–7998.
   PubMed Web of Science ®Google Scholar
• Kingman JFC. The coalescent. Stoch Process Appl 1982; 13: 235–248.
   Google Scholar
• Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG. Measurably evolving populations. Trends Ecol Evol 2003; 18: 481–488.
   Web of Science ®Google Scholar
• Emersona BC, Paradis E, Thébaud C. Revealing the demographic histories of species using DNA sequences. Trends Ecol Evol 2001; 16: 707–716.
   Google Scholar
• Kouyos RD, Althaus CL, Bonhoeffer S. Stochastic or deterministic: what is the effective population size of HIV-1? Trends Microbiol 2006; 14: 507–511.
   Google Scholar
• Pybus OG, Rambaut A. GENIE: estimating demographic history from molecular phylogenies. Bioinformatics 2002; 18: 1404–1405.
   Google Scholar
• Strimmer K, Pybus OG. Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol Biol Evol 2001; 18: 2298–2305.
   Google Scholar
• Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 2005; 22: 1185–1192.
   PubMed Web of Science ®Google Scholar
• Fouchier RA, Munster V, Wallensten A, Bestebroer TM, Herfst S, Smith D, Rimmelzwaan GF, Olsen B, Osterhaus AD. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. J Virol 2005; 79: 2814–2822.
   PubMed Web of Science ®Google Scholar
• Webster RG, Yakhno M, Hinshaw VS, Bean WJ, Murti KG. Intestinal influenza: replication and characterization of influenza viruses in ducks. Virology 1978; 84: 268–278.
   PubMed Web of Science ®Google Scholar
• Webster RG, Geraci J, Petursson G, Skirnisson K. Conjunctivitis in human beings caused by influenza A virus of seals. N Engl J Med1981; 304: 911.
   PubMed Web of Science ®Google Scholar
• Hinshaw VS, Bean WJ, Geraci J, Fiorelli P, Early G, Webster RG. Characterization of two influenza A viruses from a pilot whale. J Virol 1986; 58: 655–656.
   Web of Science ®Google Scholar
• Kuiken T, Rimmelzwaan G, van Riel D, van Amerongen G, Baars M, Fouchier R, Osterhaus A. Avian H5N1 influenza in cats. Science 2004; 306: 241.
   PubMed Web of Science ®Google Scholar
• Giese M, Harder TC, Teifke JP, Klopfleisch R, Breithaupt A, Mettenleiter TC, Vahlenkamp TW. Experimental infection and natural contact exposure of dogs with avian influenza virus (H5N1). Emerg Infect Dis 2008; 14: 308–310.
   Google Scholar
• Bean WJ, Kawaoka Y, Wood JM, Pearson JE, Webster RG. Characterization of virulent and avirulent A/chicken/Pennsylvania/83 influenza A viruses: potential role of defective interfering RNAs in nature. J Virol 1985; 54: 151–160.
   PubMed Web of Science ®Google Scholar
• Horimoto T, Rivera E, Pearson J, Senne D, Krauss S, Kawaoka Y, Webster RG. Origin and molecular changes associated with emergence of a highly pathogenic H5N2 influenza virus in Mexico. Virology 1995; 213: 223–230.
   PubMed Web of Science ®Google Scholar
• Webster RG, Govorkova EA. H5N1 influenza—continuing evolution and spread. N Engl J Med 2006; 355: 2174–2177.
   PubMed Web of Science ®Google Scholar
• Parrish CR, Kawaoka Y. The origins of new pandemic viruses: the acquisition of new host ranges by canine parvovirus and influenza A viruses. Annu Rev Microbiol 2005; 59: 553–586.
   PubMed Web of Science ®Google Scholar
• Shinde V, Bridges CB, Uyeki TM, Shu B, Balish A, Xu X, Lindstrom S, Gubareva LV, Deyde V, Garten RJ, Harris M, Gerber S, Vagasky S, Smith F, Pascoe N, Martin K, Dufficy D, Ritger K, Conover C, Quinlisk P, Klimov A, Bresee JS, Finelli L. Triple-reassortant swine influenza A (H1) in humans in the United States, 2005–2009. N Engl J Med 2009; 360: 2616–2625.
   PubMed Web of Science ®Google Scholar
• Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JS, Guan Y, Rambaut A. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 2009; 459:1122–1125.
   PubMed Web of Science ®Google Scholar
• Dawood FS, Jain S, Finelli L, Shaw MW, Lindstrom S, Garten RJ, Gubareva LV, Xu X, Bridges CB, Uyeki TM. Emergence of a novel swine-origin influenza A (H1N1) virus in humans. N Engl J Med 2009; 360: 2605–2615.
   PubMed Web of Science ®Google Scholar
• Webster RG, Laver WG. The origin of pandemic influenza. Bull World Health Organ 1972; 47: 449–452.
   Google Scholar
• Scholtissek C, Rohde W, Von Hoyningen V, Rott R. On the origin of the human influenza virus subtypes H2N2 and H3N2. Virology 1978; 87: 13–20.
   PubMed Web of Science ®Google Scholar
• Kawaoka Y, Krauss S, Webster RG. Avian-to-human transmission of the PB1 gene of influenza A viruses in the 1957 and 1968 pandemics. J Virol 1989; 63: 4603–4608.
   PubMed Web of Science ®Google Scholar
• Gorman OT, Donis RO, Kawaoka Y, Webster RG. Evolution of influenza A virus PB2 genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus. J Virol 1990; 64: 4893–4902.
   Google Scholar
• Gorman OT, Bean WJ, Kawaoka Y, Donatelli I, Guo YJ, Webster RG. Evolution of influenza A virus nucleoprotein genes: implications for the origins of H1N1 human and classical swine viruses. J Virol 1991; 65: 3704–3714.
   Google Scholar
• Ito T, Gorman OT, Kawaoka Y, Bean WJ, Webster RG. Evolutionary analysis of the influenza A virus M gene with comparison of the M1 and M2 proteins. J Virol 1991; 65: 5491–5498.
   PubMed Web of Science ®Google Scholar
• Reid AH, Fanning TG, Hultin JV, Taubenberger JK. Origin and evolution of the 1918 “Spanish” influenza virus hemagglutinin gene. Proc Natl Acad Sci USA 1999; 96: 1651–1656.
   PubMed Web of Science ®Google Scholar
• Reid AH, Fanning TG, Janczewski TA, Taubenberger JK. Characterization of the 1918 “Spanish” influenza virus neuraminidase gene. Proc Natl Acad Sci USA 2000; 97: 6785–6790.
   PubMed Web of Science ®Google Scholar
• Basler CF, Reid AH, Dybing JK, Janczewski TA, Fanning TG, Zheng H, Salvatore M, Perdue ML, Swayne DE, Garcia-Sastre A, Palese P, Taubenberger JK. Sequence of the 1918 pandemic influenza virus nonstructural gene (NS) segment and characterization of recombinant viruses bearing the 1918 NS genes. Proc Natl Acad Sci USA 2001; 98: 2746–2751.
