Evolution and epidemic spread of SARS-CoV-2 in Brazil

Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.

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Evolution and epidemic spread of SARS-CoV-2 in Brazil

10.1101/2020.06.11.20128249 ◽

2020 ◽

Cited By ~ 1

Author(s):

Darlan S. Candido ◽

Ingra M. Claro ◽

Jaqueline G. de Jesus ◽

William M. Souza ◽

Filipe R. R. Moreira ◽

...

Keyword(s):

Average Distance ◽

Virus Transmission ◽

Joint Analysis ◽

Epidemic Spread ◽

Urban Centers ◽

Genomic Dataset ◽

Time Period ◽

The Impact ◽

Transmission Models

AbstractBrazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Due to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus transmission and epidemic spread remain challenging. We investigate the impact of NPIs in Brazil using epidemiological, mobility and genomic data. Mobility-driven transmission models for São Paulo and Rio de Janeiro cities show that the reproduction number (Rt) reached below 1 following NPIs but slowly increased to values between 1 to 1.3 (1.0–1.6). Genome sequencing of 427 new genomes and analysis of a geographically representative genomic dataset from 21 of the 27 Brazilian states identified >100 international introductions of SARS-CoV-2 in Brazil. We estimate that three clades introduced from Europe emerged between 22 and 27 February 2020, and were already well-established before the implementation of NPIs and travel bans. During this first phase of the epidemic establishment of SARS-CoV-2 in Brazil, we find that the virus spread mostly locally and within-state borders. Despite sharp decreases in national air travel during this period, we detected a 25% increase in the average distance travelled by air passengers during this time period. This coincided with the spread of SARS-CoV-2 from large urban centers to the rest of the country. In conclusion, our results shed light on the role of large and highly connected populated centres in the rapid ignition and establishment of SARS-CoV-2, and provide evidence that current interventions remain insufficient to keep virus transmission under control in Brazil.One Sentence SummaryJoint analysis of genomic, mobility and epidemiological novel data provide unique insight into the spread and transmission of the rapidly evolving epidemic of SARS-CoV-2 in Brazil.

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

10.21203/rs.3.rs-130264/v1 ◽

2021 ◽

Author(s):

Ganna Rozhnova ◽

Christiaan van Dorp ◽

Patricia Bruijning-Verhagen ◽

Martin Bootsma ◽

Janneke van de Wijgert ◽

...

Keyword(s):

Reproduction Number ◽

Additional Benefit ◽

Transmission Model ◽

Time Points ◽

School Based ◽

Admission Data ◽

Age Structured ◽

The Impact ◽

Pandemic Wave

Abstract The role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. We used 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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A Mathematical Model for Nipah Virus Infection

Journal of Applied Mathematics ◽

10.1155/2020/6050834 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Assefa Denekew Zewdie ◽

Sunita Gakkhar

Keyword(s):

Virus Infection ◽

Reproduction Number ◽

Initial Conditions ◽

Nipah Virus ◽

Virus Transmission ◽

Globally Asymptotically Stable ◽

Dead Bodies ◽

Manifold Theory ◽

The Impact ◽

The Given

It has been reported that unprotected contact with the dead bodies of infected individuals is a plausible way of Nipah virus transmission. An SIRD model is proposed in this paper to investigate the impact of unprotected contact with dead bodies of infected individuals before burial or cremation and their disposal rate on the dynamics of Nipah virus infection. The model is analyzed, and the reproduction number is computed. It is established that the disease-free state is globally asymptotically stable when the reproduction number is less than unity and unstable if it is greater than unity. By using the central manifold theory, we observe that the endemic equilibrium is locally stable near to unity. It is concluded that minimizing unsafe contact with the infected dead body and/or burial or cremation as fast as possible contributes positively. Further, the numerical simulations for the given choice of data and initial conditions illustrate that the endemic state is stable and the disease persists in the community when the reproduction number is greater than one.

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COVID-19 in China: Risk Factors and R0 Revisited

10.1101/2020.05.18.20104703 ◽

2020 ◽

Author(s):

Irtesam Mahmud Khan ◽

Wenyi Zhang ◽

Sumaira Zafar ◽

Yong Wang ◽

Junyu He ◽

...

