bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2
Authors: Smithgall Marie C. , Scherberkova Ioana , Whittier Susan , Green Daniel A.
Published: April 2020

The SARS-CoV-2 pandemic has created an urgent and unprecedented need for rapid large-scale diagnostic testing to inform timely patient management. This study compared two recently-authorized rapid tests, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID Now SARS-CoV-2 to the Roche cobas SARS-CoV-2 assay. A total of 113 nasopharyngeal swabs were tested, including 88 positives spanning the full range of observed Ctvalues on the cobas assay. Compared to cobas, the overall positive agreement was 73.9% with ID Now and 98.9% with Xpert. Negative agreement was 100% and 92.0% for ID Now and Xpert, respectively. Both ID Now and Xpert showed 100% positive agreement for medium and high viral concentrations (Ctvalue <30). However, for Ctvalues >30, positive agreement was 34.3% for ID Now and 97.1% for Xpert. These findings highlight an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Further studies are needed to evaluate the performance of ID Now for direct swabs.
Self-amplifying RNA SARS-CoV-2 lipid nanoparticle vaccine induces equivalent preclinical antibody titers and viral neutralization to recovered COVID-19 patients
Authors: McKay Paul F. , Hu Kai , Blakney Anna K. , Samnuan Karnyart , Bouton Clément R. , Rogers Paul , Polra Krunal , Lin Paulo J.C. , Barbosa Christopher , Tam Ying , Shattock Robin J.
Published: April 2020

The spread of the SARS-CoV-2 into a global pandemic within a few months of onset motivates the development of a rapidly scalable vaccine. Here, we present a self-amplifying RNA encoding the SARS-CoV-2 spike protein encapsulated within a lipid nanoparticle as a vaccine and demonstrate induction of robust neutralization of a pseudo-virus, proportional to quantity of specific IgG and of higher quantities than recovered COVID-19 patients. These data provide insight into the vaccine design and evaluation of immunogenicity to enable rapid translation to the clinic.
rdmc: an open source R package implementing convergent adaptation models of Lee and Coop (2017)
Authors: Tittes Silas
Published: April 2020

The availability of whole genome sequencing data from multiple related populations creates opportunities to test sophisticated population genetic models of convergent adaptation. Recent work by Lee and Coop (2017) developed models to infer modes of convergent adaption at local genomic scales, providing a rich framework for assessing how selection has acted across multiple populations at the tested locus. Here I present,rdmc, an R package that builds on the existing software implementation of Lee and Coop (2017) that prioritizes ease of use, portability, and scalability. I demonstrate installation and comprehensive overview of the package’s current utilities.
Inequality in acute respiratory infection outcomes in the United States: A review of the literature and its implications for public health policy and practice
Authors: Moran Elizabeth , Kubale John , Noppert Grace , Malosh Ryan , Zelner Jon
Published: April 2020

Seasonal and pandemic respiratory viruses such as influenza and the novel coronavirus (SARS-COV-2) currently sweeping the globe have often been described as ‘equal opportunity infectors’, implying little socioeconomic disparity in susceptibility. However, early data from the COVID-19 pandemic has underscored that the burden of respiratory viruses actually reflect and magnify existing socioeconomic inequalities. We review the literature on socioeconomic and racial disparities in acute respiratory infection (ARI), as well as ARI-associated hospitalization and mortality. Our goal is to identify key principles of the relationship between socioeconomic inequality and ARI outcomes, as well as highlighting poorly understood areas that need to be addressed by research and policy in the wake of the COVID-19 pandemic. We find that there has been descriptive work in this area, but that there is a distinct lack of cohesive methodology in the literature exploring social determinants and ARI. We propose the fundamental cause theory is a useful framework for guiding future research of disparities in ARI and for the design of interventions to alleviate these disparities.
Taking Account of Asymptomatic Infections – A Modeling Study on the COVID-19 Outbreak on the Diamond Princess Cruise Ship
Authors: Huang Li-Shan , Li Li , Dunn Lucia , He Mai
Published: April 2020

Background

The COVID-19 outbreak on the Diamond Princess (DP) cruise ship provided empirical data to study the transmission potential of COVID-19 under quarantine with the presence of asymptomatic cases.

Methods

We studied the changes in R0 on the DP from January 21 to February 19, 2020 based on chain-binomial models under two scenarios: no quarantine assuming a random mixing condition, and quarantine of passengers in cabins — passengers may get infected either by an infectious case in a shared cabin or by asymptomatic crew who continued to work.

Results

Estimates of R0 at the beginning of the epidemic were 3.27 (95% CI, 3.02-3.54) and 3.78 (95% CI, 3.49-4.09) respectively for serial intervals of 5 and 6 days; and when quarantine started, with the reported asymptomatic ratio 0.505, R0 rose to 4.18 (95%CI, 3.86-4.52) and 4.73 (95%CI, 4.37-5.12) respectively for passengers who might be exposed to the virus due to contacts with asymptomatic crew. The overall R0 for both crew and passengers was decreased to 2.55 (95%CI, 2.36-2.76) and 2.90 (95% CI, 2.67-3.13). Results show that the higher the asymptomatic ratio is, the more infectious contacts would happen.

