Stochastic discrete epidemic modeling of COVID-19 transmission in the Province of Shaanxi incorporating public health intervention and case importation

AbstractBefore the lock-down of Wuhan/Hubei/China, on January 23rd 2020, a large number of individuals infected by COVID-19 moved from the epicenter Wuhan and the Hubei province due to the Spring Festival, resulting in an epidemic in the other provinces including the Shaanxi province. The epidemic scale in Shaanxi was comparatively small and with half of cases being imported from the epicenter. Based on the complete epidemic data including the symptom onset time and transmission chains, we calculate the control reproduction number (1.48-1.69) in Xi’an. We could also compute the time transition, for each imported or local case, from the latent, to infected, to hospitalized compartment, as well as the effective reproduction number. This calculation enables us to revise our early deterministic transmission model to a stochastic discrete epidemic model with case importation and parameterize it. Our model-based analyses reveal that the newly generated infections decay to zero quickly; the cumulative number of case-driven quarantined individuals via contact tracing stabilize at a manageable level, indicating that the intervention strategies implemented in the Shaanxi province have been effective. Risk analyses, important for the consideration of “resumption of work”, show that a large second outbreak is expected if the level of case importation remains at the same level as between January 10th and February 4th 2020. However, if the case importation decreases by 30%, 60% and 90%, the second outbreak if happening will be of small-scale assuming contact tracing and quarantine/isolation remain as effective as before. Finally, we consider the effects of intermittent inflow with a Poisson distribution on the likelihood of multiple outbreaks. We believe the developed methodology and stochastic model provide an important model framework for the evaluation of revising travel restriction rules in the consideration of resuming social-economic activities while managing the disease control with potential case importation.

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Relative role of border restrictions, case finding and contact tracing in controlling SARS-CoV-2 in the presence of undetected transmission

10.1101/2021.05.05.21256675 ◽

2021 ◽

Author(s):

Rachael Pung ◽

Hannah E. Clapham ◽

Vernon J. Lee ◽

Adam J Kucharski ◽

Keyword(s):

Reproduction Number ◽

Relative Effectiveness ◽

Case Finding ◽

Contact Tracing ◽

Transmission Model ◽

Relative Role ◽

Outbreak Control ◽

Combining Data ◽

Different Types

Background Several countries have controlled the spread of COVID-19 through varying combinations of border restrictions, case finding, contact tracing and careful calibration on the resumption of domestic activities. However, evaluating the effectiveness of these measures based on observed cases alone is challenging as it does not reflect the transmission dynamics of missed infections. Methods Combining data on notified local COVID-19 cases with known and unknown sources of infections (i.e. linked and unlinked cases) in Singapore in 2020 with a transmission model, we reconstructed the incidence of missed infections and estimated the relative effectiveness of different types of outbreak control. We also examined implications for estimation of key real-time metrics -- the reproduction number and ratio of unlinked to linked cases, using observed data only as compared to accounting for missed infections. Findings Prior to the partial lockdown in Singapore, initiated in April 2020, we estimated 89% (95%CI 75-99%) of the infections caused by notified cases were contact traced, but only 12.5% (95%CI 2-69%) of the infections caused by missed infectors were identified. We estimated that the reproduction number was 1.23 (95%CI 0.98-1.54) after accounting for missed infections but was 0.90 (95%CI 0.79-1.1) based on notified cases alone. At the height of the outbreak, the ratio of missed to notified infections was 34.1 (95%CI 26.0-46.6) but the ratio of unlinked to linked infections was 0.81 (95%CI 0.59-1.36). Our results suggest that when case finding and contact tracing identifies at least 50% and 20% of the infections caused by missed and notified cases respectively, the reproduction number could be reduced by more than 14%, rising to 20% when contact tracing is 80% effective. Interpretation Depending on the relative effectiveness of border restrictions, case finding and contact tracing, unobserved outbreak dynamics can vary greatly. Commonly used metrics to evaluate outbreak control -- typically based on notified data -- could therefore misrepresent the true underlying outbreak. Funding Ministry of Health, Singapore.