Keyword(s):

Virus Transmission ◽

Geographic Region ◽

Machine Learning Techniques ◽

Transmission Model ◽

Health Crisis ◽

Global Pandemic ◽

Learning Techniques ◽

Visual Aid ◽

Spatiotemporal Clustering ◽

The Impact

The COVID-19 epidemic had spread rapidly through China and subsequently has proliferated globally leading to a pandemic situation around the globe. Human-to-human transmissions, as well as asymptomatic transmissions of the infection, have been confirmed. As of April 3rd, public health crisis in China due to COVID-19 is potentially under control. We compiled a daily dataset of case counts, mortality, recovery, temperature, population density, and demographic information for each prefecture during the period of January 11 to April 07, 2020 (excluding Wuhan from our analysis due to missing data). Understanding the characteristics of spatiotemporal clustering of the COVID-19 epidemic and R0 is critical in effectively preventing and controlling the ongoing global pandemic. The prefectures were grouped based on several relevant features using unsupervised machine learning techniques. We performed a computational analysis utilizing the reported cases in China to estimate the revised R0 among different regions for prevention planning in an ongoing global pandemic. Finally, our results indicate that the impact of temperature and demographic (different age group percentage compared to the total population) factors on virus transmission may be characterized using a stochastic transmission model. Such predictions will help prioritize segments of a given community/ region for action and provide a visual aid in designing prevention strategies for a specific geographic region. Furthermore, revised estimation and our methodology will aid in improving the human health consequences of COVID-19 elsewhere.

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The impact of control strategies and behavioural changes on the elimination of Ebola from Lofa County, Liberia

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2016.0302 ◽

2017 ◽

Vol 372 (1721) ◽

pp. 20160302 ◽

Cited By ~ 34

Author(s):

Sebastian Funk ◽

Iza Ciglenecki ◽

Amanda Tiffany ◽

Etienne Gignoux ◽

Anton Camacho ◽

...

Keyword(s):

Reproduction Number ◽

Control Strategies ◽

Clinical Intervention ◽

Credible Interval ◽

Transmission Model ◽

Public Health Response ◽

Healthcare Seeking ◽

Behavioural Changes ◽

Treatment Centre ◽

The Impact

The Ebola epidemic in West Africa was stopped by an enormous concerted effort of local communities and national and international organizations. It is not clear, however, how much the public health response and behavioural changes in affected communities, respectively, contributed to ending the outbreak. Here, we analyse the epidemic in Lofa County, Liberia, lasting from March to November 2014, by reporting a comprehensive time line of events and estimating the time-varying transmission intensity using a mathematical model of Ebola transmission. Model fits to the epidemic show an alternation of peaks and troughs in transmission, consistent with highly heterogeneous spread. This is combined with an overall decline in the reproduction number of Ebola transmission from early August, coinciding with an expansion of the local Ebola treatment centre. We estimate that healthcare seeking approximately doubled over the course of the outbreak, and that isolation of those seeking healthcare reduced their reproduction number by 62% (mean estimate, 95% credible interval (CI) 59–66). Both expansion of bed availability and improved healthcare seeking contributed to ending the epidemic, highlighting the importance of community engagement alongside clinical intervention. This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’.

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Evolution of disease transmission rate during the course of SARS-COV-2: Patterns and determinants

10.21203/rs.3.rs-44647/v1 ◽

2020 ◽

Author(s):

Jie Zhu ◽

Blanca Gallego

Keyword(s):

Public Health ◽

Disease Transmission ◽

Reproduction Number ◽

Transmission Rate ◽

Region Of Interest ◽

Health Interventions ◽

Transmission Model ◽

Public Health Interventions ◽

Containment Measures ◽

The Impact

Abstract To date, many studies have argued the potential impact of public health interventions on flattening the epidemic curve of SARS-CoV-2. Most of them have focused on simulating the impact of interventions in a region of interest by manipulating contact patterns and key transmission parameters to reflect different scenarios. Our study looks into the evolution of the daily effective reproduction number during the epidemic via a stochastic transmission model. We found this measure (although model-dependent) provides an early signal of the efficacy of containment measures. This epidemiological parameter when updated in real-time can also provide better predictions of future outbreaks. Our results found a substantial variation in the effect of public health interventions on the dynamic of SARS-CoV-2 transmission over time and across countries, that could not be explained solely by the timing and number of the adopted interventions. This suggests that further knowledge about the idiosyncrasy of their implementation and effectiveness is required. Although sustained containment measures have successfully lowered growth in disease transmission, more than half of the 101 studied countries failed to maintain the effective reproduction number close to or below 1. This resulted in continued growth in reported cases. Finally, we were able to predict with reasonable accuracy which countries would experience outbreaks in the next 30 days.

