matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2

Cheng, Ya; Thornlow, Bryan; Hinrichs, Angie S; Krämer, Alexander; Mirchandani, Cade D; Torvi, Devika; Lanfear, Robert; Corbett‐Detig, Russ; Turakhia, Yatish

doi:10.1093/bioinformatics/btac401

Cited by 24 publications

(24 citation statements)

References 45 publications

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“…Sequences excluded in a previous step were appended to the next batch for reconsideration. The resulting tree was then optimised through 6 iterations of matOptimize ( 54 ) with SPR radius of 40 and 100 for the first 5 and final iteration respectively. This iterative tree building process resulted in a phylogeny of 115,634 sequences (with 25,921 (18.3%) sequences excluded due to uncertainty in sample placement).…”

Section: Methodsmentioning

confidence: 99%

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Tsui

Lambert

Bajaj

et al. 2023

Preprint

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SARS-CoV-2 variants of concern (VOCs) arise against the backdrop of increasingly heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron genomes, we identified >6,000 independent introductions of the antigenically distinct virus into England and reconstructed the dispersal history of resulting local transmission. Travel restrictions on southern Africa did not reduce BA.1 importation intensity as secondary hubs became major exporters. We explored potential drivers of BA.1 spread across England and discovered an early period during which viral lineage movements mainly occurred between larger cities, followed by a multi-focal spatial expansion shaped by shorter distance mobility patterns. We also found evidence that disease incidence impacted human commuting behaviours around major travel hubs. Our results offer a detailed characterisation of processes that drive the invasion of an emerging VOC across multiple spatial scales and provide unique insights on the interplay between disease spread and human mobility.

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Section: Methodsmentioning

confidence: 99%

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Tsui

Lambert

Bajaj

et al. 2023

Preprint

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“…Dispersal dynamics of SARS-CoV-2 variants tree using Online matOptimize [49] and used the resulting tree as a starting candidate tree to infer a ML tree IQ-TREE under a HKY85 nucleotide substitution model with empirical base frequencies. For the Delta variant, the tree was inferred without rate heterogeneity in the substitution model due to the computational demands required and, in the case of the Omicron (BA.1) variant, the tree was inferred using gamma-distributed rate variation among sites.…”

Section: Plos Pathogensmentioning

confidence: 99%

Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron

et al. 2023

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Since the latter part of 2020, SARS-CoV-2 evolution has been characterised by the emergence of viral variants associated with distinct biological characteristics. While the main research focus has centred on the ability of new variants to increase in frequency and impact the effective reproductive number of the virus, less attention has been placed on their relative ability to establish transmission chains and to spread through a geographic area. Here, we describe a phylogeographic approach to estimate and compare the introduction and dispersal dynamics of the main SARS-CoV-2 variants–Alpha, Iota, Delta, and Omicron–that circulated in the New York City area between 2020 and 2022. Notably, our results indicate that Delta had a lower ability to establish sustained transmission chains in the NYC area and that Omicron (BA.1) was the variant fastest to disseminate across the study area. The analytical approach presented here complements non-spatially-explicit analytical approaches that seek a better understanding of the epidemiological differences that exist among successive SARS-CoV-2 variants of concern.

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“…MrBayes (4), BEAST (5)), maximum parsimony (e.g. MPBoot (6), matOptimize (7), TNT (8)), or distance methods (e.g. BioNJ (9), FastME (10), QuickTree (11), RapidNJ (12)).…”

Section: Introductionmentioning

confidence: 99%

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees

Wong

Cherryh

Rodrigo

et al. 2022

Preprint

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Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting, introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce the mixture across sites and trees (MAST) model, which uses a mixture of bifurcating trees to represent multiple histories in a single concatenated alignment. The MAST model allows each tree to have its own topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites. We implemented the MAST model in a maximum-likelihood framework in the popular phylogenetic software, IQ-TREE. Simulations show that we can accurately recover the true model parameters, including branch lengths and tree weights (i.e. frequencies) for a given set of tree topologies. We also show that we can use standard statistical inference approaches to reject a single-tree model when data are simulated under multiple trees (and vice versa). We applied the MAST model to multiple primate datasets and found that it can recover the signal of incomplete lineage sorting in the Great Apes, as well as the asymmetry in minor trees caused by introgression among several macaque species. When applied to a dataset of four Platyrrhine species for which standard concatenated maximum likelihood and gene tree approaches disagree, we find that MAST gives the highest weight to the tree favored by gene tree approaches. These results suggest that the MAST model is able to analyse a concatenated alignment using maximum likelihood, while avoiding some of the biases that come with assuming there is only a single tree. The MAST model can therefore offer unique biological insights when applied to datasets with multiple evolutionary histories. We discuss how it can be extended in the future.

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matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2

Cited by 24 publications

References 45 publications

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees

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