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CoVID-19 in Singapore: Impact of Contact Tracing and Self-awareness on Healthcare Demand

10.1101/2020.06.04.20122879 ◽

2020 ◽

Author(s):

Qiuyang Huang ◽

Lin Wang ◽

Yongjian Yang ◽

Liping Huang ◽

Zhanwei Du ◽

...

Keyword(s):

Mathematical Model ◽

Reproduction Number ◽

Early Stage ◽

Control Strategies ◽

Contact Tracing ◽

Self Awareness ◽

Mass Gathering ◽

Minor Contribution ◽

Branching Model ◽

Local Case

AbstractBackgroundA great concern around the globe now is to mitigate the COVID-19 pandemic via contact tracing. Analyzing the control strategies during the first five months of 2020 in Singapore is important to estimate the effectiveness of contacting tracing measures.MethodsWe developed a mathematical model to simulate the COVID-19 epidemic in Singapore, with local cases stratified into 5 categories according to the conditions of contact tracing and self-awareness. Key parameters of each category were estimated from local surveillance data. We also simulated a set of possible scenarios to predict the effects of contact tracing and self-awareness for the following month.FindingsDuring January 23 - March 16, 2020, the success probabilities of contact tracing and self-awareness were estimated to be 31% (95% CI 28%-33%) and 54% (95% CI 51%-57%), respectively. During March 17 - April 7, 2020, several social distancing measures (e.g., limiting mass gathering) were introduced in Singapore, which, however, were estimated with minor contribution to reduce the non-tracing reproduction number per local case (Rι,2). If contact tracing and self-awareness cannot be further improved, we predict that the COVID-19 epidemic will continue to spread in Singapore if Rι,2 ≥ 1.5.ConclusionContact tracing and self-awareness can mitigate the COVID-19 transmission, and can be one of the key strategies to ensure a sustainable reopening after lifting the lockdown.SummaryWe evaluate the efficiency of contact tracing and self-awareness in Singapore’s early-stage control of COVID-19. Then use a branching model to simulate and evaluate the possible prospective outcomes of Singapore’s COVID-19 control in different scenarios.

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Isolation and contact tracing can tip the scale to containment of COVID-19 in populations with social distancing

10.1101/2020.03.10.20033738 ◽

2020 ◽

Cited By ~ 4

Author(s):

Mirjam E. Kretzschmar ◽

Ganna Rozhnova ◽

Michiel van Boven

Keyword(s):

