scholarly journals Possible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics

2021 ◽  
Author(s):  
Louise Dyson ◽  
Edward M Hill ◽  
Sam Moore ◽  
Jacob Curran-Sebastian ◽  
Michael J Tildesley ◽  
...  
Keyword(s):  
Immune Escape ◽  
Deterministic Model ◽  
Control Measures ◽  
Transmission Model ◽  
Vaccination Rates ◽  
Infection Dynamics ◽  
Potential Impact ◽  
Age Structured ◽  
Ongoing Infection ◽  
Viral Reproduction

Ongoing infection with, and associated viral reproduction of, SARS-CoV-2 provides opportunities for the virus to acquire advantageous mutations, which may alter viral transmissibility and disease severity, and allow escape from natural or vaccine-derived immunity. The number of countries reporting Variants of Concern (VOCs) with such mutations continues to rise. Here, we investigate two scenarios for third waves of the COVID pandemic: one driven by increased transmissibility, and another driven by immune escape. We do this using three mathematical models: a parsimonious susceptible-latent-infectious-recovered (SEIR) deterministic model with homogeneous mixing, an age-structured SARS-CoV-2 transmission model and a stochastic importation model. We calibrated our models to the situation in England in May 2021, although the insights will generalise to other contexts. We therefore accurately captured infection dynamics and vaccination rates, and also used these to explore the potential impact of a putative new VOC-targeted vaccine. Epidemiological trajectories for putative VOCs are wide-ranging and heavily dependent on their transmissibility, immune escape capability, and the time at which a postulated VOC-targeted vaccine may be introduced. We demonstrate that a VOC with either a substantial transmission advantage over resident variants, or the ability to evade vaccine-derived and prior immunity, is expected to generate a wave of infections and hospitalisations comparable to those seen in the winter 2020-21 wave. Moreover, a variant that is less transmissible, but shows partial immune-escape could provoke a wave of infection that would not be revealed until control measures are further relaxed.

scholarly journals Possible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Louise Dyson ◽  
Edward M. Hill ◽  
Sam Moore ◽  
Jacob Curran-Sebastian ◽  
Michael J. Tildesley ◽  
...  
Keyword(s):  
Mathematical Models ◽  
Disease Severity ◽  
Immune Escape ◽  
Deterministic Model ◽  
Control Measures ◽  
Structured Model ◽  
Age Structured ◽  
Age Structured Model ◽  
Viral Reproduction ◽  
Importation Model

AbstractViral reproduction of SARS-CoV-2 provides opportunities for the acquisition of advantageous mutations, altering viral transmissibility, disease severity, and/or allowing escape from natural or vaccine-derived immunity. We use three mathematical models: a parsimonious deterministic model with homogeneous mixing; an age-structured model; and a stochastic importation model to investigate the effect of potential variants of concern (VOCs). Calibrating to the situation in England in May 2021, we find epidemiological trajectories for putative VOCs are wide-ranging and dependent on their transmissibility, immune escape capability, and the introduction timing of a postulated VOC-targeted vaccine. We demonstrate that a VOC with a substantial transmission advantage over resident variants, or with immune escape properties, can generate a wave of infections and hospitalisations comparable to the winter 2020-2021 wave. Moreover, a variant that is less transmissible, but shows partial immune-escape could provoke a wave of infection that would not be revealed until control measures are further relaxed.

THE IMPACT OF VACCINATION ON MALARIA PREVALENCE: A VACCINE-AGE-STRUCTURED MODELING APPROACH

2020 ◽  
Vol 28 (02) ◽  
pp. 475-513
Author(s):  
KATIA VOGT-GEISSE ◽  
CALISTUS N. NGONGHALA ◽  
ZHILAN FENG
Keyword(s):  
Booster Dose ◽  
Deterministic Model ◽  
Vaccine Dose ◽  
Threshold Value ◽  
Disease Prevalence ◽  
Control Measures ◽  
Disease Eradication ◽  
Vaccination Programs ◽  
Age Structured ◽  
The Impact

