Overview

MeSH Disease

Disease (66)

Infections (62)

Death (43)

Human Phenotype

Falls (10)

Pneumonia (6)

Hypertension (1)

Fever (1)

Transmission

Seroprevalence
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A "Tail" of Two Cities: Fatality-based Modeling of COVID-19 Evolution in New York City and Cook County, IL

Authors: Joshua Frieman

doi:10.1101/2020.08.10.20170506 Date: 2020-08-12 Source: medRxiv

I describe SIR modeling of the COVID-19 pandemic in two U.S. urban environments, New York City (NYC) and Cook County, IL, from onset through the month of June, 2020. Since testing was not widespread early in the pandemic in the U.S., I do not use data on confirmed cases TRANS and rely solely on public fatality data to estimate model parameters. Fits to the first 20 days of data determine a degenerate combination of the basic reproduction number TRANS, R0 TRANS, and the mean time to removal from the infectious population, 1/{gamma} with {gamma}( R0 TRANS - 1) = 0.25(0.21) inverse days for NYC (Cook County). Equivalently, the initial doubling time was td = 2.8(3.4) days for NYC (Cook). The early fatality data suggest that both locations had infections MESHD in early February. I model the mitigation measures implemented in mid-March in both locations (distancing, quarantine, isolation, etc) via a time-dependent reproduction number TRANS Rt that declines monotonically from R0 TRANS to a smaller asymptotic TRANS value, with a parameterized functional form. The timing (mid-March) and duration (several days) of the transitions in Rt appear well determined by the data. However, the fatality data determine only a degenerate combination of the parameters R0 TRANS, the percentage reduction in social contact due to mitigation measures, X, and the infection MESHD fatality rate (IFR), f . With flat priors, based on simulations the NYC model parameters have 95.45% credible intervals of R0 TRANS = 3.0 - 5.4, X = 80 - 99.9% and f = 2 - 6%, with 5 - 13% of the population asymptotically infected. A strong external prior indicating a lower value of f or of 1/{gamma} would imply lower values of R0 TRANS and X and higher percentage infection MESHD of the population. For Cook County, the evolution was qualitatively different: after mitigation measures were implemented, the daily fatality counts reached a plateau for about a month before tailing off. This is consistent with an SIR model that exhibits "critical slowing-down", in which Rt plateaus at a value just above unity. For Cook County, the 95.45% credible intervals for the model parameters are much broader and shifted downward, R0 TRANS = 1.4 - 4.7, X = 26 - 54%, and f = 0.1 - 0.6% with 15 - 88% of the population asymptotically infected. Despite the apparently lower efficacy of its social contact reduction measures, Cook County has had significantly fewer fatalities per population than NYC, D{infty}/N = 100 vs. 270 per 100,000. In the model, this is attributed to the lower inferred IFR for Cook; an external prior pointing to similar values of the IFR for the two locations would instead chalk up the difference in D/N to differences in the relative growth rate of the disease MESHD. I derive a model-dependent threshold, Xcrit, for "safe" re-opening, that is, for easing of contact reduction that would not trigger a second wave; for NYC, the models predict that increasing social contact by more than 20% from post-mitigation levels will lead to renewed spread, while for Cook County the threshold value is very uncertain, given the parameter degeneracies. The timing of 2nd-wave growth will depend on the amplitude of contact increase relative to Xcrit and on the asymptotic TRANS growth rate, and the impact in terms of fatalities will depend on the parameter f .

Epidemiological Characteristics of COVID-19 under Government-mandated Control Measures in Inner Mongolia, China

Authors: Sha Du; Haiwen Lu; Yuenan Su; Shufeng Bi; Jing Wu; Wenrui Wang; Xinhui Yu; Min Yang; Huiqiu Zheng; Xuemei Wang

