Corpus overview


MeSH Disease

Human Phenotype


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    Mathematical Modelling of COVID-19 Pandemic with Demographic Effects

    Authors: Abdul Alimamy Kamara; Lagès N. Mouanguissa; Godfrey Barasa

    doi:10.21203/ Date: 2020-08-10 Source: ResearchSquare

    In this paper, an asymptomatic infection MESHD asymptomatic TRANS transmission TRANS Susceptible-Exposed-Infectious-Recovered (SEIR) model with demographic effects is used to understand the dynamics of the COVID-19 pandemics. We calculate the basic reproduction number TRANS ( R0 TRANS), and prove the global stability of the model by solving the differential equations of the model using the disease MESHD-free equilibrium (DFE) and endemic equilibrium (EE) equations, respectively. We showed that when the R0 TRANS less than one or less than and equal to one, and greater than one or greater than and equal to one the DFE and EE asymptotic TRANS stability exist theoretically and numerically, respectively. We also demonstrate the detrimental impact of the direct and asymptomatic infections MESHD asymptomatic TRANS for the COVID-19 pandemic. 

    Lymphopenia MESHD Lymphopenia HP-induced T cell proliferation is a hallmark of severe COVID-19

    Authors: Sarah Adamo; Stéphane Chevrier; Carlo Cervia; Yves Zurbuchen; Miro E. Räber; Liliane Yang; Sujana Sivapatham; Andrea Jacobs; Esther Bächli; Alain Rudiger; Melina Stüssi-Helbling; Lars C. Huber; Dominik Schaer; Bernd Bodenmiller; Onur Boyman; Jakob Nilsson

    doi:10.1101/2020.08.04.236521 Date: 2020-08-04 Source: bioRxiv

    Coronavirus disease MESHD 2019 (COVID-19), caused by infection MESHD infection with severe HP with severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2), has a broad clinical presentation ranging from asymptomatic infection MESHD asymptomatic TRANS to fatal disease MESHD. Different features associated with the immune response to SARS-CoV-2, such as hyperinflammation and reduction of peripheral CD8+ T cell counts are strongly associated with severe disease MESHD. Here, we confirm the reduction in peripheral CD8+ T cells both in relative and absolute terms and identify T cell apoptosis and migration into inflamed tissues as possible mechanisms driving peripheral T cell lymphopenia MESHD lymphopenia HP. Furthermore, we find evidence of elevated serum SERO interleukin-7, thus indicating systemic T cell paucity and signs of increased T cell proliferation in patients with severe lymphopenia MESHD lymphopenia HP. Following T cell lymphopenia MESHD lymphopenia HP in our pseudo-longitudinal time course, we observed expansion and recovery of poly-specific antiviral T cells, thus arguing for lymphopenia MESHD lymphopenia HP-induced T cell proliferation. In summary, this study suggests that extensive T cell loss and subsequent T cell proliferation are characteristic of severe COVID-19.

    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.

    Estimates of the rate of infection and asymptomatic MESHD asymptomatic TRANS COVID-19 disease MESHD in a population sample from SE England

    Authors: Philippa M Wells; Katie M Doores; Simon Couvreur; Rocio Martin Martinez; Jeffrey Seow; Carl Graham; Sam Acors; Neophytos Kouphou; Stuart Neil; Richard Tedder; Pedro Matos; Kate Poulton; Maria Jose Lista; Ruth Dickenson; Helin Sertkaya; Thomas Maguire; Edward Scourfield; Ruth Bowyer; Deborah Hart; Aoife O'Byrne; Kathryn Steele; Oliver Hemmings; Carolina Rosadas; Myra McClure; Joan Capedevila-Pujol; Jonathan wolf; Sebastien Ourseilin; Matthew Brown; Michael Malim; Timothy Spector; Claire Steves

    doi:10.1101/2020.07.29.20162701 Date: 2020-07-30 Source: medRxiv

    Background: Understanding of the true asymptomatic TRANS rate of infection MESHD of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence SERO after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. Methods: We undertook enzyme linked immunosorbent assay SERO characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged TRANS 19-86 (median age TRANS 48; 85% female TRANS). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. Findings: We demonstrated a seroprevalence SERO of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic TRANS, and 16 (27%) were asymptomatic TRANS for core COVID-19 symptoms: fever MESHD fever HP, cough MESHD cough HP or anosmia HP. Specificity of anosmia HP for seropositivity was 95%, compared to 88% for fever MESHD fever HP cough MESHD cough HP and anosmia HP combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive. Interpretation: Seroprevalence SERO amongst adults TRANS from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic TRANS throughout the study. Anosmia HP demonstrated the highest symptom specificity for SARS-CoV-2 antibody SERO response. Funding: NIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC

    Epidemic Dynamics of COVID-19 Based on SEAIUHR Model Considering Asymptomatic TRANS Cases in Henan Province, China

    Authors: Chunyu Li; Yuchen Zhu; Chang Qi; Lili Liu; Dandan Zhang; Xu Wang; Kaili She; Yan Jia; Tingxuan Liu; Momiao Xiong; Xiujun Li

    doi:10.21203/ Date: 2020-07-28 Source: ResearchSquare

    Background New coronavirus disease MESHD (COVID-19), an infectious disease MESHD caused by a type of novel coronavirus, has emerged in various countries since the end of 2019 and caused a global pandemic. Many infected people went undetected because their symptoms were mild or asymptomatic TRANS, but the proportion and infectivity of asymptomatic infections MESHD asymptomatic TRANS remained unknown. Therefore, in this paper, we analyzed the proportion and infectivity of asymptomatic TRANS cases, as we as the prevalence SERO of COVID-19 in Henan province.Methods We constructed SEAIUHR model based on COVID-19 cases reported from 21 January to 26 February 2020 in Henan province to estimate the proportion and infectivity of asymptomatic TRANS cases, as we as the change of effective reproductive number TRANS, \({R}_{t}\). At the same time, we simulated the changes of cases in different scenarios by changing the time and intensity of the implementation of prevention and control measures.Results The proportion of asymptomatic TRANS cases among COVID-19 infected individuals was 42% and infectivity of asymptomatic TRANS cases was 10% of that symptomatic ones. The basic reproductive number\({R TRANS}_{0}\)=2.73, and \({R}_{t}\) dropped below 1 on 1 February under a series of measures. If measures were taken five days earlier, the number of cases would be reduced by 2/3, and after 5 days the number would more than triple.Conclusions In Henan Province, the COVID-19 epidemic spread rapidly in the early stage, and there were a large number of asymptomatic TRANS infected individuals with relatively low infectivity. However, the epidemic was quickly brought under control with national measures, and the earlier measures were implemented, the better.

    Modeling Control, Lockdown & Exit Strategies for COVID-19 Pandemic in India

    Authors: Madhab Barman; Snigdhashree Nayak; Manoj Kumar Yadav; Soumyendu Raha; Nachiketa Mishra

    doi:10.1101/2020.07.25.20161992 Date: 2020-07-28 Source: medRxiv

    COVID-19--a viral infectious disease MESHD--has quickly emerged as a global pandemic infecting millions of people with a significant number of deaths MESHD across the globe. The symptoms of this disease MESHD vary widely. Depending on the symptoms an infected person is broadly classified into two categories namely, asymptomatic TRANS and symptomatic. Asymptomatic TRANS individuals display mild or no symptoms but continue to transmit the infection MESHD to otherwise healthy individuals. This particular aspect of asymptomatic infection MESHD asymptomatic TRANS poses a major obstacle in managing and controlling the transmission TRANS of the infectious disease MESHD. In this paper, we attempt to mathematically model the spread of COVID-19 in India under various intervention strategies. We consider SEIR type epidemiological models, incorporated with India specific social contact matrix representing contact structures among different age groups TRANS of the population. Impact of various factors such as presence of asymptotic TRANS individuals, lockdown strategies, social distancing practices, quarantine, and hospitalization on the disease MESHD transmission TRANS is extensively studied. Numerical simulation of our model is matched with the real COVID-19 data of India till May 15, 2020, for the purpose of estimating the model parameters. Our model with zone-wise lockdown is seen to give a decent prediction for July 20, 2020.

    Seroprevalence SERO of SARS-CoV-2 IgG Antibodies SERO in Utsunomiya City, Greater Tokyo, after first pandemic in 2020 (U-CORONA): a household- and population-based study

    Authors: Nobutoshi Nawa; Jin Kuramochi; Shiro Sonoda; Yui Yamaoka; Yoko Nukui; Yasunari Miyazaki; Takeo Fujiwara

