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1.
BMC Infect Dis ; 21(1): 1145, 2021 Nov 09.
Article in English | MEDLINE | ID: covidwho-1608950

ABSTRACT

BACKGROUND: The global spread of the novel coronavirus pneumonia is still continuing, and a new round of more serious outbreaks has even begun in some countries. In this context, this paper studies the dynamics of a type of delayed reaction-diffusion novel coronavirus pneumonia model with relapse and self-limiting treatment in a temporal-spatial heterogeneous environment. METHODS: First, focus on the self-limiting characteristics of COVID-19, incorporate the relapse and self-limiting treatment factors into the diffusion model, and study the influence of self-limiting treatment on the diffusion of the epidemic. Second, because the traditional Lyapunov stability method is difficult to determine the spread of the epidemic with relapse and self-limiting treatment, we introduce a completely different method, relying on the existence conditions of the exponential attractor of our newly established in the infinite-dimensional dynamic system to determine the diffusion of novel coronavirus pneumonia. Third, relapse and self-limiting treatment have led to a change in the structure of the delayed diffusion COVID-19 model, and the traditional basic reproduction number [Formula: see text] no longer has threshold characteristics. With the help of the Krein-Rutman theorem and the eigenvalue method, we studied the threshold characteristics of the principal eigenvalue and found that it can be used as a new threshold to describe the diffusion of the epidemic. RESULTS: Our results prove that the principal eigenvalue [Formula: see text] of the delayed reaction-diffusion COVID-19 system with relapse and self-limiting treatment can replace the basic reproduction number [Formula: see text] to describe the threshold effect of disease transmission. Combine with the latest official data and the prevention and control strategies, some numerical simulations on the stability and global exponential attractiveness of the diffusion of the COVID-19 epidemic in China and the USA are given. CONCLUSIONS: Through the comparison of numerical simulations, we find that self-limiting treatment can significantly promote the prevention and control of the epidemic. And if the free activities of asymptomatic infected persons are not restricted, it will seriously hinder the progress of epidemic prevention and control.


Subject(s)
COVID-19 , Epidemics , Basic Reproduction Number , Humans , Models, Biological , SARS-CoV-2
2.
PLoS Negl Trop Dis ; 16(1): e0010048, 2022 01.
Article in English | MEDLINE | ID: covidwho-1606114

ABSTRACT

BACKGROUND: The first community transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant of concern (VOC) in Guangzhou, China occurred between May and June 2021. Herein, we describe the epidemiological characteristics of this outbreak and evaluate the implemented containment measures against this outbreak. METHODOLOGY/PRINCIPAL FINDINGS: Guangzhou Center for Disease Control and Prevention provided the data on SARS-CoV-2 infections reported between 21 May and 24 June 2021. We estimated the incubation period distribution by fitting a gamma distribution to the data, while the serial interval distribution was estimated by fitting a normal distribution. The instantaneous effective reproductive number (Rt) was estimated to reflect the transmissibility of SARS-CoV-2. Clinical severity was compared for cases with different vaccination statuses using an ordinal regression model after controlling for age. Of the reported local cases, 7/153 (4.6%) were asymptomatic. The median incubation period was 6.02 (95% confidence interval [CI]: 5.42-6.71) days and the means of serial intervals decreased from 5.19 (95% CI: 4.29-6.11) to 3.78 (95% CI: 2.74-4.81) days. The incubation period increased with age (P<0.001). A hierarchical prevention and control strategy against COVID-19 was implemented in Guangzhou, with Rt decreasing from 6.83 (95% credible interval [CrI]: 3.98-10.44) for the 7-day time window ending on 27 May 2021 to below 1 for the time window ending on 8 June and thereafter. Individuals with partial or full vaccination schedules with BBIBP-CorV or CoronaVac accounted for 15.3% of the COVID-19 cases. Clinical symptoms were milder in partially or fully vaccinated cases than in unvaccinated cases (odds ratio [OR] = 0.26 [95% CI: 0.07-0.94]). CONCLUSIONS/SIGNIFICANCE: The hierarchical prevention and control strategy against COVID-19 in Guangzhou was timely and effective. Authorised inactivated vaccines are likely to contribute to reducing the probability of developing severe disease. Our findings have important implications for the containment of COVID-19.


