scholarly journals Determination of critical decision points for COVID-19 measures in Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Junu Kim ◽  
Kensaku Matsunami ◽  
Kozue Okamura ◽  
Sara Badr ◽  
Hirokazu Sugiyama
Keyword(s):  
Time Delay ◽  
Infection Rate ◽  
Reproduction Number ◽  
Sir Model ◽  
Infection Rates ◽  
Seir Model ◽  
Decision Points ◽  
Medical Institutions ◽  
The World

AbstractCoronavirus disease 2019 (COVID-19) has spread throughout the world. The prediction of the number of cases has become essential to governments’ ability to define policies and take countermeasures in advance. The numbers of cases have been estimated using compartment models of infectious diseases such as the susceptible-infected-removed (SIR) model and its derived models. However, the required use of hypothetical future values for parameters, such as the effective reproduction number or infection rate, increases the uncertainty of the prediction results. Here, we describe our model for forecasting future COVID-19 cases based on observed data by considering the time delay (tdelay). We used machine learning to estimate the future infection rate based on real-time mobility, temperature, and relative humidity. We then used this calculation with the susceptible-exposed-infectious-removed (SEIR) model to forecast future cases with less uncertainty. The results suggest that changes in mobility affect observed infection rates with 5–10 days of time delay. This window should be accounted for in the decision-making phase especially during periods with predicted infection surges. Our prediction model helps governments and medical institutions to take targeted early countermeasures at critical decision points regarding mobility to avoid significant levels of infection rise.

scholarly journals The Effect of Vaccination Rates on the Infection of COVID-19 under the Vaccination Rate below the Herd Immunity Threshold

2021 ◽  
Vol 18 (14) ◽  
pp. 7491
Author(s):  
Yi-Tui Chen
Keyword(s):  
Infection Rate ◽  
Herd Immunity ◽  
The United States ◽  
Vaccination Rate ◽  
Infection Rates ◽  
Vaccination Rates ◽  
The United Kingdom ◽  
The World ◽  
Almost All ◽  
The Impact

Although vaccination is carried out worldwide, the vaccination rate varies greatly. As of 24 May 2021, in some countries, the proportion of the population fully vaccinated against COVID-19 has exceeded 50%, but in many countries, this proportion is still very low, less than 1%. This article aims to explore the impact of vaccination on the spread of the COVID-19 pandemic. As the herd immunity of almost all countries in the world has not been reached, several countries were selected as sample cases by employing the following criteria: more than 60 vaccine doses per 100 people and a population of more than one million people. In the end, a total of eight countries/regions were selected, including Israel, the UAE, Chile, the United Kingdom, the United States, Hungary, and Qatar. The results find that vaccination has a major impact on reducing infection rates in all countries. However, the infection rate after vaccination showed two trends. One is an inverted U-shaped trend, and the other is an L-shaped trend. For those countries with an inverted U-shaped trend, the infection rate begins to decline when the vaccination rate reaches 1.46–50.91 doses per 100 people.

EPIDEMIC SPREADING ON THREE-LAYER INTERDEPENDENT NETWORKS

2016 ◽  
Vol 24 (04) ◽  
pp. 469-494 ◽  
Author(s):  
LINGNA WANG ◽  
GUANGHU ZHU ◽  
HUIYAN KANG ◽  
XINCHU FU
Keyword(s):  
Infection Rate ◽  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Mean Field ◽  
Network Size ◽  
Infection Rates ◽  
Epidemic Spreading ◽  
Interdependent Networks ◽  
Coupled Networks ◽  
The Basic Reproduction Number

