Corpus overview


MeSH Disease

Human Phenotype

Pneumonia (200)

Hypertension (135)

Fever (122)

Cough (105)

Respiratory distress (88)


    displaying 31 - 40 records in total 2378
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    Reconciling epidemiological models with misclassified case-counts for SARS-CoV-2 with seroprevalence SERO surveys: A case study in Delhi, India

    Authors: Rupam Bhattacharyya; Ritwik Bhaduri; Ritoban Kundu; Maxwell Salvatore; Bhramar Mukherjee

    doi:10.1101/2020.07.31.20166249 Date: 2020-08-04 Source: medRxiv

    Underreporting of COVID-19 cases and deaths MESHD is a hindrance to correctly modeling and monitoring the pandemic. This is primarily due to limited testing, lack of reporting infrastructure and a large number of asymptomatic infections MESHD asymptomatic TRANS. In addition, diagnostic tests (RT-PCR tests for detecting current infection MESHD) and serological antibody tests SERO for IgG (to assess past infections MESHD) are imperfect. In particular, the diagnostic tests have a high false negative rate. Epidemiologic models with a latent compartment for unascertained infections MESHD like the Susceptible-Exposed-Infected-Removed (SEIR) models can provide predictions for unreported cases and deaths MESHD under certain assumptions. Typically, the number of unascertained cases is unobserved and thus we cannot validate these estimates for a real study except for simulation studies. Population-based seroprevalence SERO studies can provide a rough estimate of the total number of infections MESHD and help us check epidemiologic model projections. In this paper, we develop a method to account for high false negative rates in RT-PCR in an extension to the classic SEIR model. We apply this method to Delhi, the national capital region of India, with a population of 19.8 million and a COVID-19 hotspot of the country, obtaining estimates of underreporting factor for cases at 34-53 times and that for deaths MESHD at 8-13 times. Based on a recently released serological survey for Delhi with an estimated 22.86% seroprevalence SERO, we compute adjusted estimates of the true number of infections MESHD reported by the survey (after accounting for misclassification of the antibody test SERO results) which is largely consistent with the model outputs, yielding an underreporting factor for cases from 30-42. Together with the model and the serosurvey, this implies approximately 96-98% cases in Delhi remained unreported and whereas only 109,140 cases were reported on July 10, the true number of infections MESHD varied somewhere between 4.4-4.6 million across different estimates. While repeated serological monitoring is resource intensive, model-based adjustments, run with the most up to date data, can provide a viable option to keep track of the unreported cases and deaths MESHD and gauge the true extent of transmission TRANS of this insidious virus.

    Comparing the impact on COVID-19 mortality of self-imposed behavior change and of government regulations across 13 countries

    Authors: Julian Jamison; Donald Bundy; Dean Jamison; Jacob Spitz; Stephane Verguet

    doi:10.1101/2020.08.02.20166793 Date: 2020-08-04 Source: medRxiv

    Background: Countries have adopted different approaches, at different times, to reduce the transmission TRANS of coronavirus disease MESHD 2019 (COVID-19). Cross-country comparison could indicate the relative efficacy of these approaches. We assess various non-pharmaceutical interventions (NPIs) over time, comparing the effects of self-imposed (i.e. voluntary) behavior change and of changes enforced via official regulations, by statistically examining their impacts on subsequent death MESHD rates in 13 European countries. Methods and findings: We examine two types of NPI: the introduction of government-enforced closure policies over time; and self-imposed alteration of individual behaviors in response to awareness of the epidemic, in the period prior to regulations. Our proxy for the latter is Google mobility data, which captures voluntary behavior change when disease MESHD salience is sufficiently high. The primary outcome variable is the rate of change in COVID-19 fatalities per day, 16-20 days after interventions take place. Linear multivariate regression analysis is used to evaluate impacts. Voluntarily reduced mobility, occurring prior to government policies, decreases the percent change in deaths MESHD per day by 9.2 percentage points (95% CI 4.5-14.0 pp). Government closure policies decrease the percent change in deaths MESHD per day by 14.0 percentage points (95% CI 10.8-17.2 pp). Disaggregating government policies, the most beneficial are intercity travel TRANS restrictions, cancelling public events, and closing non-essential workplaces. Other sub-components, such as closing schools and imposing stay-at-home rules, show smaller and statistically insignificant impacts. Conclusions: This study shows that NPIs have substantially reduced fatalities arising from COVID-19. Importantly, the effect of voluntary behavior change is of the same order of magnitude as government-mandated regulations. These findings, including the substantial variation across dimensions of closure, have implications for the phased withdrawal of government policies as the epidemic recedes, and for the possible reimposition of regulations if a second wave occurs, especially given the substantial economic and human welfare consequences of maintaining lockdowns.

