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. 2021 Jan 19;10:e64509. doi: 10.7554/eLife.64509

Figure 1. Phylogenetic trees for spike gene of seasonal human coronaviruses (HCoVs) OC43 and 229E.

Phylogenies built from (A) OC43 spike sequences from 389 isolates over 53 years, and (B) 229E spike sequences from 54 isolates over 31 years. OC43 bifurcates immediately after the root and is split into two lineages: lineage A (dark teal) and lineage B (light teal). 229E contains just one lineage (dark blue). For the analyses in this paper, the evolution of each gene (or genomic region) is considered separately, so phylogenies are built for each viral gene, and those phylogenies are used to split isolates into lineages for each gene. These are temporally resolved phylogenies with year shown on the x-axis. The clock rate estimate is 5 × 10–4 substitutions per nucleotide site per year for OC43 and 6 × 10–4 for 229E.

Figure 1.

Figure 1—figure supplement 1. Recombination occurs between human coronavirus (HCoV) isolates.

Figure 1—figure supplement 1.

A tanglegram draws lines between an isolate’s position on two phylogenies built on different genes (or genomic regions). Dramatic differences in an isolate’s position on one tree versus another are indicative of recombination. (A) Phylogenetic relationships between OC43 isolates based on spike sequences (left) versus relationships based on RdRp sequences (right). Light teal lines that connect isolates classified as lineage A based on their RdRp sequence to isolates classified as lineage B based on their spike sequence suggest that recombination occurred in these isolates or their ancestors. (B) Phylogenetic reconstruction of OC43 isolates based on S1 sequences (left) versus S2 sequences (right). Year is shown on the x-axis.
Figure 1—figure supplement 2. Phylogenetic trees for seasonal human coronaviruses (HCoVs) NL63 and HKU1.

Figure 1—figure supplement 2.

Phylogenies built from (A) NL63 spike sequences from 159 isolates over 37 years, and (B) HKU1 spike sequences from 41 isolates over 13 years. HKU1 bifurcates immediately after the root and is split into lineage A (darker blue) and lineage B (lighter blue). NL63 contains just one lineage (green). Both HCoVs are rooted on an outgroup sequence. For the analyses in this paper, the evolution of each gene (or genomic region) is considered separately, so phylogenies are built for each viral gene and those phylogenies are used to split isolates into lineages for each gene. These are temporally resolved phylogenies with year shown on the x-axis. The clock rate of each HCoV is listed in the section ‘Phylogenetic inference’.