SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method.

"the multiple sequence alignment was performed using multiple alignment using fast fourier transform (mafft) v7 486 ( ) with options--anysymbol--keeplength--6merpair--addfragments on sequences from the local dataset that had less than 10 per cent unknown positions ( n ) as well as lineage consensus reference sequences (available at https://github com/corneliusroemer/pango-sequences ) for a total of 62719 genome sequences.; sequence data with less than 90 per cent genome coverage that were not found in public databases were made available in a public github repository.; the list of the accessions along with metadata and genomic sequences of the global and local datasets used in this study are available on github at https://github com/nychealth/covid-consensus-genomes-pangolin-analysis ."

"the multiple sequence alignment was performed using multiple alignment using fast fourier transform (mafft) v7 486 ( ) with options--anysymbol--keeplength--6merpair--addfragments on sequences from the local dataset that had less than 10 per cent unknown positions ( n ) as well as lineage consensus reference sequences (available at https://github com/corneliusroemer/pango-sequences ) for a total of 62719 genome sequences.; sequence data with less than 90 per cent genome coverage that were not found in public databases were made available in a public github repository.; the list of the accessions along with metadata and genomic sequences of the global and local datasets used in this study are available on github at https://github com/nychealth/covid-consensus-genomes-pangolin-analysis ."

"Conflict of interest: None declared."

"Funding A.d.B.S. acknowledges support from the California Department of Public Health (Contract No. 20-11088). The findings and conclusions in this article are those of the authors and do not necessarily represent the views or opinions of the California Department of Public Health or the California Health and Human Services Agency. COVID sequencing in NYC was supported (in part) by the Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases Cooperative Agreement (Grant Number: ELC DETECT (6NU50CK000517-01-07) funded by the Centers for Disease Control and Prevention (CDC). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of CDC or the Department of Health and Human Services."