Emergence and Potential Extinction of Genetic Lineages of Human Metapneumovirus between 2005 and 2021

Figures

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  FIG 1. Maximum likelihood phylogenetic tree based on 199 whole HMPV genome sequences. The tree was reconstructed using the Maximimum-Likelihood (GTR+G+I) substitution model with 1,000 bootstraps. The tree with bootstrap values and virus names is shown in Fig. S1 in the supplemental material. Markers on the right indicate the main virus lineages A and B, which could be divided in 6 sublineages (A1, A2.1, A2.2.1, A2.2.2, B1, and B2). Lineage A2.2.2 viruses with a 180-nt duplication (▽, red line) or a 111-nt duplication (△, blue line) in the G gene are highlighted. Different names that have been used for each lineage are shown.

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  FIG 2. (a to c) Scatterplots of p distances between viruses from phylogenetic trees reconstructed from whole-genome sequences versus full-length F gene sequences (a), whole-genome sequences versus partial F gene sequences (b), and full-length F gene sequences versus partial F gene sequences (c). The trees from which p distances were compared are shown in Fig. S1, S2, and S3.

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  FIG 3. Genetic evolution of HMPV based on full-length F gene sequences. (a and b) A genetic map was generated from full-length F gene sequences obtained in this study combined with those from GenBank (n = 744) with color coding per lineage (a) or year of isolation (b). The axes represent genetic distance, with each square of the grid representing a 10-nucleotide distance. Sequences were color coded by year of isolation using a greyscale. (c) Maximum likelihood phylogenetic tree based on 744 full-length HMPV F gene sequences. The tree was reconstructed using the GTR +G +I substitution model with 1,000 bootstraps. The tree is color coded according to the colors used in the map shown in a. The tree with bootstrap values and isolate names is shown in Fig. S5. Markers on the right indicate virus lineages and sublineages.

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  FIG 4. (a) The number of obtained sequences from each lineage of viruses isolated from hospitalized patients suffering from RTIs per epidemiologic season. Seasons started in week 40 and ended in week 39 of the next year. Samples were selected based on a CT value of ≤25.0, with exceptions as described in the Materials and Methods section, and genotyped by phylogenetic analyses of whole-genome sequences. (b) Clustering of viruses isolated from patients suffering from RTIs visiting general practitioners per year. Samples were selected as described in the Materials and Methods section and genotyped based on phylogenetic analyses of partial F and G gene sequences.

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  FIG 5. Maximum likelihood phylogenetic tree reconstructed from partial F gene sequences from viruses obtained from patients with RTIs visiting general practitioners combined with those of six viruses obtained from hospitalized individuals. The tree was reconstructed using the GTR +G +I substitution model with 1,000 bootstraps. The tree with bootstrap values and isolate names is shown in Fig. S6. Lines indicate virus lineages (e.g., A2).