23 June, 2021

Anti-prothrombin autoantibodies enriched after infection with SARS-CoV-2 and influenced by strength of antibody response against SARS-CoV-2 proteins -

Antiphospholipid antibodies (aPL), assumed to cause antiphospholipid syndrome (APS), are notorious for their heterogeneity and detect phospholipids and phospholipid-binding proteins. The persistent presence of Lupus anticoagulant and/or aPL against cardiolipin and/or {beta}2 glycoprotein I have been shown to be independent risk factors for vascular thrombosis and pregnancy morbidity in APS. Among others, viral infections have been proposed to trigger the production of aPL while mostly being considered non-pathogenic. Yet, the potential pathogenicity of infection-associated aPL has gained momentum since an increasing number of patients infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been described with coagulation abnormalities and hyperinflammation, together with the presence of aPL. Here, we present data from a multicentric, mixed-severity study including three cohorts of individuals who contracted SARS-CoV-2 as well as non-infected blood donors. We simultaneously measured 10 different criteria and non-criteria aPL (IgM and IgG) by using a line immunoassay. Further, IgG antibody response against three SARS-CoV-2 proteins was investigated using tripartite automated blood immunoassay technology. Our analyses revealed that select non-criteria aPL are enriched concomitant to or after an infection with SARS-CoV-2. Linear mixed-effect models suggest an association of aPL to prothrombin (PT) with the strength of the antibody response against SARS-CoV-2 and further influenced by SARS-CoV-2 disease severity and sex of the individuals. In conclusion, our study is the first to report an association between disease severity, anti-SARS-CoV-2 immunoreactivity and aPL against PT in patients with SARS-CoV-2.

🖺 Full Text HTML: Anti-prothrombin autoantibodies enriched after infection with SARS-CoV-2 and influenced by strength of antibody response against SARS-CoV-2 proteins

Tools for Public Health Policy: Nudges and Boosts as Active Support of the Law in Special Situations such as the COVID-19 Pandemic -

In recent years, “nudging” has become a standard behavioral intervention at the individual level and for the design of social policies. Although nudges are effective, such interventions seem to be limited to a given space and time, and there is only scant evidence to support the contrary view. On the other hand, choice architects may utilize another type of intervention called “boosting,” which shows the promise of generalized and lasting behavioral change. The government can use these tools to shape public policy. Behavioral interventions such as policy-making tools have their boundaries, as does the law. We argue that nudging and boosting may serve as active aids in support of the legal system under certain circumstances. Nudging and boosting can also support the legal system especially in relation to emerging social issues or events that are unprecedented, such as the recent COVID-19 pandemic, where certain behavioral patterns are expected, but it would be hard or impossible to enforce them through the law alone.

🖺 Full Text HTML: Tools for Public Health Policy: Nudges and Boosts as Active Support of the Law in Special Situations such as the COVID-19 Pandemic

SequenceBouncer: A method to remove outlier entries from a multiple sequence alignment -

Phylogenetic analyses can take advantage of multiple sequence alignments as input. These alignments typically consist of homologous nucleic acid or protein sequences, and the inclusion of outlier or aberrant sequences can compromise downstream analyses. Here, I describe a program, SequenceBouncer, that uses the Shannon entropy values of alignment columns to identify and remove outlier entries in a manner responsive to overall alignment context. I demonstrate the utility of this software using alignments of mammalian reference mitochondrial genomes, bird cytochrome c oxidase-derived sequence barcodes, and COVID-19 sequences.

🖺 Full Text HTML: SequenceBouncer: A method to remove outlier entries from a multiple sequence alignment

Adherance to Public Health Measures in Adolescents versus Adults duing the COVID-19 Pandemic in Canada -

To mitigate the burden of COVID-19 on healthcare systems and to reduce infections and associated deaths, public health measures including physical distancing and mask-wearing have been recommended. We know little regarding important predictors of adherence and motivation to engage in public guidelines among at-risk populations, such as adolescents. Objectives. The purpose of the present study was to examine differences in adherence to public health measures across provinces, and to examine developmental differences in both adherence and motivations to engage in public health among adolescents and adults across Canada during the COVID-19 pandemic. Methods. Participants from two samples, including adolescents (N=788, 56.7% female, M=15.68, SD=1.36) and adults (N=578, 94.6% female; M=45.12, SD=5.83) completed online quesionnaires during the summer 2020. Results. Both adolescents and adults in provinces mandating masks were more likely to wear a mask. There were no provincial differences in adherence to social distancing. Adolescents were more likely to be motivated by social reasons, while adults were motivated by social responsibility. For both adults and adoeslcents, social responsibility was associated with more adherence to public health measures, while social concerns(e.g., maintaining social ties, social judgment) was associated with less adherence. Conclusion. Adherence to public health measures was mixed, with most participants reporting socializing in-person with people outside of their home. At the time of the survey, provincial mask mandates were associated with more mask-wearing. Results also suggest social responsibility was the main predictor of increased adherence to public health measures.

