Genetic diversity and molecular characterization of HRSV-A on the coast of Peru, 2009–2020

Figures

• 

  Figure 1. Maximum-likelihood phylogenetic tree of HRSV-A reconstructed with IQ-TREE v2.4 from the second hypervariable region of the G gene under the GTR + G model and 1,000 bootstrap replicates. Bootstrap support values are shown at the nodes. Branches are colored according to the assigned lineages or clades, as indicated in the legend. Sequences generated in this study are labeled in red, whereas reference sequences are shown in black and identified as accession number_annotated lineage. Dashed boxes indicate magnified views of the clades containing the sequences obtained in this study. The scale bar represents the number of substitutions per site per branch.

• 

  Figure 2. Amino acid profile of positions 212–321 of the second hypervariable region of the HRSV-A G protein, corresponding to the sequences grouped within the A. D. (ON1) lineages detected in this study. Compared with the prototype strain ON67-1210 (GenBank accession number: JN257693), all sequences included show the characteristic 24-aa duplication between positions 285 and 308. Asterisks at the end of each sequence indicate stop codons. Circles above the amino acid position ruler indicate potential O-glycosylation sites in the reference strain; bold circles correspond to positions with a glycosylation potential G ≥ 0.5. Potential N-glycosylation sites are indicated by black dashed rectangles. Colored boxes group sequences that share specific amino acid substitutions. Labels on the right indicate the characteristic mutations observed in each annotated lineage.

• 

  Figure 3. Amino acid profile of positions 212–297 of the second hypervariable region of the HRSV-A G protein, corresponding to the sequences grouped within lineage A.3.1/A.3.1.1 (NA1) detected in this study, in comparison with the prototype strain NG-016-04 (GenBank accession number: AB470478). Asterisks at the end of each sequence indicate stop codons. Circles above the amino acid position ruler indicate potential O-glycosylation sites in the reference strain; bold circles correspond to positions with a glycosylation potential G ≥ 0.5. Potential N-glycosylation sites are indicated by black dashed rectangles. Colored boxes group sequences that share specific amino acid substitutions. Labels on the right indicate the characteristic mutations observed in each annotated lineage.

• 

  Figure 4. Root-to-tip regression of the HRSV-A A. D (ON1) sequences included in the temporal analysis. Each point represents an individual sequence and is colored according to its country of origin, as indicated in the legend. The black line indicates the linear regression between root-to-tip divergence and sampling year. The red dashed line marks the x-intercept, corresponding to an exploratory tMRCA estimate around April 2008. The regression slope was 0.0027 substitutions per site per year, with a correlation of 0.65 and a coefficient of determination R2 = 0.42. Sequence PER1.05_2009 is highlighted as one of the earliest sequences included in this study.

• 

  Figure 5. Maximum clade credibility (MCC) tree of the second hypervariable region of the G gene of the A. D (ON1) lineages, reconstructed using Bayesian Markov chain Monte Carlo (MCMC) inference and summarized using median heights. The tree shows the five major clades of the A. D lineages, colored according to the legend. Circles on the branches correspond to sequences obtained in Peru; red circles represent sequences generated in this study, whereas black circles represent annotated Peruvian sequences retrieved from public databases. The dashed box shows exclusively the lineages and nested sublineages reported in Peru. The root node indicates the estimated tMRCA for the entire A. D lineage, whereas the upper node shows the tMRCA of the oldest A. D sequences from Peru. Bars on the nodes represent the 95% highest posterior density (95% HPD) intervals, and the black bar below the tree indicates the temporal scale.