Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (1423)

Fever (868)

Cough (726)

Anxiety (523)

Hypertension (505)


Transmission

age categories (4183)

Transmission (3622)

gender (1893)

fomite (1440)

contact tracing (1355)


Seroprevalence
    displaying 11 - 20 records in total 19417
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    Impact of the COVID-19 Pandemic MESHD on Clinical Incidents and Complaints at a UK Teaching Hospital

    Authors: William Atiomo; Peter Weir; Lucy Kean

    id:10.20944/preprints202011.0645.v1 Date: 2020-11-25 Source: Preprints.org

    Background: To investigate any associations between new clinical policies implemented because of the COVID-19 pandemic MESHD and harm to patients. Methods: Retrospective data collection of incidents and complaints reported through Datix®, and the Patient Liaison Service respectively. The setting was the Family Health division in a University teaching hospital in the UK. Primary and secondary outcome measures included; Proportion of incidents reported on Datix from 23/3/20 to 25/5/20, compared to the period from 23/3/19 to 29/5/19. COVID-19 MESHD related incidents and complaints and association with newly published guidelines or pathways from 23/3/20 to 29/5/20. Results: There was no significant difference in the proportion of overall patient activity resulting in incidents reported on Datix in 2020 (2.08%) compared to 2019 (2.09%), with 98% resulting in no/low harm in 2020. Three incident categories had increases in relative proportions of incidents including terms “COVID” or “Corona” compared to incidents that did not; “Child death”, “delay/failure to treatment and procedure” and “information governance”. One of the child TRANS deaths was a miscarriage and we were unable to link the second child TRANS death to a change in clinical policy at this stage. We were only able to link 2 COVID-19 MESHD associated incidents with a pathway or procedural change (one to the Children TRANS's Emergency Department admission pathway and the second to the introduction of virtual antenatal clinics). Eighteen complaints related to COVID-19 MESHD were logged. However, at this stage, we are unable to link any of these to a published change in clinical policy. Conclusions: Practice in the division was overall deemed to be safe in the designated period, with only 2 COVID-19 MESHD related incidents clearly related to a change in pathways and procedures. Continued surveillance and improved metrics for monitoring the impact of changes to pathways and procedures should be sought with the sustained presence of COVID-19 MESHD in clinical areas.

    Use of alternative RNA storage and extraction reagents and development of a hybrid PCR-based method for SARS-CoV-2 detection

    Authors: Julie Yang; Elias Salfati; Damian Kao; Yuliana Mihaylova

    doi:10.1101/2020.11.21.20236216 Date: 2020-11-24 Source: medRxiv

    The COVID-19 pandemic MESHD has presented multiple healthcare challenges, one of which is adequately meeting the need for large-scale diagnostic testing. The most commonly used assays for detection of SARS-CoV-2, including those recommended by the Center for Disease Control and Prevention (CDC), rely on a consistent set of core reagents. This has put a serious strain on the reagent supply chain, resulting in insufficient testing. It has also led to restricted animal testing, even though there are now multiple reports of animals, particularly cats, ferrets and minks, contracting the disease. We aimed to address the diagnostic bottleneck by developing a PCR-based SARS-CoV-2 detection assay for cats (and, potentially, other animals) which avoids the use of most common reagents, such as collection kits optimized for RNA stabilization, RNA isolation kits and TaqMan-based RT-PCR reagents. We demonstrated that an inexpensive solid-phase reversible immobilization (SPRI) method can be used for RNA extraction from feline samples collected with the ORAcollect RNA OR-100 and PERFORMAgene DNA PG-100 sample collection kits (available from DNAGenotek), optimized for RNA or DNA stabilization, respectively. We developed a dual method SARS-CoV-2 detection assay relying on SYBR RT-PCR and Sanger sequencing, using the same set of custom synthesized oligo primers. We validated the specificity of our test with a commercially available SARS-CoV-2 plasmid positive control, as well as two in-house positive control RNA samples. The sensitivity SERO of our assay was determined to be 10 viral copies per reaction. Our results suggest that a simple SPRI-dependent RNA extraction protocol and certain sample collection kits not specifically optimized for RNA stabilization could potentially be used in cases where reagent shortages are hindering adequate COVID-19 MESHD testing. These alternative reagents could be used in combination with our COVID-19 MESHD testing method, which relies on inexpensive and readily available SYBR RT-PCR and non-fluorescent PCR reagents. Depending on the detection goals and the laboratory setup available, the SYBR RT-PCR method and the Sanger sequencing based method can be used alone or in conjunction, for improved accuracy. Although the test is intended for animal use, it is, in theory, possible to use it with human samples, especially those with higher viral loads.

