Phylogenetic Structure and Sequential Dominance of Sub-Lineages of PRRSV Type-2 Lineage 1 in the United States

Figure 1. Characteristics of the DPCA used to create sub-lineages within Lineage 1. (A) 80% variance was explained when retaining 70 principal components. (B) Grouping sequences into eight sub-lineage clusters yielded the lowest BIC while still preserving previously documents sub-lineage structure.

Figure 2. Flowchart describing the number of PRRSV sequences classified into each lineage and sub-lineage L1 after removing duplicates and sequences without a date.

Figure 3. (A) Phylogenetic tree of L1 sequences classified into sub-lineages according to discriminant analysis of principle components. The gray tips in the tree represent sub-lineage 1D-beta sequences, which are not displayed in other analysis. (B) Absolute frequency of sequences per sub-lineage per year.

Figure 4. Estimated viral population through time for each L1 sub-lineage. The area in gray denotes the period in which no sequences were available.

Figure 5. Consensus amino acid sequences of the ectodomain portion of GP5 (AA positions 27–61) for each sub-lineage, wherein the amino acid is present in >50% of sequences in a given sub-lineage. Sub-lineages in this figure are ordered according to their time of emergence to give a better idea of the immune landscape immediately prior to each sub-lineage’s emergence. *5: papers considered include [23,44,45,46,47].

Figure 6. (A) Nextstrain tree illustrating sequences from the UMN VDL and from GenBank according to its source, and (B) according to its lineage/sub-lineage.