Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    Analyzing the dominant SARS-CoV-2 transmission TRANS routes towards an ab-initio SEIR model

    Authors: Swetaprovo Chaudhuri; Saptarshi Basu; Abhishek Saha

    id:2007.13596v2 Date: 2020-07-27 Source: arXiv

    Identifying the relative importance of the different transmission TRANS routes of the SARS-CoV-2 virus is an urgent research priority. To that end, the different transmission TRANS routes, and their role in determining the evolution of the Covid-19 pandemic are analyzed in this work. Probability of infection MESHD caused by inhaling virus-laden droplets (initial, ejection diameters between $0.5-750\mu m$) and the corresponding desiccated nuclei that mostly encapsulate the virions post droplet evaporation, are individually calculated. At typical, air-conditioned yet quiescent indoor space, for average viral loading, cough MESHD cough HP droplets of initial diameter between $10-50 \mu m$ have the highest infection MESHD probability. However, by the time they are inhaled, the diameters reduce to about $1/6^{th}$ of their initial diameters. While the initially near unity infection MESHD probability due to droplets rapidly decays within the first $25s$, the small yet persistent infection MESHD probability of desiccated nuclei decays appreciably only by $\mathcal{O} (1000s)$, assuming the virus sustains equally well within the dried droplet nuclei as in the droplets. Combined with molecular collision theory adapted to calculate frequency of contact TRANS frequency of contact SERO between the susceptible population and the droplet/nuclei cloud, infection MESHD rate constants are derived ab-initio, leading to a SEIR model applicable for any respiratory event - vector combination. Viral load, minimum infectious dose, sensitivity SERO of the virus half-life to the phase of its vector and dilution of the respiratory jet/puff by the entraining air are shown to mechanistically determine specific physical modes of transmission TRANS and variation in the basic reproduction number TRANS $\mathcal{R}_0$, from first principle calculations.

    Probability of aerosol transmission TRANS of SARS-CoV-2

    Authors: Daniel Bonn; Scott Howard Smith; Aernout Somsen; Cees van Rijn; Stefan Kooij; Lia van der Hoek; Reinout A Bem

    doi:10.1101/2020.07.16.20155572 Date: 2020-07-18 Source: medRxiv

    Transmission TRANS of SARS-CoV-2 leading to COVID-19 occurs through exhaled respiratory droplets from infected humans. Currently, however, there is much controversy over whether respiratory aerosol microdroplets play an important role as a route of transmission TRANS. By measuring and modeling the dynamics of exhaled respiratory droplets we can assess the relative contribution of aerosols in the spreading of SARS-CoV-2. We measure size distribution, total numbers and volumes of respiratory droplets, including aerosols, by speaking and coughing MESHD coughing HP from healthy subjects. Dynamic modelling of exhaled respiratory droplets allows to account for aerosol persistence times in confined public spaces. The probability of infection MESHD by inhalation of aerosols when breathing in the same space can then be estimated using current estimates of viral load and infectivity of SARS-CoV-2. In line with the current known reproduction numbers TRANS, our study of transmission TRANS of SARS-CoV-2 suggests that aerosol transmission TRANS is an inefficient route, in particular from non or mildly symptomatic individuals.

    Epidemiological and clinical characteristics of COVID-19 in Indian children TRANS in the initial phase of the pandemic: A cross-sectional study

    Authors: Bhakti Sarangi; Venkat Sandeep Reddy; Jitendra S. Oswal; Nandini Malshe; Ajinkya Patil; Manojit Chakraborty; Sanjay Lalwani