Conclusions

We find evidence to support a US CDC report that “a high proportion of asymptomatic infections could partially explain the high attack rate among cruise ship passengers and crew.” Our study suggests that the effects of quarantine may be limited if the asymptomatic ratio is high, implying that a combination of preventive measures is needed to stop the spread of virus.
Clinical utility of genetic and genomic testing in the precision diagnosis and management of pediatric patients with kidney and urinary tract diseases
Authors: Bekheirnia Nasim , Glinton Kevin E. , Rossetti Linda , Manor Joshua , Chen Wuyan , Lamb Dolores J. , Braun Michael C. , Bekheirnia Mir Reza
Published: April 2020

As genetic and genomic testing increasingly integrates into the practice of nephrology, our understanding of the basis of many kidney disorders has exponentially increased. Given this, we recently initiated a Renal Genetics Clinic (RGC) at our large, urban children’s hospital for patients with either a personal or strong family history of renal disorders. Genetic testing was performed in Clinical Laboratory Improvement Amendments (CLIA) certified laboratories using single gene testing, multi-gene panels, chromosomal microarray (CMA), or exome sequencing (ES). A total of 192 patients (185 probands) were evaluated in this clinic, with cystic kidney disease (49/192) being the most common reason for referral followed by Congenital Anomalies of the Kidney and Urinary Tract (CAKUT: 41/192) and hematuria (38/192). Genetic testing was performed for 153 probands with an overall diagnostic yield of 75/153 (49%). In the patients who reached a molecular diagnosis, 13/75 (17.3%), medical or surgical treatment of the patients were impacted, and in 12/75 (16%), previous clinical diagnoses were changed to more accurate molecular diagnoses. Such testing provided an accurate diagnosis for children and in some cases led to further diagnosis in seemingly asymptomatic family members and changes to overall medical management. Molecular testing, as facilitated by such a specialized clinical setting, thus appears to have clear utility in the diagnosis and counseling of patients with a wide range of renal manifestations.
Non-Linear Fitting of Sigmoidal Growth Curves to predict a maximum limit to the total number of COVID-19 cases in the United States
Authors: Dutra Carlos Maximiliano
Published: April 2020

In the present work is used non-linear fitting of the “Gompert” and “Logistic” growth models to the number of total COVID-19 cases from the United States as a country and individually by states. The methodology allowed us to estimate that the maximum limit for the total number of cases of COVID-19 patients such as those registered with the World Health Organization will be approximately one million and one hundred thousand cases to the United States. Up to 04/19/20 the models indicate that United States reached 70% of this maximum number of “total cases” and the United States will reach 95% of this limit by 05/14/2020. The application of the nonlinear fitting of growth curves to the individual data of each American state showed that only 25% of them did not reach, on 04/19/20, the percentage of 59% of the maximum limit of “total cases” and that 17 of the 50 states still will not have reached 95% of that limit on 05/14/20.
Antibody tests in detecting SARS-CoV-2 infection: a meta-analysis
Authors: Kontou Panagiota I , Braliou Georgia G , Dimou Niki L , Nikolopoulos Georgios , Bagos Pantelis G
Published: April 2020

Background

With the emergence of SARS-CoV-2 and the associated Coronavirus disease 2019 (COVID-19), there is an imperative need for diagnostic tests that can identify the infection. Although Nucleic Acid Test (NAT) is considered to be the gold standard, serological tests based on antibodies could be very helpful. However, individual studies measuring the accuracy of the various tests are usually underpowered and inconsistent, thus, a comparison of different tests is needed.

Methods

We performed a systematic review and meta-analysis following the PRISMA guidelines. We conducted the literature search in PubMed, medRxiv and bioRxiv. For the statistical analysis we used the bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities. We evaluated IgM and IgG tests based on Enzyme-linked immunosorbent assay (ELISA), Chemiluminescence Enzyme Immunoassays (CLIA), Fluorescence Immunoassays (FIA) and the point-of-care (POC) Lateral Flow Immunoassays (LFIA) that are based on immunochromatography.

Findings

In total, we identified 38 eligible studies that include data from 7,848 individuals. The analyses showed that tests using the S antigen are more sensitive than N antigen-based tests. IgG tests perform better compared to IgM ones, and show better sensitivity when the samples were taken longer after the onset of symptoms. Moreover, irrespective of the method, a combined IgG/IgM test seems to be a better choice in terms of sensitivity than measuring either antibody type alone. All methods yielded high specificity with some of them (ELISA and LFIA) reaching levels around 99%. ELISA- and CLIA-based methods performed better in terms of sensitivity (90-94%) followed by LFIA and FIA with sensitivities ranging from 80% to 86%.

Interpretation

ELISA tests could be a safer choice at this stage of the pandemic. POC tests (LFIA), that are more attractive for large seroprevalence studies show high specificity but lower sensitivity and this should be taken into account when designing and performing seroprevalence studies.

Funding

None
Machine learning algorithm for early mortality prediction in patients with advanced penile cancer
Authors: Chen Robert , Kudelka Matthew R , Rosado Aaron M , Zhang James
Published: April 2020

Penile cancer remains a rare cancer with an annual incidence of 1 in 100,000 men in the United States, accounting for 0.4-0.6% of all malignancies. Furthermore, to date there are no predictive models of early mortality in penile cancer. Meanwhile, machine learning has potential to serve as a prognostic tool for patients with advanced disease.