    Cold-adapted live attenuated SARS-CoV-2 vaccine completely protects human ACE2 transgenic mice from SARS-CoV-2 infection MESHD

    Authors: Sang Heui Seo; Yunyueng Jang

    doi:10.1101/2020.08.04.235689 Date: 2020-08-04 Source: bioRxiv

    Severe acute respiratory syndrome MESHD coronavirus (SARS-CoV-2) has infected more than 16,000,000 people and has caused the death MESHD of more than 650,000 individuals since December 2019. A safe and effective vaccine that can provide herd immunity against SARS-CoV-2 is urgently needed to stop the spread of this virus among humans. Many human viral vaccines are live attenuated forms of viruses that elicit humoral and cellular immunity. Here, we describe the development of a cold-adapted live attenuated vaccine (SARS-CoV-2/human/Korea/CNUHV03-CA22{degrees}C/2020) by gradually adapting the growth of SARS-CoV-2 from 37{degrees}C to 22{degrees}C in Vero cells. This vaccine can be potentially administered to humans through nasal spray. Its single dose was observed to strongly induce the neutralising antibody SERO (>640), cellular immunity, and mucosal IgA antibody SERO in intranasally immunised K18-hACE2 mice, which are very susceptible to SARS-CoV-2 and SARS-CoV infection MESHD. The one-dose vaccinated mice were completely protected from SARS-CoV-2 infection MESHD and did not show loss of body weight MESHD, death MESHD, and the presence of virus in tissues, such as the nasal turbinates, brain, lungs, and kidneys. Taken together, the cold-adapted live attenuated SARS-CoV-2 vaccine developed by us may contribute to saving of human lives from the threat of SARS-CoV-2.

    A Study on Survival Scenario of COVID-19 patients in India: An Application of Survival Analysis on patient demographics

    Authors: Sampurna Kundu; Kirti; Debarghya Mandal

    doi:10.1101/2020.08.01.20162115 Date: 2020-08-04 Source: medRxiv

    The study of transmission TRANS dynamics of COVID-19, have depicted the rate, patterns and predictions of the pandemic cases. In order to combat the disease MESHD transmission TRANS in India, the Government had declared lockdown on the 25th of March. Even after a strict lockdown nationwide, the cases are increasing and have crossed 4.5 lakh positive cases. A positive point to be noted amongst all that the recovered cases are slowly exceeding the active cases. The survival of the patients, taking death MESHD as the event that varies over age groups TRANS and gender TRANS wise is noteworthy. This study aims in carrying out a survival analysis to establish the variability in survivorship among age groups TRANS and sex, at different levels, that is, national, state and district level. The open database of COVID-19 tracker ( of India has been utilized to fulfill the objectives of the study. The study period has been taken from the beginning of the first case which was on 30th Jan 2020 till 30th June. Due to the amount of under-reporting of data and dropping missing columns a total of 26,815 sample patients were considered. The entry point of each patient is different and event of interest is death MESHD in the study. Kaplan Meier survival estimation, Cox proportional hazard model and multilevel survival model has been used to perform survival analysis. Kaplan Meier survival function, shows that the probability of survival has been declining during the study period of five months. A significant variability has been observed in the age groups TRANS, as evident from all the survival estimates, with increasing age TRANS the risk of dying from COVID-19 increases. When Western and Central India show ever decreasing survival rate in the framed time period then Eastern , North Eastern and Southern India shows a slightly better picture in terms of survival. Maharashtra, Gujarat, Delhi, Rajasthan and West bengal showed alrmingly poor survival as well. This study has depicted a grave scenario of gradation of ever decreasing survival rates in various regions and shows the variability by age TRANS and gender TRANS.

    Possible Cross-Reactivity Between SARS-CoV-2 Proteins, CRM197 and Proteins in Pneumococcal Vaccines May Protect Against Symptomatic SARS-CoV-2 Disease MESHD and Death MESHD

    Authors: Robert Root-Bernstein

    id:10.20944/preprints202007.0141.v2 Date: 2020-08-04 Source:

    Various studies indicate that vaccination, especially with pneumococcal vaccines, protects against symptomatic cases of SARS-CoV-2 infection MESHD and death MESHD. This paper explores the possibility that pneumococcal vaccines in particular, but perhaps other vaccines as well, contain antigens that might be cross-reactive with SARS-CoV-2 antigens. Comparison of the glycosylation structures of SARS-CoV-2 with the polysaccharide structures of pneumococcal vaccines yielded no obvious similarities. However, while pneumococcal vaccines are primarily composed of capsular polysaccharides, some are conjugated to CRM197, a modified diphtheria MESHD toxin, and all contain about three percent protein contaminants, including the pneumococcal surface proteins PsaA, PspA and probably PspC. All of these proteins have very high degrees of similarity, using very stringent criteria, with several SARS-CoV-2 proteins including the spike protein, membrane protein and replicase 1a. CRM197 is also present in Hib and meningitis MESHD meningitis HP vaccines. Equivalent similarities were found at statistically significantly lower rates, or were completely absent, among the proteins in diphtheria MESHD, tetanus MESHD, pertussis, measles MESHD, mumps MESHD, rubella MESHD, and poliovirus vaccines. Notably, PspA and PspC are highly antigenic and new pneumococcal vaccines based on them are currently in human clinical trials so that their effectiveness against SARS-CoV-2 disease MESHD is easily testable.

