11 February, 2021

The impact of coronavirus (COVID-19) related public-health measures on training behaviours of individuals previously participating in resistance training: A cross-sectional survey study -

Introduction: Understanding the impact of lockdown upon RT, and how people adapted their RT behaviours, is expected to have implications for strategies to maintain engagement in positive health behaviours such as this during- restrictive pandemic-related public health measures. Further, doing so will provide a baseline for investigation of the long-term effects of these measures upon behaviours and perceptions and facilitate future follow-up study. Objectives: To determine how the onset of coronavirus (COVID-19), and the associated ‘lockdown’, affected resistance training (RT) behaviours, in addition to motivation, perceived effectiveness, enjoyment, and intent to continue, in those who regularly performed resistance training RT prior to the pandemic. Methods: We conducted an observational, cross-sectional study using online surveys in multiple languages (English, Danish, French, German, Italian, Portuguese, Slovakian, Swedish, and Japanese) distributed across social media platforms and through authors professional and personal networks. Adults (n = 5389 after data cleaning; median age = 31 years [interquartile range (IQR) = 25, 38]), who were previously engaged in RT prior to lockdown (median prior RT experience = 7 years [IQR = 4, 12]) participated. Outcomes were self-reported RT behaviours including: continuation of RT during lockdown, location of RT, purchase of specific equipment for RT, method of training (e.g. alone, supervision etc.), full-body or split routine, types of training, repetition ranges, exercise number, set volumes (per exercise and muscle group), weekly frequency of training, perception of effort, whether training was planned/recorded, time of day, and training goals. Secondary outcomes included motivation, perceived effectiveness, enjoyment, and intent to continue RT. Results: A majority of individuals (82.8%) maintained participation in some form of RT during- lockdown. Marginal probabilities from generalised linear models and generalised estimating equations of engaging in certain RT behaviours were largely similar from pre- to during- lockdown (particularly numbers of exercises, sets per exercise or muscle group, and weekly frequencies). There was reduced probability of training in privately owned gyms (~59% to ~7%) and increased probability of training at home (~18% to ~89%); greater probability of training using a full-body routine (~38% to ~51%); reduced probability of resistance machines (~66% to ~13%) and free weight use (~96% to ~81%), and increased probability of bodyweight training (~62% to ~82%); reduced probability of moderate repetition ranges (~62-82% to ~55-66%) and greater probability of higher repetition ranges (~27% to ~49%); and moderate reduction in the perception of effort experienced during- training (r = 0.31). Further, individuals were slightly less likely to plan or record training during- lockdown and many changed their training goals as a result of lockdown. Additionally, perceived effectiveness, enjoyment, and likelihood of continuing current training were all lower during- lockdown. Conclusions: Those engaged in RT prior to lockdown appeared mostly able to maintain these behaviours with only slight adaptations in both the location and types of training performed. However, people employed less effort, had lower motivation, and perceived training as less effective and enjoyable, reporting that their likelihood of continuing current training was similar or lower than pre- lockdown. These results have implications for strategies to maintain engagement in positive health behaviours such as RT during- restrictive pandemic-related public health measures.

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Investigating orthographic versus auditory cross-situational word learning with online and lab-based research -

In recent years, cross-situational word learning (CSWL) paradigms have shown that novel words can be learned through implicit statistical learning. So far, CSWL studies using adult populations have focused on the presentation of spoken words (auditory information), however, words can also be learned through their written form (orthographic information). This study compares auditory and orthographic presentation of novel words with different degrees of phonological overlap using the CSWL paradigm. Additionally, we also present a lab-based and online-based approach to testing behavioural experiments. Due to the COVID-19 pandemic, lab testing was prematurely terminated, and testing was continued online using a newly created online testing protocol. Analyses first compared accuracy and response times across modalities, with our findings showing better and faster recognition performance for CSWL when novel words are presented through their written (orthographic condition) than through their spoken forms (auditory condition). As well, Bayesian modelling found that accuracy for the auditory condition was higher online compared to the lab-based experiment, whereas performance in the orthography condition was high in both experiments and generally outperformed the auditory condition. We discuss the implications of our findings for modality of presentation, as well as the benefits of our online testing protocol and its implementation for future research.

