Cryptic spread of SARS-CoV-2 undermined targeted travel restrictions

Abstract The effectiveness of travel restrictions in mitigating the spread of novel viral variants remains understudied, particularly in regions with sparse genomic surveillance. We evaluated the efficacy of these restrictions in Western Asia, where countries sequenced less than one percent of SARS-CoV-2 cases in 2021, focusing on Iraq’s travel ban on India and the tourist travel restriction. We generated 535 SARS-CoV-2 whole-genome sequences from clinical samples collected in Duhok, Iraq, between June 2021 and March 2022, encompassing the Delta and Omicron variant waves. Using discrete Bayesian phylogeographic modeling, we reconstructed spatiotemporal viral spread patterns to determine whether travel restrictions delayed the introduction of the variants into the country, postponed community transmission onset, or altered the geographic sources of viral introductions over time. We found that the Delta variant was introduced into Iraq three months before the targeted travel ban was enacted, predominantly from Western and Southern Asia, whereas the Omicron variant was introduced despite the tourist travel restriction already being in place. We also show that both variants had established community transmission within the country despite travel restrictions, rendering these measures ineffective. Analysis of travel restrictions on a global scale reveals similar patterns of limited efficacy in mitigating the introductions of novel SARS-CoV-2 variants, challenging the usefulness of such measures. Competing Interest Statement The authors have declared no competing interest. Funding Statement The research leading to these results has received funding from the National Institutes of Health grants U19AI135995 and U01AI151812. Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: N/A I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the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 Footnotes ↵# These authors jointly supervised this work Data availability The data for our analyses can be found at https://github.com/andersen-lab/paper_2025_SARS-CoV-2_Cryptic_Spread. All sequence data generated were made available via the GISAID database (GISAID EPI_SET ID: EPI_SET_221201da, EPI_SET_250114rz, and four additional sequences EPI_ISL_1227819, EPI_ISL_12604523, EPI_ISL_12604439, EPI_ISL_12278224). Air travel data can be requested for release from Bluedot (info{at}bluedot.global).