doi:10.21203/rs.3.rs-57472/v1 Date: 2020-08-11 Source: ResearchSquare

BackgroundThere were 75 local confirmed cases TRANS during the COVID-19 epidemic followed by an outbreak of Wuhan in Inner Mongolia. The aims of our study were to provide reference to control measures of COVID-19 and scientific information for supporting government decision-making for serious infectious disease MESHD, in remote regions with relatively insufficient medical resources like Inner Mongolia.MethodsThe data published by Internet were summarized in order to describe the epidemiological and clinical characteristics of patients with COVID-19. The basic reproductive number (R TRANS 0 ), incubation period TRANS, time from illness onset to confirmed and the duration of hospitalization were analyzed. The composition of imported and local secondary cases TRANS and the mild/common and severe/critical cases among different ages TRANS, genders TRANS and major clinical symptoms were compared.ResultsIn 2020, from January 23 to February 19 (less than 1 month), 75 local cases of COVID-19 were confirmed in Inner Mongolia. Among them, the median age TRANS was 45 years old (34.0, 57.0), and 61.1% were male TRANS and 33 were imported (44.0%). 29 (38.7%) were detected through close contact TRANS tracking, more than 80.0% were mild/common cases. The fatality rate was 1.3% and the basic reproductive number (R TRANS 0 ) was estimated to be 2.3. The median incubation period TRANS was 8.5 days (6.0~12.0) and the maximum incubation period TRANS reached 28 days. There was a statistically difference in the incubation period TRANS between imported and local secondary cases TRANS ( P <0.001). The duration of hospitalization of patients with incubation period TRANS <8.5 days was higher than that of patients with incubation period TRANS ≥8.5 days (30.0 vs. 24.0 days).ConclusionIn Inner Mongolia, an early and mandatory control strategy by government associated with the rapidly reduced incidence of COVID-19, by which the epidemic growth was controlled completely. And the fatality rate of COVID-19 was relatively low.

Genomic epidemiology reveals transmission TRANS patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

Authors: Jemma L Geoghegan; Xiaoyun Ren; Matthew Storey; James Hadfield; Lauren Jelley; Sarah Jefferies; Jill Sherwood; Shevaun Paine; Sue Huang; Jordan Douglas; Fabio K L Mendes; Andrew Sporle; Michael G Baker; David R Murdoch; Nigel French; Colin R Simpson; David Welch; Alexei J Drummond; Edward C Holmes; Sebastian Duchene; Joep de Ligt

doi:10.1101/2020.08.05.20168930 Date: 2020-08-06 Source: medRxiv

New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nation-wide lockdown of all non-essential services to curb the spread of COVID-19. New Zealand has now effectively eliminated the virus, with low numbers of new cases limited to new arrivals in managed quarantine facilities at the border. Here, we generated 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected between 26 February and 22 May 2020, representing 56% of all confirmed cases TRANS in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. The proportion of D614G variants in the virus spike protein increased over time due to an increase in their importation frequency, rather than selection within New Zealand. These data also helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number TRANS, Re, of New Zealand's largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in a transmission TRANS lineage of more than one additional case. Most of the cases that resulted in a transmission TRANS lineage originated from North America, rather than from Asia where the virus first emerged or from the nearest geographical neighbour, Australia. Genomic data also helped link more infections MESHD to a major transmission TRANS cluster than through epidemiological data alone, providing probable sources of infections MESHD for cases in which the source was unclear. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease MESHD mitigation.

Inhomogeneous mixing and asynchronic transmission TRANS between local outbreaks account for the spread of COVID-19 epidemics

Authors: Carlos I Mendoza

doi:10.1101/2020.08.04.20168443 Date: 2020-08-06 Source: medRxiv

The ongoing epidemic of COVID-19 originated in China has reinforced the need to develop epidemiological models capable of describing the progression of the disease MESHD to be of use in the formulation of mitigation policies. Here, this problem is addressed using a metapopulation approach to show that the delay in the transmission TRANS of the spread between different subsets of the total population, can be incorporated into a SIR framework through a time-dependent transmission TRANS rate. Thus, the reproduction number TRANS decreases with time despite the population dynamics remains uniform and the depletion of susceptible individuals is small. The obtained results are consistent with the early subexponential growth observed in the cumulated number of confirmed cases TRANS even in the absence of containment measures. We validate our model by describing the evolution of the COVID-19 using real data from different countries with an emphasis in the case of Mexico and show that it describes correctly also the long-time dynamics of the spread. The proposed model yet simple is successful at describing the onset and progression of the outbreak and considerably improves accuracy of predictions over traditional compartmental models. The insights given here may probe be useful to forecast the extent of the public health risks of epidemics and thus improving public policy-making aimed at reducing such risks.

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.

