Abstract
BackgroundGenomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide.MethodsBy applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal.ResultsWe detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed.ConclusionsHere we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.
Highlights
1234567890():,; Abstract Background Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide
We explored the diversity of Institute of Health Doutor Ricardo Jorge (INSA) sequences using a variety of nomenclature strategies, namely Nextstrain, GISAID and Phylogenetic Assignment of Named Global Outbreak LINeages[17]
The first COVID-19 confirmed cases in Portugal were reported on 2 March 2020 after laboratory confirmation by the National Institute of Health (INSA) Doutor Ricardo Jorge
Summary
The excess sequences in a country-specific monophyletic clade do not contribute any additional information to the between-country diffusion process we aim to infer
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