    doi:10.21203/rs.3.rs-36303/v1 Date: 2020-06-17 Source: ResearchSquare

    Background: India saw the largest and the most stringent lockdown in the world when the number of COVID-19 cases reached around 550. With some early benefits in containing the surge and restricting the R0 TRANS of the virus, the current relaxation of lockdown norms has witnessed an exponential rise in positive cases. With scarcity of Pediatric data from the Indian subcontinent, early observations in the pandemic are pivotal in improving the understanding of physiologic behaviors, identifying risks, and guiding clinicians in assessing time-tested interventions and augmenting the awareness in the masses about the manifold clinical profiles of an evolving disease MESHD.Objective: To assess the epidemiological and clinical characteristics of children TRANS admitted with COVID-19 infection MESHD early in the pandemic.Study Design: A cross-sectional studyParticipants: Fifty children TRANS between one month and 18 years of age TRANS whose nasopharyngeal swab tested positive for SARS-CoV-2 by RT- PCR. Results: 28 (56%) children TRANS were male TRANS. 41 (82%) came from government declared containment zones with only one child TRANS having history of travel TRANS to affected area. Home overcrowding was observed in 33 (66%). Of the 50 children TRANS, 29 (58%) were asymptomatic TRANS while 20 (40%) and one (2%) had mild and moderate symptoms respectively. Fever MESHD Fever HP, cough MESHD cough HP, and sore throat were the most common symptoms. 49 (98%) children TRANS had BCG scar HP. Leucopenia was seen in three (6%) only. Mean (SD) Neutrophil-Lymphocyte-Ratio (NLR) was 0.78 (0.48) while mean (SD) CRP was 10.98 (23.90). All 50 (100%) were cured. Conclusion: Our study reasserts the increasing pediatric burden of COVID-19 with all age groups TRANS affected and overcrowding as a risk factor for continued community transmission TRANS, thus beckoning that public health policies be directed to ensuring further preventive measures. It also re-iterates the milder disease MESHD pattern in children TRANS with COVID-19 in the initial phase of the pandemic with a high proportion of asymptomatic TRANS and mild illness. Though abnormal CRP values are synonymous with the illness in children TRANS; leucopenia may not be a consistent finding.  

    Eat, Pray, Work: A meta-analysis of COVID-19 Transmission Risk TRANS in Common Activities of Work and Leisure

    Authors: Meher K Prakash

    doi:10.1101/2020.05.22.20110726 Date: 2020-05-24 Source: medRxiv

    ABSTRACT. BACKGROUND. When the lockdowns are relaxed, the responsibility of mitigating the COVID-19 spread shifts from the governments to the individuals. To know how to conduct one-self, it is important for everyone to know the risks of transmission TRANS during the quotidian activities - meetings, meals, etc, from individuals who are known to them and looking healthy. METHODS. The detailed case-studies corresponding to 425 infections MESHD upon point-exposures over a specified duration are curated. The data from the case studies is summarized and reorganized to reflect different situations from the daily life. A meta-analysis of the attack rates TRANS of transmission TRANS and the number of infections MESHD per infected person are performed. RESULTS. The attack rates TRANS are very high in family dinners (66.7% (48.8-80.8%)) compared to sit-down dinners with lesser mixing among people eating at different tables (15.7% (12.1-20.1%)), both lasting a couple of hours. In an open workspace office floor organized in a two-half structure with shared elevators and restrooms and the employees speaking continuously, the average attack rate TRANS over the course of a few days was much higher in one half (78.7% (70.3-85.3%)) than the one for the entire floor (43.5% (37.0-50.1%)). Inferred data suggests that the transmission TRANS in elevators and trains may be lower under the conditions of using masks. In most of the instances we studied, the infected individuals spreading (35/44) and even super-spreading (3/6) were mostly without symptoms of coughing MESHD coughing HP, sneezing MESHD sneezing HP or a fever MESHD fever HP. CONCLUSIONS. Although the basic reproduction number TRANS R0 TRANS is around 3.0, the number of infections MESHD caused, including the super-spreading events, seem to be limited by the number of personal interactions in a group and their proximity. By acknowledging the risks in daily life, from healthy-looking persons, one may be able to organize their interactions better to reduce the chances of spreading or super-spreading infections MESHD.

    Epidemiologic, Clinical, and Laboratory Findings of the COVID-19 in the current pandemic: Systematic Review and Meta-analysis

    Authors: Yewei Xie; Zaisheng Wang; Huipeng Liao; Gifty Marley; Dan Wu; Weiming Tang