Analysis of COVID-19 and comorbidity co- infection MESHD Model with Optimal Control

Authors: Dr. Andrew Omame; Nometa Ikenna

doi:10.1101/2020.08.04.20168013 Date: 2020-08-04 Source: medRxiv

The new coronavirus disease MESHD 2019 (COVID-19) infection MESHD is a double challenge for people infected with comorbidities such as cardiovascular and cerebrovascular diseases MESHD and diabetes. Comorbidities have been reported to be risk factors for the complications of COVID-19. In this work, we develop and analyze a mathematical model for the dynamics of COVID-19 infection MESHD in order to assess the impacts of prior comorbidity on COVID-19 complications and COVID-19 re- infection MESHD. The model is simulated using data relevant to the dynamics of the diseases MESHD in Lagos, Nigeria, making predictions for the attainment of peak periods in the presence or absence of comorbidity. The model is shown to undergo the phenomenon of backward bifurcation caused by the parameter accounting for increased susceptibility to COVID-19 infection MESHD by comorbid susceptibles as well as the rate of re- infection MESHD by those who have recovered from a previous COVID-19 infection MESHD. Sensitivity SERO analysis of the model when the population of individuals co-infected with COVID-19 and comorbidity is used as response function revealed that the top ranked parameters that drive the dynamics of the co- infection MESHD model are the effective contact rate for COVID-19 transmission TRANS, $\beta\sst{cv}$, the parameter accounting for increased susceptibility to COVID-19 by comorbid susceptibles, $\chi\sst{cm}$, the comorbidity development rate, $\theta\sst{cm}$, the detection rate for singly infected and co-infected individuals, $\eta_1$ and $\eta_2$, as well as the recovery rate from COVID-19 for co-infected individuals, $\varphi\sst{i2}$. Simulations of the model reveal that the cumulative confirmed cases TRANS (without comorbidity) may get up to 180,000 after 200 days, if the hyper susceptibility rate of comorbid susceptibles is as high as 1.2 per day. Also, the cumulative confirmed cases TRANS (including those co-infected with comorbidity) may be as high as 1000,000 cases by the end of November, 2020 if the re- infection MESHD rates for COVID-19 is 0.1 per day. It may be worse than this if the re- infection MESHD rates increase higher. Moreover, if policies are strictly put in place to step down the probability of COVID-19 infection MESHD by comorbid susceptibles to as low as 0.4 per day and step up the detection rate for singly infected individuals to 0.7 per day, then the reproduction number TRANS can be brought very low below one, and COVID-19 infection MESHD eliminated from the population. In addition, optimal control and cost-effectiveness analysis of the model reveal that the the strategy that prevents COVID-19 infection MESHD by comorbid susceptibles has the least ICER and is the most cost-effective of all the control strategies for the prevention of COVID-19.

COVID-19 pandemic in Djibouti: epidemiology and the response strategy followed to contain the virus during the first two months, 17 March to 16 May 2020

Authors: Mohamed Elhakim; Saleh Banoita Tourab; Ahmed Zouiten

doi:10.1101/2020.08.03.20167692 Date: 2020-08-04 Source: medRxiv

Background: First cases of COVID-19 were reported from Wuhan, China, in December 2019, and it progressed rapidly. On 30 January, WHO declared the new disease MESHD as a PHEIC, then as a Pandemic on 11 March. By mid-March, the virus spread widely; Djibouti was not spared and was hit by the pandemic with the first case detected on 17 March. Djibouti worked with WHO and other partners to develop a preparedness and response plan, and implemented a series of intervention measures. MoH together with its civilian and military partners, closely followed WHO recommended strategy based on four pillars: testing, isolating, early case management, and contact tracing TRANS. From 17 March to 16 May, Djibouti performed the highest per capita tests in Africa and isolated, treated and traced the contacts TRANS of each positive case, which allowed for a rapid control of the epidemic. Methods: COVID-19 data included in this study was collected through MoH Djibouti during the period from 17 March to 16 May 2020. Results: A total of 1,401 confirmed cases TRANS of COVID-19 were included in the study with 4 related deaths MESHD (CFR: 0.3%) and an attack rate TRANS of 0.15%. Males TRANS represented (68.4%) of the cases, with the age group TRANS 31-45 years old (34.2%) as the most affected. Djibouti conducted 17,532 tests, and was considered as a champion for COVID-19 testing in Africa with 18.2 tests per 1000 habitant. All positive cases were isolated, treated and had their contacts traced TRANS, which led to early and proactive diagnosis of cases and in turn yielded up to 95-98% asymptomatic TRANS cases. Recoveries reached 69% of the infected cases with R0 TRANS (0.91). The virus was detected in 4 regions in the country, with the highest percentage in the capital (83%). Conclusion: Djibouti responded to COVID-19 pandemic following an efficient and effective strategy, using a strong collaboration between civilian and military health assets that increased the response capacities of the country. Partnership, coordination, solidarity, proactivity and commitment were the pillars to confront COVID-19 pandemic.