We developed a machine learning model for predicting early mortality in penile cancer (survival less than 11 months after initial diagnosis. A cohort of 88 patients with advanced penile cancer was extracted from the Surveillance, Epidemiology and End Results (SEER) program. In the cohort, patients with advanced penile cancer exhibited a median overall survival of 21 months, with the 25th percentile of overall survival being 11 months. We constructed predictive features based on patient demographics, staging, metastasis, lymph node biopsy criteria, and metastatic sites. We trained a multivariate logistic regression model, tuning parameters with respect to regularization, and feature selection criteria.

Upon evaluation with 5-fold cross validation, our model achieved 68.2% accuracy with AUC 0.696. Criteria for advanced staging (T4, group stage IV), as well as higher age, white race and squamous cell histology, were the most predictive of early mortality. Tumor size was the strongest negative predictor of early mortality.

Our study showcases the first known predictive model for early mortality in patients with advanced penile cancer and should serve as a framework for approaching the clinical problem in future studies. Future work should aim to incorporate other data sources such as genomic and metabolomic data, increase patient counts, incorporate clinical characteristics such as ECOG and RECIST criteria, and assess the performance of the model in a prospective fashion.
Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes
Authors: Lopera Esteban , van der Graaf Adriaan , Lanting Pauline , van der Geest Marije ,   Lifelines Cohort Study, Fu Jingyuan , Swertz Morris , Franke Lude , Wijmenga Cisca , Deelen Patrick , Zhernakova Alexandra , Sanna Serena
Published: April 2020

Coronavirus disease 2019 (COVID-19) shows a wide variation in expression and severity of symptoms, from very mild or no symptomes, to flu-like symptoms, and in more severe cases, to pneumonia, acute respiratory distress syndrome and even death. Large differences in outcome have also been observed between males and females. The causes for this variability are likely to be multifactorial, and to include genetics. The SARS-CoV-2 virus responsible for the infection uses the human receptor angiotensin converting enzyme 2 (ACE2) for cell invasion, and the serine protease TMPRSS2 for S protein priming. Genetic variation in these two genes may thus modulate an individual’s genetic predisposition to infection and virus clearance. While genetic data on COVID-19 patients is being gathered, we carried out a phenome-wide association scan (PheWAS) to investigate the role of these genes in other human phenotypes in the general population. We examined 178 quantitative phenotypes including cytokines and cardio-metabolic biomarkers, as well as 58 medications in 36,339 volunteers from the Lifelines population biobank, in relation to 1,273 genetic variants located in or near ACE2 and TMPRSS2. While none reached our threshold for significance, we observed a suggestive association of polymorphisms within the ACE2 gene with (1) the use of angiotensin II receptor blockers (ARBs) combination therapies (p=5.7×10−4), an association that is significantly stronger in females (pdiff=0.01), and (2) with the use of non-steroid anti-inflammatory and antirheumatic products (p=5.5×10−4). While these associations need to be confirmed in larger sample sizes, they suggest that these variants play a role in diseases such as hypertension and chronic inflammation that are often observed in the more severe COVID-19 cases. Further investigation of these genetic variants in the context of COVID-19 is thus promising for better understanding of disease variability. Full results are available at https://covid19research.nl.
Heat treatment for reuse of disposable respirators during Covid-19 pandemic: Is filtration and fit adversely affected?
Authors: Loh Miranda , Clark Ross , Cherrie John
Published: April 2020

A number of methods for decontaminating disposable filtering face piece respirators have been explored for use in health care settings during epidemics where respirators are in short supply, such as the current Covid-19 pandemic. Heating to temperatures above 65°C has been shown to successfully inactivate the SARS-CoV-2 virus on various surfaces. Ovens or similar heating devices are likely already widely available in hospitals globally. We did a quantitative fit test on nine models of FFP2 and FFP3 respirators before and after heat treatment in an oven. These included both flat fold and moulded cup styles. All passed the initial fit test, and all but two passed the post-treatment fit test. This study demonstrates that FFP respirators can still retain both filtration efficiency and fit after wear and heat treatment, but that it is necessary to understand the probability for failure of fit after decontamination. Heat shows promise as a simple and effective way of treating FFP respirators. Further evaluation of longer-term wear and disinfection effectiveness of heat treatment should be done before widespread use.
White matter variability, cognition, and disorders: a systematic review
Authors: Forkel Stephanie J. , Friedrich Patrick , de Schotten Michel Thiebaut , Howells Henrietta
Published: April 2020

Inter-individual differences can inform treatment procedures and - if accounted for - have the potential to significantly improve patient outcomes. However, when studying brain anatomy, these inter-individual variations are commonly unaccounted for, despite reports of differences in gross anatomical features, cross-sectional and connectional anatomy. Brain connections are essential to facilitate functional organisation and, when severed, cause impairments or complete loss of function. Hence the study of cerebral white matter may be an ideal compromise to capture inter-individual variability in structure and function. We reviewed the wealth of studies that associate functions and clinical symptoms with individual tracts using diffusion tractography. Our systematic review indicates that tractography has proven to be a sensitive method in neurology, psychiatry, and healthy populations to identify variability and its functional correlates. However, the literature may be biased, as we determined that the most commonly studied tracts are not necessarily those with the highest sensitivity to cognitive functions and pathologies. Additionally, the hemisphere of the studied tract is often unreported, thus neglecting functional laterality and asymmetries. Finally, we demonstrate that tracts, as we define them, are not usually correlated with only one, but rather multiple cognitive domains or pathologies. While our systematic review identified some methodological caveats, it also suggests that tract-function correlations might be a promising biomarker for precision medicine. It characterises variations in brain anatomy, differences in functional organisation, and predicts resilience and recovery in patients.
Detection of COVID-19 Infection from Routine Blood Exams with Machine Learning: a Feasibility Study
Authors: Brinati Davide , Campagner Andrea , Ferrari Davide , Locatelli Massimo , Banfi Giuseppe , Cabitza Federico
Published: April 2020