Subject(s)
COVID-19 Vaccines/therapeutic use , COVID-19/epidemiology , COVID-19/prevention & control , Communicable Disease Control/methods , SARS-CoV-2/isolation & purification , Adult , Aged , Basic Reproduction Number , COVID-19/transmission , China/epidemiology , Female , Humans , Male , Middle Aged , Primary Prevention/methods , Severity of Illness Index , Vaccination/statistics & numerical data , Young Adult
3.
Sci Rep ; 11(1): 24477, 2021 12 29.
Article in English | MEDLINE | ID: covidwho-1599359

ABSTRACT

Assessing the impact of temperature on COVID-19 epidemiology is critical for implementing non-pharmaceutical interventions. However, few studies have accounted for the nature of contagious diseases, i.e., their dependent happenings. We aimed to quantify the impact of temperature on the transmissibility and virulence of COVID-19 in Tokyo, Japan, employing two epidemiological measurements of transmissibility and severity: the effective reproduction number ([Formula: see text]) and case fatality risk (CFR). We estimated the [Formula: see text] and time-delay adjusted CFR and to subsequently assess the nonlinear and delayed effect of temperature on [Formula: see text] and time-delay adjusted CFR. For [Formula: see text] at low temperatures, the cumulative relative risk (RR) at the first temperature percentile (3.3 °C) was 1.3 (95% confidence interval (CI): 1.1-1.7). As for the virulence to humans, moderate cold temperatures were associated with higher CFR, and CFR also increased as the temperature rose. The cumulative RR at the 10th and 99th percentiles of temperature (5.8 °C and 30.8 °C) for CFR were 3.5 (95% CI: 1.3-10.0) and 6.4 (95% CI: 4.1-10.1). Our results suggest the importance to take precautions to avoid infection in both cold and warm seasons to avoid severe cases of COVID-19. The results and our proposed approach will also help in assessing the possible seasonal course of COVID-19 in the future.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , Temperature , Basic Reproduction Number , Cold Temperature , Humans , Mortality , Pandemics/prevention & control , Risk , SARS-CoV-2/pathogenicity , Seasons , Severity of Illness Index , Tokyo/epidemiology , Virulence
4.
PLoS One ; 16(12): e0261424, 2021.
Article in English | MEDLINE | ID: covidwho-1599330

ABSTRACT

The COVID-19 outbreak has caused two waves and spread to more than 90% of Canada's provinces since it was first reported more than a year ago. During the COVID-19 epidemic, Canadian provinces have implemented many Non-Pharmaceutical Interventions (NPIs). However, the spread of the COVID-19 epidemic continues due to the complex dynamics of human mobility. We develop a meta-population network model to study the transmission dynamics of COVID-19. The model takes into account the heterogeneity of mitigation strategies in different provinces of Canada, such as the timing of implementing NPIs, the human mobility in retail and recreation, grocery and pharmacy, parks, transit stations, workplaces, and residences due to work and recreation. To determine which activity is most closely related to the dynamics of COVID-19, we use the cross-correlation analysis to find that the positive correlation is the highest between the mobility data of parks and the weekly number of confirmed COVID-19 from February 15 to December 13, 2020. The average effective reproduction numbers in nine Canadian provinces are all greater than one during the time period, and NPIs have little impact on the dynamics of COVID-19 epidemics in Ontario and Saskatchewan. After November 20, 2020, the average infection probability in Alberta became the highest since the start of the COVID-19 epidemic in Canada. We also observe that human activities around residences do not contribute much to the spread of the COVID-19 epidemic. The simulation results indicate that social distancing and constricting human mobility is effective in mitigating COVID-19 transmission in Canada. Our findings can provide guidance for public health authorities in projecting the effectiveness of future NPIs.