   Web of Science ®Google Scholar
• Reid AH, Fanning TG, Janczewski TA, McCall S, Taubenberger JK. Characterization of the 1918 “Spanish” influenza virus matrix gene segment. J Virol 2002; 76: 10717–10723.
   Web of Science ®Google Scholar
• Reid AH, Fanning TG, Janczewski TA, Lourens RM, Taubenberger JK. Novel origin of the 1918 pandemic influenza virus nucleoprotein gene. J Virol 2004; 78: 12462–12470.
   Web of Science ®Google Scholar
• Taubenberger JK, Reid AH, Lourens RM, Wang R, Jin G, Fanning TG. Characterization of the 1918 influenza virus polymerase genes. Nature 2005; 437: 889–893.
   PubMed Web of Science ®Google Scholar
• Gibbs MJ, Gibbs AJ. Molecular virology: was the 1918 pandemic caused by a bird flu? Nature 2006; 440: E8; discussion E9–E10.
   Google Scholar
• Gibbs MJ, Armstrong JS, Gibbs AJ. Recombination in the hemagglutinin gene of the 1918 “Spanish flu.” Science 2001; 293: 1842–1845.
   PubMedGoogle Scholar
• Worobey M, Rambaut A, Pybus OG, Robertson DL. Questioning the evidence for genetic recombination in the 1918 “Spanish flu” virus. Science 2002; 296: 211.
   Google Scholar
• Karasin AI, Schutten MM, Cooper LA, Smith CB, Subbarao K, Anderson GA, Carman S, Olsen CW. Genetic characterization of H3N2 influenza viruses isolated from pigs in North America, 1977–1999: evidence for wholly human and reassortant virus genotypes. Virus Res 2000; 68: 71–85.
   Google Scholar
• Zhou NN, Senne DA, Landgraf JS, Swenson SL, Erickson G, Rossow K, Liu L, Yoon K, Krauss S, Webster RG. Genetic reassortment of avian, swine, and human influenza A viruses in American pigs. J Virol 1999; 73: 8851–8856.
   PubMed Web of Science ®Google Scholar
• Karasin AI, Olsen CW, Anderson GA. Genetic characterization of an H1N2 influenza virus isolated from a pig in Indiana. J Clin Microbiol 2000; 38: 2453–2456.
   Google Scholar
• Ma W, Gramer M, Rossow K, Yoon KJ. Isolation and genetic characterization of new reassortant H3N1 swine influenza virus from pigs in the midwestern United States. J Virol 2006; 80: 5092–5096.
   PubMedGoogle Scholar
• Ma W, Vincent AL, Gramer MR, Brockwell CB, Lager KM, Janke BH, Gauger PC, Patnayak DP, Webby RJ, Richt JA. Identification of H2N3 influenza A viruses from swine in the United States. Proc Natl Acad Sci USA 2007; 104: 20949–20954.
   PubMed Web of Science ®Google Scholar
• Nardelli L, Pascucci S, Gualandi GL, Loda P. Outbreaks of classical swine influenza in Italy in 1976. Zentralbl Veterinarmed B 1978; 25: 853–857.
   Google Scholar
• Castrucci MR, Campitelli L, Ruggieri A, Barigazzi G, Sidoli L, Daniels R, Oxford JS, Donatelli I. Antigenic and sequence analysis of H3 influenza virus haemagglutinins from pigs in Italy. J Gen Virol 1994; 75(Pt 2): 371–379.
   Google Scholar
• Brown IH, Ludwig S, Olsen CW, Hannoun C, Scholtissek C, Hinshaw VS, Harris PA, McCauley JW, Strong I, Alexander DJ. Antigenic and genetic analyses of H1N1 influenza A viruses from European pigs. J Gen Virol 1997; 78(Pt 3): 553–562.
   Google Scholar
• Castrucci MR, Donatelli I, Sidoli L, Barigazzi G, Kawaoka Y, Webster RG. Genetic reassortment between avian and human influenza A viruses in Italian pigs. Virology 1993; 193: 503–506.
   PubMed Web of Science ®Google Scholar
• Brown IH, Harris PA, McCauley JW, Alexander DJ. Multiple genetic reassortment of avian and human influenza A viruses in European pigs, resulting in the emergence of an H1N2 virus of novel genotype. J Gen Virol 1998; 79(Pt 12): 2947–2955.
   Google Scholar
• Taubenberger JK, Morens DM, Fauci AS. The next influenza pandemic: can it be predicted? JAMA 2007; 297: 2025–2027.
   PubMed Web of Science ®Google Scholar
• Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, Spiro DJ, Sitz J, Koo H, Bolotov P, Dernovoy D, Tatusova T, Bao Y, St George K, Taylor J, Lipman DJ, Fraser CM, Taubenberger JK, Salzberg SL. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 2005; 437: 1162–1166.
   PubMed Web of Science ®Google Scholar
• Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ, Taubenberger JK. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol 2005; 3: e300.
   Web of Science ®Google Scholar
• Nelson MI, Viboud C, Simonsen L, Bennett RT, Griesemer SB, St George K, Taylor J, Spiro DJ, Sengamalay NA, Ghedin E, Taubenberger JK, Holmes EC. Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathog 2008; 4: e1000012.
   Google Scholar
• Monne I, Joannis TM, Fusaro A, De Benedictis P, Lombin LH, Ularamu H, Egbuji A, Solomon P, Obi TU, Cattoli G, Capua I. Reassortant avian influenza virus (H5N1) in poultry, Nigeria, 2007. Emerg Infect Dis 2008; 14: 637–640.
   Google Scholar
• Vijaykrishna D, Bahl J, Riley S, Duan L, Zhang JX, Chen H, Peiris JS, Smith GJ, Guan Y. Evolutionary dynamics and emergence of panzootic H5N1 influenza viruses. PLoS Pathog 2008; 4: e1000161.
   PubMed Web of Science ®Google Scholar
• Simonsen L, Viboud C, Grenfell BT, Dushoff J, Jennings L, Smit M, Macken C, Hata M, Gog J, Miller MA, Holmes EC. The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance. Mol Biol Evol 2007; 24: 1811–1820.
   PubMedGoogle Scholar
• Hill AW, Guralnick RP, Wilson MJ, Habib F, Janies D. Evolution of drug resistance in multiple distinct lineages of H5N1 avian influenza. Infect Genet Evol 2009; 9: 169–178.
   PubMed Web of Science ®Google Scholar
• Krumbholz A, Schmidtke M, Bergmann S, Motzke S, Bauer K, Stech J, Durrwald R, Wutzler P, Zell R. High prevalence of amantadine resistance among circulating European porcine influenza A viruses. J Gen Virol 2009; 90(Pt 4): 900–908.
