Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology

Joseph R Fauver; Mary E. Petrone; Emma B Hodcroft; Kayoko Shioda; Hanna Y Ehrlich; Alexander G. Watts; Chantal B.F. Vogels; Anderson F. Brito; Tara Alpert; Anthony Muyombwe; Jafar Razeq; Randy Downing; Nagarjuna R. Cheemarla; Anne L Wyllie; Chaney C. Kalinich; Isabel Ott; Josh Quick; Nicholas J. Loman; Karla M. Neugebauer; Alexander L. Greninger; Keith R. Jerome; Pavitra Roychoundhury; Hong Xie; Lasata Shrestha; Meei-Li Huang; Virginia E. Pitzer; Akiko Iwasaki; Saad B. Omer; Kamran Khan; Isaac Bogoch; Richard A. Martinello; Ellen F. Foxman; Marie-Louise Landry; Richard A Neher; Albert I Ko; Nathan D. Grubaugh

A total of 24 ng of the low titer group was loaded onto a MinION R9.4.1 flow cell and sequenced for a total of 5.5 hours and generated 2.1 million reads. The flow cell was nuclease treated, flushed, and primed prior to loading 25 ng of the high titer group library. These samples were sequenced for a total of 9 hours and generated 1.4 million reads ( Data S1 ). The RAMPART software from the ARTIC Network was used to monitor the sequencing run to estimate the depth of coverage across the genome for each barcoded sample in both runs https://github.com/artic-network/rampart ). Following completion of the sequencing runs, .fast5 files were basecalled with Guppy (v3.5.1, ONT) using the high accuracy module. Basecalling was performed on a single GPU node on the Yale HPC. Consensus genomes were generated for input into phylogenetic analysis according to the ARTIC Network bioinformatic pipeline ( Artic Network ). Variants in the consensus genomes were called using nanopolish per the bioinformatic pipeline (Loman et al., 2015) . Amplicons that were not sequenced to depth of 20x were not included in the final consensus genome, and these positions are represented by stretches of NNN's ( Data S1 ).