Subject(s)
COVID-19/prevention & control , COVID-19/transmission , Epidemics/prevention & control , SARS-CoV-2 , Travel/statistics & numerical data , Basic Reproduction Number/statistics & numerical data , COVID-19/epidemiology , Canada/epidemiology , Humans , Incidence , Models, Statistical , Physical Distancing , Quarantine/methods
6.
Nat Microbiol ; 7(1): 97-107, 2022 01.
Article in English | MEDLINE | ID: covidwho-1596437

ABSTRACT

Global and national surveillance of SARS-CoV-2 epidemiology is mostly based on targeted schemes focused on testing individuals with symptoms. These tested groups are often unrepresentative of the wider population and exhibit test positivity rates that are biased upwards compared with the true population prevalence. Such data are routinely used to infer infection prevalence and the effective reproduction number, Rt, which affects public health policy. Here, we describe a causal framework that provides debiased fine-scale spatiotemporal estimates by combining targeted test counts with data from a randomized surveillance study in the United Kingdom called REACT. Our probabilistic model includes a bias parameter that captures the increased probability of an infected individual being tested, relative to a non-infected individual, and transforms observed test counts to debiased estimates of the true underlying local prevalence and Rt. We validated our approach on held-out REACT data over a 7-month period. Furthermore, our local estimates of Rt are indicative of 1-week- and 2-week-ahead changes in SARS-CoV-2-positive case numbers. We also observed increases in estimated local prevalence and Rt that reflect the spread of the Alpha and Delta variants. Our results illustrate how randomized surveys can augment targeted testing to improve statistical accuracy in monitoring the spread of emerging and ongoing infectious disease.


Subject(s)
COVID-19/epidemiology , Models, Statistical , SARS-CoV-2/isolation & purification , Basic Reproduction Number , Bias , COVID-19/diagnosis , COVID-19/transmission , COVID-19 Testing/statistics & numerical data , Forecasting , Humans , Prevalence , Reproducibility of Results , SARS-CoV-2/genetics , Spatio-Temporal Analysis , United Kingdom/epidemiology
7.
Sci Rep ; 11(1): 24124, 2021 12 16.
Article in English | MEDLINE | ID: covidwho-1585805

ABSTRACT

The quantification of spreading heterogeneity in the COVID-19 epidemic is crucial as it affects the choice of efficient mitigating strategies irrespective of whether its origin is biological or social. We present a method to deduce temporal and individual variations in the basic reproduction number directly from epidemic trajectories at a community level. Using epidemic data from the 98 districts in Denmark we estimate an overdispersion factor k for COVID-19 to be about 0.11 (95% confidence interval 0.08-0.18), implying that 10 % of the infected cause between 70 % and 87 % of all infections.


Subject(s)
Algorithms , Basic Reproduction Number/statistics & numerical data , COVID-19/transmission , Models, Theoretical , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/virology , Denmark/epidemiology , Epidemics/prevention & control , Geography , Humans , SARS-CoV-2/physiology
8.
PLoS Med ; 18(12): e1003879, 2021 12.
Article in English | MEDLINE | ID: covidwho-1573611

ABSTRACT

BACKGROUND: The epidemiology of the SARS-CoV-2 B.1.1.7 (or Alpha) variant is insufficiently understood. This study's objective was to describe the introduction and expansion of this variant in Qatar and to estimate the efficacy of natural infection against reinfection with this variant. METHODS AND FINDINGS: Reinfections with the B.1.1.7 variant and variants of unknown status were investigated in a national cohort of 158,608 individuals with prior PCR-confirmed infections and a national cohort of 42,848 antibody-positive individuals. Infections with B.1.1.7 and variants of unknown status were also investigated in a national comparator cohort of 132,701 antibody-negative individuals. B.1.1.7 was first identified in Qatar on 25 December 2020. Sudden, large B.1.1.7 epidemic expansion was observed starting on 18 January 2021, triggering the onset of epidemic's second wave, 7 months after the first wave. B.1.1.7 was about 60% more infectious than the original (wild-type) circulating variants. Among persons with a prior PCR-confirmed infection, the efficacy of natural infection against reinfection was estimated to be 97.5% (95% CI: 95.7% to 98.6%) for B.1.1.7 and 92.2% (95% CI: 90.6% to 93.5%) for variants of unknown status. Among antibody-positive persons, the efficacy of natural infection against reinfection was estimated to be 97.0% (95% CI: 92.5% to 98.7%) for B.1.1.7 and 94.2% (95% CI: 91.8% to 96.0%) for variants of unknown status. A main limitation of this study is assessment of reinfections based on documented PCR-confirmed reinfections, but other reinfections could have occurred and gone undocumented. CONCLUSIONS: In this study, we observed that introduction of B.1.1.7 into a naïve population can create a major epidemic wave, but natural immunity in those previously infected was strongly associated with limited incidence of reinfection by B.1.1.7 or other variants.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Reinfection/epidemiology , Reinfection/virology , SARS-CoV-2 , Adolescent , Adult , Aged , Aged, 80 and over , Basic Reproduction Number , Child , Female , Humans , Immunity, Innate , Male , Middle Aged , Models, Theoretical , Polymerase Chain Reaction , Qatar/epidemiology , Retrospective Studies , Time Factors , Young Adult
9.
Viruses ; 13(12)2021 12 10.
Article in English | MEDLINE | ID: covidwho-1572658