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‘Phytopathological strolls’ in the dual context of COVID-19 lockdown and IYPH2020: transforming constraints into an opportunity for public education about plant pathogens -

The experience presented here relates to 2020, a particularly timely year for plant disease-related communication (‘International Year of Plant Health’ IYPH2020), but also a unique year because of the COVID-19 pandemic. Our goal was to illustrate the diversity and beauty of fungal plant pathogens through a naturalist approach that could be followed by any amateur. We achieved this end through ‘phytopathological strolls’, in which we observed and determined the origin of symptoms on diseased plants found in our garden, in the local streets, in nearby open spaces, and sharing this matter with a broad public. The lockdown imposed in France created an additional motivation to take up the challenge, and to involve our children, even under strong constraints, such as movement restrictions. We observed and described fungal pathogens through hundreds of photographs, shared our findings with a large audience on Twitter, and received feedback. The material used was deliberately simple and transportable: a digital reflex camera, an old microscope, a mobile phone, some books and an Internet connexion. Between March 17, 2020 and June 20, 2021 we found 196 plant pathogens, including 97 rusts, 27 powdery mildews and 28 septoria-like diseases. We discuss here the importance of promoting searches for plant pathogens, their description and conservation, through a combination of classical approaches and digital tools in tune with the times, such as Twitter, by treating pathogen identification like a detective game and, more surprisingly, by making use of the addictive nature of collection approaches, drawing a parallel with Pokemon Go.

🖺 Full Text HTML: ‘Phytopathological strolls’ in the dual context of COVID-19 lockdown and IYPH2020: transforming constraints into an opportunity for public education about plant pathogens

The Knowledge and Attitude of Physicians Regarding Vaccinations in Yerevan, Armenia: Challenges for COVID-19 -

Background This primary-data analysis investigates the current level of awareness and medical knowledge of physicians in 20 health facilities in Yerevan, Armenia regarding vaccination, specifically with regard to HPV infection and the recently-introduced Gardasil vaccine used against HPV infection that may have implications for successful roll-outs of national programmes for new vaccines, including those for COVID-19. Methods A questionnaire-based cross-sectional study was completed by 348 physicians who met the study inclusion criteria, from 20 out of 36 randomly selected healthcare facilities in Yerevan, Armenia, between Dec 2017 to Sep 2018. The aim of the questionnaire was to identify physicians awareness of and attitudes to HPV-related cervical cancer and the Gardasil vaccine. Responses were analysed using SPSS software (Version 16). Results The responding physicians displayed a respectable level of knowledge and awareness regarding vaccination with regard to some characteristics (e.g. more than 81% knew that HPV infection was commonly asymptomatic, 87% were knew that HPV infection was implicated in most cervical cancers and 87% knew that cervical cancer is the most prevalent cancer amongst women) but low knowledge in others and poor understanding of key issues such as the age at which women were most likely to develop cervical cancer (only 15% answered correctly); whether or not the vaccine should be administered to people who had already been affected (27% answered correctly) and whether sexually active young people should be treated for infection before vaccination (26%). Lack of confidence within the surveyed groups regarding the value of vaccination and, in particular concerns over the reasons for administering it to certain age cohorts, was driven by misconceptions. Conclusions Armenian physicians awareness of vaccine characteristics, the reasons for their inclusion in the national vaccination programme and the characteristics of the diseases they treat can be poor. The study further suggests that drivers of vaccine hesitancy are complex, may not be consistent from vaccine to vaccine, and may vary from generation to generation. The Armenian healthcare sector may need to provide additional training, awareness-raising and educational activities to improve understanding of and trust in vaccination programmes. Further studies are warranted to better understand knowledge, attitudes and practices (KAP) regarding immunization and vaccination programmes amongst Armenian healthcare workers.