    doi:10.21203/rs.3.rs-28367/v2 Date: 2020-05-11 Source: ResearchSquare

    Background: The COVID-19 pandemic has affected the world deeply, with more than 3,000,000 people infected and nearly 200,000 deaths MESHD. This review aimed to summarize the epidemiologic traits, clinical spectrum, CT results and laboratory findings of the COVID-19 pandemic.Methods: We scoped for relevant literatures published during 1st Dec 2019 to 23rd Apr 2020 based on four databases using English and Chinese languages. We reviewed and analyzed the relevant clinic outcomes of COVID-19.Results: The COVID-19 pandemic was found to have a higher transmission TRANS rate compared to SARS and MERS and involved 4 stages of evolution. The basic reproduction number TRANS ( R0 TRANS) is 3.32 (95% CI:3.24-3.39), the incubation period TRANS was 5.24 days (95% CI:3.97-6.50, 5 studies) on average, and the average time for symptoms onset TRANS varied by countries. Common clinical spectrums identified included fever MESHD fever HP (38.1-39.0℃), cough MESHD cough HP and fatigue MESHD fatigue HP, with Acute Respiratory Distress HP Syndrome MESHD (ARDS) being the most common complication reported. Body temperatures above 39.0 ℃, dyspnea MESHD dyspnea HP, and anorexia MESHD anorexia HP were more common symptoms in severe patients. Aged TRANS over 60 years old, having co-morbidities, and developing complications were the commonest high-risk factors associated with severe conditions. Leucopenia and lymphopenia MESHD lymphopenia HP were the most common signs of infection MESHD while liver and kidney damage were rare but may cause bad outcomes for patients. The bilateral, multifocal Ground-Glass Opacification (GGO) on peripheral, and the consolidative pulmonary opacity HP were the most frequent CT results and the tendency of mortality rates differed by region.Conclusions: We provided a bird’s-eye view of the COVID-19 during the current pandemic, which will help better understanding the key traits of the disease MESHD. The findings could be used for disease’s future research, control and prevention.

    Epidemic Peak for COVID-19 in India, 2020

    Authors: Chaitanya S. Wagh; Parikshit N. Mahalle; Sanjeev J. Wagh

    id:10.20944/preprints202005.0176.v1 Date: 2020-05-10 Source: Preprints.org

    In India the first case of coronavirus disease MESHD 2019 (COVID-19) reported on 30 January 2020, and thereafter cases were increasing daily after the last week of Feb. 2020. COVID-19 identified as family member TRANS of coronaviridae where previously Middle East Respiratory Syndrome MESHD MERS and Severe Acute Respiratory Syndrome MESHD SARS belongs to same family. The COVID-19 attacks on respiratory system signing fever MESHD fever HP, cough MESHD cough HP and breath shortness, in severe cases may cause pneumonia MESHD pneumonia HP, SARS or some time death MESHD. The aim of this study work is to develop model which predicts the epidemic peak for COVID-19 in India by using the real-time data from 30 Jan to 10 May 2020. There are uncertainties while identifying the population information due to the incomplete and inaccurate data, we initiate the most popular model for epidemic prediction i.e Susceptible, Exposed, Infectious, & Recovered SEIR initially the compartmental model for the prediction. Based on the solution of the state estimation problem for polynomial system with Poisson noise, we estimate that the epidemic peak may reach the early-middle July 2020, initializing recovered R0 TRANS to 0 and Infected I0 to 1. The outcomes of the model will help epidemiologist to isolate the source of the disease MESHD geospatially and analyze the death MESHD. Also government authorities will be able to target their interventions for rapidly checking the spread of the epidemic.

    Exit strategies: optimising feasible surveillance for detection, elimination and ongoing prevention of COVID-19 community transmission TRANS

    Authors: Kamalini Lokuge; Emily Banks; Stephanie Davis; Leslee Roberts; Tatum Street; Grazia Caleo; Kathryn Glass

    doi:10.1101/2020.04.19.20071217 Date: 2020-04-23 Source: medRxiv

    Background Following successful implementation of strong containment measures by the community, Australia is now close to the point of eliminating detectable community transmission TRANS of COVID-19. We aimed to develop an efficient, rapid and scalable surveillance strategy for detecting all remaining COVID-19 community transmission TRANS through exhaustive identification of every active transmission chain TRANS. We also identified measures to enable early detection and effective management of any reintroduction of transmission TRANS once containment measures are lifted to ensure strong containment measures do not need to be reinstated. Methods We compared efficiency and sensitivity SERO to detect community transmission chains TRANS through testing of: hospital cases; primary TRANS care fever MESHD fever HP and cough MESHD cough HP patients; or asymptomatic TRANS community members, using surveillance evaluation methods and mathematical modelling, varying testing capacities and prevalence SERO of COVID-19 and non-COVID-19 fever MESHD fever HP and cough MESHD cough HP, and the reproduction number TRANS. System requirements for increasing testing to allow exhaustive identification of all transmission chains TRANS, and then enable complete follow-up of all cases and contacts within each chain, were assessed per million population. Findings Assuming 20% of cases are asymptomatic TRANS and all symptomatic COVID-19 cases present to primary care, with high transmission TRANS (R=2.2) there are a median of 13 unrecognised community cases (5 infectious) when a transmission chain TRANS is identified through hospital surveillance versus 3 unrecognised cases (1 infectious) through primary care surveillance. 3 unrecognised community upstream community cases themselves are estimated to generate a further 22-33 contacts requiring follow-up. The unrecognised community cases rise to 5 if only 50% of symptomatic cases present to primary care. Screening for asymptomatic disease MESHD asymptomatic TRANS in the community cannot exhaustively identify all transmission TRANS under any of the scenarios assessed. The additional capacity required to screen all fever MESHD fever HP and cough MESHD cough HP primary care patients would be approximately 2,000 tests/million population per week using 1/16 pooling of samples. Interpretation Screening all syndromic fever MESHD fever HP and cough MESHD cough HP primary care presentations, in combination with exhaustive and meticulous case and contact identification and management, enables appropriate early detection and elimination of community transmission TRANS of COVID-19. If testing capacity is limited, interventions such as pooling allow increased case detection, even given reduced test sensitivity SERO. Wider identification and testing of all upstream contacts, (i.e. potential sources of infection MESHD for identified cases, and their related transmission chains TRANS) is critical, and to be done exhaustively requires more resources than downstream contact tracing TRANS. The most important factor in determining the performance SERO of such a surveillance system is community participation in screening and follow up, and as such, appropriate community engagement, messaging and support to encourage presentation and compliance is essential. We provide operational guidance on implementing such a system.