ABSTRACT

Domestic cats are susceptible to SARS-CoV-2 virus infection and given that they are in close contact with people, assessing the potential risk cats represent for the transmission and maintenance of SARS-CoV-2 is important. Assessing this risk implies quantifying transmission from humans-to-cats, from cats-to-cats and from cats-to-humans. Here we quantified the risk of cat-to-cat transmission by reviewing published literature describing transmission either experimentally or under natural conditions in infected households. Data from these studies were collated to quantify the SARS-CoV-2 reproduction number R0 among cats. The estimated R0 was significantly higher than one, hence cats could play a role in the transmission and maintenance of SARS-CoV-2. Questions that remain to be addressed are the risk of transmission from humans-to-cats and cats-to-humans. Further data on household transmission and data on virus levels in both the environment around infected cats and their exhaled air could be a step towards assessing these risks.


Subject(s)
Basic Reproduction Number , COVID-19/transmission , COVID-19/veterinary , Animals , Cats , Databases, Factual , Humans , SARS-CoV-2
10.
Zhonghua Liu Xing Bing Xue Za Zhi ; 42(10): 1763-1768, 2021 Oct 10.
Article in Chinese | MEDLINE | ID: covidwho-1534278

ABSTRACT

Objective: To analyze the epidemiological characteristics of a local outbreak of COVID-19 caused by SARS-CoV-2 B.1.617.2(Delta) variant in Liwan district, Guangzhou, and provide evidence for the further prevention and control of the Delta variant of COVID-19. Methods: From May 21 to June 18, 2021, the incidence data of COVID-19 caused by Delta variant were obtained from National Notifiable Disease Report System of Chinese Disease Prevention and Control Information System and Liwan District Center for Disease Control and Prevention of Guangzhou.Frequency analysis (proportions), histograms, and percentage stacked area plots were used to describe the epidemiological characteristics of the outbreaks. The incubation period and time-varying reproduction numbers (Rt) estimations were used for the further analysis. Results: By June 18, 2021, a total of 127 COVID-19 cases caused by Delta variant was reported in Liwan district. The youngest case was aged 2 years and the oldest was aged 85 years. There were 18.9% (24/127) aged <18 years, 43.3% (55/127) aged 18-59 years, and 37.8% (48/127) aged ≥60 years, the male to female ratio of the cases was 1∶1.35 (54∶73). The cases were mainly retired people (32.3%, 41/127), the jobless or unemployed (18.1%, 23/127), and students (16.5%, 21/127). The infections mainly occurred in Baihedong (70.1%, 89/127) and Zhongnan street (23.6%, 30/127) communities in the southern area of Liwan district. The median incubation period of the Delta variant infection was 6 days (range: 1-15 days). The clinical classification were mainly common type (64.6%, 82/127). The basic reproduction number (R0) was 5.1, Rt which once increased to 7.3. The transmissions mainly occurred in confined spaces, such as home (26.8%), restaurant (29.1%), neighborhood (3.9%), and market (3.1%), the household clustering was predominant. Close contacts tracing (66.1%) and community screening (33.1%) were the main ways to find the infections. Conclusion: The COVID-19 outbreak caused by Delta variant in Liwan district of Guangzhou was highly contagious, with the obvious characteristics of household clustering and high proportions of cases in adults aged 18-59 years and elderly people aged ≥60 years.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , Aged , Basic Reproduction Number , Disease Outbreaks , Female , Humans , Male
11.
Clin Infect Dis ; 73(9): 1735-1741, 2021 11 02.
Article in English | MEDLINE | ID: covidwho-1501053