Reproduction Number ◽

Added Value ◽

Contact Tracing ◽

Transmission Model ◽

Critical Threshold ◽

Strong Impact ◽

Social Distancing ◽

Household Contacts ◽

Novel Coronavirus ◽

The Impact

AbstractBackgroundNovel coronavirus (SARS-CoV-2) has extended its range of transmission in all parts of the world, with substantial variation in rates of transmission and severity of associated disease. Many countries have implemented social distancing as a measure to control further spread.MethodsWe evaluate whether and under which conditions containment or slowing down COVID-19 epidemics are possible by isolation and contact tracing in settings with various levels of social distancing. We use a stochastic transmission model in which every person generates novel infections according to a probability distribution that is affected by the incubation period distribution (time from infection to symptoms), distribution of the latent period (time from infection to onset of infectiousness), and overall transmissibility. The model distinguishes between close contacts (e.g., within a household) and other contacts in the population. Social distancing affects the number of contacts outside but not within the household.FindingsThe proportion of asymptomatic or unascertained cases has a strong impact on the controllability of the disease. If the proportion of asymptomatic infections is larger than 30%, contact tracing and isolation cannot achieve containment for an R0 of 2.5. Achieving containment by social distancing requires a reduction of numbers of non-household contacts by around 90%. Depending on the realized level of contact reduction, tracing and isolation of only household contacts, or of household and non-household contacts are necessary to reduce the effective reproduction number to below 1. A combination of social distancing with isolation and contact tracing leads to synergistic effects that increase the prospect of containment.InterpretationIsolation and contact tracing can be an effective means to slow down epidemics, but only if the majority of cases are ascertained. In a situation with social distancing, contact tracing can act synergistically and tip the scale towards containment, and can therefore be a tool for controlling COVID-19 epidemics as part of an exit strategy from current lockdown measures.FundingThis research was partly funded by ZonMw project number 91216062.Research in contextEvidence before this studyAs of 8 April 2020, the novel coronavirus (SARS-CoV-2) has spread to more than 170 countries and has caused near 90,000 deaths of COVID-19 worldwide. In the absence of effective medicines and vaccines, the preventive measures are limited to social distancing, isolation of confirmed and suspected cases, and identification and quarantining of their contacts. Evidence suggests that a substantial portion of transmission may occur before the onset of symptoms and before cases can be isolated, and that many cases remain unascertained. This has potentially important implications for the prospect of containment by combinations of these measures.Added value of this studyUsing a stochastic transmission model armed with current best estimates of epidemiological parameters, we evaluated under which conditions containment could be achieved with combinations of social distancing, isolation and contact tracing. We investigated the level of social distancing needed for containment, and how an additional implementation of isolation and contact tracing may likely help to in reducing the effective reproduction number to below 1, the critical threshold. We analyzed what proportion of household and non-household contacts need to be isolated effectively to achieve containment depending on the level of social distancing in the population. We estimated the impact of combinations of these measures on epidemic growth rate and doubling time for the number of infections. We find that under realistic assumptions on the level of social distancing, additional isolation and contact tracing are needed for stopping the epidemic. Whether quarantining only household contacts is sufficient, depends on levels of social distancing and timeliness of tracing and isolation.Implications of all the available evidenceOur analyses based on best understanding of the epidemiology of COVID-19, highlight that if social distancing is not complete, isolation and contact tracing at least of household contacts can help to delay and lower the epidemic peak. High levels of timely contact tracing of household and non-household contacts may be sufficient to control the epidemic.

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Determining the optimal strategy for reopening schools, work and society in the UK: balancing earlier opening and the impact of test and trace strategies with the risk of occurrence of a secondary COVID-19 pandemic wave

10.1101/2020.06.01.20100461 ◽

2020 ◽

Author(s):

Jasmina Panovska-Griffiths ◽

Cliff Kerr ◽

Robyn Margaret Stuart ◽

Dina Mistry ◽

Daniel Klein ◽

...

Keyword(s):