Many epidemic diseases spread among three different populations with different contact patterns and infection rates. In response to such diseases, we propose two new types of three-layer interdependent networks — string-coupled networks and circular-coupled networks. We investigate an epidemic spreading on the two types of interdependent networks, propose two mathematical models through heterogeneous mean field approach and prove global stability of the disease-free and endemic equilibria. Through theoretical and numerical analysis, we find the following: the increase of each infection rate affects effectively only its own subnetwork and neighbors; in a string-coupled network, the middle subnetwork has bigger impact on the basic reproduction number than the end subnetworks with the growth of network size or infection rates; the basic reproduction number on a circular-coupled network is larger than that on a string-coupled network for a fixed network size; but the change of the basic reproduction number (or the average infection densities) is almost the same on both string-coupled and circular-coupled networks with the increasing of certain infection rate.

scholarly journals An SEIR Model with Contact Tracing and Age-Structured Social Mixing for COVID-19 outbreak

2020 ◽  
Author(s):  
Ali Teimouri
Keyword(s):  
Reproduction Number ◽  
Contact Tracing ◽  
Seir Model ◽  
Expectation Value ◽  
Proposed Model ◽  
Social Mixing ◽  
The World ◽  
Age Structured ◽  
And Control ◽  
Explicit Relation

AbstractIn December 2019 a severe acute respiratory syndrome now known as SARS-CoV-2 began to surge in Wuhan, China. The virus soon spread throughout the world to become a pandemic. Since the outbreak various measures were put in place to contain and control the spread, these interventions were mostly based on compartmental models in epidemiology with the main goal of controlling and monitoring the rate of the basic and effective reproduction number. In this paper, we propose an SEIR model where we incorporate contact tracing and age-structured social mixing. We show the explicit relation between contact tracing and social mixing and other relevant parameters of the proposed model. We derive a formula for the effective reproduction number which is expressed in terms of reported cases, tracing quantities and social mixing. We use this formula to determine the expectation value of the effective reproduction number in London, UK.

scholarly journals The basic reproduction number of COVID-19 across Africa

2021 ◽  
Author(s):  
Sarafa Adewale Iyaniwura ◽  
Muhammad Rabiu Musa ◽  
Jummy F. David ◽  
Jude Dzevela Kong
Keyword(s):  
Bayesian Inference ◽  
Severe Acute Respiratory Syndrome ◽  
Basic Reproduction Number ◽  
Reproduction Number ◽  
Transmission Dynamics ◽  
Clear Understanding ◽  
Seir Model ◽  
The World ◽  
Bayesian Inference Framework ◽  
The Basic Reproduction Number

The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) took the world by surprise. Following the first outbreak of COVID-19 in December 2019, several models have been developed to study and understand its transmission dynamics. Although the spread of COVID-19 is being slowed down by vaccination and other interventions, there is still a need to have a clear understanding of the evolution of the pandemic across countries, states and communities. To this end, there is a need to have a clearer picture of the initial spread of the disease in different regions. In this project, we used a simple SEIR model and a Bayesian inference framework to estimate the basic reproduction number of COVID-19 across Africa. Our estimates vary between 1.98 (Sudan) and 9.66 (Mauritius), with a median of 3.67 (90% CrI: 3.31 - 4.12). The estimates provided in this paper will help to inform COVID-19 modeling in the respective countries/regions.

scholarly journals The approximately universal shapes of epidemic curves in the Susceptible-Exposed-Infectious-Recovered (SEIR) model

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Kevin Heng ◽  
Christian L. Althaus
Keyword(s):  
Analytical Solution ◽  
Reproduction Number ◽  
Sir Model ◽  
Seir Model ◽  
Stretch Factor ◽  
Invaluable Tool ◽  
Appl Math ◽  
Transmission Models ◽  
Approximate Characteristic ◽  
Initial Fraction