   Google Scholar
• Schafer JR, Kawaoka Y, Bean WJ, Suss J, Senne D, Webster RG. Origin of the pandemic 1957 H2 influenza A virus and the persistence of its possible progenitors in the avian reservoir. Virology 1993; 194: 781–788.
   PubMed Web of Science ®Google Scholar
• Suarez DL. Evolution of avian influenza viruses. Vet Microbiol 2000; 74: 15–27.
   PubMed Web of Science ®Google Scholar
• Chen R, Holmes EC. Avian influenza virus exhibits rapid evolutionary dynamics. Mol Biol Evol 2006; 23: 2336–2341.
   PubMed Web of Science ®Google Scholar
• Bush RM, Fitch WM, Bender CA, Cox NJ. Positive selection on the H3 hemagglutinin gene of human influenza virus A. Mol Biol Evol 1999; 16: 1457–1465.
   PubMedGoogle Scholar
• Yang Z. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J Mol Evol 2000; 51: 423–432.
   PubMed Web of Science ®Google Scholar
• Suzuki Y. Positive selection operates continuously on hemagglutinin during evolution of H3N2 human influenza A virus. Gene 2008; 427: 111–116.
   Google Scholar
• Tang JW, Ngai KL, Lam WY, Chan PK. Seasonality of influenza A (H3N2) virus: a Hong Kong perspective (1997–2006). PLoS One 2008; 3: e2768.
   Web of Science ®Google Scholar
• Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Rimmelzwaan GF, Osterhaus AD, Fouchier RA. Mapping the antigenic and genetic evolution of influenza virus. Science 2004; 305: 371–376.
   PubMed Web of Science ®Google Scholar
• Wolf YI, Viboud C, Holmes EC, Koonin EV, Lipman DJ. Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct 2006; 1: 34.
   PubMed Web of Science ®Google Scholar
• Kosakovsky Pond SL, Poon AF, Leigh Brown AJ, Frost SD. A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol 2008; 25: 1809–1824.
   PubMed Web of Science ®Google Scholar
• Kryazhimskiy S, Bazykin GA, Plotkin J, Dushoff J. Directionality in the evolution of influenza A haemagglutinin. Proc Biol Sci 2008; 275: 2455–2464.
   Google Scholar
• Carrat F, Flahault A. Influenza vaccine: the challenge of antigenic drift. Vaccine 2007; 25: 6852–6862.
   PubMed Web of Science ®Google Scholar
• Wallace RG, Hodac H, Lathrop RH, Fitch WM. A statistical phylogeography of influenza A H5N1. Proc Natl Acad Sci USA 2007; 104: 4473–4478.
   PubMed Web of Science ®Google Scholar
• Wallace RG, Fitch WM. Influenza A H5N1 immigration is filtered out at some international borders. PLoS ONE 2008; 3: e1697.
   PubMedGoogle Scholar
• Chen R, Holmes EC. Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds. Virology 2009; 383: 156–161.
   PubMed Web of Science ®Google Scholar
• Krauss S, Obert CA, Franks J, Walker D, Jones K, Seiler P, Niles L, Pryor SP, Obenauer JC, Naeve CW, Widjaja L, Webby RJ, Webster RG. Influenza in migratory birds and evidence of limited intercontinental virus exchange. PLoS Pathog 2007; 3: e167.
   PubMed Web of Science ®Google Scholar
• Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC. Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog 2007; 3: 1220–1228.
   Google Scholar
• Hirsch VM, Olmsted RA, Murphey-Corb M, Purcell RH, Johnson PR. An African primate lentivirus (SIVsm) closely related to HIV-2. Nature 1989; 339: 389–392.
   PubMed Web of Science ®Google Scholar
• Gao F, Yue L, White AT, Pappas PG, Barchue J, Hanson AP, Greene BM, Sharp PM, Shaw GM, Hahn BH. Human infection by genetically diverse SIVSM-related HIV-2 in west Africa. Nature 1992; 358: 495–499.
   PubMed Web of Science ®Google Scholar
• Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM, Michael SF, Cummins LB, Arthur LO, Peeters M, Shaw GM, Sharp PM, Hahn BH. Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 1999; 397: 436–441.
   PubMed Web of Science ®Google Scholar
• Hillis DM. AIDS. Origins of HIV. Science 2000; 288: 1757–1759.
   PubMed Web of Science ®Google Scholar
• Leitner T, Albert J. The molecular clock of HIV-1 unveiled through analysis of a known transmission history. Proc Natl Acad Sci USA 1999; 96: 10752–10757.
   Google Scholar
• Leitner T, Escanilla D, Franzen C, Uhlen M, Albert J. Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc Natl Acad Sci USA 1996; 93: 10864–10869.
   PubMed Web of Science ®Google Scholar
• Leitner T, Kumar S, Albert J. Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J Virol 1997; 71: 4761–4770.
   Google Scholar
• Lemey P, Pybus OG, Wang B, Saksena NK, Salemi M, Vandamme AM. Tracing the origin and history of the HIV-2 epidemic. Proc Natl Acad Sci USA 2003; 100: 6588–6592.
   PubMed Web of Science ®Google Scholar
• Paraskevis D, Lemey P, Salemi M, Suchard M, Van De Peer Y, Vandamme AM. Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using bayesian inference: implications for the origin of HIV-1. Mol Biol Evol 2003; 20: 1986–1996.
   PubMed Web of Science ®Google Scholar
• Robbins KE, Lemey P, Pybus OG, Jaffe HW, Youngpairoj AS, Brown TM, Salemi M, Vandamme AM, Kalish ML. U.S. human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains. J Virol 2003; 77: 6359–6366.
   PubMedGoogle Scholar
• Thomson MM, Perez-Alvarez L, Najera R. Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy. Lancet Infect Dis 2002; 2: 461–471.
   PubMed Web of Science ®Google Scholar
• Requejo HI. Worldwide molecular epidemiology of HIV. Rev Saude Publica 2006; 40: 331–345.
   Web of Science ®Google Scholar
• Buonaguro L, Tornesello ML, Buonaguro FM. Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications. J Virol 2007; 81: 10209–10219.
   PubMed Web of Science ®Google Scholar
• Gao F, Robertson DL, Morrison SG, Hui H, Craig S, Decker J, Fultz PN, Girard M, Shaw GM, Hahn BH, Sharp PM. The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. J Virol 1996; 70: 7013–7029.
   PubMed Web of Science ®Google Scholar
• Gao F, Robertson DL, Carruthers CD, Li Y, Bailes E, Kostrikis LG, Salminen MO, Bibollet-Ruche F, Peeters M, Ho DD, Shaw GM, Sharp PM, Hahn BH. An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I). J Virol 1998; 72: 10234–10241.
