Epidemiology of human adenovirus and molecular characterization of human adenovirus 55 in China, 2009–2012

Lu, Qing-Bin; Tong, Yi-Gang; Wo, Ying; Wang, Hong-Yu; Liu, En-Mei; Gray, Gregory C; Liu, Wei; Cao, Wu-Chun

The rate of substitutions in HAdV-55 strains, their divergence over time, and the time to the most recent common ancestor (TMRCA) were estimated using a Bayesian Markov chain Monte Carlo (MCMC) approach as implemented in the Bayesian Evolutionary Sampling Tree package, version 1.7.2. 16 The best-fit substitution model was chosen by performing a maximum likelihood analysis using the jModeltest package, version 0.1.1. 17 Relaxed lognormal molecular clocks were employed and followed by allowing substitution rate variations among branches on the trees. The Bayesian MCMC chain lengths were 1 million generations with sampling every 1000 chain and discarding 10% of the chain as burn-in. Convergence of the chains was achieved by computational run over a sufficient time with inspection of MCMC samples using TRACER, version 1.5 (http://beast. bio.ed.ac.uk/). The resulting tree of each run was summarized using Tree Annotator, and the maximum clade credibility tree was visualized with FigTree software, version 1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/). All GenBank accession numbers for the sequences obtained in this study, as well as those used for comparison are listed in Table 1 .