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Antenatal Depression and the Impact of COVID-19 Mitigation Efforts in Australia -

The mitigation efforts of COVID-19 have led to significant changes to the delivery of routine healthcare globally. In Australia, the way maternal health services have been delivered since the beginning of the pandemic has also changed. Maternity care and support are known to influence maternal mental health. One hundred and eighty-eight English speaking pregnant women residing in Australia were recruited using social media advertising between September and November 2020 as part of a larger study. Participants were aged between 19 and 42 (M = 31.05, SD = 4.68). Compared with previous Australian prevalence rates of around 7% for antenatal depression, rates in this study were 15.9% overall and 19% for those in Melbourne. It is suggested that increased vigilance with screening and assessment will be required to identify and support this cohort of mothers who are not coping.

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Bifurcated monocyte states are predictive of mortality in severe COVID-19 -

Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection presents with varied clinical manifestations, ranging from mild symptoms to acute respiratory distress syndrome (ARDS) with high mortality. Despite extensive analyses, there remains an urgent need to delineate immune cell states that contribute to mortality in severe COVID-19. We performed high-dimensional cellular and molecular profiling of blood and respiratory samples from critically ill COVID-19 patients to define immune cell genomic states that are predictive of outcome in severe COVID-19 disease. Critically ill patients admitted to the intensive care unit (ICU) manifested increased frequencies of inflammatory monocytes and plasmablasts that were also associated with ARDS not due to COVID-19. Single-cell RNAseq (scRNAseq)-based deconvolution of genomic states of peripheral immune cells revealed distinct gene modules that were associated with COVID-19 outcome. Notably, monocytes exhibited bifurcated genomic states, with expression of a cytokine gene module exemplified by CCL4 (MIP-1{beta}) associated with survival and an interferon signaling module associated with death. These gene modules were correlated with higher levels of MIP-1{beta} and CXCL10 levels in plasma, respectively. Monocytes expressing genes reflective of these divergent modules were also detectable in endotracheal aspirates. Machine learning algorithms identified the distinctive monocyte modules as part of a multivariate peripheral immune system state that was predictive of COVID-19 mortality. Follow-up analysis of the monocyte modules on ICU day 5 was consistent with bifurcated states that correlated with distinct inflammatory cytokines. Our data suggests a pivotal role for monocytes and their specific inflammatory genomic states in contributing to mortality in life-threatening COVID-19 disease and may facilitate discovery of new diagnostics and therapeutics.

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The effect of respiratory activity, ventilatory therapy and facemasks on total aerosol emissions -

Background Exhaled respirable aerosols (<5 μm diameter) present a high risk of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission. Many guidelines recommend using aerosol precautions during “aerosol generating procedures” (AGPs) and droplet (>5 μm) precautions at other times. However, there is emerging evidence that respiratory activities such as cough and not AGPs are the important source of aerosols. Methods We used a novel chamber with an optical particle counter sampling at 100 L/min to count and size-fractionate all exhaled particles (0.5-25 μm). We compared emissions from ten healthy subjects during respiratory “activities” (quiet breathing, talking, shouting, forced expiratory maneuvers, exercise and coughing) with respiratory “therapies” designated as AGPs: high flow nasal oxygen (HFNO) and single or dual circuit non-invasive positive pressure ventilation, NIPPV-S and NIPPV-D, respectively. Activities were repeated wearing facemasks. Results Compared to quiet breathing, respiratory activities increased particle counts between 34.6-fold (95% confidence interval [CI], 15.2 to 79.1) during talking, to 370.8-fold (95% CI, 162.3 to 847.1) during coughing (p<0.001). During quiet breathing, HFNO at 60 L/min increased counts 2.3-fold (95% CI, 1.2 to 4.4) (p=0.03) and NIPPV-S and NIPPV-D at 25/10 cm H₂O increased counts by 2.6-fold (95% CI, 1.7 to 4.1) and 7.8-fold (95% CI, 4.4 to 13.6) respectively (p<0.001). During activities, respiratory therapies and facemasks reduced emissions compared to activities alone. Conclusion Talking, exertional breathing and coughing generate substantially more aerosols than the respiratory therapies HFNO and NIPPV which can reduce total emissions. The risk of aerosol exposure is underappreciated and warrants widespread targeted interventions.