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Investigating the Impact of Social Awareness and Rapid Test on A COVID-19 Transmission Model

Communication in Biomathematical Sciences ◽

10.5614/cbms.2021.4.1.5 ◽

2021 ◽

Vol 4 (1) ◽

pp. 46-64

Author(s):

Muhammad Afief Balya ◽

Bunga Oktaviani Dewi ◽

Faza Indah Lestari ◽

Gayatri Ratu ◽

Hanna Rosuliyana ◽

...

Keyword(s):

Basic Reproduction Number ◽

Reproduction Number ◽

Equilibrium Points ◽

Rapid Test ◽

Social Awareness ◽

Transmission Model ◽

Media Campaign ◽

Single Intervention ◽

The Impact ◽

The Basic Reproduction Number

In this article, we propose and analyze a mathematical model of COVID-19 transmission among a closed population, with social awareness and rapid test intervention as the control variables. For this, we have constructed the model using a compartmental system of the ordinary differential equations. Dynamical analysis regarding the existence and local stability of equilibrium points is conducted rigorously. Our analysis shows that COVID-19 will disappear from the population if the basic reproduction number is less than one, and persist if the basic reproduction number is greater than one. In addition, we have shown a trans-critical bifurcation phenomenon based on our proposed model when the basic reproduction number equals one. From the elasticity analysis, we have observed that rapid testing is more promising in reducing the basic reproduction number as compared to a media campaign to improve social awareness on COVID-19. Using the Pontryagin Maximum Principle (PMP), the characterization of our optimal control problem is derived analytically and solved numerically using the forward-backward iterative algorithm. Our cost-effectiveness analysis shows that using rapid test and media campaigns partially are the best intervention strategy to reduce the number of infected humans with the minimum cost of intervention. If the intervention is to be implemented as a single intervention, then using solely the rapid test is a more promising and low-cost option in reducing the number of infected individuals vis-a-vis a media campaign to increase social awareness as a single intervention.

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Mitigating COVID-19 outbreaks in workplaces and schools by hybrid telecommuting

PLoS Computational Biology ◽

10.1371/journal.pcbi.1009264 ◽

2021 ◽

Vol 17 (8) ◽

pp. e1009264

Author(s):

Simon Mauras ◽

Vincent Cohen-Addad ◽

Guillaume Duboc ◽

Max Dupré la Tour ◽

Paolo Frasca ◽

...

Keyword(s):

High School ◽

Primary School ◽

Primary Schools ◽

Reproduction Number ◽

Real Life ◽

Transmission Model ◽

Image Position ◽

Local Reproduction ◽

The Impact ◽

Day By Day

The COVID-19 epidemic has forced most countries to impose contact-limiting restrictions at workplaces, universities, schools, and more broadly in our societies. Yet, the effectiveness of these unprecedented interventions in containing the virus spread remain largely unquantified. Here, we develop a simulation study to analyze COVID-19 outbreaks on three real-life contact networks stemming from a workplace, a primary school and a high school in France. Our study provides a fine-grained analysis of the impact of contact-limiting strategies at workplaces, schools and high schools, including: (1) Rotating strategies, in which workers are evenly split into two shifts that alternate on a daily or weekly basis; and (2) On-Off strategies, where the whole group alternates periods of normal work interactions with complete telecommuting. We model epidemics spread in these different setups using a stochastic discrete-time agent-based transmission model that includes the coronavirus most salient features: super-spreaders, infectious asymptomatic individuals, and pre-symptomatic infectious periods. Our study yields clear results: the ranking of the strategies, based on their ability to mitigate epidemic propagation in the network from a first index case, is the same for all network topologies (workplace, primary school and high school). Namely, from best to worst: Rotating week-by-week, Rotating day-by-day, On-Off week-by-week, and On-Off day-by-day. Moreover, our results show that below a certain threshold for the original local reproduction number R 0 l o c a l within the network (< 1.52 for primary schools, < 1.30 for the workplace, < 1.38 for the high school, and < 1.55 for the random graph), all four strategies efficiently control outbreak by decreasing effective local reproduction number to R 0 l o c a l < 1. These results can provide guidance for public health decisions related to telecommuting.

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