A deterministic model for the effects on disease prevalence of the most advanced pre-erythrocytic vaccine against malaria is proposed and studied. The model includes two vaccinated classes that correspond to initially vaccinated and booster dose vaccinated individuals. These two classes are structured by time-since-initial-vaccination (vaccine-age). This structure is a novelty for vector–host models; it allows us to explore the effects of parameters that describe timed and delayed delivery of a booster dose, and immunity waning on disease prevalence. Incorporating two vaccinated classes can predict more accurately threshold vaccination coverages for disease eradication under multi-dose vaccination programs. We derive a vaccine-age-structured control reproduction number [Formula: see text] and establish conditions for the existence and stability of equilibria to the system. The model is bistable when [Formula: see text]. In particular, it exhibits a backward (sub-critical) bifurcation, indicating that [Formula: see text] is no longer the threshold value for disease eradication. Thus, to achieve eradication we must identify and implement control measures that will reduce [Formula: see text] to a value smaller than unity. Therefore, it is crucial to be cautious when using [Formula: see text] to guide public health policy, although it remains a key quantity for decision making. Our results show that if the booster vaccine dose is administered with delay, individuals may not acquire its full protective effect, and that incorporating waning efficacy into the system improves the accuracy of the model outcomes. This study suggests that it is critical to follow vaccination schedules closely, and anticipate the consequences of delays in those schedules.

scholarly journals The Impact of Universal Mask Use on SARS-COV-2 in Victoria, Australia on the Epidemic Trajectory of COVID-19

2021 ◽  
Vol 9 ◽  
Author(s):  
Valentina Costantino ◽  
Chandini Raina MacIntyre
Keyword(s):  
Mathematical Modeling ◽  
Deterministic Model ◽  
Face Mask ◽  
Control Measures ◽  
Contact Tracing ◽  
Epidemic Size ◽  
Community Transmission ◽  
Age Structured ◽  
The Impact ◽  
Mask Effectiveness

Objective(s): To estimate the impact of universal community face mask use in Victoria, Australia along with other routine disease control measures in place.Methods: A mathematical modeling study using an age structured deterministic model for Victoria, was simulated for 123 days between 1 June 2020 and 1 October 2020, incorporating lockdown, contact tracing, and case findings with and without mask use in varied scenarios. The model tested the impact of differing scenarios of the universal use of face masks in Victoria, by timing, varying mask effectiveness, and uptake.Results: A six-week lockdown with standard control measures, but no masks, would have resulted in a large resurgence by September, following the lifting of restrictions. Mask use can substantially reduce the epidemic size, with a greater impact if at least 50% of people wear a mask which has an effectiveness of at least 40%. Early mask use averts more cases than mask usage that is only implemented closer to the peak. No mask use, with a 6-week lockdown, results in 67,636 cases and 120 deaths by 1 October 2020 if no further lockdowns are used. If mask use at 70% uptake commences on 23 July 2020, this is reduced to 7,961 cases and 42 deaths. We estimated community mask effectiveness to be 11%.Conclusion(s): Lockdown and standard control measures may not have controlled the epidemic in Victoria. Mask use can substantially improve epidemic control if its uptake is higher than 50% and if moderately effective masks are used. Early mask use should be considered in other states if community transmission is present, as this has a greater effect than later mask wearing mandates.

scholarly journals The effect of non-pharmaceutical interventions on COVID-19 cases, deaths and demand for hospital services in the UK: a modelling study

2020 ◽  
Author(s):  
Nicholas G. Davies ◽  
Adam J. Kucharski ◽  
Rosalind M. Eggo ◽  
Amy Gimma ◽  
W. John Edmunds ◽  
...  
Keyword(s):  
Intensive Care ◽  
Healthcare System ◽  
Control Measures ◽  
Transmission Model ◽  
School Closures ◽  
Social Distancing ◽  
Age Structured ◽  
The Uk ◽  
The Impact ◽  
Pharmaceutical Interventions