Large Scale ◽

Reproduction Number ◽

Epidemiological Data ◽

Contact Tracing ◽

Cumulative Number ◽

Social Distancing ◽

Uk Government ◽

The Uk ◽

The Impact ◽

Pandemic Wave

Background In order to slow down the spread of SARS-CoV-2, the virus causing the COVID-19 pandemic, the UK government has imposed strict physical distancing (lockdown) measures including school 'dismissals' since 23 March 2020. As evidence is emerging that these measures may have slowed the spread of the pandemic, it is important to assess the impact of any changes in strategy, including scenarios for school reopening and broader relaxation of social distancing. This work uses an individual-based model to predict the impact of a suite of possible strategies to reopen schools in the UK, including that currently proposed by the UK government. Methods We use Covasim, a stochastic agent-based model for transmission of COVID-19, calibrated to the UK epidemic. The model describes individuals' contact networks stratified as household, school, work and community layers, and uses demographic and epidemiological data from the UK. We simulate a range of different school reopening strategies with a society-wide relaxation of lockdown measures and in the presence of different non-pharmaceutical interventions, to estimate the number of new infections, cumulative cases and deaths, as well as the effective reproduction number with different strategies. To account for uncertainties within the stochastic simulation, we also simulated different levels of infectiousness of children and young adults under 20 years old compared to older ages. Findings We found that with increased levels of testing of people (between 25% and 72% of symptomatic people tested at some point during an active COVID-19 infection depending on scenarios) and effective contact-tracing and isolation for infected individuals, an epidemic rebound may be prevented across all reopening scenarios, with the effective reproduction number (R) remaining below one and the cumulative number of new infections and deaths significantly lower than they would be if testing did not increase. If UK schools reopen in phases from June 2020, prevention of a second wave would require testing 51% of symptomatic infections, tracing of 40% of their contacts, and isolation of symptomatic and diagnosed cases. However, without such measures, reopening of schools together with gradual relaxing of the lockdown measures are likely to induce a secondary pandemic wave, as are other scenarios for reopening. When infectiousness of <20 year olds was varied from 100% to 50% of that of older ages, our findings remained unchanged. Interpretation To prevent a secondary COVID-19 wave, relaxation of social distancing including reopening schools in the UK must be implemented alongside an active large-scale population-wide testing of symptomatic individuals and effective tracing of their contacts, followed by isolation of symptomatic and diagnosed individuals. Such combined measures have a greater likelihood of controlling the transmission of SARS-CoV-2 and preventing a large number of COVID-19 deaths than reopening schools and society with the current level of implementation of testing and isolation of infected individuals.

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Discrete epidemic modelling of COVID-19 transmission in Shaanxi Province with media reporting and imported cases

Mathematical Biosciences and Engineering ◽

10.3934/mbe.2022064 ◽

2021 ◽

Vol 19 (2) ◽

pp. 1388-1410

Author(s):

Jin Guo ◽

◽

Aili Wang ◽

Weike Zhou ◽

Yinjiao Gong ◽

...

Keyword(s):

Media Coverage ◽

Large Scale ◽

Public Awareness ◽

Shaanxi Province ◽

Contact Tracing ◽

Cumulative Number ◽

Global Public Health ◽

Final Size ◽

Media Reporting ◽

Imported Cases

<abstract><p>The large-scale infection of COVID-19 has led to a significant impact on lives and economies around the world and has had considerable impact on global public health. Social distancing, mask wearing and contact tracing have contributed to containing or at least mitigating the outbreak, but how public awareness influences the effectiveness and efficiency of such approaches remains unclear. In this study, we developed a discrete compartment dynamic model to mimic and explore how media reporting and the strengthening containment strategies can help curb the spread of COVID-19 using Shaanxi Province, China, as a case study. The targeted model is parameterized based on multi-source data, including the cumulative number of confirmed cases, recovered individuals, the daily number of media-reporting items and the imported cases from the rest of China outside Shaanxi from January 23 to April 11, 2020. We carried out a sensitivity analysis to investigate the effect of media reporting and imported cases on transmission. The results revealed that reducing the intensity of media reporting, which would result in a significant increasing of the contact rate and a sizable decreasing of the contact-tracing rate, could aggravate the outbreak severity by increasing the cumulative number of confirmed cases. It also demonstrated that diminishing the imported cases could alleviate the outbreak severity by reducing the length of the epidemic and the final size of the confirmed cases; conversely, delaying implementation of lockdown strategies could prolong the length of the epidemic and magnify the final size. These findings suggest that strengthening media coverage and timely implementing of lockdown measures can significantly reduce infection.</p></abstract>

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Model-based evaluation of school- and non-school-related measures to control the COVID-19 pandemic

Nature Communications ◽

10.1038/s41467-021-21899-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ganna Rozhnova ◽

Christiaan H. van Dorp ◽

Patricia Bruijning-Verhagen ◽

Martin C. J. Bootsma ◽

Janneke H. H. M. van de Wijgert ◽

...