   PubMed Web of Science ®Google Scholar
• Abecasis AB, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, Vandamme AM. Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. J Virol 2007; 81: 8543–8551.
   PubMedGoogle Scholar
• Yamaguchi J, Ndembi N, Ngansop C, Mbanya D, Kaptue L, Gurtler LG, Devare SG, Brennan CA. HIV type 1 group M subtype G in Cameroon: five genome sequences. AIDS Res Hum Retroviruses 2009; 25: 469–473.
   Google Scholar
• Blackard JT, Renjifo B, Fawzi W, Hertzmark E, Msamanga G, Mwakagile D, Hunter D, Spiegelman D, Sharghi N, Kagoma C, Essex M. HIV-1 LTR subtype and perinatal transmission. Virology 2001; 287: 261–265.
   Google Scholar
• Yang C, Li M, Newman RD, Shi YP, Ayisi J, van Eijk AM, Otieno J, Misore AO, Steketee RW, Nahlen BL, Lal RB. Genetic diversity of HIV-1 in western Kenya: subtype-specific differences in mother-to-child transmission. AIDS 2003; 17: 1667–1674.
   PubMed Web of Science ®Google Scholar
• Murray MC, Embree JE, Ramdahin SG, Anzala AO, Njenga S, Plummer FA. Effect of human immunodeficiency virus (HIV) type 1 viral genotype on mother-to-child transmission of HIV-1. J Infect Dis 2000; 181: 746–749.
   Google Scholar
• Tapia N, Franco S, Puig-Basagoiti F, Menendez C, Alonso PL, Mshinda H, Clotet B, Saiz JC, Martinez MA. Influence of human immunodeficiency virus type 1 subtype on mother-to-child transmission. J Gen Virol 2003; 84(Pt 3): 607–613.
   Google Scholar
• Kanki PJ, Hamel DJ, Sankale JL, Hsieh C, Thior I, Barin F, Woodcock SA, Gueye-Ndiaye A, Zhang E, Montano M, Siby T, Marlink R, NDoye I, Essex ME, MBoup S. Human immunodeficiency virus type 1 subtypes differ in disease progression. J Infect Dis 1999; 179: 68–73.
   PubMed Web of Science ®Google Scholar
• Kaleebu P, French N, Mahe C, Yirrell D, Watera C, Lyagoba F, Nakiyingi J, Rutebemberwa A, Morgan D, Weber J, Gilks C, Whitworth J. Effect of human immunodeficiency virus (HIV) type 1 envelope subtypes A and D on disease progression in a large cohort of HIV-1-positive persons in Uganda. J Infect Dis 2002; 185: 1244–1250.
   PubMed Web of Science ®Google Scholar
• Baeten JM, Chohan B, Lavreys L, Chohan V, McClelland RS, Certain L, Mandaliya K, Jaoko W, Overbaugh J. HIV-1 subtype D infection is associated with faster disease progression than subtype A in spite of similar plasma HIV-1 loads. J Infect Dis 2007; 195: 1177–1180.
   PubMed Web of Science ®Google Scholar
• Kiwanuka N, Laeyendecker O, Robb M, Kigozi G, Arroyo M, McCutchan F, Eller LA, Eller M, Makumbi F, Birx D, Wabwire-Mangen F, Serwadda D, Sewankambo NK, Quinn TC, Wawer M, Gray R. Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection. J Infect Dis 2008; 197: 707–713.
   PubMed Web of Science ®Google Scholar
• Kuritzkes DR. HIV-1 subtype as a determinant of disease progression. J Infect Dis 2008; 197: 638–639.
   PubMed Web of Science ®Google Scholar
• Tang JW, Chan PKS. Virology of human immunodeficiency virus. In Lee SS, Wu JCY, Wong KH, Eds. HIV Manual 2007. Pp 3–6. Hong Kong SAR: Centre for Health Protection, Department of Health, 2007. Available at: http://www.info.gov.hk/aids/pdf/g190htm/i_index.htm. Accessed 11 March 2010.
   Google Scholar
• Ou CY, Ciesielski CA, Myers G, Bandea CI, Luo CC, Korber BT, Mullins JI, Schochetman G, Berkelman RL, Economou AN, et al. Molecular epidemiology of HIV transmission in a dental practice. Science 1992; 256: 1165–1171.
   PubMed Web of Science ®Google Scholar
• Hillis DM, Huelsenbeck JP. Support for dental HIV transmission. Nature 1994; 369: 24–25.
   PubMed Web of Science ®Google Scholar
• Hayman A, Moss T, Simmons G, Arnold C, Holmes EC, Naylor-Adamson L, Hawkswell J, Allen K, Radford J, Nguyen-Van-Tam J, Balfe P. Phylogenetic analysis of multiple heterosexual transmission events involving subtype b of HIV type 1. AIDS Res Hum Retroviruses 2001; 17: 689–695.
   Google Scholar
• Tatt ID, Barlow KL, Clewley JP, Gill ON, Parry JV. Surveillance of HIV-1 subtypes among heterosexuals in England and Wales, 1997–2000. J Acquir Immune Defic Syndr 2004; 36: 1092–1099.
   Google Scholar
• Bobkov AF, Kazennova EV, Selimova LM, Khanina TA, Ryabov GS, Bobkova MR, Sukhanova AL, Kravchenko AV, Ladnaya NN, Weber JN, Pokrovsky VV. Temporal trends in the HIV-1 epidemic in Russia: predominance of subtype A. J Med Virol 2004; 74: 191–196.
   PubMed Web of Science ®Google Scholar
• Aggarwal I, Smith M, Tatt ID, Murad S, Osner N, Geretti AM, Easterbrook PJ. Evidence for onward transmission of HIV-1 non-B subtype strains in the United Kingdom. J Acquir Immune Defic Syndr 2006; 41: 201–209.
   Google Scholar
• Gottlieb GS, Heath L, Nickle DC, Wong KG, Leach SE, Jacobs B, Gezahegne S, van’t Wout AB, Jacobson LP, Margolick JB, Mullins JI. HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study. J Infect Dis 2008; 197: 1011–1015.
   PubMed Web of Science ®Google Scholar
• Kakehasi FM, Tupinambas U, Cleto S, Aleixo A, Lin E, Melo VH, Aguiar RA, Pinto JA. Persistence of genotypic resistance to nelfinavir among women exposed to prophylactic antiretroviral therapy during pregnancy. AIDS Res Hum Retroviruses 2007; 23: 1515–1520.
   Google Scholar
• Kiptoo M, Ichimura H, Wembe RL, Ng’Ang’a Z, Mueke J, Kinyua J, Lagat N, Okoth F, Songok EM. Prevalence of nevirapine-associated resistance mutations after single dose prophylactic treatment among antenatal clinic attendees in north rift Kenya. AIDS Res Hum Retroviruses 2008; 24: 1555–1559.