Background

The COVID-19 pandemia due to the SARS-CoV-2 coronavirus, in its first 4 months since its outbreak, has to date reached more than 200 countries worldwide with more than 2 million confirmed cases (probably a much higher number of infected), and almost 200,000 deaths. Amplification of viral RNA by (real time) reverse transcription polymerase chain reaction (rRT-PCR) is the current gold standard test for confirmation of infection, although it presents known shortcomings: long turnaround times (3-4 hours to generate results), potential shortage of reagents, false-negative rates as large as 15-20%, the need for certified laboratories, expensive equipment and trained personnel. Thus there is a need for alternative, faster, less expensive and more accessible tests.

Material and methods

We developed two machine learning classification models using hematochemical values from routine blood exams (namely: white blood cells counts, and the platelets, CRP, AST, ALT, GGT, ALP, LDH plasma levels) drawn from 279 patients who, after being admitted to the San Raffaele Hospital (Milan, Italy) emergency-room with COVID-19 symptoms, were screened with the rRT-PCR test performed on respiratory tract specimens. Of these patients, 177 resulted positive, whereas 102 received a negative response.

Results

We have developed two machine learning models, to discriminate between patients who are either positive or negative to the SARS-CoV-2: their accuracy ranges between 82% and 86%, and sensitivity between 92% e 95%, so comparably well with respect to the gold standard. We also developed an interpretable Decision Tree model as a simple decision aid for clinician interpreting blood tests (even off-line) for COVID-19 suspect cases.

Discussion

This study demonstrated the feasibility and clinical soundness of using blood tests analysis and machine learning as an alternative to rRT-PCR for identifying COVID-19 positive patients. This is especially useful in those countries, like developing ones, suffering from shortages of rRT-PCR reagents and specialized laboratories. We made available a Web-based tool for clinical reference and evaluation1.
Model the transmission dynamics of COVID-19 propagation with public health intervention
Authors: Mamo Dejen Ketema
Published: April 2020

In this work, a researcher develop SHEIQRD (Susceptible-Stay at home-Exposed-Infected-Quarantine-Recovery-Death) coronavirus pandemic spread model. The disease-free and endemic equilibrium points are calculated and analyzed. The basic reproductive number ℛ0 is derived and its sensitivity analysis is done. COVID-19 pandemic spread is die out when ℛ0 ≤ 1 and its persist in the community whenever ℛ0 > 1. Efficient stay at home rate, high coverage of precise identification and isolation of expose and infected individuals, and redaction of transmission and stay at home return rate can be mitigate the pandemics. Finally, theoretical analysis and numerical results are consistent.
Modelling the transmission dynamics of COVID-19 in six high burden countries
Authors: Rahman Azizur , Kuddus Md Abdul
Published: April 2020

The new coronavirus disease, officially known as COVID-19, originated in China in 2019 and has since spread around the globe. We presented a modified Susceptible-Latent-Infected-Removed (SLIR) compartmental model of COVID-19 disease transmission with nonlinear incidence during the epidemic period. We provided the model calibration to estimate parameters with day wise corona virus (COVID-19) data i.e. reported cases by worldometer from the period of 15th February to 30th March, 2020 in six high burden countries including Australia, Italy, Spain, USA, UK and Canada. We estimate transmission rates for each countries and found that the highest transmission rate country in Spain, which may be increase the new cases and deaths in Spain than the other countries. Sensitivity analysis was used to identify the most important parameters through the partial rank correlation coefficient method. We found that the transmission rate of COVID-19 had the largest influence on the prevalence. We also provides the prediction of new cases in COVID-19 until May 18, 2020 using the developed model and recommends, control strategies of COVID-19. The information that we generated from this study would be useful to the decision makers of various organizations across the world including the Ministry of Health in Australia, Italy, Spain, USA, UK and Canada to control COVID-19.
SARS-CoV-2 RNA titers in wastewater anticipated COVID-19 occurrence in a low prevalence area
Authors: Randazzo Walter , Truchado Pilar , Cuevas-Ferrando Enric , Simón Pedro , Allende Ana , Sánchez Gloria
Published: April 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 200,000 reported COVID-19 cases in Spain resulting in more than 20,800 deaths as of April 21, 2020. Faecal shedding of SARS-CoV-2 RNA from COVID-19 patients has extensively been reported. Therefore, we investigated the occurrence of SARS-CoV-2 RNA in six wastewater treatments plants (WWTPs) serving the major municipalities within the Region of Murcia (Spain), the area with the lowest COVID-19 prevalence within Iberian Peninsula. Firstly, an aluminum hydroxide adsorption-precipitation concentration method was tested using a porcine coronavirus (Porcine Epidemic Diarrhea Virus, PEDV) and mengovirus (MgV). The procedure resulted in average recoveries of 10.90 ± 3.54% and 10.85 ± 2.11% in influent water and 3.29 ± 1.58% and 6.19 ± 1.00% in effluent water samples for PEDV and MgV, respectively. Then, the method was used to monitor the occurrence of SARS-CoV-2 from March 12 to April 14, 2020 in influent, secondary and tertiary effluent water samples. By using the real-time RT-PCR (RT-qPCR) Diagnostic Panel validated by US CDC that targets three regions of the virus nucleocapsid (N) gene, we estimated quantification of SARS-CoV-2 RNA titers in untreated wastewater waters of 5.38 ± 0.21 log genomic copies/L on average. Two secondary water samples resulted positive (2 out of 18) and all tertiary water samples tested as negative (0 out 12). This environmental surveillance data were compared to declared COVID-19 cases at municipality level, revealing that SARS-CoV-2 was circulating among the population even before the first cases were reported by local or national authorities in many of the cities where wastewaters have been sampled. The detection of SARS-CoV-2 in wastewater in early stages of the spread of COVID-19 highlights the relevance of this strategy as an early indicator of the infection within a specific population. At this point, this environmental surveillance could be implemented by municipalities right away as a tool, designed to help authorities to coordinate the exit strategy to gradually lift its coronavirus lockdown.
Measuring Italian Citizens’ Engagement in the First Wave of the COVID-19 Pandemic Containment Measures: A Cross-sectional Study
Authors: Graffigna Guendalina , Barello Serena , Savarese Mariarosaria , Palamenghi Lorenzo , Castellini Greta , Bonanomi Andrea , Lozza Edoardo
Published: April 2020