AbstractBackgroundNon-pharmaceutical interventions have been implemented to reduce transmission of SARS-CoV-2 in the UK. Projecting the size of an unmitigated epidemic and the potential effect of different control measures has been critical to support evidence-based policymaking during the early stages of the epidemic.MethodsWe used a stochastic age-structured transmission model to explore a range of intervention scenarios, including the introduction of school closures, social distancing, shielding of elderly groups, self-isolation of symptomatic cases, and extreme “lockdown”-type restrictions. We simulated different durations of interventions and triggers for introduction, as well as combinations of interventions. For each scenario, we projected estimated new cases over time, patients requiring inpatient and critical care (intensive care unit, ICU) treatment, and deaths.FindingsWe found that mitigation measures aimed at reducing transmission would likely have decreased the reproduction number, but not sufficiently to prevent ICU demand from exceeding NHS availability. To keep ICU bed demand below capacity in the model, more extreme restrictions were necessary. In a scenario where “lockdown”-type interventions were put in place to reduce transmission, these interventions would need to be in place for a large proportion of the coming year in order to prevent healthcare demand exceeding availability.InterpretationThe characteristics of SARS-CoV-2 mean that extreme measures are likely required to bring the epidemic under control and to prevent very large numbers of deaths and an excess of demand on hospital beds, especially those in ICUs.Research in ContextEvidence before this studyAs countries have moved from early containment efforts to planning for the introduction of large-scale non-pharmaceutical interventions to control COVID-19 outbreaks, epidemic modelling studies have explored the potential for extensive social distancing measures to curb transmission. However, it remains unclear how different combinations of interventions, timings, and triggers for the introduction and lifting of control measures may affect the impact of the epidemic on health services, and what the range of uncertainty associated with these estimates would be.Added value of this studyUsing a stochastic, age-structured epidemic model, we explored how eight different intervention scenarios could influence the number of new cases and deaths, as well as intensive care beds required over the projected course of the epidemic. We also assessed the potential impact of local versus national targeting of interventions, reduction in leisure events, impact of increased childcare by grandparents, and timing of triggers for different control measures. We simulated multiple realisations for each scenario to reflect uncertainty in possible epidemic trajectories.Implications of all the available evidenceOur results support early modelling findings, and subsequent empirical observations, that in the absence of control measures, a COVID-19 epidemic could quickly overwhelm a healthcare system. We found that even a combination of moderate interventions – such as school closures, shielding of older groups and self-isolation – would be unlikely to prevent an epidemic that would far exceed available ICU capacity in the UK. Intermittent periods of more intensive lockdown-type measures are predicted to be effective for preventing the healthcare system from being overwhelmed.

scholarly journals The contribution of asymptomatic SARS-CoV-2 infections to transmission on the Diamond Princess cruise ship

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Jon C Emery ◽  
Timothy W Russell ◽  
Yang Liu ◽  
Joel Hellewell ◽  
Carl AB Pearson ◽  
...  
Keyword(s):  
Reproduction Number ◽  
Disease Onset ◽  
Control Measures ◽  
Transmission Model ◽  
Cruise Ship ◽  
Transmission Control ◽  
Asymptomatic Infections ◽  
Potential Impact ◽  
Asymptomatic Individuals ◽  
Net Reproduction

A key unknown for SARS-CoV-2 is how asymptomatic infections contribute to transmission. We used a transmission model with asymptomatic and presymptomatic states, calibrated to data on disease onset and test frequency from the Diamond Princess cruise ship outbreak, to quantify the contribution of asymptomatic infections to transmission. The model estimated that 74% (70–78%, 95% posterior interval) of infections proceeded asymptomatically. Despite intense testing, 53% (51–56%) of infections remained undetected, most of them asymptomatic. Asymptomatic individuals were the source for 69% (20–85%) of all infections. The data did not allow identification of the infectiousness of asymptomatic infections, however low ranges (0–25%) required a net reproduction number for individuals progressing through presymptomatic and symptomatic stages of at least 15. Asymptomatic SARS-CoV-2 infections may contribute substantially to transmission. Control measures, and models projecting their potential impact, need to look beyond the symptomatic cases if they are to understand and address ongoing transmission.

scholarly journals The effect of control strategies that reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China