Abstract Compartmental transmission models have become an invaluable tool to study the dynamics of infectious diseases. The Susceptible-Infectious-Recovered (SIR) model is known to have an exact semi-analytical solution. In the current study, the approach of Harko et al. (Appl. Math. Comput. 236:184–194, 2014) is generalised to obtain an approximate semi-analytical solution of the Susceptible-Exposed-Infectious-Recovered (SEIR) model. The SEIR model curves have nearly the same shapes as the SIR ones, but with a stretch factor applied to them across time that is related to the ratio of the incubation to infectious periods. This finding implies an approximate characteristic timescale, scaled by this stretch factor, that is universal to all SEIR models, which only depends on the basic reproduction number and initial fraction of the population that is infectious.

scholarly journals Modifikasi Model SIR pada Penyebaran Penyakit Demam Berdarah Dengue di Kabupaten Bone

2019 ◽  
Vol 1 (2) ◽  
pp. 169
Author(s):  
Syafruddin Side ◽  
A Alimuddin ◽  
Alvioni Bani
Keyword(s):  
Dengue Fever ◽  
Basic Reproduction Number ◽  
Epidemic Model ◽  
Reproduction Number ◽  
Equilibrium Points ◽  
Sir Model ◽  
District Health Office ◽  
District Health ◽  
Reproduction Numbers

Abstrak. Artikel ini membahas mengenai modifikasi model epidemik SIR pada penyebaran penyakit DBD di Kabupaten Bone dengan penembahan asumsi baru bahwa 20% penderita DBD yang sembuh akan kembali terinfeksi dan 80 % dari individu yang telah sembuh, tidak akan kembali menjadi rentan. Data yang digunakan adalah jumlah penderita DBD di Kabupaten Bone tahun 2016 dari Dinas Kesehatan Kabupaten Bone. Pembahasan dimulai dari penentuan titik equilibrium, stabilitas, bilangan reproduksi dasar  dan simulasi menggunakan Maple. Dalam penelitian ini diperoleh dua titik equilibrium dengan nilai reproduksi dasar . Hal ini menunjukkan bahwa penyakit DBD di Kabupaten Bone akan terus meningkat dan menjadi endemik.Kata Kunci: Titik Equilibrium, Bilangan Reproduksi Dasar, DBD, Modifikasi Model SIR.  Abstract. The research discusses a modification of epidemic model SIR on the spreadof dengue fever disease in Bone District. With some addition of the assumption that 20% of patients who recovered will be re-infected and 80% of individuals who have recovered will not be susceptible. The data used in the number of dengue fever patients in Bone District in 2016 from Bone District Health Office. The discussion starts by the determination of equilibrium points, stability and basic reproduction numbers . In this study, we obtained that two equilibrium points and basic reproduktion value . This indicates that dengue fever disease in Bone District will increase and become endemic.Keywords: Equilibrium Point, Basic Reproduction Number, Dengue Fever, The Modification of SIR Model. 

scholarly journals Modeling the Impact of Lock-down on COVID-19 Spread in Malaysia

2020 ◽  
Author(s):  
Altahir A. Altahir ◽  
Nirbhay Mathur ◽  
Loshini Thiruchelvam ◽  
Ghulam E. Mustafa Abro ◽  
Syaimaa’ S. M. Radzi ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Reproduction Number ◽  
Formal Analysis ◽  
Time Frame ◽  
Immature Stage ◽  
Epidemic Spread ◽  
Prevention Measures ◽  
Seir Model ◽  
The World ◽  
The Impact

