Table 1.
Strain Information for all 40 HPIV-1 Genomes Sequenced.
Table 2.
HPIV-1 Primer Information for Amplification and Sequencing.
Figure 1.
The phylogenetic relationships of the 40 genomes and sequence AF457102 using the BEAST program.
The phylogeny of 40 recently sequenced HPIV-1 genomes and one sequence from GenBank (AF457102) was estimated using a Bayesian Markov Chain Monte Carlo (MCMC) method with a strict molecular clock. Strain HPIV-1/c-35/1957 showed the greatest distance from the 39 1997–2010 Milwaukee viruses which is consistent with its isolation time. Colored rectangles (labeled clade 1–3) represent the three clades of the 39 1997–2010 Milwaukee viruses. The sequence from strain HPIV-1/WI/629-007/1997 is a singleton. The scale bar shows the unit for branch age. The numbers following the underscore in each name represent the collection date in number of years since collection date of the oldest HPIV-1 strain. To make the figure more legible identical sequences were removed from the table.
Figure 2.
The phylogenetic relationships of HN genes including 37 present sequences and 221 sequences from GenBank.
The phylogeny of 258 HN gene sequences was analyzed using a Bayesian Markov Chain Monte Carlo (MCMC) method with a strict molecular clock in the BEAST program. Colored rectangles labeled clades 1–3 represent the three clades identified in Figure 1 containing the 36 HPIV-1 sequences from the present study. Colored rectangles labeled genotypes C and D represent the HN gene sequences from HPIV-1 viruses collected in Milwaukee, WI in 1991. The number following the underscore in each name represents the collection date in years since collection date of the oldest HPIV-1 strain. Branch color corresponds to clade name/HN sequence seen in Figure 3.
Figure 3.
Amino acid sequence of the HN protein across all HPIV-1 clades.
This figure shows the amino acid sequence of the HN protein across all HPIV-1 clades. Amino acid substitutions were determined with the MacClade program and the consensus HN gene sequence for each clade. The color of the branches in Figure 2 correspond to the color of the clade name in this figure indicating which viruses have each of the sequences listed above.
Table 3.
Clade-Scale Amino Acid Substitutions from the N, P, M, F and L Proteins of 40 Recently Sequenced HPIV-1 Complete Genomes (the HN protein is described in greater detail in Table 4 and is not included here).
Table 4.
Amino Acid substitutions of the Seven Regions of HN Gene (calculated using all available sequences from GenBank).
Table 5.
Genetic Diversity Across the HPIV-1 Genome.
Figure 4.
Sliding Scale Analysis of Nucleotide Diversity of the HPIV-1 Genome.
Analysis of nucleotide diversity was done in 100 nt windows in 25 nt increments. A table showing each window and its diversity can be seen in supplementary document 1. A schematic of the HPIV-1 genome can be found at the bottom of the figure. The coding region of each gene is labeled.
Table 6.
Nonsynonymous (Ka) vs. Synonymous Mutations in the Coding Region of HPIV-1 Genes.