Distribution of the isolation countries for 1000 sequences resampled by the CNT algorithm.

<p>Distribution of the isolation countries for 1000 sequences resampled by the CNT algorithm.</p

Changes of the distribution of the isolation years by means of (A) CNT, (B) NHC, and (C) kMC.

<p>Changes of the distribution of the isolation years by means of (A) CNT, (B) NHC, and (C) kMC.</p

Relationship between nucleotide diversity and the fraction of discarded sequences.

<p>Relationship between nucleotide diversity and the fraction of discarded sequences.</p

Execution time of the four resampling algorithms against the nucleotide sequences of human H3N2 influenza virus with 1000 sequences.

<p>The time units are seconds.</p

Statistics of the sequences of HA of human H3N2 influenza virus. (A) distribution of isolation years and (B) distribution of isolation countries.

<p>More than 92% were sequences isolated after 1992 and more than 30% were sequences of influenza viruses isolated from the USA. Moreover, there is a large gap on the number of nucleotide sequences of HA of human H3N2 influenza virus isolated before 1991 and after 1992, when the PCR technique had been in widespread use.</p

Relationship between average sequence identity between and sequences and the fraction of discarded sequences.

<p>The horizontal axis represents the percentage of discarded sequences and the vertical axis represents identity . It can be seen that the performance of ZAS05 is worse than those of the other three algorithms.</p

Description of the CNT algorithm. (A) the pseudocode and (B) a schematic image.

<p>Description of the CNT algorithm. (A) the pseudocode and (B) a schematic image.</p

HI activity of MAb S139/1 with various influenza virus strains.

a<p>HI titers are expressed as the lowest concentrations of purified MAb S139/1 that completely inhibited hemagglutination.</p>b<p>No detectable hemagglutination inhibition at 50 µg/ml by MAb S139/1.</p

Protective efficacy of passive immunization with MAb S139/1 in mice.

<p>Mice were passively immunized before (A) or after (B) virus challenge with Aichi (H3) or WSN (H1). Control mice were given MAb ZGP12/1.1 or PBS. Virus titers of the lung were determined by a plaque assay. The means and standard deviations are shown. For statistical purposes, samples with undetectable virus titers were given the value 2.0 log₁₀PFU/g. The data of pre-immunized mice were analyzed using the nonparametric Kruskal-Wallis ANOVA on ranks, followed by the Mann-Whitney U-test with the Bonferroni correction for multiple comparisons. The data of post-immunized mice were analyzed using the Mann-Whitney U-test. Two-sided <i>p</i> values less than 0.05 were considered statistically significant. Significant differences were indicated by asterisks (*** <i>p</i><0.001, ** <i>p</i><0.01, * <i>p</i><0.05). All statistical analyses were performed with the computer program R (version 2.8.1).</p

Structure of the MAb S139/1 epitope on the globular head of HA trimer models.

<p>Three-dimensional models of Aichi (H3) (A), PR8 (H1) (D), and VN1194 (H5) (E) HAs were constructed from the coordinates obtained from the Protein Data Bank (PDB codes: 1HGF, 1RVX, and 2IBX, respectively). The structures of WSN (H1) (B) and Adachi (H2) (C) were constructed by homology modeling as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000350#s4" target="_blank">Materials and Methods</a>. Images were prepared by using DS Visualizer (version 1.7, Accelrys, Inc.). Residue numbering is thoroughly on the basis of the H3 HA sequence.</p