Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.
Nat Genet
; 53(6): 809-816, 2021 06.
Article
in English
| MEDLINE | ID: covidwho-1223103
ABSTRACT
As the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering in a new era of 'genomic contact tracing'-that is, using viral genomes to trace local transmission dynamics. However, because the viral phylogeny is already so large-and will undoubtedly grow many fold-placing new sequences onto the tree has emerged as a barrier to real-time genomic contact tracing. Here, we resolve this challenge by building an efficient tree-based data structure encoding the inferred evolutionary history of the virus. We demonstrate that our approach greatly improves the speed of phylogenetic placement of new samples and data visualization, making it possible to complete the placements under the constraints of real-time contact tracing. Thus, our method addresses an important need for maintaining a fully updated reference phylogeny. We make these tools available to the research community through the University of California Santa Cruz SARS-CoV-2 Genome Browser to enable rapid cross-referencing of information in new virus sequences with an ever-expanding array of molecular and structural biology data. The methods described here will empower research and genomic contact tracing for SARS-CoV-2 specifically for laboratories worldwide.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Phylogeny
/
Software
/
Computational Biology
/
SARS-CoV-2
/
COVID-19
Type of study:
Observational study
/
Prognostic study
/
Randomized controlled trials
Limits:
Humans
Language:
English
Journal:
Nat Genet
Journal subject:
Genetics, Medical
Year:
2021
Document Type:
Article
Affiliation country:
S41588-021-00862-7
Similar
MEDLINE
...
LILACS
LIS