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Explaining ethnic disparities in COVID-19 mortality: population-based, prospective cohort study -

Ethnic disparities in COVID-19 hospitalizations and mortality have been reported but there is scant understanding of how these inequalities are embodied. The UK Biobank prospective cohort study comprises around half a million people who were aged 40-69 years at study induction between 2006 and 2010 when information on ethnic background and potential explanatory factors was captured. Study members were linked to a national mortality registry. In an analytical sample of 448,664 individuals (248,820 women), 354 deaths were ascribed to COVID-19 between 5th March and the end of follow-up on 17th September 2020. In age- and sex-adjusted analyses, relative to White participants, Black study members experienced around seven times the risk of COVID-19 mortality (odds ratio; 95% confidence interval: 7.25; 4.65, 11.33), while there was a doubling in the Asian group (1.98; 1.02, 3.84). Controlling for baseline comorbidities, socioeconomic circumstances, and lifestyle factors explained 53% of the differential in risk for Asian people (1.37; 0.68, 2.77) and 27% in Black study members (4.28; 2.67, 6.86). The residual risk in ethnic minority groups for COVID-19 deaths may be ascribed to unknown genetic factors or unmeasured phenotypes, most obviously racial discrimination.

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COVID-19 vaccination rate and protection attitudes can determine the best prioritisation strategy to reduce fatalities -

Background: The unprecedented rapid development of vaccines against the SARS-CoV-2 virus creates in itself a new challenge for governments and health authorities: the effective vaccination of large numbers of people in a short time and, possibly, with shortage of vaccine doses. To whom vaccinate first and in what sequence, if any at all, to avoid the most fatalities remains an open question. Methods: A compartmental model considering age-related groups was developed to evaluate and compare vaccine distribution strategies in terms of the total avoidable fatalities. Population groups are established based on relevant differences in mortality (due to e.g. their age) and risk-related traits (such as their behaviour and number of daily person-to-person interactions). Vaccination distribution strategies were evaluated for different vaccine effectiveness levels, population coverage and vaccination rate using data mainly from Spain. Findings: Our results show that, if children could also be included in the vaccination, a rollout by priority to groups with the highest number of daily person-to-person interactions can achieve large reductions in total fatalities. This is due to the importance of the avoided subsequent infections inflicted on the rest of the population by highly interactive individuals. If children are excluded from the vaccination, the differences between priority strategies become smaller and appear highly depending on rollout rate, coverage and the levels of self-protection and awareness exercised by the population. Interpretation: These results are in possible contradiction with several published plans for COVID-19 vaccination and highlight the importance of conducting an open comprehensive and thorough analysis of this problem leaving behind possible preconceptions.

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The COVID States Project #27: Trajectory of COVID-19-related behaviors in Illinois -

The number of COVID-19 cases in Illinois has risen sharply over the last two months, from about 2,000 new cases a day in late September to 10,000 or so currently. In this report we evaluate whether there have been significant changes in the behaviors that facilitate the spread of the disease. The COVID States Project has been conducting a 50-state survey roughly once a month since April about attitudes and behaviors around COVID-19. Here we focus on public-health related behaviors that facilitate/inhibit the spread of the disease. It has become apparent that behaviors of particular importance are (1) those which bring people into indoor proximity; and (2) mask wearing.

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SARS-CoV-2 infection models using in vivo and in vitro hACE2-lentivirus transduction -

SARS-CoV-2 uses the human ACE2 receptor (hACE2), with mouse ACE2 (mACE2) unable to support infection. Herein we describe an ACE2-lentivirus system and illustrate its utility in vitro and in vivo. Transduction of non-permissive cell lines with hACE2 imparted replication competence, and transduction with mACE2 containing N30D, N31K, F83Y and H353K mutations, to match hACE2, rescued SARS-CoV-2 replication. hACE2-lentivirus transduction of C57BL/6J, IFNAR-/- and IL-28RA-/- mice lungs indicated type I and III IFN receptor knockout had minimal effect on virus replication. However, RNA-Seq illustrated that they were required for inflammatory responses in C57BL/6J mice, which were similar to those seen in COVID-19 patients. Finally, we illustrate the utility of hACE2 transduction for vaccine evaluation in C57BL/6J mice. The hACE2-lentivirus system thus has broad application in SARS-CoV-2 research, in particular allowing access to GM mice, while also offering the inherent advantages of lentiviral transduction such as stable genomic integration.

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In vitro evolution of Remdesivir resistance reveals genome plasticity of SARS-CoV-2 -

Remdesivir (RDV) is used widely for COVID-19 patients despite varying results in recent clinical trials. Here, we show how serially passaging SARS-CoV-2 in vitro in the presence of RDV selected for drug-resistant viral populations. We determined that the E802D mutation in the RNA-dependent RNA polymerase was sufficient to confer decreased RDV sensitivity without affecting viral fitness. Analysis of more than 200,000 sequences of globally circulating SARS-CoV-2 variants show no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we also observed changes in the Spike (i.e., H69 E484, N501, H655) corresponding to mutations identified in emerging SARS-CoV-2 variants indicating that they can arise in vitro in the absence of immune selection. This study illustrates SARS-CoV-2 genome plasticity and offers new perspectives on surveillance of viral variants.

