Corpus overview


MeSH Disease

Human Phenotype

Pneumonia (34)

Cough (26)

Fever (24)

Diarrhea (8)

Falls (6)


    displaying 1 - 10 records in total 278
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    Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

    Authors: Joshua S. Bloom; Eric M. Jones; Molly Gasperini; Nathan B. Lubock; Laila Sathe; Chetan Munugala; A. Sina Booeshaghi; Oliver F. Brandenberg; Longhua Guo; Scott W. Simpkins; Isabella Lin; Nathan LaPierre; Duke Hong; Yi Zhang; Gabriel Oland; Bianca Judy Choe; Sukantha Chandrasekaran; Evann E. Hilt; Manish J. Butte; Robert Damoiseaux; Aaron R. Cooper; Yi Yin; Lior Pachter; Omai B. Garner; Jonathan Flint; Eleazar Eskin; Chongyuan Luo; Sriram Kosuri; Leonid Kruglyak; Valerie A. Arboleda

    doi:10.1101/2020.08.04.20167874 Date: 2020-08-06 Source: medRxiv

    The rapid spread of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission TRANS by individuals who are asymptomatic TRANS at the time of transmission TRANS. Frequent, widespread testing of the asymptomatic TRANS population for SARS-CoV-2 is essential to suppress viral transmission TRANS and is a key element in safely reopening society. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic TRANS individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. We show that SwabSeq can test nasal and oral specimens for SARS-CoV-2 with or without RNA extraction while maintaining analytical sensitivity SERO better than or comparable to that of fluorescence-based RT-qPCR tests. SwabSeq is simple, sensitive, flexible, rapidly scalable, inexpensive enough to test widely and frequently, and can provide a turn around time of 12 to 24 hours.

    SARS-CoV-2 infection MESHD, disease MESHD and transmission TRANS in domestic cats

    Authors: Natasha N Gaudreault; Jessie D Trujillo; Mariano Carossino; David A Meekins; Igor Morozov; Daniel W Madden; Sabarish V Indran; Dashzeveg Bold; Velmurugan Balaraman; Taeyong Kwon; Bianca Libanori Artiaga; Konner Cool; Adolfo Garcia-Sastre; Wenjun Ma; William C Wilson; Jamie Henningson; Udeni BR Balasuriya; Juergen A Richt

    doi:10.1101/2020.08.04.235002 Date: 2020-08-04 Source: bioRxiv

    Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2) is the cause of Coronavirus Disease MESHD 2019 (COVID-19) and responsible for the current pandemic. Recent SARS-CoV-2 susceptibility and transmission TRANS studies in cats show that the virus can replicate in these companion animals and transmit to other cats. Here, we present an in-depth study of SARS-CoV-2 infection MESHD, associated disease MESHD and transmission TRANS dynamics in domestic cats. Six 4- to 5-month-old cats were challenged with SARS-CoV-2 via intranasal and oral routes simultaneously. One day post challenge (DPC), two sentinel contact cats were co-mingled with the principal infected animals. Animals were monitored for clinical signs, clinicopathological abnormalities and viral shedding throughout the 21 DPC observation period. Postmortem examinations were performed at 4, 7 and 21 DPC to investigate disease progression MESHD. Viral RNA was not detected in blood SERO but transiently in nasal, oropharyngeal and rectal swabs and bronchoalveolar lavage fluid as well as various tissues. Tracheobronchoadenitis of submucosal glands with the presence of viral RNA and antigen was observed in airways of the infected cats on 4 and 7 DPC. Serology showed that both, principal and sentinel cats, developed SARS-CoV-2-specific and neutralizing antibodies to SARS-CoV-2 SERO detectable at 7 DPC or 10 DPC, respectively. All animals were clinically asymptomatic TRANS during the course of the study and capable of transmitting SARS-CoV-2 to sentinels within 2 days of comingling. The results of this study are critical for our understanding of the clinical course of SARS-CoV-2 in a naturally susceptible host species, and for risk assessment of the maintenance of SARS-CoV-2 in felines and transmission TRANS to other animals and humans.