AbstractAfter a breakdown notified in Wuhan, China in December 2019, COVID-19 is declared as pandemic diseases. To the date more than 13 million confirmed cases and more than half a million are dead around the world. This virus also attached Malaysia in its immature stage where 8718 cases were confirmed and 122 were declared as death. Malaysia responsibly controlled the spread by enforcing MCO. Hence, it is required to visualize the pattern of Covid-19 spread. Also, it is necessary to estimate the impact of the enforced prevention measures. In this paper, an infectious disease dynamic modeling (SEIR) is used to estimate the epidemic spread in Malaysia. The main assumption is to update the reproduction number Rt with respect to the implemented prevention measures. For a time-frame of five month, the Rt was assumed to vary between 2.9 and 0.3. Moreover, the manuscript includes two possible scenarios: the first will be the extension of the stricter measures all over the country, and the second will be the gradual lift of the lock-down. After implementing several stages of lock-down we have found that the estimated values of the Rt with respect to the strictness degree varies between 0.2 to 1.1. A continuous strict lock-down may reduce the Rt to 0.2 and accordingly the estimated active cases will be reduced to 20 by the beginning of September 2020. In contrast, the second scenario considers a gradual lift of the enforced prevention measures by the end of June 2020, here we have considered three possible outcomes according to the MCO relaxation. Thus, the estimated values of Rt = 0.7, 0.9, 1.1, which shows a rapid increase in the number of active cases. The implemented SEIR model shows a close resemblance with the actual data recorded from 10, March till 7, July 2020.Author summaryConceptualization, A.A.A; methodology, A.A.A, N.M; validation, A.A.A, N.M; formal analysis, A.A.A; investigation, N.M, A.A.A; resources, G.E.M.A, L.T; data collection, L.T, N.M; writing—original draft preparation, A.A.A, L.T, G.E.M.A, N.M; writing—review and editing, V.S.A, S.C.D, B.S.G, P.S, S.A.B.M.Z, N.M; visualization, N.M; supervision, V.S.A; project administration, V.S.A. All authors have read and agreed to the published version of the manuscript

scholarly journals New reproduction number and acceleration parameter introduced and applied to COVID-19

2021 ◽  
Author(s):  
Eckhard Rebhan
Keyword(s):  
Exponential Growth ◽  
Reproduction Number ◽  
Analytical Form ◽  
Precise Determination ◽  
Acceleration Parameter ◽  
Infection Dynamics ◽  
The World

Abstract To characterize the progression of a pandemic, a well interpretable reproduction number is introduced which is easily applicable to many different situations due to its handy analytical form. On the basis of its derivation it can be understood as a cross between a volatile instantaneous reproduction number and the more robust effective reproduction number commonly used. Starting from it, a further quantity, termed acceleration parameter, is introduced, which facilitates a more differentiated characterization of the infection dynamics. In particular, it enables the precise determination of when the limit to exponential growth is reached and exceeded. A variety of possible developments is examined, including linear and exponential growth of the infection numbers as well as sub- and super-exponential growth. It turned out useful to incorporate the incidence as a further epidemiological indicator. It is used for calculating the trace that the progression of the pandemic leaves behind on a plain spanned by itself and the acceleration parameter. This plane can be divided into a dangerous area, where the pandemic becomes uncontrollable, and a safer area that must be the target of mitigation efforts. At present, many countries and the world as a whole are mired in the dangerous area.

scholarly journals Tracking R of COVID-19: A new real-time estimation using the Kalman filter

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0244474 ◽  
Author(s):  
Francisco Arroyo-Marioli ◽  
Francisco Bullano ◽  
Simas Kucinskas ◽  
Carlos Rondón-Moreno
Keyword(s):  
Growth Rate ◽  
Kalman Filter ◽  
Reproduction Number ◽  
Time Estimation ◽  
Sir Model ◽  
Time Varying ◽  
The World ◽  
Real Time Estimation ◽  
Image Position ◽  
Pharmaceutical Interventions

We develop a new method for estimating the effective reproduction number of an infectious disease (R) and apply it to track the dynamics of COVID-19. The method is based on the fact that in the SIR model, R is linearly related to the growth rate of the number of infected individuals. This time-varying growth rate is estimated using the Kalman filter from data on new cases. The method is easy to implement in standard statistical software, and it performs well even when the number of infected individuals is imperfectly measured, or the infection does not follow the SIR model. Our estimates of R for COVID-19 for 124 countries across the world are provided in an interactive online dashboard, and they are used to assess the effectiveness of non-pharmaceutical interventions in a sample of 14 European countries.

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