Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal

Funding This study is co-funded by Fundação para a Ciência e a Tecnologia and Agência de Investigação Clínica e Inovação Biomédica [grant number 234_596874175] on behalf of the Research 4 COVID-19 call. This work is also a result of the GenomePT project [grant number POCI-01-0145- FEDER-022184], supported by COMPETE 2020 – Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).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.publishersversionpublishe

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

© The Author(s) 2022.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.publishersversionpublishe

The Rhubarb Connection and Other Revelations: The Everyday World of Metal Ions

Pink warships that vanish at dusk, urinary maladies of an emperor, and a gold test for cocaine – behold the chemistry of metal ions as never before.In this book you will learn about the sarcophagus molecule, the Chen-Kao test, and how murderers can be caught blue-handed with the wonders of glowing luminol. You will also meet the hidden chemistry of metal ions in everyday life, from the clever modern devices that measure blood-sugar levels, to the leather on your shoes and chewing gum stuck to their soles.Expect to encounter a fair share of heroes and villains, real and fictional, scientist and layperson. Such characters include an ex-MI5 employee running a hospital ward in London amid falling German V1 rockets, a notorious racing cyclist, a proud butler and the lady who first proposed nuclear fission (it’s not who you think it is).With engaging, humorous and intelligent prose, the reader will discover the fascinating back-stories of chemical discoveries and inventions where metal ions have played a major role.Featuring a foreword by popular science communicator Dr Raychelle Burks of St. Edward\u27s University, Texas

Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China.

Background: A novel coronavirus disease (COVID-19) outbreak has now spread to a number of countries worldwide. While sustained transmission chains of human-to-human transmission suggest high basic reproduction number R 0, variation in the number of secondary transmissions (often characterised by so-called superspreading events) may be large as some countries have observed fewer local transmissions than others. Methods: We quantified individual-level variation in COVID-19 transmission by applying a mathematical model to observed outbreak sizes in affected countries. We extracted the number of imported and local cases in the affected countries from the World Health Organization situation report and applied a branching process model where the number of secondary transmissions was assumed to follow a negative-binomial distribution. Results: Our model suggested a high degree of individual-level variation in the transmission of COVID-19. Within the current consensus range of R 0 (2-3), the overdispersion parameter k of a negative-binomial distribution was estimated to be around 0.1 (median estimate 0.1; 95% CrI: 0.05-0.2 for R0 = 2.5), suggesting that 80% of secondary transmissions may have been caused by a small fraction of infectious individuals (~10%). A joint estimation yielded likely ranges for R 0 and k (95% CrIs: R 0 1.4-12; k 0.04-0.2); however, the upper bound of R 0 was not well informed by the model and data, which did not notably differ from that of the prior distribution. Conclusions: Our finding of a highly-overdispersed offspring distribution highlights a potential benefit to focusing intervention efforts on superspreading. As most infected individuals do not contribute to the expansion of an epidemic, the effective reproduction number could be drastically reduced by preventing relatively rare superspreading events

The impact of COVID-19 on epilepsy care: Perspectives from UK healthcare workers

The COVID-19 pandemic has created an immense pressure on healthcare providers, resulting in a shift to remote consultations and the redeployment of healthcare workers (HCWs). We present survey data from the United Kingdom (UK) HCWs to outline how changes in healthcare provision impact clinicians' wellbeing and ability to provide adequate care. We designed an online survey to gather the experiences of HCWs providing care to people with epilepsy. We received seventy-nine responses from UK-based HCWs, of whom 43% reported an impact on their mental health. Changes to service delivery have resulted in 71% of clinicians performing > 75% of their consultations remotely. Diagnosing and treating epilepsy has changed, with a fifth of respondents being significantly less confident in diagnosing epilepsy. Ultimately, these results show that COVID-19 has had an overall negative impact on HCWs and their ability to provide epilepsy care. These results must be considered when reorganizing health services to ensure optimal outcomes for people with epilepsy

Laboratory capability and surveillance testing for Middle East respiratory syndrome coronavirus infection in the WHO European Region, June 2013

Since September 2012, over 90 cases of respiratory disease caused by a novel coronavirus, now named Middle East respiratory syndrome coronavirus (MERSCoV), have been reported in the Middle East and Europe. To ascertain the capabilities and testing experience of national reference laboratories across the World Health Organization (WHO) European Region to detect this virus, the European Centre for Disease Prevention and Control (ECDC) and the WHO Regional Office for Europe conducted a joint survey in November 2012 and a follow-up survey in June 2013. In 2013, 29 of 52 responding WHO European Region countries and 24 of 31 countries of the European Union/European Economic Area (EU/EEA) had laboratory capabilities to detect and confirm MERS-CoV cases, compared with 22 of 46 and 18 of 30 countries, respectively, in 2012. By June 2013, more than 2,300 patients had been tested in 23 countries in the WHO European Region with nine laboratory-confirmed MERS-CoV cases. These data indicate that the Region has developed significant capability to detect this emerging virus in accordance with WHO and ECDC guidance. However, not all countries had developed capabilities, and the needs to do so should be addressed. This includes enhancing collaborations between countries to ensure diagnostic capabilities for surveillance of MERS-CoV infections across the European Region.S

Effects of non-pharmaceutical interventions on COVID-19 cases, deaths, and demand for hospital services in the UK: a modelling study.

