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

We sequenced SARS-CoV-2 genomes from nine of the first COVID-19 cases reported in Connecticut (CT), with sample collection dating from March 6-14, 2020 ( Data S1 ). These individuals are residents of eight different cities in Connecticut. According to the Connecticut State Department of Public Health, none of the cases were associated with international travel. Using our amplicon sequencing approach, 'PrimalSeq' (Grubaugh et al., 2019b; Quick et al., 2017) , with the portable Oxford Nanopore Technologies (ONT) MinION platform, we generated the first SARS-CoV-2 genome approximately 14 hours after receiving the sample (CT-Yale-006), demonstrating our ability to perform near real-time clinical sequencing and bioinformatics. Our complete workflow included RNA extraction, PCR testing, validation of PCR results, library preparation, sequencing, and live base calling and read mapping. We shared the genomes of these viruses publicly as we generated them (GISAID EPI_ISL_416416-416424). We combined our genomes with other publicly available sequences for a final dataset of 168 SARS-CoV-2 genomes ( Figure 1, Data S2 ). The dataset can be visualized on our 'community' Nextstrain page ( https://nextstrain.org/community/grubaughlab/CT-SARS-CoV-2 ).