Background

In January 2020, the coronavirus disease 2019 (COVID-19) started to spread in Italy. The Italian government adopted urgent measures to hold its spread. Enforcing compliance to such measures is crucial in order to enhance their effectiveness. Engaging citizens in the COVID-19 preventive process is today urgent in Italy and around the world. However, to the best of our knowledge, no previous studies have investigated the role of health engagement in predicting citizens’ compliance to health emergency containment measures.

Method

An online survey was administered between February 28th and March 4th 2020 on a representative sample of 1000 Italians. The questionnaire included a measure of Health Engagement (PHE-S) and a series of ad hoc items intended to measure both affective and behavioral responses of the citizens to the emergency in terms of perceived susceptibility to and severity of the disease, orientation towards health management, change in habits and in purchases. To investigate the relationship between Health Engagement and these variables, a series of ANOVAs, Logistic regressions and crosstabs have been carried out.

Results

Less engaged people show higher levels of perceived susceptibility to the virus and of severity of the disease; they trust less scientific and healthcare authorities, they feel less self-effective in managing their own health - both in normal conditions and under stress - and are less prone to cooperate with healthcare professionals. Low levels of Health Engagement are also associated with a change in the usual purchase behavior.

Conclusions

The Patient Health Engagement Model (PHE) provides a useful framework for understanding how people will respond to health threats such as pandemics. Therefore, intervention studies should focus on particular groups and on raising their levels of engagement to increase the effectiveness of educational initiatives devoted to promote preventive behaviors.
Knowledge and Beliefs of General Public of India on COVID-19: A Web-based Cross-sectional Survey
Authors: Krishna Puvvada Rahul , Undela Krishna , Palaksha Shilpa , Gupta Balaji Sathyanarayana
Published: April 2020

Context

Despite many awareness programs conducted by the governments and other agencies, there are certain false beliefs among the general public of India towards the transmission, prevention, and treatment of COVID-19.

Aims

To assess the knowledge and beliefs of the general public of India on COVID-19.

Materials and Methods

A web-based cross-sectional survey was conducted between 20th March and 15th April 2020. A 17-item questionnaire was developed, validated, and used for the study. The questionnaire was randomly distributed among the public using Google forms through social media networks. Descriptive analysis was performed to represent the study characteristics, Chi-square test for assessing the associations among the study variables, and logistic regression analysis for identifying the factors influencing the beliefs.

Results

A total of 462 participants with a mean (SD) age of 30.66 (11.31) years were responded to the questionnaire. Study participants are having fairly good knowledge of the basic aspects of COVID-19. However, a considerable fraction of participants were having false beliefs towards the transmission of new coronavirus, and prevention & treatment of COVID-19. It was observed that the participants who were aged 31-60 years and >60 years, education level of intermediate or diploma and high school certificate, and occupation as the unskilled workers had more of false beliefs towards COVID-19 compared to their counterparts.

Conclusion

Though the overall knowledge on COVID-19 was good enough among the general public of India, still there is a need for education to avoid false beliefs especially among the people who are elderly, having a low level of education, and non-professional workers.

Key Messages

A cross-sectional web-based online survey was conducted to assess the knowledge and beliefs of general public of India on COVID-19. It was identified that the knowledge among the general public on COVID-19 is fairly good. However, still there are some false beliefs among the population towards transmission of new coronavirus, and prevention & treatment of COVID-19, especially among the people who are elderly, having low level of education, and non-professional workers.
Chest computed tomography (CT) scan findings in patients with COVID-19: a systematic review and meta-analysis
Authors: Karimian Mohammad , Azami Milad
Published: April 2020

Objectives

Numerous cases of pneumonia of caused by coronavirus disease 2019 (COVID-19) were reported in Wuhan, China. Chest computed tomography (CT) scan is highly important in the diagnosis and follow-up of lung disease treatment. The present meta-analysis was performed to evaluate chest CT findings in COVID-19 patients.