   Google Scholar
• Church JD, Omer SB, Guay LA, Huang W, Lidstrom J, Musoke P, Mmiro F, Jackson JB, Eshleman SH. Analysis of nevirapine (NVP) resistance in Ugandan infants who were HIV infected despite receiving single-Dose (SD) NVP versus SD NVP plus daily NVP up to 6 weeks of age to prevent HIV vertical transmission. J Infect Dis 2008; 198: 1075–1082.
   PubMedGoogle Scholar
• Steain MC, Wang B, Saksena NK. Analysis of HIV-1 sequences vertically transmitted to infants in Kisumu, Kenya. J Clin Virol 2006; 36: 298–302.
   Google Scholar
• Kwiek JJ, Russell ES, Dang KK, Burch CL, Mwapasa V, Meshnick SR, Swanstrom R. The molecular epidemiology of HIV-1 envelope diversity during HIV-1 subtype C vertical transmission in Malawian mother-infant pairs. AIDS 2008; 22: 863–871.
   Google Scholar
• Hoffmann FG, He X, West JT, Lemey P, Kankasa C, Wood C. Genetic variation in mother-child acute seroconverter pairs from Zambia. AIDS 2008; 22: 817–824.
   Google Scholar
• Albert J, Wahlberg J, Leitner T, Escanilla D, Uhlen M. Analysis of a rape case by direct sequencing of the human immunodeficiency virus type 1 pol and gag genes. J Virol 1994; 68: 5918–5924.
   PubMed Web of Science ®Google Scholar
• Metzker ML, Mindell DP, Liu XM, Ptak RG, Gibbs RA, Hillis DM. Molecular evidence of HIV-1 transmission in a criminal case. Proc Natl Acad Sci USA 2002; 99: 14292–14297.
   PubMed Web of Science ®Google Scholar
• Pillay D, Rambaut A, Geretti AM, Brown AJ. HIV phylogenetics. BMJ 2007; 335: 460–461.
   Google Scholar
• Blanchard A, Ferris S, Chamaret S, Guetard D, Montagnier L. Molecular evidence for nosocomial transmission of human immunodeficiency virus from a surgeon to one of his patients. J Virol 1998; 72: 4537–4540.
   Google Scholar
• Goujon CP, Schneider VM, Grofti J, Montigny J, Jeantils V, Astagneau P, Rozenbaum W, Lot F, Frocrain-Herchkovitch C, Delphin N, Le Gal F, Nicolas JC, Milinkovitch MC, Deny P. Phylogenetic analyses indicate an atypical nurse-to-patient transmission of human immunodeficiency virus type 1. J Virol 2000; 74: 2525–2532.
   Google Scholar
• Hirsch MS. Initiating therapy: when to start, what to use. J Infect Dis 2008; 197(Suppl 3): S252–S260.
   Google Scholar
• Wilson JW, Bean P, Robins T, Graziano F, Persing DH. Comparative evaluation of three human immunodeficiency virus genotyping systems: the HIV-GenotypR method, the HIV PRT GeneChip assay, and the HIV-1 RT line probe assay. J Clin Microbiol 2000; 38: 3022–3028.
   Google Scholar
• Erali M, Page S, Reimer LG, Hillyard DR. Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods. J Clin Microbiol 2001; 39: 2157–2165.
   PubMed Web of Science ®Google Scholar
• Yam WC, Chen JH, Wong KH, Chan K, Cheng VC, Lam HY, Lee SS, Zheng BJ, Yuen KY. Clinical utility of genotyping resistance test on determining the mutation patterns in HIV-1 CRF01_AE and subtype B patients receiving antiretroviral therapy in Hong Kong. J Clin Virol 2006; 35: 454–457.
   PubMed Web of Science ®Google Scholar
• Chen JH, Wong KH, Chan K, Lam HY, Lee SS, Li P, Lee MP, Tsang DN, Zheng BJ, Yuen KY, Yam WC. Evaluation of an in-house genotyping resistance test for HIV-1 drug resistance interpretation and genotyping. J Clin Virol 2007; 39: 125–131.
   Google Scholar
• Zazzi M, Romano L, Catucci M, Venturi G, De Milito A, Valensin PE. Clinical evaluation of an in-house reverse transcription-competitive PCR for quantitation of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol 1999; 37: 333–338.
   Google Scholar
• Jennings C, Fiscus SA, Crowe SM, Danilovic AD, Morack RJ, Scianna S, Cachafeiro A, Brambilla DJ, Schupbach J, Stevens W, Respess R, Varnier OE, Corrigan GE, Gronowitz JS, Ussery MA, Bremer JW. Comparison of two human immunodeficiency virus (HIV) RNA surrogate assays to the standard HIV RNA assay. J Clin Microbiol 2005; 43: 5950–5956.
   PubMed Web of Science ®Google Scholar
• Lam HY, Chen JH, Wong KH, Chan K, Li P, Lee MP, Tsang DN, Yuen KY, Yam WC. Evaluation of NucliSens EasyQ HIV-1 assay for quantification of HIV-1 subtypes prevalent in South-east Asia. J Clin Virol 2007; 38: 39–43.
   PubMed Web of Science ®Google Scholar
• Hirsch MS, Gunthard HF, Schapiro JM, Brun-Vezinet F, Clotet B, Hammer SM, Johnson VA, Kuritzkes DR, Mellors JW, Pillay D, Yeni PG, Jacobsen DM, Richman DD. Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis 2008; 47: 266–285.
   PubMed Web of Science ®Google Scholar
• Eron JJ. Managing antiretroviral therapy: changing regimens, resistance testing, and the risks from structured treatment interruptions. J Infect Dis 2008; 197(Suppl 3): S261–S271.
   Google Scholar
• Johnson VA, Brun-Vezinet F, Clotet B, Gunthard HF, Kuritzkes DR, Pillay D, Schapiro JM, Richman DD. Update of the drug resistance mutations in HIV-1: Spring 2008. Top HIV Med 2008; 16: 62–68.
   PubMedGoogle Scholar
• Tang JW, Pillay D. Transmission of HIV-1 drug resistance. J Clin Virol 2004; 30: 1–10.
   PubMed Web of Science ®Google Scholar
• Oette M, Kaiser R, Daumer M, Akbari D, Fatkenheuer G, Rockstroh JK, Stechel J, Rieke A, Mauss S, Schmaloer D, Gobels K, Vogt C, Wettstein M, Haussinger D. Primary drug-resistance in HIV-positive patients on initiation of first-line antiretroviral therapy in Germany. Eur J Med Res 2004; 9: 273–278.
   Google Scholar
• Fox J, Dustan S, McClure M, Weber J, Fidler S. Transmitted drug-resistant HIV-1 in primary HIV-1 infection; incidence, evolution and impact on response to antiretroviral therapy. HIV Med 2006; 7: 477–483.
