Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

Abstract

Extended Data Fig. 2 | Addition of two perfectly correlated errors significantly reduces UShER accuracy. As in Fig. 2, the Robinson-Foulds distances, proportion of sister nodes identical to the reference tree, distance from true placement and equally parsimonious placements, respecitvely, are shown for UShER experiments in placing 10 lineages, with two perfectly correlated errors added to 1, 2 … 10 of the lineages to be placed. To the far right in the left-most panel, labeled 'Null', the distribution of scores across 100 replicates in which 10 lineages were added randomly to the phylogeny is shown as a null model for comparison. N = 100 independent replicates for each experiment. The whiskers in the boxplot on the left are centered on the median of the data and extend to the first and third quartiles. In the error bars panel (second from the left), the data points are centered on the mean of the data and extend to the bounds of the 95% confidence interval, calculated by 1,000 iterations of bootstrapping. NATURE GENETICS | www.nature.com/naturegeneticsArticles NATURE GENETICS Extended Data Fig. 3 | UShER can output multiple trees to accommodate phylogenetic uncertainty. (A): Composite of 239 trees with 424 samples, representing all possible parsimony-optimal placements of two samples on a starting tree having 422 samples, computed using DensiTree 52 and plotted using the phangorn package (https://cran.r-project.org/web/packages/phangorn). All trees were scaled to be the same height. (B): Two of the trees from (A) compared in a tanglegram, colored according to COG-UK lineage assignments, with linker lines shown only for the two placed samples whose placements differ between topologies. As in Fig. 4, both trees in this tanglegram are ultrametric and branch lengths are arbitrary.Extended Data Fig. 6 | A demonstration of our distance metric for placements. To evaluate the accuracy of each placement in a new phylogeny, we compute the distance for each newly placed sample in the UShER tree (Tree 1) with the reference tree (Tree 2). The clade sets in the two trees are shown for each N1 and N2 value, representing the number of generations from the Sample D in Tree 1 and Tree 2, respectively. We compute the values of N1+N2-2 such that the descendant clades for both trees are identical. In case of newly placed Sample D, clades are identical when N1=2 and N2=2 and when N1=3 and N2=3, which are highlighted in bold. Hence the distance (smallest N1+N2-2) from the true placement is equal to 2.

Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India

“…The alignment file was then used to build phylogenetic tree by maximum-likelihood method using general time reversal (GTR) statistical model with 1000 bootstrap replicates [ 18 ]. We also performed the phylogenetic analysis of the 129 sequences of the new variant with the Ultafast Sample Placement of Existing Trees (UShER) that has been integrated in the UCSC SARS-CoV-2 Genome Browser [ 21 ]. We accessed to the UCSC SARS-CoV-2 Genome Browser ( https://genome.ucsc.edu/cgi-bin/hgPhyloPlace ) and uploaded the sequence IDs of 129 sequences (Table S1) for the construction of the phylogenetic tree.…”

Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples

“…Bases with less than 20X coverage were masked in accordance with public SARS-CoV-2 sequencing guidelines ( https://www.aphl.org/programs/preparedness/Crisis-Management/Documents/APHL-SARS-CoV-2-Sequencing.pdf ). SARS-CoV-2 lineages were assessed using Pangolin (Version 3.1.5, github.com/cov-lineages/pangolin ), and phylogenetic analysis was performed with UShER [ 24 ] (Database: GISAID, GenBank, COG-UK and CNCB [2021-07-11]). Phylogenetic trees were constructed using augur [ 25 ], rooted at the SARS-CoV-2 reference sequence, and visualized in iTOL [ 26 ].…”

Application of omics technology to combat the COVID‐19 pandemic

“… 19 On this basis, the disclosure of enough SARA‐CoV‐2 genomes for genomic surveillance is of great importance to track the mutations, evolution, and adaptation of SARS‐CoV‐2, 6 , 20 , 21 and series of efforts were made to realize real‐time genomic surveillance. 22 , 23 …”