Data-driven modeling and forecasting of COVID-19 outbreak for public policy making

Authors: Agus Hasan; Endah Putri; Hadi Susanto; Nuning Nuraini

doi:10.1101/2020.07.30.20165555 Date: 2020-08-02 Source: medRxiv

This paper presents a data-driven approach for COVID-19 outbreak modeling and forecasting, which can be used by public policy and decision makers to control the outbreak through Non-Pharmaceutical Interventions (NPI). First, we apply an extended Kalman filter (EKF) to a discrete-time stochastic augmented compartmental model to estimate the time-varying effective reproduction number TRANS Rt. We use daily confirmed cases TRANS, active cases, recovered cases, deceased cases, Case-Fatality-Rate (CFR), and infectious time as inputs for the model. Furthermore, we define a Transmission TRANS Index (TI) as a ratio between the instantaneous and the maximum value of the effective reproduction number TRANS. The value of TI shows the disease MESHD transmission TRANS in a contact between a susceptible and an infectious individual due to current measures such as physical distancing and lock-down relative to a normal condition. Based on the value of TI, we forecast different scenarios to see the effect of relaxing and tightening public measures. Case studies in three countries are provided to show the practicability of our approach.

Isolation Considered Epidemiological Model for the Prediction of COVID-19 Trend in Tokyo, Japan

Authors: Motoaki Utamura; Makoto Koizumi; Seiichi Kirikami

doi:10.1101/2020.07.31.20165829 Date: 2020-07-31 Source: medRxiv

Background: Coronavirus Disease MESHD 2019 (COVID19) currently poses a global public health threat. Although no exception, Tokyo, Japan was affected at first by only a small epidemic. Medical collapse nevertheless nearly happened because no predictive method existed for counting patients. A standard SIR epidemiological model and its derivatives predict susceptible, infectious, and removed (recovered/ deaths MESHD) cases but ignore isolation of confirmed cases TRANS. Predicting COVID19 trends with hospitalized and infectious people in field separately is important to prepare beds and develop quarantine strategies. Methods: Time-series COVID19 data from February 28 to May 23, 2020 in Tokyo were adopted for this study. A novel epidemiological model based on delay differential equation was proposed. The model can evaluate patients in hospitals and infectious cases in the field. Various data such as daily new cases, cumulative infections MESHD, patients in hospital, and PCR test positivity ratios were used to examine the model. This approach derived an alternative formulation equivalent to the standard SIR model. Its results were compared quantitatively with those of the present isolation model. Results: The basic reproductive number TRANS, inferred as 2.30, is a dimensionless parameter composed of modeling parameters. Effects of intervention to mitigate the epidemic spread were assessed a posteriori. An exit policy of how and when to release a statement of emergency MESHD was also assessed using the model. Furthermore, results suggest that the rapid isolation of infectious cases has a large potential to effectively mitigate the spread of infection MESHD and restores social and economic activities safely. Conclusions: A novel mathematical model was proposed and examined using COVID19 data for Tokyo. Results show that shortening the period from infection MESHD to hospitalization is effective against outbreak without rigorous public health intervention and control. Faster and precise case cluster detection and wider and quicker introduction of testing measures are strongly recommended.

The effective reproductive number TRANS (Rt) of COVID-19 and its relationship with social distancing

Authors: Lucas Jardim Sr.; Jose Alexandre Diniz-Filho Sr.; Thiago Fernando Rangel Sr.; Cristiana Maria Toscano II

doi:10.1101/2020.07.28.20163493 Date: 2020-07-29 Source: medRxiv

The expansion of the new coronavirus disease MESHD (COVID-19) triggered a renewed public interest in epidemiological models and on how parameters can be estimated from observed data. Here we investigated the relationship between average number of transmissions TRANS though time, the reproductive number TRANS Rt, and social distancing index as reported by mobile phone data service inloco, for Goias State, Brazil, between March and June 2020. We calculated Rt values using EpiEstim package in R-plataform for confirmed cases TRANS incidence curves. We found a correlation equal to -0.72 between Rt values for confirmed cases TRANS and isolation index at a time lag of 8 days. As the Rt values were paired with center of the moving window of 7 days, the delay matches the mean incubation period TRANS of the virus. Our findings reinforce that isolation index can be an effective surrogate for modeling and epidemiological analyses and, more importantly, can be an useful metrics for anticipating the need for early interventions, a critical issue in public health.

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 All None MeSH Disease Human Phenotype Transmission Seroprevalence

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