SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal
Authors: Borges Vítor , Isidro Joana , Trovão Nídia Sequeira , Duarte Sílvia , Cortes-Martins Helena , Martiniano Hugo , Gordo Isabel , Leite Ricardo , Vieira Luís ,   Portuguese network for SARS-CoV-2 genomics (Consortium), Lira Agostinho José S. , Sousa Fernandes Aida M. , Estrada Alexandra , Nunes Alexandra , Rodrigues Alfredo , Caldas Ana , Constança Ana , Henriques Ana Margarida , Matos Ana Miguel , Oliveira Ana , Dias Ana Paula , Pelerito Ana , Couto Ana Rita , Vilares Anabela , Albuquerque António , Nunes Baltazar , Gouveia Bruna R. , de Fátima Rodrigues Carina , Feliciano Carla , Roque Carla , Cardoso Carlos , Sousa Carlos , Paulino Cathy , Bettencourt Célia Rodrigues , Branco Claudia C. , dos Santos Cláudia Nunes , Godinho Conceição , Caetano Constantino P. , Correia Cristina , Toscano Cristina , Veríssimo Cristina , Silva Daniela , da Silva Diana Patrícia Pinto , Costa Eliana , Pádua Elizabeth , Martins Fátima , Vale Fátima , Vilarinho Fernanda , Branca Fernando , Caldeira Filomena , Lacerda Filomena , Rocha Francisca , Andrade Graça , Ribeiro Helena , Rodrigues Helena , Jesus Herberto , Sousa Hugo , Ferreira Idalina , Baldaque Inês , Costa Inês , Gomes Inês , Slobidnyk Inna , Albergaria Isabel , Dias Isabel , Fernandes Isabel , de Carvalho Isabel Lopes , Água-Doce Ivone , Armas Jácome Bruges , Ramos Joana , Sousa João Carlos , Costa João , Dias João , Rodrigues João , Sobral João , Machado Jorge , Meneses Jorge , Alves José , Constantino José Vicente , Brum Laura , Silveira Leonor , Zé-Zé Líbia , Santos Lidia , Freitas Ludivina , Silva Luís , Mota-Vieira Luisa , Lopes Lurdes , Monteiro Lurdes , Faria Márcia , Farinha Margarida , Vaz Margarida , Pinto Maria Alice , Pessanha Maria Ana , Tomaz Maria Beatriz , Vellés Maria Calle , Maciel de Soveral Maria da Graça , Ramos Maria Helena , Veiga Maria Isabel , Gargate Maria João , Peres Maria João , Borrego Maria José , Figueiredo Maria Matos , Martins Mariana , Viana Mariana , Melim Maurício , Jorreto Miguel Babarro , Fevereiro Miguel , Pinheiro Miguel , Oleastro Mónica , Seixas Nair , Ventura Nelson , Verdasca Nuno , Costa Olga , Barros Patrícia , Fonseca Patricia , Miguel Patricia , Bajanca-Lavado Paula , Branquinho Paula , Palminha Paula , Soares Paula , Valente Paula , Leandro Paulo , Pereira Paulo , Cardoso Pedro , Pechirra Pedro , Ramos Pedro , Neves Raquel , Rocha Raquel , Rodrigues Raquel , Sabino Raquel , Sá Regina , Ferreira Ricardo Filipe Romão , Rodrigues Ricardo , Veloso Rita C. , Cordeiro Rita , Côrte-Real Rita , de Sousa Rita , Gralha Rita , Macedo Rita , Matos Rita , Rodrigues Rita , Paulo Sandra , Sousa Sara , Lopo Sílvia , Magalhães Sónia Marta Santos , Rodrigues Sónia , Silva Sónia , Ladeiro Susana , Martins Susana , Silva Susana , Salvado Teresa , Luís Tiago , Alves Valquíria , Manageiro Vera , Guiomar Raquel , Gomes João Paulo 
Published: January 2022

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.

Methods
By 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.

Results
We 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.

Conclusions
Here 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.