Materials and Methods

All research steps were taken according to the MOOSE protocol and the final report was based on PRISMA guidelines. Each stage of the study was conducted by two independent authors. We searched the Web of Science, Ovid, Science Direct, Scopus, EMBASE, PubMed/Medline, Cochrane Library, EBSCO, CINAHL and Google scholar databases. The search was conducted on March 20, 2020. Grey literature was searched at medrxiv website. All analyses were performed using Comprehensive Meta-Analysis. The adapted Newcastle Ottawa Scale was used to evaluate the risk of bias. We registered this review at PROSPERO (registration number: CRD42019127858).

Results

Finally, 40 eligible studies with 4,183 patients with COVID-19 were used for meta- analysis. The rate of positive chest CT scan in patients with COVID-19 was 94.5% (95%CI: 91.7-96.3). Bilateral lung involvement, pure ground-glass opacity (GGO), mixed (GGO pulse consolidation or reticular), consolidation, reticular, and presence of nodule findings in chest CT scan of COVID-19 pneumonia patients were respectively estimated to be 79.1% (95% CI: 70.8- 85.5), 64.9% (95%CI: 54.1-74.4), 49.2% (95%CI: 35.7-62.8), 30.3% (95%CI: 19.6-43.6), 17.0% (95%CI: 3.9-50.9) and 16.6% (95%CI: 13.6-20.2). The distribution of lung lesions in patients with COVID-19 pneumonia was peripheral (70.0% [95%CI: 57.8-79.9]), central (3.9% [95%CI: 1.4-10.6]), and peripheral and central (31.1% [95%CI: 19.5-45.8]). The most common pulmonary lobes involved were right lower lobe (86.5% [95%CI: 57.7-96.8]) and left lower lobe (81.0% [95%CI: 50.5-94.7]).

Conclusion

Our study showed that chest CT scan has little weakness in diagnosis of COVID-19 combined to personal history, clinical symptoms, and initial laboratory findings, and may therefore serve as a standard method for diagnosis of COVID-19 based on its features and transformation rule, before initial RT-PCR screening.
Aphasia in Bilinguals
Authors: Ardila Alfredo , Lahiri Durjoy
Published: April 2020

Background

Little is known about the influence of bilingualism in aphasia.

Aims

To analyze the effect of bilingualism in a group of patients with aphasia.

Methods

Data from155 monolingual and 53 bilingual aphasia patients were analyzed.

Results

It was found that aphasia was significantly less severe in bilinguals when compared to monolinguals (p=0.023)

Conclusion

Bilingualism represents a protecting factor in aphasia. Aphasia is less severe and consequently, recovery is expected to be better in bilingual patients.
Inclusion of medical fitness to drive in medical postgraduate training curricula
Authors: Azawi Laith Al , O’Byrne Aisling , Roche Lily , O’Neill Desmond , Ryan Margaret
Published: April 2020

Background

Transport mobility, and access to driving, is an important factor in social inclusion and well-being. Doctors have an important role to play in supporting safe mobility through applying the knowledge developed in the field of traffic medicine and incorporating state of the art national and international medical fitness to drive (MFTD) guidelines. Little is known about the profile of MFTD in postgraduate curricula for core and higher specialist training.

Aims

We profiled the inclusion of MFTD in the curricula of postgraduate core, higher and streamlined medical and surgical specialties in the Republic of Ireland and the UK. Methods: All publicly available syllabi of basic and higher/ streamlined specialist training in postgraduate medical and surgical colleges in both jurisdictions were analysed (N = 122).

Results

In Ireland, 25% of basic training schemes included MFTD in the curriculum. Two-thirds of curricula of higher specialty and streamlined training schemes also included MFTD. For the UK, 44% of core and 36% of higher training schemes curricula included MFTD. Just under one-quarter of all curricula reviewed included MFTD for more than one medical condition or treatment. Common topics in both Irish and UK curricula included seizures/epilepsy, syncope and visual disturbances.

Conclusion

There are notable deficits in MFTD training for specialists in Ireland and the UK. Common conditions which can significantly impair MFTD such as stroke, diabetes and alcohol use disorders are severely underrepresented and curricula should be revisited to include relevant training and guidance for MFTD for trainees.

Main Messages

Doctors have an important role in supporting safe driving among patients with a range of medical conditions

Basic and higher specialist training curricula in a range of specialities in the British Isles are deficient in content relating to medical fitness to drive

Curricular development for specialist training should include provision of concise and speciality-relevant guidance on medical fitness to drive

Research Questions

What barriers exist currently to the inclusion of medical fitness to drive and how could these be mitigated?

What are the specialty-relevant prioritizations of medical conditions related to medical fitness to drive for inclusion in each curriculum?