    Altitude as a protective factor from COVID-19

    Authors: Timothy M Thomson; Fresia Casas; Harold Andre Guerrero; Rómulo Figueroa-Mujica; Francisco C Villafuerte; Claudia Machicado

    doi:10.1101/2020.08.03.20167262 Date: 2020-08-04 Source: medRxiv

    The COVID-19 pandemic had a delayed onset in South America compared to Asia (outside of China), Europe or North America. In spite of the presumed time advantage for the implementation of preventive measures to help contain its spread, the pandemic in that region followed growth rates that paralleled, and currently exceed, those observed several weeks before in Europe. Indeed, in early August, 2020, many countries in South and Central America presented among the highest rates in the world of COVID-19 confirmed cases TRANS and deaths MESHD per million inhabitants. Here, we have taken an ecological approach to describe the current state of the pandemic in Peru and its dynamics. Our analysis supports a protective effect of altitude from COVID-19 incidence and mortality. Further, we provide circumstantial evidence that internal migration through a specific land route is a significant factor progressively overriding the protection from COVID-19 afforded by high altitude. Finally, we show that protection by altitude is independent of poverty indexes and is inversely correlated with the prevalence SERO in the population of risk factors associated with severe COVID-19, including hypertension MESHD hypertension HP and hypercholesterolemia MESHD hypercholesterolemia HP. We discuss long-term multisystemic adaptations to hypobaric hypoxia MESHD as possible mechanisms that may explain the observed protective effect of high altitude from death MESHD from COVID-19.

    Correlation between daily infections MESHD and fatality rate due to Covid-19 in Germany

    Authors: Dieter Mergel

    doi:10.1101/2020.08.03.20167304 Date: 2020-08-04 Source: medRxiv

    The daily Covid-19 fatality rate is modelled with a trend line based on nominal day-to-day reproduction rates and a cosine to take account of weekly fluctuations. The fatality trajectory represented by this trend line can be projected from the number of daily infections MESHD by assuming a time lapse between symptom onset TRANS and death MESHD between 17 and 19 days and a nominal time-dependent fatality rate. The time trajectory of this fatality rate suggests a change of the infection MESHD dynamics at April 3, with an increase from 2.5% to 6% within 20 days perhaps indicating spread of infection MESHD to more vulnerable people. Later in summer, the nominal fatality rate decreases down to 1% in mid-July raising the question whether Covid-19 is intrinsically less lethal in summer. Although the time trajectories of infections MESHD and fatality are pronouncedly different, the reproduction rates obtained therefrom are similar indicating that the infection MESHD dynamics may reasonably well be deduced from the potentially biased reported infection MESHD rate if it is biased consistently, i.e. the same way, over an extended period of time. The administrative measures to contain the pandemic seem not to have an immediate effect on the infection MESHD dynamics but well the ease of restrictions. An effect of mask wearing on decreasing lethality cannot be excluded.

    Waves of COVID-19 pandemic. Detection and SIR simulations

    Authors: Igor Nesteruk

    doi:10.1101/2020.08.03.20167098 Date: 2020-08-04 Source: medRxiv

    Background. Unfortunately, the COVID-19 pandemic is still far from stabilizing. Of particular concern is the sharp increase in the number of diseases MESHD in June-July 2020. The causes and consequences of this sharp increase in the number of cases are still waiting for their researchers, but there is already an urgent need to assess the possible duration of the pandemic, the expected number of patients and deaths MESHD. The resumption of international passenger traffic needs the information for deciding which countries' citizens are welcome guests. Correct simulation of the infectious disease MESHD dynamics needs complicated mathematical models and many efforts for unknown parameters identification. Constant changes in the pandemic conditions (in particular, the peculiarities of quarantine and its violation, situations with testing and isolation of patients) cause various epidemic waves, lead to changes in the parameter values of the mathematical models. Objective. In this article, pandemic waves in Ukraine and in the world will be detected, calculated and discussed. The estimations for hidden periods, epidemic durations and final numbers of cases will be presented. The probabilities of meeting a person spreading the infection MESHD and reproduction numbers TRANS will be calculated for different countries and regions. Methods. We propose a simple method for the epidemic waves detection based on the differentiation of the smoothed number of cases. We use the known SIR (susceptible-infected-removed) model for the dynamics of the epidemic waves. The known exact solution of the SIR differential equations and statistical approach were modified and used. Results. The optimal values of the SIR model parameters were identified for four waves of pandemic dynamics in Ukraine and five waves in the world. The number of cases and the number of patients spreading the infection MESHD versus time were calculated. In particular, the pandemic probably began in August 2019. If current trends continue, the end of the pandemic should be expected no earlier than in March 2021 both in Ukraine and in the world, the global number of cases will exceed 20 million. The probabilities of meeting a person spreading the infection MESHD and reproduction numbers TRANS were calculated for different countries and regions. Conclusions. The SIR model and statistical approach to the parameter identification are helpful to make some reliable estimations of the epidemic waves. The number of persons spreading the infection MESHD versus time was calculated during all the epidemic waves. The obtained information will be useful to regulate the quarantine activities, to predict the medical and economic consequences of the pandemic and to decide which countries' citizens are welcome guests.