    doi:10.1101/2020.07.20.20155945 Date: 2020-07-26 Source: medRxiv

    Background: The number of confirmed cases TRANS of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infections MESHD in Japan are substantially lower in comparison to the US and UK, potentially due to the under-implementation of polymerase chain reaction (PCR) tests. Studies reported that more than half of the SARS-CoV-2 infections are asymptomatic MESHD asymptomatic TRANS, confirming the importance for conducting seroepidemiological studies. Although the seroepidemiological studies in Japan observed a reported prevalence SERO of 0.10% in Tokyo, 0.17% in Osaka, and 0.03% in Miyagi, sampling bias was not considered. The study objective was to assess the seroprevalence SERO of SARS-CoV-2 in a random sample of households in Utsunomiya City in Tochigi Prefecture, Greater Tokyo, Japan. Methods: We launched the Utsunomiya COVID-19 seROprevalence SERO Neighborhood Association (U-CORONA) Study to assess the seroprevalence SERO of COVID-19 in Utsunomiya City. The survey was conducted between 14 June 2020 and 5 July 2020, in between the first and second wave of the pandemic. Invitations enclosed with a questionnaire were sent to 2,290 people in 1,000 households randomly selected from Utsunomiya basic resident registry. Written informed consent was obtained from all participants. The level of IgG antibodies SERO to SARS-CoV-2 was assessed by chemiluminescence immunoassay SERO analysis. Results: Among 2,290 candidates, 753 returned the questionnaire and 742 received IgG tests (32.4 % participation rate). Of the 742 participants, 86.8% were 18 years or older, 52.6% were women, 71.1% were residing within 10 km from the test clinic, and 89.2% were living with another person. The age TRANS and sex distribution, distance to clinic and police district were similar with those of non-participants, while the proportion of single-person households was higher among non-participants than participants (16.2% vs. 10.8%). We confirmed three positive cases through quantitative antibody testing SERO. No positive cases were found among the people who live in the same household as someone with positive. All cases were afebrile. The estimated unweighted and weighted prevalence SERO of SARS-CoV-2 infection MESHD were 0.40% (95% confidence interval: 0.08-1.18%) and 1.23% (95% confidence interval: 0.17-2.28%), respectively. Conclusion: This study suggests the importance of detecting all cases using PCR or antigen testing, not only at a hospital, but also in areas where people assemble. Further prospective studies using this cohort are needed to monitor SARS-CoV-2 antibody SERO levels.

    The Asymptomatic Infection MESHD Asymptomatic TRANS of COVID-19 Risen in Imported Population in Shenzhen, China

    Authors: Mu-Xin Chen; Lin Ai; Da-Na Huang; Tie-Jian Feng; Jia-Xu Chen; Shu-Jiang Mei; Ya-Lan Huang; Ying Sun; Jun Meng; Gai-Ge Yang; Ling-Hong Xiong; Xiao-Min Zhang; Bo Peng; Shi-Song Fang; Shun-Xian Zhang; Ren-Li Zhang

    doi:10.21203/ Date: 2020-07-25 Source: ResearchSquare

    Background As of July 24 2020, the global reported number of COVID-19 cases was > 15.4 millions, with over 640,000 deaths MESHD. The present study aimed to carry out an epidemiological analysis of confirmed cases TRANS and asymptomatic infections MESHD asymptomatic TRANS in Shenzhen City to provide scientific reference for the prevention and control of COVID-19.Methods The epidemiological information of the 462 confirmed cases TRANS and 45 asymptomatic infections MESHD asymptomatic TRANS from January 19th to June 30th was collected in Shenzhen City, Southern China, and a descriptive analysis was performed.Results A total of 462 confirmed COVID-19 cases from January 19 to April 30, 2020 were reported in Shenzhen City, including 423 domestic cases (91.56%) and 39 imported cases (8.44%) who came back from other countries. Among domestic cases, the majority were cases imported from Hubei Province (n = 312, 67.53%), followed by local ones (n = 69, 14.94%). During the same period, a total of 45 asymptomatic infections MESHD asymptomatic TRANS were reported in Shenzhen City, including 31 local ones (68.89%) and 14 imported from abroad (31.11%). The proportion of asymptomatic infections MESHD asymptomatic TRANS in Shenzhen City was increasing over time (Z = 13.1888, P < 0.0001). The total number of local asymptomatic infections MESHD asymptomatic TRANS in Shenzhen City exceeded as the same pattern as that in other provinces (χ2 = 118.830, P < 0.0001). The proportion of asymptomatic infections MESHD asymptomatic TRANS among cases imported from abroad was higher than that of the same in domestic cases (χ2 = 22.5121, P < 0.0001, OR = 4.8983, 95%: 2.4052, 9.9756). No statistical significance was noted in the proportions of asymptomatic infections MESHD asymptomatic TRANS among imported cases from different countries (χ2 = 7.7202, P = 0.6561).Conclusions The majority of COVID-19 cases in Shenzhen City were imported cases who came back from Hubei Province in the early stage (before 1st March, 2020) and from abroad in the later stage (after 1st April, 2020). Scientific and effective prevention and control measures have resulted in only a few local infections MESHD in Shenzhen City. Asymptomatic infections MESHD Asymptomatic TRANS accounted for an increasing proportion among cases imported from abroad, indicating that the prevention measures carried out in Shenzhen City did avoid the import of infected cases. Improving the detection capability to identify asymptomatic infections MESHD asymptomatic TRANS as early as possible will be of significance for the control outbreak of COVID-19.