🖺 Full Text HTML: The Knowledge and Attitude of Physicians Regarding Vaccinations in Yerevan, Armenia: Challenges for COVID-19

Detection of antibodies neutralizing historical and emerging SARS-CoV-2 strains using a thermodynamically coupled de novo biosensor system -

With global vaccination efforts against SARS-CoV-2 underway, there is a need for rapid quantification methods for neutralizing antibodies elicited by vaccination and characterization of their strain dependence. Here, we describe a designed protein biosensor that enables sensitive and rapid detection of neutralizing antibodies against wild type and variant SARS-CoV-2 in serum samples. More generally, our thermodynamic coupling approach can better distinguish sample to sample differences in analyte binding affinity and abundance than traditional competition based assays.

🖺 Full Text HTML: Detection of antibodies neutralizing historical and emerging SARS-CoV-2 strains using a thermodynamically coupled de novo biosensor system

Cytoplasmic tail truncation of SARS-CoV-2 Spike protein enhances titer of pseudotyped vectors but masks the effect of the D614G mutation -

The high pathogenicity of SARS-CoV-2 requires it to be handled under biosafety level 3 conditions. Consequently, Spike protein pseudotyped vectors are a useful tool to study viral entry and its inhibition, with retroviral, lentiviral (LV) and vesicular stomatitis virus (VSV) vectors the most commonly used systems. Methods to increase the titer of such vectors commonly include concentration by ultracentrifugation and truncation of the Spike protein cytoplasmic tail. However, limited studies have examined whether such a modification also impacts the proteins function. Here, we optimized concentration methods for SARS-CoV-2 Spike pseudotyped VSV vectors, finding that tangential flow filtration produced vectors with more consistent titers than ultracentrifugation. We also examined the impact of Spike tail truncation on transduction of various cell types and sensitivity to convalescent serum neutralization. We found that tail truncation increased Spike incorporation into both LV and VSV vectors and resulted in enhanced titers, but had no impact on sensitivity to convalescent serum inhibition. In addition, we analyzed the effect of the D614G mutation, which became a dominant SARS-CoV-2 variant early in the pandemic. Our studies revealed that, similar to the tail truncation, D614G independently increases Spike incorporation and vector titers, but that this effect is masked by also including the cytoplasmic tail truncation. Therefore, the use of full-length Spike protein, combined with tangential flow filtration, is recommended as a method to generate high titer pseudotyped vectors that retain native Spike protein functions.

🖺 Full Text HTML: Cytoplasmic tail truncation of SARS-CoV-2 Spike protein enhances titer of pseudotyped vectors but masks the effect of the D614G mutation

Coverage and effectiveness of mRNA SARS-CoV-2 vaccines among United States Veterans -

Importance: The scope of vaccination rollout and effectiveness of mRNA SARS-CoV-2 vaccines in the United States (US), and US Veterans specifically, has not been fully assessed. Objective: To estimate receipt of SARS-CoV-2 vaccines, and vaccine effectiveness (VE) against SARS-CoV-2 infection, subsequent disease-related severity and mortality. Design, Setting, and Participants: First, receipt of any SARS-CoV-2 vaccine by March 7, 2021 was described for all enrolled and alive Veterans within the Veterans Health Administration (VHA). Second, to evaluate mRNA SARS-CoV-2 VE, a matched test negative case-control evaluation was conducted across all VHA facilities utilizing SARS-CoV-2 positive (cases [n=16,690]) and negative (controls [n=61,610]) tests from Veterans aged ≥18 years old who routinely sought care at a VHA facility and were tested for SARS-CoV-2 from December 14, 2020, through March 14, 2021. Exposures: Vaccination histories were obtained from pharmacy and medical records to determine if patients were unvaccinated, partially vaccinated (from 7 days after first dose until day of second dose of mRNA SARS-CoV-2 vaccine), or fully vaccinated (from 7 days after second dose of mRNA SARS-CoV-2 vaccine) at time of SARS-CoV-2 test. Main Outcome Measures: Primary outcomes were (1) vaccine receipt among Veterans and specific subpopulations, (2) VE calculated from odds ratios (ORs) with 95% confidence intervals (95% CI) for the association between SARS-CoV-2 infection and full vs. no vaccination, and (3) VE against infection for partial vs. no vaccination. VE against COVID-19-related hospitalization and death were also estimated. Results: By March 7, 2020, among 6,170,750 Veterans, 1,547,045 (23.1%) received at least one SARS-CoV-2 vaccine. Based on the analysis of mRNA SARS-CoV-2 vaccines, VE against infection was 93.7% (95% CI 92.0-95.0) and 57.7% (95% CI 53.5-61.5) for full and partial vaccination (vs. no vaccination), respectively. VE was similar for subpopulations. VE against COVID-19-related hospitalization and death for full vs. no vaccination was 90.7% (95% CI 90.0-91.3) and 94.7% (95% CI 91.3-98.1), respectively. Conclusion and Relevance: Vaccines are effective in reducing SARS-CoV-2 infections and disease-related severity and mortality in the Veteran population. Effective vaccine, as well as their efficient and equitable distribution, are important for reducing COVID-19 disease burden among Veterans.