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Naive human B cells can neutralize SARS-CoV-2 through recognition of its receptor binding domain -

Exposure to a pathogen elicits an adaptive immune response aimed to control and eradicate. This initial exposure is imprinted on the immune system, so that a subsequent encounter to the same pathogen or a variant will result in a memory recall response that is often protective. Interrogating the naive B cell repertoire in terms of both abundance and specificity to said pathogen may contribute to an understanding of how to potentially elicit protective responses. Here, we isolated naive B cells across 8 human donors, targeting the SARS-CoV-2 receptor-binding domain (RBD). Single B cell sorting, and subsequent sequence analysis, showed diverse gene usage and pairing with no apparent restriction on complementarity determining region length in either the heavy or light chains. We show that recombinantly expressed IgGs and Fabs of these germline precursors bind SARS-CoV-2 RBD. Importantly, a subset of these naive antibodies also bind SARS-CoV, an emergent variant (501Y.V2) and a potential pandemic (WIV-1) coronavirus. Furthermore, naive antibodies can also neutralize SARS-CoV-2 pseudoviruses in the absence of any somatic hypermutation, suggesting that protective immunity to coronaviruses, more broadly, may be genetically encoded. Future studies aimed at understanding the naive repertoire to other coronaviruses may ultimately reveal shared specificities that could be leveraged to develop pan-coronavirus vaccines aimed at priming encoded germline responses.

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Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2 -

COVID-19 has widely spread across the world, and much research is being conducted on the causative virus SARS-CoV-2. To help control the infection, we developed the Coronavirus GenBrowser (CGB) to monitor the pandemic. With CGB, 178,765 high quality SARS-CoV-2 genomic sequences were analyzed, and 121,522 mutations were identified. In total, 1,041 mutation cold spots were found, suggesting that these spots are key functional elements of SARS-CoV-2 and can be used for detection and vaccine development. CGB revealed 203 accelerated evolutions of SARS-CoV-2, but variants with accelerated evolution were not found to be highly contagious, suggesting that most of these evolutions are neutral. The B.1.1.7 (CGB75056.84017) lineage previously identified in the UK was not found to be significantly accelerated although its adaptive evolution was detected. Moreover, 2,297 strains with a significantly reduced evolutionary rate were identified, including three closely related variants widely spreading in Europe with no mutations in three months. By lineage tracing, a strain dated early March 2020 was determined to be the most recent common ancestor of nine strains collected from six different regions in three continents. This strain was also found to cause the outbreak in Xinfadi, Beijing, China in June 2020. CGB allows visualization and analysis of hundreds of thousands of SARS-CoV-2 genomic sequences. Distributed genome alignments and its effective analysis pipeline ensure timely update of the latest genomic data of SARS-CoV-2. CGB is an efficient platform for the general public to monitor the transmission and evolution of SARS-CoV-2.

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Socio-economic indicators correlate with daily mobility during the second-wave of the Covid-19 pandemic -

Non-pharmaceutical interventions are being used globally to limit the spread of Covid-19, which are in turn affecting individual mobility patterns. Mobility measures were found to be strongly associated with regional socio-economic indicators during the first wave of the pandemic. Here, we use network mobility data from an ~3.5 million person sample of individuals in Ontario, Canada to study the association between three different individual-mobility measures and four socio-economic indicators throughout the first and second wave of Covid-19 (January to December 2020). We demonstrate that understanding how mobility behaviours have changed in response to Covid-19 varies considerably depending on how mobility is measured. We find a strong positive association between different mobility levels and the economic deprivation index, which demonstrates that inequities in the changes to mobility across economic gradients observed during the initial lockdown have persisted into the later stages of the pandemic. However, the associations between mobility and other socio-economic indicators vary over time. We capture a strong day-of-week pattern of association between socio-economic indicators and mobility levels. Our findings have important implications for understanding if and how mobility data should be used to study the impact of non-pharmaceutical interventions on the socio-economic conditions across geographical space, and over time. Our results support that Covid-19 non-pharmaceutical interventions have resulted in geographically disparate responses to mobility behaviour, and quantifying mobility changes at fine geographical scales is crucial to understanding the impacts of Covid-19 on local populations.

