G Protein Entropy Plot and Positive Selected Sites.

<p>This is an entropy plot of the G protein sequences with positively selected sites also shown. Entropy values were calculated using BioEdit 7.0 from the alignments used for the positive selection analysis and the plot was generated using Microsoft Excel. Black bars are for RSVA sequences and red bars are for RSVB sequences. Sites predicted to be under positive selection in this study are shown with black diamonds for RSVA and red diamonds for RSVB. Near the top are shown sites predicted to be under positive selection or diversifying selection from previously published studies with black pluses for RSVA and red pluses for RSVB.</p

Information on the RSV Strains Sequenced.

<p>^a These sequences were sequenced by Next-Gen sequencing.</p><p>^b Partial G CDS sequences have previously been published for these samples with different strain names. Accession numbers for these sequences are HQ711732, HQ711709, HQ711688, and HQ711801 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120098#pone.0120098.ref011" target="_blank">11</a>].</p><p>^c These sequences were produced from viruses isolated in tissue culture.</p><p>Information on the RSV Strains Sequenced.</p

Tree of RSVB Genome Sequences.

<p>This is a maximum clade credibility tree of RSVB genome sequences generated in this study and retrieved from GenBank. Tip times correspond to date of collection with the scale axis across the bottom showing the years. Tip labels show the accession number, country of isolation, and collection date. The labels are color coded with black for sequences from this study (FTS), grey for sequences with an undetermined genotype (UND), and the remaining colors corresponding to previous published genotypes as show in the key in the upper left corner. Brackets highlight the major clades. Bayesian posterior probabilities are shown for key nodes.</p

CDS Evolutionary Rates.

<p>This plot shows the estimated evolutionary rates for each CDS in RSVA and RSVB. Error bars represent the 95% HPD values. Rates were determined using BEAST v1.8.0 with the GTR model of nucleotide substitution, a gamma-distributed rate variation among sites, an uncorrelated lognormal relaxed molecular clock, and a flexible Bayesian skyline tree prior. Each CDS was ran with a chain length of 50 million and sampled 10,000 times.</p

Protein Entropy Plots.

<p>This is an entropy plot of the concatenated predicted protein sequences of all of the viruses sequenced in this study. Entropy values were calculated using BioEdit 7.0 and the plot was generated using Microsoft Excel. Black bars are for RSVA sequences and red bars are for RSVB sequences. The higher the bar is the greater the variation at that position in the protein sequence. Across the top of the plot are listed the abbreviated protein sequence names in the order in which the CDS sequences for the proteins appear in the genome.</p

Tree of RSVA Genome Sequences.

<p>This is a maximum clade credibility tree of RSVA genome sequences generated in this study and retrieved from GenBank. Tip times correspond to date of collection with the scale axis across the bottom showing the years. Tip labels show the accession number, country of isolation, and collection date. The labels are color coded with black for sequences from this study (FTS), grey for sequences with an undetermined genotype (UND), and the remaining colors corresponding to previous published genotypes as show in the key in the upper left corner. Brackets highlight the major clades. Bayesian posterior probabilities are shown for key nodes.</p

Pathogens identified by NGS in children with lower respiratory tract infections.

a<p>Number of valids DNA reads in the sample por the corresponding pathogen.</p><p>Pathogens identified by NGS in children with lower respiratory tract infections.</p

DNA reads obtained after NGS sequencing of LRTI samples.

a<p>Valid DNA reads after discarding those that did not pass the quality filter, and removing repeated reads (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113570#s2" target="_blank">Methods</a>).</p><p>DNA reads obtained after NGS sequencing of LRTI samples.</p

DNA reads obtained after NGS sequencing of URTI samples.

a<p>The samples that were pooled for sequencing are indicated.</p>b<p>Valid DNA reads after discarding those that did not pass the quality filter, and removing repeated reads (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113570#s2" target="_blank">Methods</a>).</p><p>DNA reads obtained after NGS sequencing of URTI samples.</p

Frequency of viral pathogens in children with URTI and LRTI.

a<p>The number of viruses include those present in single and mixed infections. The percentage refers to the total number of viruses detected.</p><p>Frequency of viral pathogens in children with URTI and LRTI.</p