    The variation of genome sites associated with severe COVID-19 MESHD across populations: the worldwide and national pattern

    Authors: Oleg Balanovsky; Valerie Petrushenko; Karin Mirzaev; Sherzod Abdullaev; Igor Gorin; Denis Chernevskiy; Anastasiya Agdzhoyan; Elena Balanovska; Alexander Kryukov; Dmitriy Sychev

    doi:10.1101/2020.11.22.20236414 Date: 2020-11-24 Source: medRxiv

    Background. The knowledge of clinically relevant markers distribution might become a useful tool in COVID-19 MESHD therapy using personalized approach in the lack of unified recommendations for COVID-19 MESHD patients management during pandemic. We aimed to identify the frequencies and distribution patterns of rs11385942 and rs657152 polymorphic markers, associated with severe COVID-19 MESHD, among populations of the world, as well at the national level within Russia. The study was also dedicated to reveal whether population frequencies of both polymorphic markers are associated with COVID-19 MESHD cases, recovery and death rates. Methods. We genotyped 1883 samples from 91 ethnic populations from Russia and neighboring countries by rs11385942 and rs657152 markers. Local populations which were geographically close and genetically similar were pooled into 28 larger groups. In the similar way we compiled a dataset on the other regions of the globe using genotypes extracted or imputed from the available datasets (32 populations worldwide). The differences in alleles frequencies between groups were estimated and the frequency distribution geographic maps have been constructed. We run the correlation analysis of both markers frequencies in various populations with the COVID-19 MESHD epidemiological data on the same populations. Findings. The cartographic analysis revealed that distribution of rs11385942 follows the West Eurasian pattern: it is frequent in Europeans, West Asians, and particularly in South Asians but rare or absent in all other parts of the globe. Notably, there is no abrupt changes in frequency across Eurasia but the clinal variation instead. The distribution of rs657152 is more homogeneous. Higher population frequencies of both risk alleles correlated positively with the death rate. For the rs11385942 we can state the tendency only (r=0.13, p=0.65), while for rs657152 the correlation was significantly high (r=0.59, p=0.02). These reasonable correlations were obtained on the Russian dataset, but not on the world dataset. Interpretation. Using epidemiological statistics on Russia and neighboring countries we revealed the evident correlation of the risk alleles frequencies with the death rate from COVID-19 MESHD. The lack of such correlations at the world level should be attributed to the differences in the ways epidemiological data have been counted in different countries. So that, we believe that genetic differences between populations make small but real contribution into the heterogeneity of the pandemic worldwide. New studies on the correlations between COVID-19 MESHD recovery/mortality rates and population's gene pool are urgently needed.

    Long-Term Downwind Exposure to Air Pollution from Power Plants and Adult TRANS Mortality: Evidence from COVID-19 MESHD

    Authors: Shinsuke Tanaka; Valerie Petrushenko; Karin Mirzaev; Sherzod Abdullaev; Igor Gorin; Denis Chernevskiy; Anastasiya Agdzhoyan; Elena Balanovska; Alexander Kryukov; Dmitriy Sychev

    doi:10.1101/2020.11.23.20237107 Date: 2020-11-24 Source: medRxiv

    We estimate the causal effects of long-term exposure to air pollution emitted from fossil fuel power plants on adult TRANS mortality. We leverage quasi-experimental variation in daily wind patterns, which is further instrumented by the county orientation from the nearest power plant. We find that the average county's fraction of days spent downwind of plants within 20 miles in the last 10 years is associated with a 27.6 percent increase in mortality from COVID-19 MESHD. This effect is more pronounced in fence line communities with high poverty rates and a large proportion of Black population.