    A longitudinal survey for genome-based identification of SARS-CoV-2 in sewage water in selected lockdown areas of Lahore city, Pakistan; a potential approach for future smart lockdown strategy

    Authors: Tahir Yaqub; Muhammad Nawaz; Muhammad Zubair Shabbir; Muhammad Asad Ali; Imran Altaf; Sohail Raza; Muhammad Abu Bakr Shabbir; Muhammad Adnan Ashraf; Syed Zahid Aziz; Sohail Qadir Cheema; Muhammad Bilal Shah; Sohail Hassan; Saira Rafique; Nageen Sardar; Adnan Mehmood; Muhammad Waqar Aziz; Sehar Fazal; Nadir Khan; Muhammad Tahir Khan; Muhammad Moavia Attique; Ali Asif; Muhammad Anwar; Nabeel Ahmad Awan; Muhammad Usman Younis; Muhammad Ajmal Bhatti; Zarfishan Tahir; Nadia Mukhtar; Huda Sarwar; Maaz Sohail Rana

    doi:10.1101/2020.07.31.20165126 Date: 2020-08-04 Source: medRxiv

    Severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infections MESHD has affected more than 15 million people and, as of 22 July 2019, caused deaths MESHD of more than 0.6 million individuals globally. With the excretion of SARS-CoV-2 in the stool of symptomatic and asymptomatic TRANS COVID-19 patients, its genome detection in the sewage water can be used as a powerful epidemiological tool to predict the number of positive cases in a population. This study was conducted to detect SARS-CoV-2 genome in sewage water during the lockdown. Sewage samples, from 28 pre-selected sites, were collected on alternate days from 13-25 July, 2020 from two selected areas [Johar Town (n = 05) and Township (n = 23)], where smart lockdown were implemented by the government authorities on 9th July, 2020. Genomic RNA was extracted and the SARS-CoV-2 was detected and quantified using commercially available kit through Real-Time PCR. Out of 28, sixteen samples were positive on day one while 19, 17, 23, 17, 05 and 09 samples were positive on day 3, 5, 7, 9, 11, and 13, respectively. These results indicate the decreasing viral copy load with the passage of time however few sites did not followed a clear pattern indicating the complexities in sewage water based surveillance i.e time of sampling. Hourly sampling from two sites for 24 hours also revealed the impact of time sampling time on detection of SARS-CoV-2 genome in sewage pipelines and lift/disposal stations. Results of current study indicate a possible role of sewage-based COVID-19 surveillance in monitoring and execution of smart lockdowns.

    Physical activity, BMI and COVID-19: an observational and Mendelian randomisation study

    Authors: Xiaomeng Zhang; Xue Li; Ziwen Sun; Yazhou He; Wei Xu; Harry Campbell; Malcolm G Dunlop; Maria Timofeeva; Evropi Theodoratou

    doi:10.1101/2020.08.01.20166405 Date: 2020-08-04 Source: medRxiv

    Physical activity (PA) is known to be a protective lifestyle factor against several non- communicable diseases MESHD while its impact on infectious diseases MESHD, including Coronavirus Disease MESHD 2019 (COVID-19) is not as clear. We performed univariate and multivariate logistic regression to identify associations between body mass index (BMI) and both objectively and subjectively measured PA collected prospectively and COVID-19 related outcomes (Overall COVID-19, inpatient COVID-19, outpatient COVID-19, and COVID-19 death MESHD) in the UK Biobank (UKBB) cohort. Subsequently, we tested causality by using two-sample Mendelian randomisation (MR) analysis. In the multivariable model, the increased acceleration vector magnitude PA (AMPA) was associated with a decreased probability of overall and outpatient COVID-19. No association was found between self-reported moderate-to-vigorous PA (MVPA) or BMI and COVID-19 related outcomes. Although no causal association was found by MR analyses, this may be due to limited power and we conclude policies to encourage and facilitate exercise at a population level during the pandemic should be considered.

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MeSH Disease
Human Phenotype

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