    A Territory-wide study of COVID-19 cases and clusters with unknown source in Hong Kong community: A clinical, epidemiological and phylogenomic investigation

    Authors: Kenneth Siu-Sing Leung; Timothy Ting-Leung Ng; Alan Ka-Lun Wu; Miranda Chong-Yee Yau; Hiu-Yin Lao; Ming-Pan Choi; Kingsley King-Gee Tam; Lam-Kwong Lee; Barry Kin-Chung Wong; Alex Yat-Man Ho; Kam-Tong Yip; Kwok-Cheung Lung; Raymond Wai-To Liu; Eugene Yuk-Keung Tso; Wai-Shing Leung; Man-Chun Chan; Yuk-Yung Ng; Kit-Man Sin; Kitty Sau-Chun Fung; Sandy Ka-Yee Chau; Wing-Kin To; Tak-Lun Que; David Ho-Keung Shum; Shea Ping Yip; Wing-Cheong Yam; Gilman Kit Hang Siu

    doi:10.1101/2020.03.30.20045740 Date: 2020-03-31 Source: medRxiv

    Background: Initial cases of coronavirus disease MESHD 2019 (COVID-19) reported in Hong Kong were mostly imported cases from Mainland China. However, most cases reported in February 2020 were local infections MESHD with unknown source, indicating local community transmissions TRANS. This study aimed to report the clinical, epidemiological and phylogenomic characteristics of the local cases of COVID-19 in our community. Methods: We extracted the demographic, clinical and epidemiological data from 50 COVID-19 patients, who accounted for 53.8% of the cases in Hong Kong by the end of February 2020. We used both Nanopore and Illumina platforms to perform whole-genome sequencing (WGS) of the severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) from these patients. Phylogenetic relatedness among these local cases and their placement in the global phylogeny were examined. The evolutionary rate and divergence time of transmission TRANS were also determined. Findings: Of these 50 patients, only three (6.0%) had visited Wuhan while 43 (86.0%) did not have recent travel TRANS records. The average interval from symptom onset TRANS to hospital admission was 8.5 days. The most common signs and symptoms MESHD on admission were cough MESHD cough HP (74.0%) and fever MESHD fever HP (58.0%). Radiographic abnormality was found in 46 (92.0%) patients. Three (6.0%) patients required ICU admission. Phylogenetic analysis concurred with epidemiological investigation that 42 (84.0%) cases could be grouped into six transmission TRANS clusters. Forty-four (88.0%) cases harboured a common mutation Orf3a G251V. Global phylogeny of SARS-CoV-2 revealed that most (88.0%) cases in Hong Kong were clustered in two subclades with the strains from other countries. The estimated time to the most recent common ancestor (tMRCA) of COVID-2019 outbreak in Hong Kong was December 24, 2019 with an evolutionary rate of 3.04x10-3 substitutions per site per year. The reproduction number TRANS value was 1.84 as of February 28, 2020 in Hong Kong. Interpretation: We provided a territory-wide overview of COVID-19 in Hong Kong, which has borders connecting to Mainland China. Transmission TRANS in closed settings especially during family and religious gatherings is a hallmark of the recently reported cases. The reproduction number TRANS value indicated an ongoing outbreak in the community. Social distancing and vigilant epidemiological control are crucial to the containment of COVID-19 transmission TRANS

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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