ABSTRACT

Universities are faced with decisions on how to resume campus activities while mitigating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) risk. To provide guidance for these decisions, we developed an agent-based network model of SARS-CoV-2 transmission to assess the potential impact of strategies to reduce outbreaks. The model incorporates important features related to risk at the University of California San Diego. We found that structural interventions for housing (singles only) and instructional changes (from in-person to hybrid with class size caps) can substantially reduce the basic reproduction number, but masking and social distancing are required to reduce this to at or below 1. Within a risk mitigation scenario, increased frequency of asymptomatic testing from monthly to twice weekly has minimal impact on average outbreak size (1.1-1.9), but substantially reduces the maximum outbreak size and cumulative number of cases. We conclude that an interdependent approach incorporating risk mitigation, viral detection, and public health intervention is required to mitigate risk.


Subject(s)
COVID-19 , Universities , Basic Reproduction Number , Disease Outbreaks/prevention & control , Humans , SARS-CoV-2
12.
Sci Rep ; 10(1): 16598, 2020 10 06.
Article in English | MEDLINE | ID: covidwho-1493167

ABSTRACT

We address the diffusion of information about the COVID-19 with a massive data analysis on Twitter, Instagram, YouTube, Reddit and Gab. We analyze engagement and interest in the COVID-19 topic and provide a differential assessment on the evolution of the discourse on a global scale for each platform and their users. We fit information spreading with epidemic models characterizing the basic reproduction number [Formula: see text] for each social media platform. Moreover, we identify information spreading from questionable sources, finding different volumes of misinformation in each platform. However, information from both reliable and questionable sources do not present different spreading patterns. Finally, we provide platform-dependent numerical estimates of rumors' amplification.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Pneumonia, Viral/epidemiology , Social Media , Basic Reproduction Number , COVID-19 , Coronavirus Infections/virology , Data Analysis , Humans , Information Dissemination , Linear Models , Neural Networks, Computer , Pandemics , Pneumonia, Viral/virology , SARS-CoV-2 , Social Behavior
13.
Chaos ; 31(10): 101107, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1493330

ABSTRACT

Forecasting epidemic scenarios has been critical to many decision-makers in imposing various public health interventions. Despite progresses in determining the magnitude and timing of epidemics, epidemic peak time predictions for H1N1 and COVID-19 were inaccurate, with the peaks delayed with respect to predictions. Here, we show that infection and recovery rate fluctuations play a critical role in peak timing. Using a susceptible-infected-recovered model with daily fluctuations on control parameters, we show that infection counts follow a lognormal distribution at the beginning of an epidemic wave, similar to price distributions for financial assets. The epidemic peak time of the stochastic solution exhibits an inverse Gaussian probability distribution, fitting the spread of the epidemic peak times observed across Italian regions. We also show that, for a given basic reproduction number R0, the deterministic model anticipates the peak with respect to the most probable and average peak time of the stochastic model. The epidemic peak time distribution allows one for a robust estimation of the epidemic evolution. Considering these results, we believe that the parameters' dynamical fluctuations are paramount to accurately predict the epidemic peak time and should be introduced in epidemiological models.


Subject(s)
COVID-19 , Epidemics , Influenza A Virus, H1N1 Subtype , Basic Reproduction Number , Humans , SARS-CoV-2
14.
J Math Biol ; 83(5): 54, 2021 11 01.
Article in English | MEDLINE | ID: covidwho-1491092

ABSTRACT

Motivated by modelling epidemics like COVID-19, this paper proposes a generalized chain binomial process which integrates two types of infectives, those with symptoms and those without. Testing of infectives and vaccination of susceptibles are then incorporated as preventive protective measures. Our interest relates to the distribution of the state of the population at the end of infection and to the reproduction number [Formula: see text] with the associated extinction condition. The method uses the construction of a family of martingales and a branching approximation for large populations, respectively. A more general branching process for epidemics is also constructed and studied. Finally, some results obtained are illustrated by numerical examples.


