Routes of importation and spatial dynamics of SARS-CoV-2 variants during localised interventions in Chile

South America suffered large SARS-CoV-2 epidemics between 2020 and 2022 caused by multiple variants of interest and concern, some causing substantial morbidity and mortality. However, their transmission dynamics are poorly characterised. The epidemic situation in Chile enables us to investigate differences in the distribution and spread of variants Alpha, Gamma, Lambda, Mu and Delta. Chile implemented non-pharmaceutical interventions and an integrated genomic and epidemiological surveillance system that included airport and community surveillance to track SARS-CoV-2 variants. Here we combine viral genomic data and anonymised human mobility data from mobile phones to characterise the routes of importation of different variants into Chile, the relative contributions of airport-based importations to viral diversity versus land border crossings and test the impact of the mobility network on the diffusion of viral lineages within the country. We find that Alpha, Lambda and Mu were identified in Chile via airport surveillance six, four and five weeks ahead of their detection via community surveillance, respectively. Further, some variants that originated in South America were imported into Chile via land rather than international air travel, most notably Gamma. Different variants exhibited similar trends of viral dissemination throughout the country following their importation, and we show that the mobility network predicts the time of arrival of imported lineages to different Chilean comunas. Higher stringency of local NPIs was also associated with fewer domestic viral importations. Our results show how genomic surveillance combined with high resolution mobility data can help predict the multi-scale geographic expansion of emerging infectious diseases. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement M.U.G.K. acknowledges funding from The Rockefeller Foundation, Google.org, the Oxford Martin School Pandemic Genomics programme (also O.G.P. and B.G.), European Union Horizon 2020 MOOD (#874850) (also V.C., R.P.D.I., B.G. and R.E-P.) and E4Warning (101086640) (also S.B.M.) projects, the John Fell Fund, a Branco Weiss Fellowship and Wellcome Trust grants 225288/Z/22/Z and 226052/Z/22/Z. L.F. and the authors thank the funding and support of Telefonica/Movistar Chile and CISCO Chile. This research was supported by FONDECYT Grant No. 1221315 (to L.F.). LF also acknowledges financial support from the Lagrange Project of the Institute for Scientific Interchange Foundation (ISI Foundation), funded by Fondazione Cassa di Risparmio di Torino (Fondazione CRT). The views expressed are those of the authors and not necessarily those of the European Commission or any other funder. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Publicly available input data (epidemiological, flight data, land border crossings data) and scripts used to generate the analyses and plots of this manuscript are available in GitHub at https://github.com/BernardoGG/SARS2_Chile.git. The authors would like to thank and acknowledge all data contributors, i.e. the Authors and their Originating laboratories responsible for obtaining the specimens, and their Submitting laboratories for generating the genetic sequence and metadata and sharing via the GISAID Initiative. A complete list of the Authors and Originating laboratories can be found at the aforementioned public GitHub repository.