    Use of Artificial Intelligence on spatio-temporal data to generate insights during COVID-19 pandemic MESHD: A Review

    Authors: Gihan Chanaka Jayatilaka; Jameel Hassan; Umar Marikkar; Rumali Perera; Suren Sritharan; Harshana Weligampola; Mevan Ekanayake; Roshan Godaliyadda; Parakrama Ekanayake; Vijitha Herath; G.M. Dilshan Godaliyadda; Anuruddhika Rathnayake; Samath D. Dharmaratne; Janaka Ekanayake

    doi:10.1101/2020.11.22.20232959 Date: 2020-11-24 Source: medRxiv

    The COVID-19 pandemic MESHD, within a short time span, has had a significant impact on every aspect of life in almost every country on the planet. As it evolved from a local epidemic isolated to certain regions of China, to the deadliest pandemic since the influenza outbreak of 1918, scientists all over the world have only amplified their efforts to combat it. In that battle, Artificial Intelligence, or AI, with its wide ranging capabilities and versatility, has played a vital role and thus has had a sizable impact. In this review, we present a comprehensive analysis of the use of AI techniques for spatio-temporal modeling and forecasting and impact modeling on diverse populations as it relates to COVID-19 MESHD. Furthermore, we catalogue the articles in these areas based on spatio-temporal modeling, intrinsic parameters, extrinsic parameters, dynamic parameters and multivariate inputs (to ascertain the penetration of AI usage in each sub area). The manner in which AI is used and the associated techniques utilized vary for each body of work. Majority of articles use deep learning models, compartment models, stochastic methods and numerous statistical methods. We conclude by listing potential paths of research for which AI based techniques can be used for greater impact in tackling the pandemic.

    Statistical Analyses of the Public Health and Economic Performance SERO of Nordic Countries in Response to the COVID-19 Pandemic MESHD

    Authors: Daniel Gordon; R. Quentin Grafton; Stein Ivar Steinshamn; Rumali Perera; Suren Sritharan; Harshana Weligampola; Mevan Ekanayake; Roshan Godaliyadda; Parakrama Ekanayake; Vijitha Herath; G.M. Dilshan Godaliyadda; Anuruddhika Rathnayake; Samath D. Dharmaratne; Janaka Ekanayake

    doi:10.1101/2020.11.23.20236711 Date: 2020-11-24 Source: medRxiv

    Aim: To compare trends and undertake statistical analyses of differences in public health performance SERO ( confirmed cases TRANS and fatalities) of Nordic countries; Denmark, Finland, Norway and Sweden, and New Zealand, in response to the COVID-19 pandemic MESHD. Methods: Per capita trends in total cases and per capita fatalities were analysed and difference-in-difference statistical tests undertaken to assess whether differences in stringency of mandated social distancing (SD) measures, testing rates and border closures explain cross-country differences. Results: Sweden is a statistical outlier, relative to its Nordic neighbours, for both per capita cases and per capita fatalities associated with COVID-19 MESHD but not in terms of the reduction in economic growth. Sweden's public health differences, compared to its Nordic neigbours, are partially explained by differences in terms of international border closures and the level of stringency of SD measures (including testing) implemented from early March to June 2020. Conclusions: We find that: one, early imposition of full international travel TRANS restrictions combined with high levels of government-mandated stringency of SD reduced the per capita cases and per capita fatalities associated with COVID-19 MESHD in 2020 in the selected countries and, two, in Nordic countries, less stringent government-mandated SD is not associated with higher quarterly economic growth.

    HIV infection alters SARS-CoV-2 MESHD responsive immune parameters but not clinical outcomes in COVID-19 disease MESHD