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Developing initial programme theory: COVID-19 Genomics UK Consortium Hospital-Onset COVID-19 study (COG-UK HOCI) -

Intervention programme theory enhances the development, evaluation, optimisation and translation of complex interventions. It clearly specifies the ways intervention context and content combine to produce intervention outcomes. We report the development of initial programme theory for a SARS-CoV-2 genome sequence-report tool (SRT). The SRT translates genome sequencing data to drive changes in the intensity and location of infection prevention and control (IPC) and related cleaning activities within UK NHS hospitals to reduce nosocomial infections. The SRT is being trialled within the COVID-19 Genomics UK Consortium Hospital-Onset COVID-19 study (HOCI). Within the HOCI study, we will assess the impact of the SRT, and its timing, when compared to no sequence data, on the occurrence and transmission location of nosocomial infection, reducing its incidence rate and identifying previously undetected nosocomial transmission. To develop the initial programme theory we used documentary analysis (e.g. trial protocol, case report forms, drafts of the SRT), informal discussions with trial team members, and the iterative development of logic models. The intervention’s causal mechanisms were conceptualised using combined insights from behavioural, implementation science and complex adaptive systems perspectives. Our initial programme theory will subsequently be used to shape a process evaluation within a diverse sample of trial sites. The planned process evaluation will use the initial programme theory and assess SRT acceptability, support for its putative causal mechanisms, issues of fidelity and adaptation, and examine how the planned intervention has worked, or not, in relation to intended and unintended consequences.

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Mitigating losses: How science diplomacy can address the impact of COVID-19 on early career researchers -

Despite the failures to tackle early coordinated responses at national and multinational levels, the global emergence of Coronavirus Disease 2019 (COVID-19) pandemic promoted unprecedented actions on the science-policy, science-communication, and science-diplomacy interfaces worldwide. With varying degrees of success, various actions within the realm of science diplomacy have accompanied the creation of knowledge related to COVID-19 through international collaboration. The COVID-19 pandemic brought the world to a standstill and also drew attention to the genuine need for science diplomacy. This pandemic highlighted the need of training opportunities in the interface of policy and diplomacy for researchers to be able to get grips on emerging health issues. Moreover, it is necessary to create specific platforms for experts to interact with decision-makers at the national and international levels, especially in the Global South. This crisis inevitably shifted the focus on scientific areas that directly address the pandemic response (epidemiology, public health, virology, immunology, pharmacology, human behavioral research, economics, among others). At the same time, some areas not related to the pandemic response have been slowed down due to inevitable physical and social restrictions that impacted certain aspects of the academic life. This does not only relate to daily access to the lab, scientific collections, or field sites, but also associates with furloughed employees and reduced funding to non-COVID-19-related research. Moreover, during the pandemic, women and (usually young) scientists with children have reduced their research efforts substantially, with future implications still difficult to quantify. While some researchers might have harnessed telecommuting and lockdown periods to focus on data analysis and publication writing, gender bias still exists. The slight increase in publications with pre-acquired data may still be followed by an immediate future impacted by the lack of data acquisition during the pandemic. These issues may create long-term effects due to reduced capacity for generating pre-requisite data for securing new funding, termination of research, reduced networking opportunities, restrictions to international collaborations, collectively having a negative impact on other disciplines. While most established researchers may not be affected hardly by the above-mentioned effects, early career researchers (ECRs), represent a more vulnerable population. ECRs usually refer to PhD students, postdoctoral fellows and scientists who have 10 years or less of experience after the doctoral degree, although there is some flexibility in this definition. Due to their career stage, ECRs often face job precarity, lack of available opportunities, low funding, and job insecurity (e.g., untenured positions and temporary contract employees). These problems are augmented by the COVID-19 pandemic and may be experienced more in countries with a developing scientific system. The impact could be higher for countries that are developing their research environment, are dependent on training their ECRs and conducting experiments abroad through international exchanges programs, which have been stopped due to the pandemic. Given these unprecedented times, it has been observed that international scientific organizations, policy-makers, scientific communities, and private stakeholders have strengthened their collaborations in response to the pandemic. We, as ECRs, strongly believe that science diplomacy can make a difference in addressing the challenges (emanated or amplified by the current pandemic) that ECRs would face inside and outside academia. Here we present such challenges, and discuss how the Global Young Academy (GYA), an independent organization of early to mid-career researchers across all disciplines and countries, has provided a platform for ECRs to practice science diplomacy, science advice, and science communication. The former by serving as a bridge between ECRs and governments, the second by hearing the voices of young researchers when enacting policies, and the latter by informing societies about the benefits of scientific research. Motivated by the described examples, we recommend measures for scientists, funding agencies, and international organizations to foster international collaboration in these unparallel times.

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Covid-19 Sentry

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