   Google Scholar
• Poggensee G, Kucherer C, Werning J, Somogyi S, Bieniek B, Dupke S, Jessen H, Hamouda O. Impact of transmission of drug-resistant HIV on the course of infection and the treatment success. Data from the German HIV-1 Seroconverter Study. HIV Med 2007; 8: 511–519.
   PubMed Web of Science ®Google Scholar
• Gonsalez CR, Alcalde R, Nishiya A, Barreto CC, Silva FE, de Almeida A, Mendonca M, Ferreira F, Fernandes SS, Casseb J, Duarte AJ. Drug resistance among chronic HIV-1-infected patients naive for use of anti-retroviral therapy in Sao Paulo city. Virus Res 2007; 129: 87–90.
   Google Scholar
• Bannister WP, Cozzi-Lepri A, Clotet B, Mocroft A, Kjaer J, Reiss P, von Wyl V, Lazzarin A, Katlama C, Phillips AN, Ruiz L, Lundgren JD. Transmitted drug resistant HIV-1 and association with virologic and CD4 cell count response to combination antiretroviral therapy in the EuroSIDA Study. J Acquir Immune Defic Syndr 2008; 48: 324–333.
   Web of Science ®Google Scholar
• Flys TS, McConnell MS, Matovu F, Church JD, Bagenda D, Khaki L, Bakaki P, Thigpen MC, Eure C, Fowler MG, Eshleman SH. Nevirapine resistance in women and infants after first versus repeated use of single-dose nevirapine for prevention of HIV-1 vertical transmission. J Infect Dis 2008; 198: 465–469.
   Google Scholar
• Han J, Wang L, Jiang Y, Zhang Q, Fang L, Yao J, Wang Q. Resistance mutations in HIV-1 infected pregnant women and their infants receiving antiretrovirals to prevent HIV-1 vertical transmission in China. Int J STD AIDS 2009; 20: 249–254.
   Google Scholar
• Machado ES, Afonso AO, Nissley DV, Lemey P, Cunha SM, Oliveira RH, Soares MA. Emergency of primary NNRTI resistance mutations without antiretroviral selective pressure in a HAART-treated child. PLoS ONE 2009; 4: e4806.
   Google Scholar
• Hue S, Gifford RJ, Dunn D, Fernhill E, Pillay D. Demonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-naive individuals. J Virol 2009; 83: 2645–2654.
   Google Scholar
• Sturmer M, Preiser W, Gute P, Nisius G, Doerr HW. Phylogenetic analysis of HIV-1 transmission: pol gene sequences are insufficient to clarify true relationships between patient isolates. AIDS 2004; 18: 2109–2113.
   Google Scholar
• Hue S, Clewley JP, Cane PA, Pillay D. HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS 2004; 18: 719–728.
   Google Scholar
• Hue S, Clewley JP, Cane PA, Pillay D. Investigation of HIV-1 transmission events by phylogenetic methods: requirement for scientific rigour. AIDS 2005; 19: 449–450.
   Google Scholar
• Lemey P, Vandamme AM. Exploring full-genome sequences for phylogenetic support of HIV-1 transmission events. AIDS 2005; 19: 1551–1552.
   Google Scholar
• Gonzalez-Candelas F, Moya A. Time and rate of evolution are the key to establish transmission cases. AIDS 2005; 19: 1552–1553.
   Google Scholar
• Lemey P, Van Dooren S, Vandamme AM. Evolutionary dynamics of human retroviruses investigated through full-genome scanning. Mol Biol Evol 2005; 22: 942–951.
   PubMed Web of Science ®Google Scholar
• Lloyd-Smith JO, Schreiber SJ, Kopp PE, Getz WM. Superspreading and the effect of individual variation on disease emergence. Nature 2005; 438: 355–359.
   PubMed Web of Science ®Google Scholar
• Chen MI, Loon SC, Leong HN, Leo YS. Understanding the super-spreading events of SARS in Singapore. Ann Acad Med Singap 2006; 35: 390–394.
   Google Scholar
• Li Y, Yu IT, Xu P, Lee JH, Wong TW, Ooi PL, Sleigh AC. Predicting super spreading events during the 2003 severe acute respiratory syndrome epidemics in Hong Kong and Singapore. Am J Epidemiol 2004; 160: 719–728.
   PubMed Web of Science ®Google Scholar
• Shen Z, Ning F, Zhou W, He X, Lin C, Chin DP, Zhu Z, Schuchat A. Superspreading SARS events, Beijing, 2003. Emerging Infect Dis 2004; 10: 256–260.
   PubMed Web of Science ®Google Scholar
• Zhong NS, Zheng BJ, Li YM, Poon Xie, ZH, Chan KH, Li PH, Tan SY, Chang Q, Xie JP, Liu XQ, Xu J, Li DX, Yuen KY, Peiris, Guan Y. Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People’s Republic of China, in February, 2003. Lancet 2003; 362: 1353–1358.
   PubMed Web of Science ®Google Scholar
• Guan Y, Peiris JS, Zheng B, Poon LL, Chan KH, Zeng FY, Chan CW, Chan MN, Chen JD, Chow KY, Hon CC, Hui KH, Li J, Li VY, Wang Y, Leung SW, Yuen KY, Leung FC. Molecular epidemiology of the novel coronavirus that causes severe acute respiratory syndrome. Lancet 2004; 363: 99–104.
   PubMed Web of Science ®Google Scholar
• Ruan YJ, Wei CL, Ee AL, Vega VB, Thoreau H, Su ST, Chia JM, Ng P, Chiu KP, Lim L, Zhang T, Peng CK, Lin EO, Lee NM, Yee SL, Ng LF, Chee RE, Stanton LW, Long PM, Liu ET. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet 2003; 361: 1779–1785.
   PubMed Web of Science ®Google Scholar
• Chinese SARS Molecular Epidemiology Consortium. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science 2004; 303: 1666–1669.
   PubMed Web of Science ®Google Scholar
• Tang JW, Cheung JL, Chu IM, Ip M, Hui M, Peiris M, Chan PK. Characterizing 56 complete SARS-CoV S-gene sequences from Hong Kong. J Clin Virol 2007; 38: 19–26.
   Google Scholar
• Zhang CY, Wei JF, He SH. Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups. BMC Microbiol 2006; 6: 88.
   Google Scholar
• Tang X, Li G, Vasilakis N, Zhang Y, Shi Z, Zhong Y, Wang LF, Zhang S. Differential stepwise evolution of SARS coronavirus functional proteins in different host species. BMC Evol Biol 2009; 9: 52.
   Google Scholar
• Tsui SK, Chim SS, Lo YM, Chinese University of Hong Kong Molecular SARS Research Group. Coronavirus genomic-sequence variations and the epidemiology of the severe acute respiratory syndrome. N Engl J Med 2003; 349: 187–188.