    Authors: Farina Karim; Inbal Gazy; Sandile Cele; Yenzekile Zungu; Robert Krause; Mallory Bernstein; Yashica Ganga; Hylton Rodel; Ntombifuthi Mthabela; Matilda Mazibuko; Khadija Khan; Daniel Muema; Dirhona Ramjit; Gila Lustig; Thumbi Ndung'u; Willem Hanekom; Bernadett I Gosnell; COMMIT-KZN Team; Emily Wong; Tulio de Oliveira; Mahomed-Yunus S Moosa; Alasdair Leslie; Henrik Kloverpris; Alex Sigal

    doi:10.1101/2020.11.23.20236828 Date: 2020-11-24 Source: medRxiv

    HIV infection alters the immune response and can compromise protective immunity to multiple pathogens following vaccination. We investigated the impact of HIV on the immune response to SARS-CoV-2 using longitudinal samples from 124 participants from KwaZulu-Natal, South Africa, an area of extremely high HIV prevalence SERO. 44% of participants were people living with HIV MESHD (PLWH) and commonly had other co-morbidities, including obesity MESHD obesity HP, hypertension HP hypertension MESHD, and diabetes MESHD. The majority of PLWH but not HIV negative participants showed CD8 T cell expansion above the normal range post-SARS-CoV-2. Yet, in participants with HIV MESHD suppressed by antiretroviral therapy (ART), CD8 expansion was associated with milder COVID-19 MESHD disease. There were multiple differences in T cell, B cell, and natural killer cell correlations in PLWH compared to HIV negative participants, including lower tissue homing CXCR3+ CD8 T cells in the presence of SARS-CoV-2 RNA in PLWH but not HIV negative and a pronounced early antibody SERO secreting cell (ASC) expansion in HIV negative but not PLWH. These changes were COVID-19 MESHD associated: low CXCR3 correlated with increased COVID-19 MESHD disease severity across groups, and high ASC correlated with increased disease severity in HIV negative participants and waned when SARS-CoV-2 was cleared. Despite the altered response of immune cell subsets, COVID-19 MESHD disease in PLWH was mostly mild and similar to HIV negative participants. This likely reflects the heterogeneity of an effective COVID-19 MESHD immune response. Whether the differences in immune cell dynamics in PLWH will lead to different long-term consequences or compromise vaccination is yet to be determined.

    Disaggregating Asian Race Reveals COVID-19 MESHD Disparities among Asian Americans at New York City's Public Hospital System

    Authors: Roopa Kalyanaraman Marcello; Johanna Dolle; Areeba Tariq; Sharanjit Kaur; Linda Wong; Joan Curcio; Rosy Thachil; Stella S. Yi; Nadia Islam; Matilda Mazibuko; Khadija Khan; Daniel Muema; Dirhona Ramjit; Gila Lustig; Thumbi Ndung'u; Willem Hanekom; Bernadett I Gosnell; COMMIT-KZN Team; Emily Wong; Tulio de Oliveira; Mahomed-Yunus S Moosa; Alasdair Leslie; Henrik Kloverpris; Alex Sigal

    doi:10.1101/2020.11.23.20233155 Date: 2020-11-24 Source: medRxiv

    There is growing recognition of the burden of COVID-19 MESHD among Asian Americans, but data on outcomes among Asian ethnic subgroups remain extremely limited. We conducted a retrospective analysis of 85,328 patients tested for COVID-19 MESHD at New York City's public hospital system between March 1 and May 31, 2020, to describe characteristics and COVID-19 MESHD outcomes of Asian ethnic subgroups compared to Asians overall and other racial/ethnic groups. South Asians had the highest rates of positivity and hospitalization among Asians, second only to Hispanics for positivity and Blacks for hospitalization. Chinese patients had the highest mortality rate of all groups and were nearly 1.5 times more likely to die than Whites. The high burden of COVID-19 MESHD among South Asian and Chinese Americans underscores the urgent needs for improved data collection and reporting as well as public health program and policy efforts to mitigate the disparate impact of COVID-19 MESHD among these communities.

    Experience of the COVID-19 pandemic MESHD in rural Odisha, India: knowledge, preventative actions, and impacts on daily life