Subject(s)
COVID-19 , Epidemics , Basic Reproduction Number , Disease Susceptibility , Humans , Models, Biological , SARS-CoV-2
15.
Emerg Infect Dis ; 27(10): 2578-2587, 2021 10.
Article in English | MEDLINE | ID: covidwho-1486731

ABSTRACT

The serial interval and effective reproduction number for coronavirus disease (COVID-19) are heterogenous, varying by demographic characteristics, region, and period. During February 1-July 13, 2020, we identified 4,080 transmission pairs in Georgia, USA, by using contact tracing information from COVID-19 cases reported to the Georgia Department of Public Health. We examined how various transmission characteristics were affected by symptoms, demographics, and period (during shelter-in-place and after subsequent reopening) and estimated the time course of reproduction numbers for all 159 Georgia counties. Transmission varied by time and place but also by persons' sex and race. The mean serial interval decreased from 5.97 days in February-April to 4.40 days in June-July. Younger adults (20-50 years of age) were involved in most transmission events occurring during or after reopening. The shelter-in-place period was not long enough to prevent sustained virus transmission in densely populated urban areas connected by major transportation links.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , Basic Reproduction Number , Contact Tracing , Georgia/epidemiology , Humans
16.
Science ; 372(6538)2021 04 09.
Article in English | MEDLINE | ID: covidwho-1476375

ABSTRACT

A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in September 2020 and is rapidly spreading toward fixation. Using a variety of statistical and dynamic modeling approaches, we estimate that this variant has a 43 to 90% (range of 95% credible intervals, 38 to 130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine rollout, COVID-19 hospitalizations and deaths across England in the first 6 months of 2021 were projected to exceed those in 2020. VOC 202012/01 has spread globally and exhibits a similar transmission increase (59 to 74%) in Denmark, Switzerland, and the United States.


Subject(s)
COVID-19/transmission , COVID-19/virology , SARS-CoV-2 , Adolescent , Adult , Aged , Aged, 80 and over , Basic Reproduction Number , COVID-19/epidemiology , COVID-19/mortality , COVID-19 Vaccines , Child , Child, Preschool , Communicable Disease Control , England/epidemiology , Europe/epidemiology , Female , Humans , Infant , Male , Middle Aged , Models, Theoretical , Mutation , SARS-CoV-2/genetics , SARS-CoV-2/growth & development , SARS-CoV-2/pathogenicity , Severity of Illness Index , Socioeconomic Factors , United States/epidemiology , Viral Load , Young Adult
17.
Sci Rep ; 11(1): 20728, 2021 10 20.
Article in English | MEDLINE | ID: covidwho-1475481

ABSTRACT

The impact of the extent of testing infectious individuals on suppression of COVID-19 is illustrated from the early stages of outbreaks in Germany, the Hubei province of China, Italy, Spain and the UK. The predicted percentage of untested infected individuals depends on the specific outbreak but we found that they typically represent 60-80% of all infected individuals during the early stages of the outbreaks. We propose that reducing the underlying transmission from untested cases is crucial to suppress the virus. This can be achieved through enhanced testing in combination with social distancing and other interventions that reduce transmission such as wearing face masks. Once transmission from silent carriers is kept under control by these means, the virus could have been fully suppressed through fast isolation and contact tracing of tested cases.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/virology , Contact Tracing/methods , Masks , SARS-CoV-2 , Basic Reproduction Number , COVID-19/prevention & control , Calibration , China/epidemiology , Disease Outbreaks , Germany/epidemiology , Humans , Italy/epidemiology , Models, Theoretical , Physical Distancing , Poisson Distribution , Spain/epidemiology , United Kingdom/epidemiology
18.
Comput Methods Programs Biomed ; 212: 106469, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1471519