BACKGROUND: Non-pharmaceutical interventions have been implemented to reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the UK. Projecting the size of an unmitigated epidemic and the potential effect of different control measures has been crucial to support evidence-based policy making during the early stages of the epidemic. This study assesses the potential impact of different control measures for mitigating the burden of COVID-19 in the UK. METHODS: We used a stochastic age-structured transmission model to explore a range of intervention scenarios, tracking 66·4 million people aggregated to 186 county-level administrative units in England, Wales, Scotland, and Northern Ireland. The four base interventions modelled were school closures, physical distancing, shielding of people aged 70 years or older, and self-isolation of symptomatic cases. We also modelled the combination of these interventions, as well as a programme of intensive interventions with phased lockdown-type restrictions that substantially limited contacts outside of the home for repeated periods. We simulated different triggers for the introduction of interventions, and estimated the impact of varying adherence to interventions across counties. For each scenario, we projected estimated new cases over time, patients requiring inpatient and critical care (ie, admission to the intensive care units [ICU]) treatment, and deaths, and compared the effect of each intervention on the basic reproduction number, R0. FINDINGS: We projected a median unmitigated burden of 23 million (95% prediction interval 13-30) clinical cases and 350 000 deaths (170 000-480 000) due to COVID-19 in the UK by December, 2021. We found that the four base interventions were each likely to decrease R0, but not sufficiently to prevent ICU demand from exceeding health service capacity. The combined intervention was more effective at reducing R0, but only lockdown periods were sufficient to bring R0 near or below 1; the most stringent lockdown scenario resulted in a projected 120 000 cases (46 000-700 000) and 50 000 deaths (9300-160 000). Intensive interventions with lockdown periods would need to be in place for a large proportion of the coming year to prevent health-care demand exceeding availability. INTERPRETATION: The characteristics of SARS-CoV-2 mean that extreme measures are probably required to bring the epidemic under control and to prevent very large numbers of deaths and an excess of demand on hospital beds, especially those in ICUs. FUNDING: Medical Research Council

Effectiveness of prevention of SARS-CoV-2 transmission among unvaccinated Italian healthcare workers

Background: We aimed to investigate the association between personal protective equipment (PPE) use and SARS-CoV-2 infection among healthcare workers (HCWs). Methods: We analyzed occupational surveillance contact forms followed by a PCR test notified between March and September 2020 by Italian HCWs. The odds ratios (ORs) and 95% Confidence Intervals (CIs) for positive PCR based on HCWs and contacts characteristics were calculated through multivariable logistic regression models. When multiple contacts were potentially effective for a PCR test, they were weighted by the inverse of their number. Results: Overall, 4,883 contacts reported by 2,952 HCWs were analyzed, and 224 contacts among 144 HCWs had positive PCR. No difference was found according to sex, age, employment, or job title, except for an OR of 0.30 (95%CI 0.11-0.78) for resident physicians, compared to administrative staff. The ORs for use of surgical mask were 0.59 (95%CI=0.40-0.86) for use only by HCW, 0.49 (95%CI=0.22-1.07) only by the infected person, and 0.40 (95%CI=0.27-0.60) by both, compared to use by neither. Use of other PPEs was not associated with infection, while the OR for hand sanitation was 0.61 (95%CI=0.40-0.93). HCWs reporting fever, cough, and asthenia had a higher risk of infection. Conclusions: Use of surgical masks was associated with a 40-60% lower risk of infection, especially when both HCWs and infected individuals used them. Our results quantify the role played by mask use and hand sanitation in preventing SARS-CoV-2 transmission in high-risk circumstances

Algoritmes de tractament dels pacients amb infecció per SARS-CoV-2

Coronavirus SARS-Cov-2; COVID-19; 2019-nCoV; Algoritme; Detecció; Tractament; Atenció primària; Hospital; ResidènciaCoronavirus SARS-Cov-2; COVID-19; 2019-nCoV; Algoritmo; Detección; Tratamiento; Atención primaria; Hospital; ResidenciaCoronavirus SARS-Cov-2; COVID-19; 2019-nCoV; Algorithm; Detection; Treatment; Primary care; Hospital; HomeAquest document inclou una síntesi breu en format d’algoritme del document Tractament farmacològic de la infecció per SARS-CoV-2 del CatSalut.This document includes a brief summary in algorithmic format of the document: Pharmacological treatment of CatSalut SARS-CoV-2 infection.Este documento incluye una breve síntesis en formato de algoritmo del documento Tratamiento farmacológicos de la infección por SARS-CoV-2 del CatSalut