2020 ◽  
Author(s):  
Kiesha Prem ◽  
Yang Liu ◽  
Timothy W Russell ◽  
Adam J Kucharski ◽  
Rosalind M Eggo ◽  
...  
Keyword(s):  
Return To Work ◽  
Control Strategies ◽  
Age Distribution ◽  
Control Measures ◽  
Transmission Model ◽  
Epidemic Size ◽  
Contact Patterns ◽  
Returning To Work ◽  
Age Structured ◽  
Gates Foundation

AbstractBACKGROUNDIn December 2019, a novel strain of SARS-CoV-2 emerged in Wuhan, China. Since then, the city of Wuhan has taken unprecedented measures and efforts in response to the outbreak.METHODSWe quantified the effects of control measures on population contact patterns in Wuhan, China, to assess their effects on the progression of the outbreak. We included the latest estimates of epidemic parameters from a transmission model fitted to data on local and internationally exported cases from Wuhan in the age-structured epidemic framework. Further, we looked at the age-distribution of cases. Lastly, we simulated lifting of the control measures by allowing people to return to work in a phased-in way, and looked at the effects of returning to work at different stages of the underlying outbreak.FINDINGSChanges in mixing patterns may have contributed to reducing the number of infections in mid-2020 by 92% (interquartile range: 66–97%). There are benefits to sustaining these measures until April in terms of reducing the height of the peak, overall epidemic size in mid-2020 and probability that a second peak may occur after return to work. However, the modelled effects of social distancing measures vary by the duration of infectiousness and the role school children play in the epidemic.INTERPRETATIONRestrictions on activities in Wuhan, if maintained until April, would likely contribute to the reduction and delay the epidemic size and peak, respectively. However, there are some limitations to the analysis, including large uncertainties around estimates of R0 and the duration of infectiousness.FUNDINGBill and Melinda Gates Foundation, National Institute for Health Research, Wellcome Trust, and Health Data Research UK.

scholarly journals Modelling the impact of COVID-19-related programme interruptions on visceral leishmaniasis in India

2020 ◽  
Author(s):  
Epke A Le Rutte ◽  
Luc E Coffeng ◽  
Johanna Muñoz ◽  
Sake J de Vlas
Keyword(s):  
Public Health ◽  
Visceral Leishmaniasis ◽  
Health Problem ◽  
Public Health Problem ◽  
Mitigation Strategy ◽  
Mitigation Strategies ◽  
Transmission Model ◽  
Potential Impact ◽  
Age Structured ◽  
The Impact

AbstractBackgroundIn March 2020, India declared a nationwide lockdown to control the spread of COVID-19. As a result, control efforts against visceral leishmaniasis (VL) were interrupted.MethodsUsing an established age-structured deterministic VL transmission model, we predicted the impact of a 6 to 24-month programme interruption on the timeline towards achieving the VL elimination target, as well as on the increase of VL cases. We also explored the potential impact of a mitigation strategy after the interruption.ResultsDelays towards the elimination target are estimated to range between 0 to 9 years. Highly endemic settings where control efforts have been ongoing for 5-8 years are most affected by an interruption, for which we identified a mitigation strategy to be most relevant. However, more importantly, all settings can expect an increase in the number of VL cases. This increase is substantial even for settings with a limited expected delay in achieving the elimination target.ConclusionBesides implementing mitigation strategies, it is of great importance to try and keep the duration of the interruption as short as possible, to prevent new individuals from becoming infected with VL, and continue the efforts towards VL elimination as a public health problem in India.

scholarly journals COVID-19: One-month impact of the French lockdown on the epidemic burden

2020 ◽  
Author(s):  
Jonathan Roux ◽  
Clément Massonnaud ◽  
Pascal Crépey
Keyword(s):  
Large Scale ◽  
National Level ◽  
Control Measures ◽  
Transmission Model ◽  
Critical Conditions ◽  
Metropolitan Regions ◽  
Hospital Deaths ◽  
Age Structured ◽  
French Hospital ◽  
Set Up