    Land Use Change and Coronavirus Emergence Risk

    Authors: Maria Cristina Rulli; Paolo D'Odorico; Nikolas Galli; David Hayman

    doi:10.1101/2020.07.31.20166090 Date: 2020-08-04 Source: medRxiv

    Coronavirus disease MESHD 2019 (COVID-19) and severe acute respiratory syndrome MESHD (SARS) causing coronaviruses are mostly discovered in Asian horseshoe bats. It is still unclear how ongoing land use changes may facilitate SARS-related coronavirus transmission TRANS to humans. Here we use a multivariate hotspot analysis of high-resolution land-use data to show that regions of China populated by horseshoe bats are hotspots of forest fragmentation, livestock and human density. We also identify areas susceptible to new hotspot emergence in response to moderate expansion of urbanization, livestock production, or forest disturbance, thereby highlighting regions vulnerable to SARS-CoV spillover under future land-use change. In China population growth and increasing meat consumption associated with urbanization and economic development have expanded the footprint of agriculture, leading to human encroachment in wildlife habitat and increased livestock density in areas adjacent to fragmented forests. The reduced distance between horseshoe-bats and humans elevates the risk for SARS-related coronavirus transmission TRANS to humans.

    Face masks prevent transmission TRANS of respiratory diseases MESHD: a meta-analysis of randomized controlled trials

    Authors: Hanna M Ollila; Markku Partinen; Jukka Koskela; Riikka Savolainen; Anna Rotkirch; Liisa T Laine

    doi:10.1101/2020.07.31.20166116 Date: 2020-08-04 Source: medRxiv

    Background: Coronavirus Disease MESHD 2019 (COVID-19) is caused by Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2) and spreads through droplet-mediated transmission TRANS on contaminated surfaces and in air. Mounting scientific evidence from observational studies suggests that face masks for the general public may reduce the spread of infections MESHD. However, results from randomized control trials (RCT) have been presented as inconclusive, and concerns related to the safety and efficacy of non-surgical face masks in non-clinical settings remain. This controversy calls for a meta-analysis which considers non-compliance in RCTs, the time-lag in benefits of universal masking, and possible adverse effects. Methods: We performed a meta-analysis of RCTs of non-surgical face masks in preventing viral respiratory infections MESHD in non-hospital and non-household settings at cumulative and maximum follow-up as primary endpoints. The search for RCTs yielded five studies published before May 29th, 2020. We pooled estimates from the studies and performed random-effects meta-analysis and mixed-effects meta-regression across studies, accounting for covariates in compliance vs. non-compliance in treatment. Results: Face masks decreased infections across MESHD all studies at maximum follow-up (p=0.0318$, RR=0.608 [0.387 - 0.956]), and particularly in studies without non-compliance bias. We found significant between-study heterogeneity in studies with bias (I^2=71.2%, p=0.0077). We also used adjusted meta-regression to account for heterogeneity. The results support a significant protective effect of masking (p=0.0006, beta=0.0214, SE= 0.0062). No severe adverse effects were detected. Interpretation: The meta-analysis of existing randomized control studies found support for the efficacy of face masks among the general public. Our results show that face masks protect populations from infections MESHD and do not pose a significant risk to users. Recommendations and clear communication concerning the benefits of face masks should be provided to limit the number of COVID-19 and other respiratory infections MESHD.

    Trends of Interventional Radiology procedures during the Covid-19 pandemic: The first 27 weeks in the eye of the storm

    Authors: Guo Yuan How; Uei Pua

    doi:10.21203/ Date: 2020-08-04 Source: ResearchSquare

    ObjectivesWhile the Novel Coronavirus (COVID-19) pandemic looks to persist, institutions promote delaying procedures. Understanding trends and demands of interventional radiology (IR) procedures in the infected and COVID-free populations are needed in long-term planning. We detail IR procedure trends in the first 27 weeks of the pandemic and compare with the pre-pandemic era. MethodsIn this IRB approved retrospective electronic case review, all IR patients in our institution from 1 January to 9 July 2020, the same period in 2019 pre-pandemic and the Severe Acute Respiratory Syndrome MESHD (SARS-CoV) outbreak were included. IR procedures were classified using Interventional Radiology – Procedure Acuity Scale (IR-PAS) and category of IR procedures. Along with descriptive frequencies, the Mann-Whitney U test and Chi-square test of independence were performed.ResultsDuring the pandemic, 3655 IR procedures were performed compared to 3851 procedures pre-pandemic. No statistically significant difference in weekly IR caseloads across IR-PAS tiers between both periods (p = .088) and category of procedure (p = .054) were noted. General intervention procedures remained the largest proportion and musculoskeletal procedures the minority, in both periods. More general intervention radiology and oncology procedures were performed during the Covid-19 pandemic compared to the SARS-CoV outbreak. Thirty-four (0.93%) IR procedures were performed on 30 COVID-19 patients. There was no IR procedure-related COVID-19 cross- transmission TRANS. ConclusionsDemand for IR procedures among COVID-free patients remains high, and IR procedures involving COVID-19 represents a fraction of the IR caseload. A sustainable model in providing timely IR services to COVID-free patients needs to be considered.