Keyword(s):

Reproduction Number ◽

Additional Benefit ◽

Transmission Model ◽

Time Points ◽

School Based ◽

Admission Data ◽

Age Structured ◽

The Impact ◽

Pandemic Wave

AbstractThe role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. We use an age-structured transmission model fitted to age-specific seroprevalence and hospital admission data to assess the effects of school-based measures at different time points during the COVID-19 pandemic in the Netherlands. Our analyses suggest that the impact of measures reducing school-based contacts depends on the remaining opportunities to reduce non-school-based contacts. If opportunities to reduce the effective reproduction number (Re) with non-school-based measures are exhausted or undesired and Re is still close to 1, the additional benefit of school-based measures may be considerable, particularly among older school children. As two examples, we demonstrate that keeping schools closed after the summer holidays in 2020, in the absence of other measures, would not have prevented the second pandemic wave in autumn 2020 but closing schools in November 2020 could have reduced Re below 1, with unchanged non-school-based contacts.

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Analysis and prediction of the coronavirus disease epidemic in China based on an individual-based model

Scientific Reports ◽

10.1038/s41598-020-76969-4 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Zuiyuan Guo ◽

Dan Xiao

Keyword(s):

Reproduction Number ◽

Control Measures ◽

Cumulative Number ◽

Individual Based Model ◽

Whole Process ◽

Coordinate Descent Algorithm ◽

Initial Stage ◽

The Government ◽

Prevention And Control Measures ◽

And Control

AbstractWe established a stochastic individual-based model and simulated the whole process of occurrence, development, and control of the coronavirus disease epidemic and the infectors and patients leaving Hubei Province before the traffic was closed in China. Additionally, the basic reproduction number (R0) and number of infectors and patients who left Hubei were estimated using the coordinate descent algorithm. The median R0 at the initial stage of the epidemic was 4.97 (95% confidence interval [CI] 4.82–5.17). Before the traffic lockdown was implemented in Hubei, 2000 (95% CI 1982–2030) infectors and patients had left Hubei and traveled throughout the country. The model estimated that if the government had taken prevention and control measures 1 day later, the cumulative number of laboratory-confirmed patients in the whole country would have increased by 32.1%. If the lockdown of Hubei was imposed 1 day in advance, the cumulative number of laboratory-confirmed patients in other provinces would have decreased by 7.7%. The stochastic model could fit the officially issued data well and simulate the evolution process of the epidemic. The intervention measurements nationwide have effectively curbed the human-to-human transmission of severe acute respiratory syndrome coronavirus 2.

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The effects of non-pharmaceutical interventions on SARS-CoV-2 transmission in different socioeconomic populations in Kuwait: a modeling study

BMC Public Health ◽

10.1186/s12889-021-10984-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Fatima Khadadah ◽

Abdullah A. Al-Shammari ◽

Ahmad Alhashemi ◽

Dari Alhuwail ◽

Bader Al-Saif ◽

...

Keyword(s):