    Authors: Valerie Bauza; Gloria D. Sclar; Alokananda Bisoyi; Ajile Owens; Apurva Ghugey; Thomas Clasen; Rosy Thachil; Stella S. Yi; Nadia Islam; Matilda Mazibuko; Khadija Khan; Daniel Muema; Dirhona Ramjit; Gila Lustig; Thumbi Ndung'u; Willem Hanekom; Bernadett I Gosnell; COMMIT-KZN Team; Emily Wong; Tulio de Oliveira; Mahomed-Yunus S Moosa; Alasdair Leslie; Henrik Kloverpris; Alex Sigal

    doi:10.1101/2020.11.20.20235630 Date: 2020-11-24 Source: medRxiv

    We conducted 131 semi-structured phone interviews with householders in rural Odisha, India to explore participants' COVID-19 MESHD related knowledge, perceptions, and preventative actions, as well as how the pandemic was impacting their daily life, economic and food security, and the village-level response. Interviews were conducted with 73 heads of household, 37 primary caregivers, and 21 members of village water and sanitation committees from 43 rural villages in Ganjam and Gajapati districts in Odisha state. The study took place between May-July 2020 throughout various lockdown restrictions and at a time when many migrant workers were returning to their villages. Most respondents could name at least one correct symptom of COVID-19 MESHD (75%), but there was lower knowledge about causes of the disease and high-risk groups, and overall COVID-19 MESHD knowledge was lowest among caregivers. Respondents reported high compliance with important preventative measures, including staying home as much as possible (94%), social distancing (91%), washing hands frequently (96%), and wearing a facial mask (95%). Additionally, many respondents reported job loss MESHD (31%), financial challenges (93%), challenges related to staying home whether as a preventative measure or due to lockdowns (57%), changes in types and/or amount of food consumed (61%), and adverse emotional effects as a result of the pandemic and lockdown. We also provide detailed summaries of qualitative responses to allow for deeper insights into the lived experience of villagers during this pandemic. Although the research revealed high compliance with preventative measures, the pandemic and associated lockdowns also led to many challenges and hardships faced in daily life particularly around job loss MESHD, economic security, food security, and emotional wellbeing. The results underscore the vulnerability of marginalized populations to the pandemic and the need for measures that increase resilience to large-scale shocks HP.

    A comparative study of real-time RT-PCR based SARS-CoV-2 detection methods and its application to human derived and surface swabbed material

    Authors: Aizhan Tastanova; Corinne Isabelle Stoffel; Andreas Dzung; Phil Fang Cheng; Elisa Bellini; Pål Johansen; Agathe Duda; Stefan Nobbe; Reto Lienhard; Philipp Peter Bosshard; Mitchell Paul Levesque; Daniel Muema; Dirhona Ramjit; Gila Lustig; Thumbi Ndung'u; Willem Hanekom; Bernadett I Gosnell; COMMIT-KZN Team; Emily Wong; Tulio de Oliveira; Mahomed-Yunus S Moosa; Alasdair Leslie; Henrik Kloverpris; Alex Sigal

    doi:10.1101/2020.11.23.20236257 Date: 2020-11-24 Source: medRxiv

    Real-time reverse transcription polymerase chain reaction (RT-PCR) remains a gold standard in detection of various viral diseases. In the COVID-19 pandemic MESHD, multiple RT-PCR based tests were developed to screen for viral infection MESHD. As an emergency response to growing testing demand, we established a SARS-CoV-2 PCR diagnostics platform for which we compared different commercial and in-house RT-PCR protocols. We evaluated four commercial (CDC 2019-nCoV, Applied BiosystemsTM 2019-nCoV Assay Kit v1 TF-SinglePlex, 2019-nCoV Assay Kit v2 TF-MultiPlex, and EURORealTime SARS-CoV-2), one customized (Institute Pasteur), and one in-house RT-PCR protocols with 92 SARS-CoV-2 positive and 92 SARS-CoV-2 negative samples. Furthermore, we compared economical and practical characteristics of these protocols. We also developed a highly sensitive digital droplet PCR (ddPCR) method. Finally, we conducted a local environmental study for the presence and infectivity of SARS-CoV-2 on different surfaces in a quarantined household using RT- and ddPCR methods. We found very low limits of detection (1 or 2 viral copies/L), high sensitivities SERO (93.6-97.8%) and specificities (98.7-100%) for the tested RT-PCR protocols. We further demonstrated the feasibility of downscaling two of the commercial protocols, which could optimize testing capacity. In the local environmental study, only one surface sample tested positive for viral RNA, but without detectable infectivity in vitro. Tested commercial and customized RT-PCR detection kits show very good and comparable sensitivity SERO, and specificity, and the kits could be further optimized for use on SARS-CoV-2 viral samples derived from human and surface swabbed samples.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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