   Google Scholar
• Song HD, Tu CC, Zhang GW, Wang SY, Zheng K, Lei LC, Chen QX, Gao YW, Zhou HQ, Xiang H, Zheng HJ, Chern SW, Cheng F, Pan CM, Xuan H, Chen SJ, Luo HM, Zhou DH, Liu YF, He JF, Qin PZ, Li LH, Ren YQ, Liang WJ, Yu YD, Anderson L, Wang M, Xu RH, Wu XW, Zheng HY, Chen JD, Liang G, Gao Y, Liao M, Fang L, Jiang LY, Li H, Chen F, Di B, He LJ, Lin JY, Tong S, Kong X, Du L, Hao P, Tang H, Bernini A, Yu XJ, Spiga O, Guo ZM, Pan HY, He WZ, Manuguerra JC, Fontanet A, Danchin A, Niccolai N, Li YX, Wu CI, Zhao GP. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci USA 2005; 102: 2430–2435.
   PubMed Web of Science ®Google Scholar
• Chim SS, Tsui SK, Chan KC, Au TC, Hung EC, Tong YK, Chiu RW, Ng EK, Chan PK, Chu CM, Sung JJ, Tam JS, Fung KP, Waye MM, Lee CY, Yuen KY, Lo YM, CUHK Molecular SARS Research Group. Genomic characterisation of the severe acute respiratory syndrome coronavirus of Amoy Gardens outbreak in Hong Kong. Lancet 2003; 362: 1807–1808.
   Google Scholar
• Lan YC, Liu TT, Yang JY, Lee CM, Chen YJ, Chan YJ, Lu JJ, Liu HF, Hsiung CA, Ho MS, Hsiao KJ, Chen HY, Chen YM. Molecular epidemiology of severe acute respiratory syndrome-associated coronavirus infections in Taiwan. J Infect Dis 2005; 191: 1478–1489.
   Google Scholar
• Shih MC, Peck K, Chan WL, Chu YP, Chen JC, Tsai CH, Chang JG. SARS-CoV infection was from at least two origins in the Taiwan area. Intervirology 2005; 48: 124–132.
   Google Scholar
• Chiu RW, Chim SS, Lo YM. Molecular epidemiology of SARS—from Amoy Gardens to Taiwan. N Engl J Med 2003; 349: 1875–1876.
   Google Scholar
• Lan YC, Liu HF, Shih YP, Yang JY, Chen HY, Chen YM. Phylogenetic analysis and sequence comparisons of structural and non-structural SARS coronavirus proteins in Taiwan. Infect Genet Evol 2005; 5: 261–269.
   Google Scholar
• Yeh SH, Wang HY, Tsai CY, Kao CL, Yang JY, Liu HW, Su IJ, Tsai SF, Chen DS, Chen PJ, National Taiwan University SARS Research Team. Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: molecular epidemiology and genome evolution. Proc Natl Acad Sci USA 2004; 101: 2542–2547.
   PubMed Web of Science ®Google Scholar
• Vega VB, Ruan Y, Liu J, Lee WH, Wei CL, Se-Thoe SY, Tang KF, Zhang T, Kolatkar PR, Ooi EE, Ling AE, Stanton LW, Long PM, Liu ET. Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003. BMC Infect Dis 2004; 4: 32.
   PubMed Web of Science ®Google Scholar
• Bi S, Qin E, Xu Z, Li W, Wang J, Hu Y, Liu Y, Duan S, Hu J, Han Y, Xu J, Li Y, Yi Y, Zhou Y, Lin W, Xu H, Li R, Zhang Z, Sun H, Zhu J, Yu M, Fan B, Wu Q, Tang L, Yang B, Li G, Peng W, Li W, Jiang T, Deng Y, Liu B, Shi J, Deng Y, Wei W, Liu H, Tong Z, Zhang F, Zhang Y, Wang C, Li Y, Ye J, Gan Y, Ji J, Li X, Tian X, Lu F, Tan G, Yang R, Liu B, Liu S, Li S, Wang J, Wang J, Cao W, Yu J, Dong X, Yang H. Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04). Genomics Proteomics Bioinformatics 2003; 1: 180–192.
   Google Scholar
• Zhao GP. SARS molecular epidemiology: a Chinese fairy tale of controlling an emerging zoonotic disease in the genomics era. Philos Trans R Soc Lond B Biol Sci 2007; 362: 1063–1081.
   PubMed Web of Science ®Google Scholar
• Liang G, Chen Q, Xu J, Liu Y, Lim W, Peiris JS, Anderson LJ, Ruan L, Li H, Kan B, Di B, Cheng P, Chan KH, Erdman DD, Gu S, Yan X, Liang W, Zhou D, Haynes L, Duan S, Zhang X, Zheng H, Gao Y, Tong S, Li D, Fang L, Qin P, Xu W. Laboratory diagnosis of four recent sporadic cases of community-acquired SARS, Guangdong Province, China. Emerg Infect Dis 2004; 10: 1774–1781.
   PubMed Web of Science ®Google Scholar
• Lam TT, Hon CC, Lam PY, Yip CW, Zeng FY, Leung FC. Comments to the predecessor of human SARS coronavirus in 2003–2004 epidemic. Vet Microbiol 2008; 126: 390–393.
   Google Scholar
• Zeng F, Chow KYC, Leung FC. Estimated timing of the last common ancestor of the SARS coronavirus. N Engl J Med 2003; 349:2469–2470.
   Google Scholar
• Salemi M, Fitch WM, Ciccozzi M, Ruiz-Alvarez MJ, Rezza G, Lewis MJ. Severe acute respiratory syndrome coronavirus sequence characteristics and evolutionary rate estimate from maximum likelihood analysis. J Virol 2004; 78: 1602–1603.
   PubMed Web of Science ®Google Scholar
• Stumpf MP, Pybus OG. Genetic diversity and models of viral evolution for the hepatitis C virus. FEMS Microbiol Lett 2002; 214: 143–152.
   Google Scholar
• Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, Khattra J, Asano JK, Barber SA, Chan SY, Cloutier A, Coughlin SM, Freeman D, Girn N, Griffith OL, Leach SR, Mayo M, McDonald H, Montgomery SB, Pandoh PK, Petrescu AS, Robertson AG, Schein JE, Siddiqui A, Smailus DE, Stott JM, Yang GS, Plummer F, Andonov A, Artsob H, Bastien N, Bernard K, Booth TF, Bowness D, Czub M, Drebot M, Fernando L, Flick R, Garbutt M, Gray M, Grolla A, Jones S, Feldmann H, Meyers A, Kabani A, Li Y, Normand S, Stroher U, Tipples GA, Tyler S, Vogrig R, Ward D, Watson B, Brunham RC, Krajden M, Petric M, Skowronski DM, Upton C, Roper RL. The genome sequence of the SARS-associated coronavirus. Science 2003; 300: 1399–1404.