Disease Transmission ◽

Reproduction Number ◽

Transmission Model ◽

Socioeconomic Groups ◽

Before And After ◽

Cross Transmission ◽

Community Transmission ◽

The Impact ◽

Pharmaceutical Interventions ◽

The Basic Reproduction Number

Abstract Background Aggressive non-pharmaceutical interventions (NPIs) may reduce transmission of SARS-CoV-2. The extent to which these interventions are successful in stopping the spread have not been characterized in countries with distinct socioeconomic groups. We compared the effects of a partial lockdown on disease transmission among Kuwaitis (P1) and non-Kuwaitis (P2) living in Kuwait. Methods We fit a modified metapopulation SEIR transmission model to reported cases stratified by two groups to estimate the impact of a partial lockdown on the effective reproduction number ($$ {\mathcal{R}}_e $$ R e ). We estimated the basic reproduction number ($$ {\mathcal{R}}_0 $$ R 0 ) for the transmission in each group and simulated the potential trajectories of an outbreak from the first recorded case of community transmission until 12 days after the partial lockdown. We estimated $$ {\mathcal{R}}_e $$ R e values of both groups before and after the partial curfew, simulated the effect of these values on the epidemic curves and explored a range of cross-transmission scenarios. Results We estimate $$ {\mathcal{R}}_e $$ R e at 1·08 (95% CI: 1·00–1·26) for P1 and 2·36 (2·03–2·71) for P2. On March 22nd, $$ {\mathcal{R}}_e $$ R e for P1 and P2 are estimated at 1·19 (1·04–1·34) and 1·75 (1·26–2·11) respectively. After the partial curfew had taken effect, $$ {\mathcal{R}}_e $$ R e for P1 dropped modestly to 1·05 (0·82–1·26) but almost doubled for P2 to 2·89 (2·30–3·70). Our simulated epidemic trajectories show that the partial curfew measure greatly reduced and delayed the height of the peak in P1, yet significantly elevated and hastened the peak in P2. Modest cross-transmission between P1 and P2 greatly elevated the height of the peak in P1 and brought it forward in time closer to the peak of P2. Conclusion Our results indicate and quantify how the same lockdown intervention can accentuate disease transmission in some subpopulations while potentially controlling it in others. Any such control may further become compromised in the presence of cross-transmission between subpopulations. Future interventions and policies need to be sensitive to socioeconomic and health disparities.

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Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

Science ◽

10.1126/science.abg3055 ◽

2021 ◽

Vol 372 (6538) ◽

pp. eabg3055 ◽

Cited By ~ 82

Author(s):

Nicholas G. Davies ◽

Sam Abbott ◽

Rosanna C. Barnard ◽

Christopher I. Jarvis ◽

Adam J. Kucharski ◽

...

Keyword(s):

United States ◽

Severe Acute Respiratory Syndrome ◽

Reproduction Number ◽

The United States ◽

Control Measures ◽

Transmission Model ◽

Educational Institutions ◽

Stringent Control ◽

Dynamic Transmission Model ◽

Credible Intervals

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.

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POLICY OF PROMOTING ALCOHOL CONSUMPTION IN TIMES OF COVID-19 LOCKDOWN IN INDIA: A MEDICAL AND CONSTITUTIONAL ANALYSIS.

10.36106/ijar/1510903 ◽

2021 ◽

pp. 21-24

Author(s):

Neha Sharma ◽

Ayush Anand ◽

Shreyas Joshi ◽

Samrat Ray

Keyword(s):

Mobile Application ◽

Prospective Observational Study ◽

Social Contact ◽

Contact Tracing ◽

Family Welfare ◽

Cumulative Number ◽

Test Results ◽

Before And After ◽

The Given ◽

Constitutional Analysis

BACKGROUND: India, with the declaration of COVID-19 as a pandemic, started imposing restrictions in the country th and initiated a nationwide lockdown under Section 6 of the Disaster Management Act, 2005 on 24 March 2020, followed by four phases of lockdown and then gradual unlock of the country. The rationale behind the same was to avoid social contact. Alcohol dispensing was also stopped during this time and was among the rst services to be reopened by the States. We propose in this paper that this lifting of ban on alcohol sale during the pandemic has led to a signicant increase in the number of COVID-19 cases in the country. METHODS: This is a prospective, observational study, done by collecting data from the Aargya Setu App, which is a mobile application launched by the Ministry of Health and Family Welfare on 2 April 2020 for contact tracing and elf assessment of COVID-19. The data of cumulative number of cases in 12 selected states of the country were compared before and after the lift of ban of alcohol and signicance was shown by the paired t test. RESULTS: The number of COVID-19 positive cases in the country during nationwide lockdown with simultaneous ban on alcohol sale when compared to cumulative number of cases after the lift of ban of alcohol sale during Lockdown and initial Unlock is statistically signicant (p = 0.04) CONCLUSION: We found that the decision to restart the sale of Alcohol could have been a factor for rise in number of cases in the country in the given timeframe. The decision to start the sale has also not been in accordance with the Indian Constitution and against the nation's founding ethics.

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