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

By combining daily passenger volumes ( Figure 2B ) with COVID-19 prevalence at the travel route origin ( Figure 2C -D ) and accounting for differences in reporting rates, we found that both domestic and international SARS-CoV-2 importation started to increase dramatically at the beginning of March, 2020 ( Figure 2E ). Without accounting for the effects of international travel restrictions, our estimated domestic importation risk from the selected five U.S. states surpassed international importation risk by March 10. Using previous assumptions around travel restrictions (Chinazzi et al., 2020) , we also modeled two scenarios where federal travel restrictions reduced passenger volume by 40% and by 90% from the restricted countries ( Figure 2E ). Due to the overall low prevalence of COVID-19 in China, we did not find any significant effects of travel restrictions from China that were enacted on February 1st ( Data S3 ). Also, we did not find significant changes to the importation risk following travel restrictions from Iran on March 1, likely due to the relatively small number of passengers arriving from that country ( Data S3 ). While we did find a dramatic decrease in international importation risk following the restrictions on travel from Europe (March 13), this decrease occurred after our estimates of domestic travel importation risk had already surpassed that of international importation ( Figure 3E ). The dramatic rises in both domestic and international importation risk preceded the state-wide COVID-19 outbreak in Connecticut ( Figure 3E ), and the recent increase in risk of domestic importation may give rise to new outbreaks in the region. We selected three international airports in the region that are commonly used by Connecticut residents: Hartford (BDL), Boston (BOS), and New York (JFK). We used data from January to March, 2019, to estimate relative differences in daily air passenger volumes from the selected origins to the airport destinations. These daily estimates were then combined by either international or domestic travel. ( C-D ) The cumulative number of daily COVID-19 cases were divided by 100,000 population to calculate normalized disease prevalence for each location. ( E ) We calculated importation risk by modelling the number of daily prevalent COVID-19 cases in each potential importation source and then estimating the number of infected travelers using the daily air travel volume from each location. Data, criteria, and analyses used to create this figure can be found in Data S3 .