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AbstractThe legal and illegal trade in wildlife for food, medicine and other products is a globally significant threat to biodiversity that is also responsible for the emergence of pathogens that threaten human and livestock health and our global economy. Trade in wildlife likely played a role in the origin of COVID-19, and viruses closely related to SARS-CoV-2 have been identified in bats and pangolins, both traded widely. To investigate the possible role of pangolins as a source of potential zoonoses, we collected throat and rectal swabs from 334 Sunda pangolins (Manis javanica) confiscated in Peninsular Malaysia and Sabah between August 2009 and March 2019. Total nucleic acid was extracted for viral molecular screening using conventional PCR protocols used to routinely identify known and novel viruses in extensive prior sampling (> 50,000 mammals). No sample yielded a positive PCR result for any of the targeted viral families—Coronaviridae, Filoviridae, Flaviviridae, Orthomyxoviridae and Paramyxoviridae. In the light of recent reports of coronaviruses including a SARS-CoV-2-related virus in Sunda pangolins in China, the lack of any coronavirus detection in our ‘upstream’ market chain samples suggests that these detections in ‘downstream’ animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. While confirmatory serologic studies are needed, it is likely that Sunda pangolins are incidental hosts of coronaviruses. Our findings further support the importance of ending the trade in wildlife globally.

[EN] The eNCLaUsTrA2 project that we present in this communication arises from the reflections made during the preparation and development of the laboratory practicals for the course Complementary Disciplinary Training (esp. Physics and Chemistry) of the Postgraduate Certificate in Secondary Teaching at the University of La Rioja. In the 2020-21 academic year, as a result of the health measures adopted due to the COVID-19 pandemic, it was impossible for many of the course students to attend the laboratory sessions. As a result of these circumstances and reflection, we considered instructing our students on the practical teaching of science using a virtual environment that favours teacher-student interaction through chats, chats and the use of collaborative murals during the development of the synchronous laboratory session. The experience gained during the eNCLaUsTrA2 workshop will hopefully have an impact on the training of future secondary school teachers, as well as providing them with a model that they can export to their teaching activity. [ES] El proyecto eNCLaUsTrA2 que presentamos en esta comunicación surge de la reflexiones que realizamos durante la preparación y desarrollo de las prácticas de laboratorio de la asignatura Complementos de Formación Disciplinar (esp. Física y Química) del Máster en Profesorado. En el curso 2020-21, consecuencia de las medidas sanitarias adoptadas debido a la pandemia de COVID-19, a buena parte de los alumnos de la asignatura les era imposible asistir a las clases de laboratorio. Fruto de las circunstancias y de la reflexión nos planteamos la instrucción de nuestro alumnado en la docencia práctica de las ciencias utilizando un entorno virtual que favorezca la interacción profesor-alumno a través de charlas, chats y el uso de murales colaborativos durante el desarrollo de la sesión de laboratorio síncrona. La experiencia adquirida durante el taller eNCLaUsTrA2 esperamos que repercuta en la formación del futuro profesorado de secundaria, además de proporcionarle un modelo que pueden exportar a su actividad docente.

What are the psychological consequences of the increasingly politicized nature of the COVID-19 pandemic in the United States relative to similar Western countries? In a two-wave study completed early (March) and later (December) in the pandemic, we found that polarization was greater in the United States ( N = 1,339) than in Canada ( N = 644) and the United Kingdom. ( N = 1,283). Political conservatism in the United States was strongly associated with engaging in weaker mitigation behaviors, lower COVID-19 risk perceptions, greater misperceptions, and stronger vaccination hesitancy. Although there was some evidence that cognitive sophistication was associated with increased polarization in the United States in December (but not March), cognitive sophistication was nonetheless consistently negatively correlated with misperceptions and vaccination hesitancy across time, countries, and party lines. Furthermore, COVID-19 skepticism in the United States was strongly correlated with distrust in liberal-leaning mainstream news outlets and trust in conservative-leaning news outlets, suggesting that polarization may be driven by differences in information environments.

In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, Gamma, Delta) and one closely related variant of interest (VoI—Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but in Omicron this enrichment is significantly higher. The progenitors of each of these VoC/VoI lineages underwent positive selection in the Spike ORF. However, once they were established, their Spike ORFs have been undergoing purifying selection, despite the application of global vaccination schemes from 2021 onwards. Our analyses reject the hypothesis that the heavily mutated receptor binding domain (RBD) of the Omicron Spike was introduced via recombination from another closely related Sarbecovirus. Thus, successive point mutations appear as the most parsimonious scenario. Intriguingly, in each of the six lineages, we observed a significant number of AAS wherein the new residue is not present at any homologous site among the other known Sarbecoviruses. Such AAS should be further investigated as potential adaptations to the human host. By studying the phylogenetic distribution of AAS shared between the six lineages, we observed that the Omicron (BA.1) lineage had the highest number (8/10) of recurrent mutations.

The impact of the COVID-19 pandemic on excess mortality from all causes in 2020 varied across and within European countries. Using data for 2015–2019, we applied Bayesian spatio-temporal models to quantify the expected weekly deaths at the regional level had the pandemic not occurred in England, Greece, Italy, Spain, and Switzerland. With around 30%, Madrid, Castile-La Mancha, Castile-Leon (Spain) and Lombardia (Italy) were the regions with the highest excess mortality. In England, Greece and Switzerland, the regions most affected were Outer London and the West Midlands (England), Eastern, Western and Central Macedonia (Greece), and Ticino (Switzerland), with 15–20% excess mortality in 2020. Our study highlights the importance of the large transportation hubs for establishing community transmission in the first stages of the pandemic. Here, we show that acting promptly to limit transmission around these hubs is essential to prevent spread to other regions and countries. In this study, the authors estimate excess mortality at the regional level for five European countries (England, Greece, Italy, Spain, and Switzerland) in 2020. They identify the regions and time periods with highest excess mortality and show how these patterns evolved through different pandemic waves.