ABSTRACT

BACKGROUND AND OBJECTIVE: In this work, we analyze the spatial-temporal dynamics of a susceptible-infected-recovered (SIR) epidemic model with time delays. To better describe the dynamical behavior of the model, we take into account the cumulative effects of diffusion in the population dynamics, and the time delays in both the Holling type II treatment and the disease transmission process, respectively. METHODS: We perform linear stability analyses on the disease-free and endemic equilibria. We provide the expression of the basic reproduction number and set conditions on the backward bifurcation using Castillo's theorem. The values of the critical time transmission, the treatment delays and the relationship between them are established. RESULTS: We show that the treatment rate decreases the basic reproduction number while the transmission rate significantly affects the bifurcation process in the system. The transmission and treatment time-delays are found to be inversely proportional to the susceptible and infected diffusion rates. The analytical results are numerically tested. The results show that the treatment rate significantly reduces the density of infected population and ensures the transition from the unstable to the stable domain. Moreover, the system is more sensible to the treatment in the stable domain. CONCLUSIONS: The density of infected population increases with respect to the infected and susceptible diffusion rates. Both effects of treatment and transmission delays significantly affect the behavior of the system. The transmission time-delay at the critical point ensures the transition from the stable (low density) to the unstable (high density) domain.


Subject(s)
Epidemics , Models, Biological , Basic Reproduction Number , Computer Simulation
19.
Sci Rep ; 11(1): 20386, 2021 10 14.
Article in English | MEDLINE | ID: covidwho-1469987

ABSTRACT

Continuous deterministic models have been widely used to guide non-pharmaceutical interventions (NPIs) to combat the spread of the coronavirus disease 2019 (COVID-19). The validity of continuous deterministic models is questionable because they fail to incorporate two important characteristics of human society: high clustering and low degree of separation. A small-world network model is used to study the spread of COVID-19, thus providing more reliable information to provide guidance to mitigate it. Optimal timing of lockdown and reopening society is investigated so that intervention measures to combat COVID-19 can work more efficiently. Several important findings are listed as follows: travel restrictions should be implemented as soon as possible; if 'flattening the curve' is the purpose of the interventions, measures to reduce community transmission need not be very strict so that the lockdown can be sustainable; the fraction of the population that is susceptible, rather than the levels of daily new cases and deaths, is a better criterion to decide when to reopen society; and society can be safely reopened when the susceptible population is still as high as 70%, given that the basic reproduction number is 2.5. Results from small-world network models can be significantly different than those from continuous deterministic models, and the differences are mainly due to a major shortfall intrinsically embedded in the continuous deterministic models. As such, small-world network models provide meaningful improvements over continuous deterministic models and therefore should be used in the mathematical modeling of infection spread to guide the present COVID-19 interventions. For future epidemics, the present framework of mathematical modeling can be a better alternative to continuous deterministic models.


Subject(s)
COVID-19/epidemiology , Basic Reproduction Number , COVID-19/prevention & control , COVID-19/transmission , Communicable Disease Control , Humans , Quarantine , SARS-CoV-2/isolation & purification
20.
Nat Commun ; 12(1): 5968, 2021 10 13.
Article in English | MEDLINE | ID: covidwho-1467102

ABSTRACT

There is conflicting evidence on the influence of weather on COVID-19 transmission. Our aim is to estimate weather-dependent signatures in the early phase of the pandemic, while controlling for socio-economic factors and non-pharmaceutical interventions. We identify a modest non-linear association between mean temperature and the effective reproduction number (Re) in 409 cities in 26 countries, with a decrease of 0.087 (95% CI: 0.025; 0.148) for a 10 °C increase. Early interventions have a greater effect on Re with a decrease of 0.285 (95% CI 0.223; 0.347) for a 5th - 95th percentile increase in the government response index. The variation in the effective reproduction number explained by government interventions is 6 times greater than for mean temperature. We find little evidence of meteorological conditions having influenced the early stages of local epidemics and conclude that population behaviour and government interventions are more important drivers of transmission.


Subject(s)
COVID-19/transmission , Meteorological Concepts , SARS-CoV-2/pathogenicity , Basic Reproduction Number , COVID-19/epidemiology , Cities , Cross-Sectional Studies , Humans , Meta-Analysis as Topic , Pandemics , Regression Analysis , Seasons , Temperature , Weather
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