The early dynamics of the SARS-CoV-2 epidemic in Portugal

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. This unprecedented collaborative effort culminated in the generation of 1275 SARS-CoV-2 genome sequences, which represent 15.5% of all confirmed cases in March 2020, making Portugal one of the countries generating the highest volumes of SARS-CoV-2 genomic data during early COVID-19 pandemic. Methods: We reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal using recent phylodynamic models that allow integration of individual-based travel history, in order to obtain a more realistic reconstruction of the viral dynamics. 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 was broadly consistent with the available travel history data, as well as with the countries with most frequent connectivity and/or with the highest number of Portuguese immigrants. Although most introductions were estimated to have occurred during the last week of February and the first week of March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal several weeks before the first confirmed local cases on March 2, 2020. Discussion and Conclusion: While the implemented preventive and early control measures seem to have been successful in mitigating community transmission from most independent introductions, our results suggest that their earlier implementation could have largely minimized the number of introductions and subsequent virus expansion. Here we lay the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlight the need for systematic, continuous and geographically-representative genomic surveillance to guide national and international public health authorities toward the characterization and control of SARS-CoV-2 circulating diversity.

Unraveling the hurdles of a large COVID-19 epidemiological investigation by viral genomics

“…61 In Portugal, such a framework is partially established, but still needs to be strengthened to automate the systematic integration of genomic and epidemiological data, and to promote timely communication of results back to local public health entities. 35 These efforts will not only require the re-design of currently implemented systems towards a more comprehensive and interactive data flow between all stakeholders, but also require that all public health teams and decision-makers are aligned with the need to embed genomics into the routine activities of infectious disease surveillance and outbreak resolution. The COVID-19 pandemic highlighted this field by establishing genomic surveillance as a key tool for Public Health decision-making towards outbreak control.…”

“…In contrast, SARS-CoV-2 with the genetic profile 2 (including Nextstrain clade 20B root sequences and 1-3 SNPs descendants) was highly prevalent worldwide (especially in Europe) during the study period (March-June 2021), 36 and was introduced multiple times (and in multiple locations) in Portugal during the early epidemics. 35 Considering the relatively low diversification of clade 20B worldwide, the power of genomics to track the source of infection and disclose direct contacts within genetic profile 2 is reduced when compared with genetic profile 1. Regarding genetic profiles 3 and 4, both represent singleton sequences in the global national phylogenetic tree (Supplementary Figure 1).…”

Controlling the pandemic during the SARS-CoV-2 vaccination rollout: a modeling study

“…The present study makes a contribution towards better understanding of when and which control measures can be relaxed as mass vaccination programmes progress in 2021. We take Portugal as a case study where good quality data for model parameterization are available but, apart from efforts of genomic surveillance [49], there are no dedicated COVID-19 modeling studies for informing policymaking in this country [50]. Using an age-structured transmission model that has been fitted in a Bayesian framework to the data from various sources (age-specific hospitalizations and seroprevalence, social contact and demographic data, national vaccination plan and vaccine rollout data etc.…”

Controlling the pandemic during the SARS-CoV-2 vaccination rollout: a modeling study

“…The present study makes a contribution towards better understanding of when and which control measures can be relaxed as mass vaccination programmes progress in 2021. We take Portugal as a case study where good quality data for model parameterization are available but, apart from efforts of genomic surveillance [49], there are no dedicated COVID-19 modeling studies for informing policymaking in this country [50]. Using an age-structured transmission model that has been fitted in a Bayesian framework to the data from various sources (age-specific hospitalizations and seroprevalence, social contact and demographic data, national vaccination plan and vaccine rollout data etc.…”