Report 3, published 19 July 2021. Fully open-access.We conducted a nationally representative online survey in Ghana (N = 1295) throughout June 2021.In our analyses, we operationalised vaccine hesitancy as respondents who answered ‘no’ and ‘I don’t know’ to the question: “When a COVID-19 vaccine becomes available to you, would you like to get vaccinated?” Some top-level findings to share - willingness to vaccinate dropped from 82% in March, to 71% in June 2021 - Therefore, to phrase another way, there was an observed and significant increase in hesitancy, from 18% to 29% across this time period. - 32% of respondents reported that they had recently seen or heard stories about the indecision surrounding the Oxford Astrazeneca vaccine rollout in Europe and North America. Of this 32% subgroup, 62.0% of them indicated that these stories made them feel worried about accepting the COVID-19 vaccine in the future. - our main predictors of hesitancy continue to include: i) education (more educated people were more likely to be hesitant; one hypothesis is perhaps more likely to have greater access to the internet and thus availability of misinformation via social media); ii) females more hesitant than males; and iii) political allegiance (voting for the opposition parties was greater predictor of hesitancy). We hope that this information can be helpful with informing the health promotion efforts from the GHS, Ministry of Health and other stakeholders. For the previous report from this series of Ghana surveys (covering surveys in August 2020 and March 2021), see https://www.researchgate.net/publication/351327020_Examining_drivers_of_COVID-19_vaccine_hesitancy_in_Ghana

Abstract Background Currently, there is a missing link in the natural history of COVID-19, from first (usually milder) symptoms to hospitalization and/or death. To fill in this gap, we characterized COVID-19 patients at the time at which they were diagnosed in outpatient settings and estimated 30-day hospital admission and fatality rates. Methods This was a population-based cohort study.   Data were obtained from Information System for Research in Primary Care (SIDIAP)—a primary-care records database covering >6 million people (>80% of the population of Catalonia), linked to COVID-19 reverse transcriptase polymerase chain reaction (RT-PCR) tests and hospital emergency, inpatient and mortality registers. We included all patients in the database who were ≥15 years old and diagnosed with COVID-19 in outpatient settings between 15 March and 24 April 2020 (10 April for outcome studies). Baseline characteristics included socio-demographics, co-morbidity and previous drug use at the time of diagnosis, and polymerase chain reaction (PCR) testing and results.   Study outcomes included 30-day hospitalization for COVID-19 and all-cause fatality. Results We identified 118 150 and 95 467 COVID-19 patients for characterization and outcome studies, respectively. Most were women (58.7%) and young-to-middle-aged (e.g. 21.1% were 45–54 years old). Of the 44 575 who were tested with PCR, 32 723 (73.4%) tested positive. In the month after diagnosis, 14.8% (14.6–15.0) were hospitalized, with a greater proportion of men and older people, peaking at age 75–84 years. Thirty-day fatality was 3.5% (95% confidence interval: 3.4% to 3.6%), higher in men, increasing with age and highest in those residing in nursing homes [24.5% (23.4% to 25.6%)]. Conclusion COVID-19 infections were widespread in the community, including all age–sex strata. However, severe forms of the disease clustered in older men and nursing-home residents. Although initially managed in outpatient settings, 15% of cases required hospitalization and 4% died within a month of first symptoms. These data are instrumental for designing deconfinement strategies and will inform healthcare planning and hospital-bed allocation in current and future COVID-19 outbreaks.

Abstract The COVID-19 pandemic has affected human mobility via lockdowns, social distancing rules, home quarantines, and the full or partial suspension of transportation. Evidence-based policy recommendations are urgently needed to ensure that transport systems have resilience to future pandemic outbreaks, particularly within Global South megacities where demand for public transport is high and reduced access can exacerbate socio-economic inequalities. This study focuses on Metro Manila – a characteristic megacity that experienced one of the most stringent lockdowns worldwide. It analyzes aggregated cell phone and GPS data from Google and Apple that provide a comprehensive representation of mobility behavior before and during the lockdown. While significant decreases are observed for all transport modes, public transport experienced the largest drop (−74.5 %, on average). The study demonstrates that: (i) those most reliant on public transport were disproportionately affected by lockdowns; (ii) public transport was unable to fulfil its role as public service; and, (iii) this drove a paradigm shift towards active mobility. Moving forwards, in the short-term policymakers must promote active mobility and prioritize public transport to reduce unequal access to transport. Longer-term, policymakers must leverage the increased active transport to encourage modal shift via infrastructure investment, and better utilize big data to support decision-making.

The ongoing COVID-19 outbreak has expanded rapidly throughout China. Major behavioral, clinical, and state interventions are underway currently to mitigate the epidemic and prevent the persistence of the virus in human populations in China and worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, have affected COVID-19 spread in China. We use real-time mobility data from Wuhan and detailed case data including travel history to elucidate the role of case importation on transmission in cities across China and ascertain the impact of control measures. Early on, the spatial distribution of COVID-19 cases in China was well explained by human mobility data. Following the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases are still indicative of local chains of transmission outside Wuhan. This study shows that the drastic control measures implemented in China have substantially mitigated the spread of COVID-19. One sentence summary: The spread of COVID-19 in China was driven by human mobility early on and mitigated substantially by drastic control measures implemented since the end of January.