ABSTRACT
Background: As countries around the world review interventions for containing the COVID-19 pandemic, movement of populations has been identified as a key factor of viral dispersal and limiting the population flow intensity has been applied to contain the current COVID-19 epidemic. Evolutionary analyses of well-annotated sequencing data can provide insights into viral transmission dynamics. Herein, we characterized the dynamics of COVID-19 transmission within California and across the Mexico-California (MX/CA) border, the busiest land border-crossing area in the world, to inform the containment policy in this binational context. Methods: All publicly available SARS-CoV-2 full genome sequences (human host) available on the GISAID database were collected (as of Nov. 16th, 2020). After sequence curation, a multistep phylogenetic approach was applied to identify putative clusters of transmission within CA (across counties), MX (across states) and across the MX/CA border. These clades were analyzed with a discrete phylogeographic model to evaluate transmission dynamics of COVID-19 in the MX/CA region. Results: From a total of 174,324 SARS-CoV-2 sequences including 5,471 sequences from Mexico (7 States, n=223)/California (29 counties, n=5,248), we identified 622 unique introduction events into the study region, including 381 clusters of size ≥3 from ≥2 locations (i.e. CA county and/or MX state). Of these, 339 (89%) clusters were from CA only across 23 counties, 5 (1.3%) were from MX only across 6 states and 38 (10%) included sequences from both CA and MX Discrete phylogeographic analysis revealed a complex viral migration network within CA/MX and across the border (Figure 1A, left panel). Analyses of the 38 clusters including sequences from CA and MEX showed bidirectional migration events across the border (Figure 1B). In particular we showed migration events in the border region from the border state of Baja California, MX to the border county of San Diego, CA and from the border county of Imperial County, CA to the border state of Sonora, MX (Figure 1A, right panel). Conclusion: This comprehensive analysis of all publicly available COVID-19 sequences showed local transmission across regions within CA and MX as well as across neighboring locations across the border. Similar to the 2009 H1N1 pandemic, the MX/CA border does not appear to be a major barrier to the spread of COVID-19, necessitating coordinated transnational intervention approaches.