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Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic -

The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH’s Sequence Read Archive. I recover the deleted files from the Google Cloud, and reconstruct partial sequences of 13 early epidemic viruses. Phylogenetic analysis of these sequences in the context of carefully annotated existing data suggests that the Huanan Seafood Market sequences that are the focus of the joint WHO-China report are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2’s bat coronavirus relatives.

🖺 Full Text HTML: Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic

Estimating Vaccination Effects on COVID-19 outbreak course in Japan -

Background: Japan started vaccinations for COVID-19 in late February, 2021, mainly using BNT162b2 mRNA COVID-19 Vaccine. Object: We evaluated COVID-19 vaccination effects on infectiousness in Japan. Method: The effective reproduction number R(t) was regressed on vaccine coverage along with data of temperature, humidity, mobility, and countermeasures. We presumed two definitions for vaccine coverage: at least a single dose with a 12-day delay and a second dose. The study period was February, 2020 through May 16, 2021. Results: Estimation results indicate that vaccine coverage significantly and drastically reduced R(t) for both definitions. Results imply that increased first shot coverage by 1% point decreased R(t) by 0.5 with a 12 day delay. Moreover, increased second shot coverage by 1% point, decreased R(t) by 1 immediately. Discussion and Conclusion: Vaccination effects might be stronger because the periods when vaccination was started and rapid spread coincide with a decreasing phase of R(t).

🖺 Full Text HTML: Estimating Vaccination Effects on COVID-19 outbreak course in Japan

Association between overcrowded households, multigenerational households, and COVID-19: a cohort study -

Introduction: The role of overcrowded and multigenerational households as a risk factor for COVID-19 remains unmeasured. The objective of this study is to examine and quantify the association between overcrowded and multigenerational households, and COVID-19 in New York City (NYC). Methods: We conducted a Bayesian ecological time series analysis at the ZIP Code Tabulation Area (ZCTA) level in NYC to assess whether ZCTAs with higher proportions of overcrowded (defined as proportion of estimated number of housing units with more than one occupant per room) and multigenerational households (defined as the estimated percentage of residences occupied by a grandparent and a grandchild less than 18 years of age) were independently associated with higher suspected COVID-19 case rates (from NYC Department of Health Syndromic Surveillance data for March 1 to 30, 2020). Our main measure was adjusted incidence rate ratio (IRR) of suspected COVID-19 cases per 10,000 population. Our final model controlled for ZCTA-level sociodemographic factors (median income, poverty status, White race, essential workers), prevalence of clinical conditions related to COVID-19 severity (obesity, hypertension, coronary heart disease, diabetes, asthma, smoking status, and chronic obstructive pulmonary disease), and spatial clustering. Results: 39,923 suspected COVID-19 cases presented to emergency departments across 173 ZCTAs in NYC. Adjusted COVID-19 case rates increased by 67% (IRR 1.67, 95% CI = 1.12, 2.52) in ZCTAs in quartile four (versus one) for percent overcrowdedness and increased by 77% (IRR 1.77, 95% CI = 1.11, 2.79) in quartile four (versus one) for percent living in multigenerational housing. Interaction between both exposures was not significant (βinteraction = 0.99, 95% CI: 0.99-1.00). Conclusions: Over-crowdedness and multigenerational housing are independent risk factors for suspected COVID-19. In the early phase of surge in COVID cases, social distancing measures that increase house-bound populations may inadvertently but temporarily increase SARS-CoV-2 transmission risk and COVID-19 disease in these populations.