What resources and evidence are available to specialist training programmes to support the guidance for medical fitness to drive in their curricula?
Forecast and interpretation of daily affected people during 21 days lockdown due to COVID 19 pandemic in India
Authors: Bhattacharyya Achintya , Bhowmik Dipak , Mukherjee Joy
Published: April 2020

The problem of facing difficulty to control the spreading of newly detected novel corona virus 2019 is a matter of attention throughout the whole world. The total numbers of infected individuals have already crossed 2 million throughout the world. The government of all the affected countries have already taken many measures like lockdown to stop the spread. Therefore, it is important to study the nature of growth and interpretations are necessary for taking needful by the government. In this paper, we have tried to interpret the spreading capability of novel corona virus in India taking into consideration of 21 days lockdown data. The prediction is based on the present number of available cases and number of new cases reporting daily. We have explained the number of infected people in India comparing with Italy, China, Spain, and USA data of 21 days individually after announcing lockdown. The plot of daily new cases with the number of days spent after lockdown is fitted by linear and polynomial function. The best fitted graph is chosen for interpretation and that is based on the parameters obtained from fitting. The forecast of maximum spreading possibility is discussed with linear and 4-degree polynomial fitting parameters. Finally, some further preventive measurements are also discussed.
Pooling of Nasopharyngeal Swab Specimens for SARS-CoV-2 detection by RT-PCR
Authors: Torres Ignacio , Albert Eliseo , Navarro David
Published: April 2020

Systematic testing of large population groups by RT-PCR is mandatory to Covid-19 case identification and contact tracing in order to minimize the likelyhood of resurgence in contagion. Sample pooling for RT-PCR has been effectively used to detect community transmission of SARS CoV-2. Nevertheless, this procedure may decrease the sensitivity of RT-PCR assays due to specimen dilution. We evaluated the efficacy of this strategy for diagnosis of Covid-19 using a sensitive commercially-available RT-PCR targeting SARS CoV-2 E and RdRp genes in a single reaction. A total of 20 mini-pools containing either 5 (n=10) or 10 (n=10) nasopharyngeal exudates collected in universal transport medium were made, each of which including a unique positive NP specimen. Positive specimens yielding CT <32 for the E gene (6 out of 10) or <35.2 for the RdRP gene (7 out of 10) were detected in mini-pools of both sizes. In contrast, most NP samples displaying CTs > 35.8 for the E gene or 35.7 for the RdRP gene remained undetected in mini-pools of 5 specimens (3/4 and 2/3, respectively) or in mini-pools of 10 samples (4/4 and 3/3, respectively.
Pre-exposure prophylaxis uptake among users of non-occupational post-exposure prophylaxis: a longitudinal analysis of attendees at a large sexual health clinic in Montréal
Authors: Xia Yiqing , Greenwald R. Zoë , Milwid M. Rachael , Trottier Claire , Boissonnault Michel , Gaul Neil , Charest Louise , Landry Gabrielle , Zahedi N. Navid , Szabo Jason , Thomas Réjean , Maheu-Giroux Mathieu
Published: April 2020

Background

Reducing HIV transmission using pre-exposure prophylaxis (PrEP) requires targeting individuals at high acquisition risk, such as men who have sex with men (MSM) with a history of non-occupational post-exposure prophylaxis (nPEP). This study aims to characterize longitudinal trends in PrEP uptake and its determinants among nPEP users in Montréal.

Methods

Eligible attendees at Clinique médicale l’Actuel were recruited prospectively starting in October 2000 (nPEP) and January 2013 (PrEP). Linking these cohorts, we characterized the PEP-to-PrEP cascade, examined the determinants of PrEP uptake after nPEP consultation using a Cox proportional-hazard model, and assessed whether PrEP persistence differed by nPEP history using Kaplan-Meier curves.

Results

As of August 2019, 31% of 2,682 MSM nPEP cohort participants had two or more nPEP consultations. Subsequent PrEP consultations occurred among 36% of nPEP users, of which 17% sought nPEP again afterwards. Among 2,718 PrEP cohort participants, 46% reported previous nPEP use. Among nPEP users, those aged 25-49 years (Hazard Ratio (HR)=1.3, 95% confidence interval (CI): 1.1-1.7), with more nPEP episodes (HR=1.4, 95%CI: 1.3-1.5), reported chemsex (HR=1.3, 95%CI: 1.1-1.7), with a STI history (HR=1.5; 95%CI: 1.3-1.7), and who returned for their first nPEP follow-up visit (HR=3.4, 95%CI: 2.7-4.2) had higher rates of PrEP linkage. There was no difference in PrEP persistence between PEP-to-PrEP and PrEP only participants.

Conclusion

Over one-third of nPEP users were subsequently prescribed PrEP. However, the large proportion of men who repeatedly use nPEP calls for more efficient PrEP-linkage services and, among those that use PrEP, improved persistence should be encouraged.
Experience with Hydroxychloroquine and Azithromycin in the COVID-19 Pandemic: Implications for QT Interval Monitoring
Authors: Ramireddy Archana , Chugh Harpriya , Reinier Kyndaron , Ebinger Joseph , Park Eunice , Thompson Michael , Cingolani Eugenio , Cheng Susan , Marban Eduardo , Albert Christine M. , Chugh Sumeet S.
Published: April 2020

Background

Despite a paucity of clinical evidence, hydroxychloroquine and azithromycin are being administered widely to patients with verified or suspected COVID-19. Both drugs may increase risk of lethal arrhythmias associated with QT interval prolongation.

