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Modeling vaccination rollouts, SARS-CoV-2 variants and the requirement for non-pharmaceutical interventions in Italy.

ABSTRACT: Despite progress in clinical care for patients with coronavirus disease 2019 (COVID-19)¹, population-wide interventions are still crucial to manage the pandemic, which has been aggravated by the emergence of new, highly transmissible variants. In this study, we combined the SIDARTHE model², which predicts the spread of SARS-CoV-2 infections, with a new data-based model that projects new cases onto casualties and healthcare system costs. Based on the Italian case study, we outline several scenarios: mass vaccination campaigns with different paces, different transmission rates due to new variants and different enforced countermeasures, including the alternation of opening and closure phases. Our results demonstrate that non-pharmaceutical interventions (NPIs) have a higher effect on the epidemic evolution than vaccination alone, advocating for the need to keep NPIs in place during the first phase of the vaccination campaign. Our model predicts that, from April 2021 to January 2022, in a scenario with no vaccine rollout and weak NPIs ([Formula: see text] = 1.27), as many as 298,000 deaths associated with COVID-19 could occur. However, fast vaccination rollouts could reduce mortality to as few as 51,000 deaths. Implementation of restrictive NPIs ([Formula: see text] = 0.9) could reduce COVID-19 deaths to 30,000 without vaccinating the population and to 18,000 with a fast rollout of vaccines. We also show that, if intermittent open-close strategies are adopted, implementing a closing phase first could reduce deaths (from 47,000 to 27,000 with slow vaccine rollout) and healthcare system costs, without substantive aggravation of socioeconomic losses.

SUBMITTER: Giordano G

PROVIDER: S-EPMC8205853 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Modeling vaccination rollouts, SARS-CoV-2 variants and the requirement for non-pharmaceutical interventions in Italy.

Giordano Giulia G Colaneri Marta M Di Filippo Alessandro A Blanchini Franco F Bolzern Paolo P De Nicolao Giuseppe G Sacchi Paolo P Colaneri Patrizio P Bruno Raffaele R

Nature medicine 20210416 6

Despite progress in clinical care for patients with coronavirus disease 2019 (COVID-19)<sup>1</sup>, population-wide interventions are still crucial to manage the pandemic, which has been aggravated by the emergence of new, highly transmissible variants. In this study, we combined the SIDARTHE model<sup>2</sup>, which predicts the spread of SARS-CoV-2 infections, with a new data-based model that projects new cases onto casualties and healthcare system costs. Based on the Italian case study, we o ...[more]

PMID: 33864052

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Project description:BackgroundUnderstanding how the COVID-19 pandemic evolved under control measures is crucial to tackle the SARS-CoV-2 virus spread. Laos, a country bordering China but with late occurrence and low burden of COVID-19 compared to its neighbouring countries, was used for a case study.MethodsA transmission model with disease reporting was proposed to investigate the impact of control measures on the SARS-CoV-2 virus spread in Laos from April 2021 to May 2022. It was assumed that the transmission rate changed with people's behaviours, control measures and emerging variants; susceptibility decreased with vaccination and infection. Bayesian inference was used for model calibration to data of confirmed cases, deaths, and recoveries, and the deviance information criterion was used to select the best model variant.ResultsOur model including Non-pharmaceutical interventions (NPIs), behaviour change, vaccination, and changing variants well explained the three waves in Laos. The Alpha variant was estimated to have a basic reproduction number of 1.55 (95% CrI: 1.47-1.64) and was replaced by the Delta variant from September 2021 which was 1.88 (95% CrI: 1.77-2.01) times more transmissible; the Delta variant was replaced by Omicron variant from March 2022 which was 3.33 (95% CrI: 2.84-3.74) times more transmissible. The Delta variant was the most severe with a case fatality rate of 1.05% (95% CrI: 0.96-1.15%) while the Alpha variant and Omicron variant were much milder. The ascertainment rate was low and variable: first decreasing from 13.2 to 1.8% by 23 May 2021, and then increasing to 23.4% by 15 March 2022. Counterfactual simulations indicated that vaccination played strong roles in reducing infections even under the emergence of immune escape variants while behaviour change delayed but might not flatten the peak of outbreaks.ConclusionsThe three waves of Laos' epidemics were due to the invasion of more transmissible and immune escape variants that affected the herd immunity built via vaccination and infection. Even with immunity waning and the escape of new variants, vaccination was still the major contributor to control COVID-19 and combining behaviour changes and vaccination would best suppress future outbreaks of COVID-19.

Project description:BackgroundEngland's COVID-19 roadmap out of lockdown policy set out the timeline and conditions for the stepwise lifting of non-pharmaceutical interventions (NPIs) as vaccination roll-out continued, with step one starting on March 8, 2021. In this study, we assess the roadmap, the impact of the delta (B.1.617.2) variant of SARS-CoV-2, and potential future epidemic trajectories.MethodsThis mathematical modelling study was done to assess the UK Government's four-step process to easing lockdown restrictions in England, UK. We extended a previously described model of SARS-CoV-2 transmission to incorporate vaccination and multi-strain dynamics to explicitly capture the emergence of the delta variant. We calibrated the model to English surveillance data, including hospital admissions, hospital occupancy, seroprevalence data, and population-level PCR testing data using a Bayesian evidence synthesis framework, then modelled the potential trajectory of the epidemic for a range of different schedules for relaxing NPIs. We estimated the resulting number of daily infections and hospital admissions, and daily and cumulative deaths. Three scenarios spanning a range of optimistic to pessimistic vaccine effectiveness, waning natural immunity, and cross-protection from previous infections were investigated. We also considered three levels of mixing after the lifting of restrictions.FindingsThe roadmap policy was successful in offsetting the increased transmission resulting from lifting NPIs starting on March 8, 2021, with increasing population immunity through vaccination. However, because of the emergence of the delta variant, with an estimated transmission advantage of 76% (95% credible interval [95% CrI] 69-83) over alpha, fully lifting NPIs on June 21, 2021, as originally planned might have led to 3900 (95% CrI 1500-5700) peak daily hospital admissions under our central parameter scenario. Delaying until July 19, 2021, reduced peak hospital admissions by three fold to 1400 (95% CrI 700-1700) per day. There was substantial uncertainty in the epidemic trajectory, with particular sensitivity to the transmissibility of delta, level of mixing, and estimates of vaccine effectiveness.InterpretationOur findings show that the risk of a large wave of COVID-19 hospital admissions resulting from lifting NPIs can be substantially mitigated if the timing of NPI relaxation is carefully balanced against vaccination coverage. However, with the delta variant, it might not be possible to fully lift NPIs without a third wave of hospital admissions and deaths, even if vaccination coverage is high. Variants of concern, their transmissibility, vaccine uptake, and vaccine effectiveness must be carefully monitored as countries relax pandemic control measures.FundingNational Institute for Health Research, UK Medical Research Council, Wellcome Trust, and UK Foreign, Commonwealth and Development Office.

Project description:BackgroundAggressive 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.MethodsWe 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 ([Formula: see text]). We estimated the basic reproduction number ([Formula: see text]) 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 [Formula: see text] 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.ResultsWe estimate [Formula: see text] at 1·08 (95% CI: 1·00-1·26) for P1 and 2·36 (2·03-2·71) for P2. On March 22nd, [Formula: see text] 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, [Formula: see text] 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.ConclusionOur 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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Modeling vaccination rollouts, SARS-CoV-2 variants and the requirement for non-pharmaceutical interventions in Italy.

Publications

Modeling vaccination rollouts, SARS-CoV-2 variants and the requirement for non-pharmaceutical interventions in Italy.

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