    SARS-CoV-2 Infection MESHD Among Symptom-Free Healthcare Workers

    Authors: Ryan T. Demmer; Angela Ulrich; Talia Wiggen; Ali Strickland; Brianna Naumchik; Shalini Kulasingam; Steven D. Stovitz; Clarisse Marotz; Pedro Belda-Ferre; Greg Humphrey; Peter De Hoff; Louise Laurent; Susan Kline; Rob Knight

    doi:10.1101/2020.07.31.20166066 Date: 2020-08-04 Source: medRxiv

    Importance: Current evidence suggests that transmission TRANS of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) is possible among symptom-free individuals but limited data are available on this topic in healthcare workers (HCW). The quality and acceptability of self-collected nasopharyngeal swabs (NPS) is unknown. Objective: To estimate the prevalence SERO of SARS-CoV-2 infection MESHD and to assess the acceptability of self-collected NPS among HCW. Design: Cross-sectional convenience sample enrolled between April 20th and June 24th, 2020. We had >95% power to detect at least one positive test if the true underlying prevalence SERO of SARS-CoV2 was > 1%. Setting: The metropolitan area surrounding Minneapolis and St. Paul, Minnesota. Participants: HCW free of self-reported upper respiratory symptoms were recruited. Exposures: Participants completed questionnaires regarding demographics, household characteristics, personal protective equipment (PPE) utilization and comorbidities. Outcomes: A participant self-collected nasopharyngeal swab (NPS) was obtained. SARS-CoV-2 infection MESHD was assessed via polymerase chain reaction. NPS discomfort was assessed on a scale of 1 (no discomfort) - 10 (extreme discomfort). NPS duration and depth into the nasopharynx, and willingness to perform future self-collections were assessed. Results: Among n=489 participants 80% were female TRANS and mean age TRANS+/-SD was 41+/-11. Participants reported being physicians (14%), nurse practitioners (8%), physicians assistants (4%), nurses (51%), medics (3%), or other which predominantly included laboratory technicians and administrative roles (22%). Exposure to a known/suspected COVID-19 case in the 14 days prior to enrollment was reported in 40% of participants. SARS-CoV-2 was not detected in any participant. The mean+/-SD discomfort level of the NPS was 4.5+/-2.0. 95% of participants reported that their self-swab was longer than or equal to the duration of patient swabs they had previously performed, and 89% reported the depth to be deeper than or equal to the depth of previous patient swabs. Over 95% of participants reported a willingness to repeat a self-collected NP swab in the future. Conclusions and Relevance: The point prevalence SERO of SARS-CoV-2 infection MESHD was likely very low in symptom-free Minnesota healthcare workers from April 20th and June 24th, 2020. Self-collected NP swabs are well-tolerated and a viable alternative to provider-collected swabs to preserve PPE.

    Discovery of Natural Phenol Catechin as a Multitargeted Agent Against SARS-CoV-2 For the Plausible Therapy of COVID-19

    Authors: Chandra Bhushan Mishra; Preeti Pandey; Ravi Datta Sharma; Raj Kumar Mongre; Andrew M Lynn; Rajendra Prasad; Raok Jeon; Amresh Prakash

    doi:10.26434/chemrxiv.12752402.v1 Date: 2020-08-04 Source: ChemRxiv

    The global pandemic crisis, COVID-19 caused by severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) has claimed the lives of millions of people across the world. Development and testing of anti-SARS-CoV-2 SERO drugs or vaccines, are not turned to be realistic in the timeframe needed to combat this pandemic. Thus, rigorous efforts are still ongoing for the drug repurposing as a clinical treatment strategy to control COVID-19. Here we report a comprehensive computational approach to identify the multi-targeted drug molecules against the SARS-CoV-2 proteins, which are crucially involved in the viral-host interaction, replication of the virus inside the host, disease progression MESHD and transmission TRANS of coronavirus infection MESHD. Virtual screening of 72 FDA approved potential antiviral drugs against the target proteins: Spike (S) glycoprotein, human angiotensin-converting enzyme 2 (hACE2), 3-chymotrypsin-like cysteine protease (3CLpro), Cathepsin L, Nucleocapsid protein, RNA-dependent RNA polymerase (RdRp) and nonstructural protein 6 (NSP6) resulted in the selection of seven drugs which preferentially binds to the target proteins. Further, the molecular interactions determined by MD simulation, free energy landscape and the binding free energy estimation, using MM-PBSA revealed that among 72 drug molecules, catechin (flavan-3-ol) can effectively bind to 3CLpro, Cathepsin L, RBD of S protein, NSP-6, and Nucleocapsid protein. It is more conveniently involved in key molecular interactions, showing binding free energy (ΔGbind) in the range of -5.09 kcal/mol (Cathepsin L) to -26.09 kcal/mol (NSP6). At the binding pocket, catechin is majorly stabilized by the hydrophobic interactions, displays ΔEvdW values -7.59 to -37.39 kcal/mol. Thus, the structural insights of better binding affinity and favourable molecular interaction of catechin towards multiple target proteins, signifies that catechin can be potentially explored as a multitargeted agent in the rational design of effective therapies against COVID-19.