   PubMed Web of Science ®Google Scholar
• Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Peñaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, Günther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 2003; 300: 1394–1399.
   PubMed Web of Science ®Google Scholar
• Zeng FY, Chan CW, Chan MN, Chen JD, Chow KY, Hon CC, Hui KH, Li J, Li VY, Wang CY, Wang PY, Guan Y, Zheng B, Poon LL, Chan KH, Yuen KY, Peiris JS, Leung FC. The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39). Exp Biol Med (Maywood) 2003; 228: 866–873.
   PubMedGoogle Scholar
• Holmes KV, Enjuanes L. Virology. The SARS coronavirus: a postgenomic era. Science 2003; 300: 1377–1378.
   Google Scholar
• Eickmann M, Becker S, Klenk HD, Doerr HW, Stadler K, Censini S, Guidotti S, Masignani V, Scarselli M, Mora M, Donati C, Han JH, Song HC, Abrignani S, Covacci A, Rappuoli R. Phylogeny of the SARS coronavirus. Science 2003; 302: 1504–1505.
   PubMed Web of Science ®Google Scholar
• Kim OJ, Lee DH, Lee CH. Close relationship between SARS-coronavirus and group 2 coronavirus. J Microbiol 2006; 44: 83–91.
   Google Scholar
• Zhu G, Chen HW. Monophyletic relationship between severe acute respiratory syndrome coronavirus and group 2 coronaviruses. J Infect Dis 2004; 189: 1676–1678.
   Google Scholar
• Gibbs AJ, Gibbs MJ, Armstrong JS. The phylogeny of SARS coronavirus. Arch Virol 2004; 149: 621–624.
   Google Scholar
• Liò P, Goldman N. Phylogenomics and bioinformatics of SARS-CoV. Trends Microbiol 2004; 12: 106–111.
   Google Scholar
• Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, Guan Y, Rozanov M, Spaan WJ, Gorbalenya AE. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol Biol 2003; 331: 991–1004.
   PubMed Web of Science ®Google Scholar
• Haijema BJ, Volders H, Rottier PJ. Switching species tropism: an effective way to manipulate the feline coronavirus genome. J Virol 2003; 77: 4528–4538.
   Google Scholar
• Rest JS, Mindell DP. SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting. Infect Genet Evol 2003; 3: 219–225.
   PubMedGoogle Scholar
• Stanhope MJ, Brown JR, Amrine-Madsen H. Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV. Infect Genet Evol 2004; 4: 15–19.
   Google Scholar
• Stavrinides J, Guttman DS. Mosaic evolution of the severe acute respiratory syndrome coronavirus. J Virol 2004; 78: 76–82.
   PubMed Web of Science ®Google Scholar
• Zhang XW, Yap YL, Danchin A. Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus. Arch Virol 2005; 150: 1–20.
   Google Scholar
• Chan CX, Beiko RG, Ragan MA. Detecting recombination in evolving nucleotide sequences. BMC Bioinformatics 2006; 7: 412.
   Google Scholar
• Holmes EC, Rambaut A. Viral evolution and the emergence of SARS coronavirus. Philos Trans R Soc Lond, B, Biol Sci 2004; 359: 1059–1065.
   PubMedGoogle Scholar
• Kan B, Wang M, Jing H, Xu H, Jiang X, Yan M, Liang W, Zheng H, Wan K, Liu Q, Cui B, Xu Y, Zhang E, Wang H, Ye J, Li G, Li M, Cui Z, Qi X, Chen K, Du L, Gao K, Zhao YT, Zou XZ, Feng YJ, Gao YF, Hai R, Yu D, Guan Y, Xu J. Molecular evolution analysis and geographic investigation of severe acute respiratory syndrome coronavirus-like virus in palm civets at an animal market and on farms. J Virol 2005; 79: 11892–11900.
   PubMed Web of Science ®Google Scholar
• Wang M, Yan M, Xu H, Liang W, Kan B, Zheng B, Chen H, Zheng H, Xu Y, Zhang E, Wang H, Ye J, Li G, Li M, Cui Z, Liu YF, Guo RT, Liu XN, Zhan LH, Zhou DH, Zhao A, Hai R, Yu D, Guan Y, Xu J. SARS-CoV infection in a restaurant from palm civet. Emerging Infect Dis 2005; 11: 1860–1865.
   PubMed Web of Science ®Google Scholar
• Lau SK, Woo PC, Li KS, Huang Y, Tsoi HW, Wong BH, Wong SS, Leung SY, Chan KH, Yuen KY. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci USA 2005; 102: 14040–14045.
   PubMed Web of Science ®Google Scholar
• Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, Wang H, Crameri G, Hu Z, Zhang H, Zhang J, McEachern J, Field H, Daszak P, Eaton BT, Zhang S, Wang LF. Bats are natural reservoirs of SARS-like coronaviruses. Science 2005; 310: 676–679.
   PubMed Web of Science ®Google Scholar
• Ren W, Li W, Yu M, Hao P, Zhang Y, Zhou P, Zhang S, Zhao G, Zhong Y, Wang S, Wang LF, Shi Z. Full-length genome sequences of two SARS-like coronaviruses in horseshoe bats and genetic variation analysis. J Gen Virol 2006; 87(Pt 11): 3355–3359.
   Google Scholar
• Vijaykrishna D, Smith GJ, Zhang JX, Peiris JS, Chen H, Guan Y. Evolutionary insights into the ecology of coronaviruses. J Virol 2007; 81: 4012–4020.
   PubMed Web of Science ®Google Scholar
• Pettersson E, Lundeberg J, Ahmadian A. Generations of sequencing technologies. Genomics 2009; 93: 105–111.
   PubMed Web of Science ®Google Scholar
• ten Bosch JR, Grody WW. Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J Mol Diagn 2008; 10: 484–492.
   PubMed Web of Science ®Google Scholar
• Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008; 452: 872–876.
   PubMed Web of Science ®Google Scholar
• Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 2009; 324: 1561–1564.
   PubMed Web of Science ®Google Scholar
• Loytynoja A, Goldman N. Evolution. Uniting alignments and trees. Science 2009; 324: 1528–1529.
   Google Scholar
• Trombetti GA, Bonnal RJ, Rizzi E, De Bellis G, Milanesi L. Data handling strategies for high throughput pyrosequencers. BMC Bioinformatics 2007; 8(Suppl 1): S22.
   Google Scholar
• Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P. A bioinformatician’s guide to metagenomics. Microbiol Mol Biol Rev 2008; 72: 557–578.
   PubMed Web of Science ®Google Scholar
• Gorecki P, Tiuryn J. Inferring phylogeny from whole genomes. Bioinformatics 2007; 23: e116–e122.
   Google Scholar