1AbstractOn March 16 2020, French authorities ordered a large scale lockdown to counter the COVID-19 epidemic wave rising in the country, stopping non-essential economic, educational, and entertainment activities, maintaining mainly food retailers and healthcare institutions. One month later, the number of new hospitalizations and ICU admissions had reached a plateau and were beginning a slow descent.We developed a spatialized, deterministic, age-structured, and compartmental SARS-CoV-2 transmission model able to reproduce the pre-lockdown dynamic of the epidemic in each of the 13 French metropolitan regions. Thanks to this model, we estimate, at regional and national levels, the total number of hospitalizations, ICU admissions, hospital beds requirements (hospitalization and ICU), and hospital deaths which may have been prevented by this massive and unprecedented intervention in France.If no control measures had been set up, between March 19 and April 19 2020, our analysis shows that almost 23% of the French population would have been affected by COVID-19 (14.8 million individuals). Hence, the French lockdown prevented 587,730 hospitalizations and 140,320 ICU admissions at the national level. The total number of ICU beds required to treat patients in critical conditions would have been 104,550, far higher than the maximum French ICU capacity. This first month of lockdown also permitted to avoid 61,739 hospital deaths, corresponding to a 83.5% reduction of the total number of predicted deaths.Our analysis shows that in absence of any control measures, the COVID-19 epidemic would have had a critical morbidity and mortality burden in France, overwhelming in a matter of weeks French hospital capacities.

scholarly journals Controlling the pandemic during the SARS-CoV-2 vaccination rollout

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
João Viana ◽  
Christiaan H. van Dorp ◽  
Ana Nunes ◽  
Manuel C. Gomes ◽  
Michiel van Boven ◽  
...  
Keyword(s):  
Vaccination Coverage ◽  
Hospital Admissions ◽  
Mass Vaccination ◽  
Control Measures ◽  
Transmission Model ◽  
Seroprevalence Data ◽  
Age Structured ◽  
Substantial Control

AbstractThere is a consensus that mass vaccination against SARS-CoV-2 will ultimately end the COVID-19 pandemic. However, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. We investigate relaxation scenarios using an age-structured transmission model that has been fitted to age-specific seroprevalence data, hospital admissions, and projected vaccination coverage for Portugal. Our analyses suggest that the pressing need to restart socioeconomic activities could lead to new pandemic waves, and that substantial control efforts prove necessary throughout 2021. Using knowledge on control measures introduced in 2020, we anticipate that relaxing measures completely or to the extent as in autumn 2020 could launch a wave starting in April 2021. Additional waves could be prevented altogether if measures are relaxed as in summer 2020 or in a step-wise manner throughout 2021. We discuss at which point the control of COVID-19 would be achieved for each scenario.

scholarly journals Modelling the impact of COVID-19-related programme interruptions on visceral leishmaniasis in India

2021 ◽  
Author(s):  
Epke A Le Rutte ◽  
Luc E Coffeng ◽  
Johanna Muñoz ◽  
Sake J de Vlas
Keyword(s):  
Public Health ◽  
Visceral Leishmaniasis ◽  
Health Problem ◽  
Public Health Problem ◽  
Mitigation Strategy ◽  
Mitigation Strategies ◽  
Transmission Model ◽  
Potential Impact ◽  
Age Structured ◽  
The Impact

Abstract Background In March 2020, India declared a nationwide lockdown to control the spread of coronavirus disease 2019. As a result, control efforts against visceral leishmaniasis (VL) were interrupted. Methods Using an established age-structured deterministic VL transmission model, we predicted the impact of a 6- to 24-month programme interruption on the timeline towards achieving the VL elimination target as well as on the increase of VL cases. We also explored the potential impact of a mitigation strategy after the interruption. Results Delays towards the elimination target are estimated to range between 0 and 9 y. Highly endemic settings where control efforts have been ongoing for 5–8 y are most affected by an interruption, for which we identified a mitigation strategy to be most relevant. However, more importantly, all settings can expect an increase in the number of VL cases. This increase is substantial even for settings with a limited expected delay in achieving the elimination target. Conclusions Besides implementing mitigation strategies, it is of great importance to try and keep the duration of the interruption as short as possible to prevent new individuals from becoming infected with VL and continue the efforts towards VL elimination as a public health problem in India.

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