Phylogenetic relationship among the 562 EV71 C4 strains isolated in mainland China from 1998 to 2010.

<p>257 China strains are from the present study, and 305 China strains are from GenBank. The bootstrap values of 1000 replicates for major lineages are displayed as numbers at the nodes. Strains isolated in Shenzhen from 1998 to 2004 were marked by the sombol •.</p

EV71 reference strains used in this study.

*<p>The GenBank numbers of the 203 reference strains are AY895129-AY895145, EU753363 - EU753418, FJ765416 - FJ765435, GQ121417 - GQ121441, GQ253391 - GQ253423, GQ487666 - GQ487689 and GU353079 - GU353106. All of these strains are part of the 305 GenBank EV71 C4 reference strains collected in Mainland China from 1998 to 2010.</p

Maximum Clade Credibility tree and Bayesian Skyline of the China EV71 C4 strains.

<p>The upper portion of the figure was maximum clade credibility tree with 95% highest posterior density (HPD) intervals for the node times (in years) and posterior probabilities for branching events. Tree was generated by the MCMC method in BEAST on the basis of a multiple alignment of VP1 nucleotide sequences of EV71 C4 strains collected in Guangdong Province from 2008 to 2010 and Genbank EV71 C4 reference strains isolated in mainland China from 1998 to 2010. Below the tree, the Bayesian Skyline with 95% HPD intervals shows the relative measure for genetic diversity through time (values plotted on y-axis).</p

Alignment of deduced amino acid sequences of the VP1 fragment of representative EV71 strains collected in mainland China from 1998 to 2010.

<p>The amino acid substitutions are marked by using small panes.</p

Cytopathic effects (CPEs) and virus replication kinetics of GD809/2011 infection.

<p>RD and Hep-2 cells were infected with GD809/2011 at an MOI of 1. (a). The CPEs were shown by the cell morphological changes at 0, 6, 12, and 24 h p.i. (original magnification, ×100); (b). Intracellular viral RNA levels were measured at 0, 3, 6, 12, and 24 h p.i. by qRT- PCR. The relative viral RNA level at 0 h p.i. was set as 1, and the viral RNA levels at other time points were expressed as fold changes. Data shown are the mean ± SD of three independent experiments.</p

Phylogenetic tree of the VP1 coding region of the EV-C96 strains available in GenBank.

<p>The locations of the Guangdong strains are indicated by a black diamond. Bar, nucleotide distance as substitutions per site. Only bootstrap values of over 70% are shown.</p

Similarity plot (a) and bootscanning analysis (b) of the complete EV-C genomes using a sliding window of 500 nt moving in 40-nt steps.

<p>The EV-96 strain GD809/2011 was used as a query sequence.</p

Phylogenetic trees constructed based on the <i>P1</i> (a), <i>P2</i> (b), and <i>P3</i> (c) coding regions of EV-C strains.

<p>The five EV-96 strains with available full genome sequences were included. The locations of the Guangdong strains are indicated by a black diamond. Bar, nucleotide distance as substitutions per site. Only bootstrap values of over 70% are shown.</p

Similarity plot (a) and bootscanning analysis (b) of the complete genome of the newly isolated EV-C96 strain GD809/2011 with other EV-C96 strains.

<p>Analysis was performed by using a sliding window of 500-nt steps. GD809/2011 was used as a query sequence.</p

Phylogenetic analysis of sequences of representative Chinese measles viruses, compared to the WHO reference sequences.

<p>These trees are based on the WHO standard sequence window within the N gene. Panel A. Phylogenetic tree of 87 representative measles isolates from China during 1993–2008 compared to the WHO reference sequences for each genotype. Sequences from Chinese viruses of H1a cluster from 1993–2008 are indicated by blue and sequences from Chinese viruses of H1b cluster from 1994–2005 are indicated by fluorescence green, and WHO reference strains are indicated by red. All isolates from China, including 3 WHO reference strains(Hunan.China93-7/H1, Beijing.China94-1/H2, MVi/Menglian.Yunnan.CHN/47.09/d11), are indicated by solid rounded dots. Panel B. Phylogenetic tree of 5 measles vaccine viruses from China compared to the A genotype strains of Edmonston wild type and other vaccine strains used worldwide. Sequences from viruses isolated in China are indicated by blue, and A genotype wild type Edmonston strain is indicated by red. Two Chinese measles vaccines are indicated by green solid triangles.</p