Genomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. The Spike Y839 variant was most likely imported from Italy in mid-late February and massively disseminated in Portugal during the early epidemic, becoming prevalent in the Northern and Central regions of Portugal where it represented 22% and 59% of the sampled genomes, respectively, by 30 April. Based on our high sequencing sampling during the early epidemics [15.5% (1275/8251) and 6.0% (1500/24987) of all confirmed cases until the end of March and April, respectively], we estimate that, between 14 March and 9 April (covering the epidemic exponential phase) the relative frequency of the Spike Y839 variant increased at a rate of 12.1% (6.1%–18.2%, CI 95%) every three days, being potentially associated with 24.8% (20.8–29.7%, CI 95%; 3177–4542 cases, CI 95%) of all COVID-19 cases in Portugal during this period. Our data supports population/epidemiological (founder) effects contributing to the Y839 variant superspread. The potential existence of selective advantage is also discussed, although experimental validation is required. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants.

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.

Mutations in the Spike motif predicted to correspond to the fusion peptide are considered of interest as this domain is a potential target for anti-viral drug development that plays a pivotal role in inserting SARS-CoV-2 into human cell membranes. We tracked the temporal and geographical spread of a SARS-CoV-2 variant with the Spike D839Y mutation in the fusion peptide, which was detected early during the COVID-19 epidemic in Portugal. We show that this variant was most likely imported from Italy in mid-late February 2020, becoming prevalent in the Northern and Central regions of Portugal, where represented 22% and 59% of the sampled genomes, respectively, until the end of April 2020. Based on our high sequencing sampling during the early epidemics [15,5% (1275/8251) and 6,0% (1500/24987) of all confirmed cases until the end of March and April, respectively)], we estimate that, between March 14th and April 9th (covering the exponential phase of the epidemic), the relative frequency of Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) at every three days, being potentially associated with one in each four (20.8-29.7%, CI 95%) COVID-19 cases in Portugal during the same period. This observation places the Spike Y839 variant in the origin of the largest SARS-CoV-2 transmission chain during the first month of the COVID-19 epidemic in Portugal. We hypothesize that population/epidemiological effects (founder effects) and enhanced selective advantage might have concomitantly contributed to the increasing frequency trajectory of the Spike Y839 variant. Screening of the D839Y mutation globally confirmed its detection in 12 additional countries, even though the huge differences in genome sampling between countries hampers any accurate estimate of D839Y global frequency. In summary, our data points out that SARS-CoV-2 Spike Y839 variants, namely the descendent variant of the globally spread G614 variant detected in Portugal, need continuous and close surveillance.

<b><i>Background:</i></b> Ovar was the first Portuguese municipality to declare active community transmission of SARS-CoV-2, with total lockdown decreed on March 17, 2020. This context provided conditions for a large-scale testing strategy, allowing a referral system considering other symptoms besides the ones that were part of the case definition (fever, cough, and dyspnea). This study aims to identify other symptoms associated with COVID-19 since it may clarify the pre-test probability of the occurrence of the disease. <b><i>Methods:</i></b> This case-control study uses primary care registers between March 29 and May 10, 2020 in Ovar municipality. Pre-test clinical and exposure-risk characteristics, reported by physicians, were collected through a form, and linked with their laboratory result. <b><i>Results:</i></b> The study population included a total of 919 patients, of whom 226 (24.6%) were COVID-19 cases and 693 were negative for SARS-CoV-2. Only 27.1% of the patients reporting contact with a confirmed or suspected case tested positive. In the multivariate analysis, statistical significance was obtained for headaches (OR 0.558), odynophagia (OR 0.273), anosmia (OR 2.360), and other symptoms (OR 2.157). The interaction of anosmia and odynophagia appeared as possibly relevant with a borderline statistically significant OR of 3.375. <b><i>Conclusion:</i></b> COVID-19 has a wide range of symptoms. Of the myriad described, the present study highlights anosmia itself and calls for additional studies on the interaction between anosmia and odynophagia. Headaches and odynophagia by themselves are not associated with an increased risk for the disease. These findings may help clinicians in deciding when to test, especially when other diseases with similar symptoms are more prevalent, namely in winter.

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