    Stringent thresholds for SARS-CoV-2 IgG assays result in under-detection of cases reporting loss of taste/smell

    Authors: David W Eyre; Sheila F Lumley; Nicole E Stoesser; Philippa C Matthews; Alison Howarth; Stephanie B Hatch; Brian D Marsden; Stuart Cox; Tim James; Richard Cornall; David I Stuart; Gavin Screaton; Daniel Ebner; Derrick W Crook; Christopher P Conlon; Katie Jeffery; Timothy M Walker; Tim EA Peto

    doi:10.1101/2020.07.21.20159038 Date: 2020-07-25 Source: medRxiv

    Thresholds for SARS-CoV-2 antibody SERO assays have typically been determined using samples from symptomatic, often hospitalised, patients. Assay performance SERO following mild/ asymptomatic infection MESHD asymptomatic TRANS is unclear. We assessed IgG responses in asymptomatic TRANS healthcare workers with a high pre-test probability of Covid-19, e.g. 807/9292(8.9%) reported loss of smell/taste. The proportion reporting anosmia HP/ ageusia MESHD increased at antibody SERO titres below diagnostic thresholds for both an in-house ELISA SERO and the Abbott Architect chemiluminescent microparticle immunoassay SERO (CMIA): 424/903(47%) reported anosmia HP/ ageusia MESHD with a positive ELISA SERO, 59/387(13.2%) with high-negative titres, and 324/7943(4.1%) with low-negative results. Adjusting for the proportion of staff reporting anosmia HP/ ageusia MESHD suggests the sensitivity SERO of both assays is lower than previously reported: Oxford ELISA SERO 90.8% (95%CI 86.1-92.1%) and Abbott CMIA 80.9% (77.5-84.3%). However, the sensitivity SERO may be lower if some anosmia HP/ ageusia MESHD in those with low-negative titres is Covid-19-associated. Samples from individuals with mild/ asymptomatic infection MESHD asymptomatic TRANS should be included in SARS-CoV-2 immunoassay SERO evaluations. Reporting equivocal SARS-CoV-2 antibody SERO results should be considered.

    Strategies to reduce the risk of SARS-CoV-2 re-introduction from international travellers

    Authors: Samuel Clifford; Billy J Quilty; Timothy W Russell; Yang Liu; Yung-Wai Desmond Chan; Carl A B Pearson; Rosalind M Eggo; Akira Endo; - CMMID COVID-19 Working Group; Stefan Flasche; W John Edmunds

    doi:10.1101/2020.07.24.20161281 Date: 2020-07-24 Source: medRxiv

    To mitigate SARS-CoV-2 transmission risks TRANS from international travellers, many countries currently use a combination of up to 14 days of self-quarantine on arrival and testing for active infection MESHD. We used a simulation model of air travellers arriving to the UK from the EU or the USA and the timing of their stages of infection MESHD to evaluate the ability of these strategies to reduce the risk of seeding community transmission TRANS. We find that a quarantine period of 8 days on arrival with a PCR test on day 7 (with a 1-day delay for test results) can reduce the number of infectious arrivals released into the community by a median 94% compared to a no quarantine, no test scenario. This reduction is similar to that achieved by a 14-day quarantine period (median 99% reduction). Shorter quarantine periods still can prevent a substantial amount of transmission TRANS; all strategies in which travellers spend at least 5 days (the mean incubation period TRANS) in quarantine and have at least one negative test before release are highly effective (e.g. a test on day 5 with release on day 6 results in a median 88% reduction in transmission TRANS potential). Without intervention, the current high prevalence SERO in the US (40 per 10,000) results in a higher expected number of infectious arrivals per week (up to 23) compared to the EU (up to 12), despite an estimated 8 times lower volume of travel TRANS in July 2020. Requiring a 14-day quarantine period likely results in less than 1 infectious traveller each entering the UK per week from the EU and the USA (97.5th percentile). We also find that on arrival the transmission risk TRANS is highest from pre-symptomatic travellers; quarantine policies will shift this risk increasingly towards asymptomatic infections MESHD asymptomatic TRANS if eventually-symptomatic individuals self-isolate after the onset of symptoms TRANS. As passenger numbers recover, strategies to reduce the risk of re-introduction should be evaluated in the context of domestic SARS-CoV-2 incidence, preparedness to manage new outbreaks, and the economic and psychological impacts of quarantine.

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MeSH Disease
Human Phenotype

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