🖺 Full Text HTML: Association between overcrowded households, multigenerational households, and COVID-19: a cohort study

Did social factors buffer against the effect of adversities on self-harm during the COVID-19 pandemic? A longitudinal analysis of 49,227 UK adults -

Background: Little is known about which factors exacerbate and buffer the impact of COVID-19 -related adversities on changes in thinking about and engaging in self-harm over time. Aims: To examine how changes in four social factors contribute to changes in self-harm thoughts and behaviours over time and how these factors in turn interact with adversities and worries about adversities to increase risk for these outcomes. Method: Data from 49,227 UK adults in the UCL COVID-19 Social Study were analysed across the first 59 weeks of the pandemic. Fixed effects logistic regressions examined time-varying associations between social support quality, loneliness, number of days of face-to-face contact for > 15 minutes, and number of days phoning/video calling for >15 minutes with self-harm thoughts and behaviours. We then examined how these four factors in turn interacted with the total number of adversities and worries about adversity on outcomes. Results: Increases in the quality of social support decreased the likelihood of both outcomes, whilst greater loneliness increased their likelihood. Associations were inconsistent for telephone/video contact and face-to-face contact with outcomes. Social support buffered and loneliness exacerbated the impact of adversity experiences with self-harm behaviours. Other interactions were inconsistent, and some were in the unexpected direction. Conclusions: These findings suggest the importance of the quality of social support, rather than the mere presence of contact, is important for reducing the likelihood of self-harm behaviours in the context of COVID-19 pandemic-related adversity and worry.

🖺 Full Text HTML: Did social factors buffer against the effect of adversities on self-harm during the COVID-19 pandemic? A longitudinal analysis of 49,227 UK adults

An Extended Susceptible-Exposed-Infected-Recovered (SEIR) Model with Vaccination for Forecasting the COVID-19 Pandemic in Sri Lanka -

The role of modelling in predicting the spread of an epidemic is important for health planning and policies. This study aims to apply a compartmental model for predicting the variations of epidemiological parameters in Sri Lanka. We used a dynamic Susceptible-Exposed-Infected-Recovered-Vaccinated (SEIRV) model, and simulated for potential vaccine strategies under a range of epidemic conditions. The predictions were based on different vaccination coverages (5% to 90%), vaccination-rates (1%, 2%, 5%) and vaccine-efficacies (40%, 60%, 80%) under different R0 (2,4,6). We observed how the above dynamics influenced the SEIRV model without COVID-19 vaccination at different R0 values, and estimated the duration, exposed and infected populations. When the R0 was increased, the days of reduction of susceptibility and the days to reach the peak of the infection were reduced gradually. At least 45% vaccine coverage is required for reducing the infected population as early as possible. The results revealed that when R0 is increased in the SEIRV model along with the increase of vaccination efficacy and vaccination rate, the population to be vaccinated is reducing. Thus, the vaccination offers greater benefits to the local population by reducing the time to reach the peak, exposed and infected population through flattening the curves.

🖺 Full Text HTML: An Extended Susceptible-Exposed-Infected-Recovered (SEIR) Model with Vaccination for Forecasting the COVID-19 Pandemic in Sri Lanka

Continuous Positive Airway Pressure (CPAP) for Moderate to Severe Covid19 Acute Respiratory Distress Syndrome (CARDS) in a Resource limited setting -

Covid19 Acute Respiratory Distress Syndrome (CARDS) poses a challenge in management particularly due to limited capacity of ventilated intensive care beds and staffing, and this is exacerbated in resource poor settings with poor patient outcomes. Within this context CPAP has been trialled for CARDS although mainly in resource rich settings. This study retrospectively analyses the survival outcomes and characteristics of a cohort of patients with moderate to severe CARDS were treated exclusively with CPAP in a rural secondary level hospital in Pakistan with limited previous critical care expertise. 32 out of the 41 patients (78%) who were treated with CPAP survived overall (30/37 (81%) who were treated according to protocol), suggesting non inferiority to CARDS outcomes of critical care units employing Intubation and Mechanical Ventilation (IMV) in resource rich settings. This suggests CPAP should be promoted as an efficacious and cost-effective method for treating CARDS within the context of the pandemic surge of Covid19 in resource poor settings.

🖺 Full Text HTML: Continuous Positive Airway Pressure (CPAP) for Moderate to Severe Covid19 Acute Respiratory Distress Syndrome (CARDS) in a Resource limited setting

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