Methods

We performed a case series of COVID-19 positive/suspected patients admitted between 2/1/2020 and 4/4/2020 who were treated with azithromycin, hydroxychloroquine or a combination. We evaluated baseline and post-medication QT interval (QTc, Bazett’s) using 12-lead ECGs. Critical QTc prolongation was defined as: a) maximum QTc ≥500 ms (if QRS <120 ms) or QTc ≥550 (if QRS ≥120 ms) and b) increased QTc of ≥60 ms. Tisdale score and Elixhauser comorbidity index were calculated.

Results

Of 490 COVID-19 positive/suspected patients, 314 (64%) received either/both drugs, and 98 (73 COVID-19 positive, 25 suspected) met study criteria (age 62±17 yrs, 61% male). Azithromycin was prescribed in 28%, hydroxychloroquine in 10%, and both in 62%. Baseline mean QTc was 448±29 ms and increased to 459±36ms (p=0.005) with medications. Significant prolongation was observed only in men (18±43 ms vs -0.2±28 ms in women, p=0.02). 12% of patients reached critical QTc prolongation. In a multivariable logistic regression, age, sex, Tisdale score, Elixhauser score, and baseline QTc were not associated with critical QTc prolongation (p>0.14). Changes in QTc were highest with the combination compared to either drug, with many-fold greater prolongation with the combination vs. azithromycin alone (17±39 vs. 0.5±40 ms, p=0.07). No patients manifested torsades de pointes.

Conclusions

Overall, 12% of patients manifested critical QTc interval prolongation, and traditional risk indices failed to flag these patients. With the drug combination, QTc prolongation was several-fold higher compared to azithromycin alone. The balance between uncertain benefit and potential risk when treating COVID-19 patients with these drugs should be carefully assessed prior to use.
Gut microbiota may underlie the predisposition of healthy individuals to COVID-19
Authors: Gou Wanglong , Fu Yuanqing , Yue Liang , Chen Geng-dong , Cai Xue , Shuai Menglei , Xu Fengzhe , Yi Xiao , Chen Hao , Zhu Yi , Xiao Mian-li , Jiang Zengliang , Miao Zelei , Xiao Congmei , Shen Bo , Wu Xiaomai , Zhao Haihong , Ling Wenhua , Wang Jun , Chen Yu-ming , Guo Tiannan , Zheng Ju-Sheng
Published: April 2020

The COVID-19 pandemic is spreading globally with high disparity in the susceptibility of the disease severity. Identification of the key underlying factors for this disparity is highly warranted. Here we describe constructing a proteomic risk score based on 20 blood proteomic biomarkers which predict the progression to severe COVID-19. We demonstrate that in our own cohort of 990 individuals without infection, this proteomic risk score is positively associated with proinflammatory cytokines mainly among older, but not younger, individuals. We further discovered that a core set of gut microbiota could accurately predict the above proteomic biomarkers among 301 individuals using a machine learning model, and that these gut microbiota features are highly correlated with proinflammatory cytokines in another set of 366 individuals. Fecal metabolomic analysis suggested potential amino acid-related pathways linking gut microbiota to inflammation. This study suggests that gut microbiota may underlie the predisposition of normal individuals to severe COVID-19.
Intermittent self-administration of fentanyl induces a multifaceted addiction state associated with persistent changes in the orexin system
Authors: Fragale Jennifer E. , James Morgan H. , Aston-Jones Gary
Published: April 2020

The orexin (hypocretin) system plays a critical role in motivated drug-taking. Cocaine self-administration with the intermittent access (IntA) procedure produces a robust addiction-like state that is orexin-dependent. Here, we sought to determine the role of the orexin system in opioid addiction using IntA self-administration of fentanyl. Different groups of male rats were either given continuous access in 1h (short access; ShA), or 6h periods (long access, LgA), or IntA (5min of access separated by 25min of no-access) to fentanyl for 14 days. IntA produced a greater escalation of fentanyl intake, motivation for fentanyl on a behavioral economics task, persistent drug seeking during abstinence, and cued-induced reinstatement compared to rats given ShA or LgA. We found that addiction behaviors induced by IntA to fentanyl were reversed by the orexin-1 receptor antagonist SB-334867. IntA to fentanyl was also associated with a persistent increase in the number of orexin-expressing neurons. Together, results indicate that the IntA model is a useful tool in the study of opioid addiction, and that the orexin system is critical for the maintenance of addiction behaviors induced by IntA self-administration of fentanyl.
A mobile sex-determining region, male-specific haplotypes, and rearing environment influence age at maturity in Chinook salmon
Authors: McKinney Garrett J , Nichols Krista M , Ford Michael J
Published: April 2020

Variation in age at maturity is an important contributor to life history and demographic variation within and among species. The optimal age at maturity can vary by sex, and the ability of each sex to evolve towards its fitness optimum depends on the genetic architecture of maturation. Using GWAS of RAD sequencing data, we show that age at maturity in Chinook salmon exhibits sex-specific genetic architecture, with age at maturity in males governed by large (up to 20Mb) male-specific haplotypes. These regions showed no such effect in females. We also provide evidence for translocation of the sex-determining gene between two different chromosomes. This has important implications for sexually antagonistic selection, particularly that sex-linkage of adaptive genes may differ within and among populations based on chromosomal location of the sex-determining gene. Our findings will facilitate research into the genetic causes of shifting demography in Chinook salmon as well as a better understanding of sex-determination in this species and Pacific salmon in general.