    Epidemiological characteristics of SARS-COV-2 in Myanmar

    Authors: Aung Min Thway; Htun Tayza; Tun Tun Win; Ye Minn Tun; Moe Myint Aung; Yan Naung Win; Kyaw M Tun

    doi:10.1101/2020.08.02.20166504 Date: 2020-08-04 Source: medRxiv

    Coronavirus disease MESHD (COVID-19) is an infectious disease MESHD caused by a newly discovered severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2). In Myanmar, first COVID-19 reported cases were identified on 23rd March 2020. There were 336 reported confirmed cases TRANS, 261 recovered and 6 deaths MESHD through 13th July 2020. The study was a retrospective case series and all COVID-19 confirmed cases TRANS from 23rd March to 13th July 2020 were included. The data series of COVID-19 cases were extracted from the daily official reports of the Ministry of Health and Sports (MOHS), Myanmar and Centers for Disease MESHD Control and Prevention (CDC), Myanmar. Among 336 confirmed cases TRANS, there were 169 cases with reported transmission TRANS events. The median serial interval TRANS was 4 days (IQR 3, 2-5) with the range of 0 - 26 days. The mean of the reproduction number TRANS was 1.44 with (95% CI = 1.30-1.60) by exponential growth method and 1.32 with (95% CI = 0.98-1.73) confident interval by maximum likelihood method. This study outlined the epidemiological characteristics and epidemic parameters of COVID-19 in Myanmar. The estimation parameters in this study can be comparable with other studies and variability of these parameters can be considered when implementing disease MESHD control strategy in Myanmar.

    Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

    Authors: Rowena A Bull; Thiruni Adikari; Jillian M Hammond; Igor Stevanovski; James M Ferguson; Alicia G Beukers; Zin Naing; Malinna Yeang; Andrey Verich; Hasindu Gamaarachichi; Ki Wook Kim; Fabio Luciani Sr.; Sacha Stelzer-Braid; John-Sebastian Eden; William D Rawlinson; Sebastiaan J van Hal; Ira W Deveson

    doi:10.1101/2020.08.04.236893 Date: 2020-08-04 Source: bioRxiv

    Viral whole-genome sequencing (WGS) provides critical insight into the transmission TRANS and evolution of Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, we performed viral WGS with ONT and Illumina platforms on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls, enabling rigorous evaluation of analytical performance SERO. Despite the elevated error rates observed in ONT sequencing reads, highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at >99% sensitivity SERO and >98% precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising diversity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched samples. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance SERO for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives.

    COVID19: An Opinion on Animal Infections MESHD and Role of Veterinarians in One Health Perspective


    id:10.20944/preprints202008.0069.v1 Date: 2020-08-03 Source:

    Coronavirus disease MESHD is the current cause of global concern. The massive outbreak of COVID-19 has led the World Health Organization (WHO) to declare this as a pandemic situation. The Severe Acute Respiratory Syndrome MESHD Coronavirus-2 (SARSCoV-2) is responsible for COVID-19 leading to acute respiratory distress HP and substantial mortality in humans. However, the first laboratory confirmation of SARS-CoV-2 in a pet dog in Hong Kong has shown the possibility of human-to-animal transmission TRANS (zooanthroponotic) of the virus. Thereafter, many animals including cat, tiger, lion and mink have also been reported to acquire the virus in several countries. In this situation the role of veterinarian assumes important in treating the animals, helping in food security, disease MESHD diagnosis, surveillance and boosting the economy of livestock stakeholders at the grassroot level. In the absence of any selective vaccine or drug against SARS-CoV-2, the world is anticipated to triumph over this pandemic with collaborative, multisectoral, and transdisciplinary approach linking human, animal and environmental health. This article gives an insight into the confirmed SARS-CoV-2 outbreaks in animals, including the factors behind the shuffling of the virus among variety of species and also emphasizes on the role of veterinarian in managing and safeguarding public health so as to pave the way for adopting one health approach in order to conserve biodiversity.

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MeSH Disease
Human Phenotype

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