Retrospective study of the first wave of COVID-19 in Spain: analysis of counterfactual scenarios

One of the most important questions on the COVID-19 pandemic is ascertaining the correct timing to introduce non-pharmaceutical interventions (NPIs), based mainly on mobility restrictions, to control the rising of the daily incidence in a specific territory. Here, we make a retrospective analysis of the first wave of the epidemic in Spain and provide a set of useful insights to optimize actions in the near future. We have reconstructed the exposure times, from infection to detectability, to correctly estimate the reproduction number Rt. This enables us to analyze counterfactual scenarios to understand the impact of earlier or later responses, decoupling containment measures from natural immunity. Our results quantify the differences in the number of fatalities for earlier and later responses to the epidemic in Spain.Teaser“We propose a backward analysis of pandemic incidence in a region to determine the correct timing of authorities’ non-pharmaceutical interventions to fight COVID-19”

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Diagnosis and treatment delay of head and neck cancers during COVID-19 era in a tertiary care academic hospital: what should we expect?

European Archives of Oto-Rhino-Laryngology ◽

10.1007/s00405-021-06834-1 ◽

2021 ◽

Author(s):

Pietro De Luca ◽

Antonella Bisogno ◽

Vito Colacurcio ◽

Pasquale Marra ◽

Claudia Cassandro ◽

...

Keyword(s):

Retrospective Study ◽

Head And Neck ◽

Retrospective Analysis ◽

Tertiary Care ◽

Diagnostic Delay ◽

Treatment Delay ◽

Head And Neck Cancers ◽

Control Measures ◽

Academic Hospital ◽

The Impact

Abstract Background Since the spreading of SARS-CoV-2 from China, all deferrable medical activities have been suspended, to redirect resources for the management of COVID patients. The goal of this retrospective study was to investigate the impact of COVID-19 on head and neck cancers’ diagnosis in our Academic Hospital. Methods A retrospective analysis of patients treated for head and neck cancers between March 12 and November 1, 2020 was carried out, and we compared these data with the diagnoses of the same periods of the 5 previous years. Results 47 patients were included in this study. We observed a significative reduction in comparison with the same period of the previous 5 years. Conclusions Our findings suggest that the COVID-19 pandemic is associated with a decrease in the number of new H&N cancers diagnoses, and a substantial diagnostic delay can be attributable to COVID-19 control measures.

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Despite vaccination, China needs non-pharmaceutical interventions to prevent widespread outbreaks of COVID-19 in 2021

Nature Human Behaviour ◽

10.1038/s41562-021-01155-z ◽

2021 ◽

Author(s):

Juan Yang ◽

Valentina Marziano ◽

Xiaowei Deng ◽

Giorgio Guzzetta ◽

Juanjuan Zhang ◽

...

Keyword(s):

Reproduction Number ◽

Synergetic Effect ◽

Data Driven ◽

Natural Immunity ◽

Epidemic Threshold ◽

Policy Makers ◽

Large Populations ◽

One Year ◽

Pharmaceutical Interventions

AbstractCOVID-19 vaccination is being conducted in over 200 countries and regions to control SARS-CoV-2 transmission and return to a pre-pandemic lifestyle. However, understanding when non-pharmaceutical interventions (NPIs) can be lifted as immunity builds up remains a key question for policy makers. To address this, we built a data-driven model of SARS-CoV-2 transmission for China. We estimated that, to prevent the escalation of local outbreaks to widespread epidemics, stringent NPIs need to remain in place at least one year after the start of vaccination. Should NPIs alone be capable of keeping the reproduction number (Rt) around 1.3, the synergetic effect of NPIs and vaccination could reduce the COVID-19 burden by up to 99% and bring Rt below the epidemic threshold in about 9 months. Maintaining strict NPIs throughout 2021 is of paramount importance to reduce COVID-19 burden while vaccines are distributed to the population, especially in large populations with little natural immunity.

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

University of Toronto Journal of Public Health ◽

10.33137/utjph.v2i2.36995 ◽

2021 ◽

Vol 2 (2) ◽

Author(s):

Fatima Khadadah ◽

Abdullah A. Al-Shammari ◽

Ahmad Alhashemi ◽

Dari Alhuwail ◽

Bader Al-Saif ◽

...

Keyword(s):

Disease Transmission ◽

Reproduction Number ◽

Public Health Intervention ◽

Population Level ◽

Socioeconomic Groups ◽

Before And After ◽

Cross Transmission ◽

Community Transmission ◽

The Impact ◽

Pharmaceutical Interventions

Background: Aggressive non-pharmaceutical interventions (NPIs) may reduce transmission of SARS-CoV2. 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 metapopulation Susceptible-Exposed-Infectious-Recovered (SEIR) model to reported cases stratified by two groups to estimate the impact of a lockdown on the effective reproduction number (Re). We estimated the basic reproduction number (R0) 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 lockdown. We estimated Re values of both groups before and after the lockdown, simulated the effect of these values on epidemic curves and explored a range of cross-transmission scenarios. Results: We estimate R0 at 1·06 (95% CI: 1·05-1·28) for P1 and 1·83 (1·58-2·33) for P2. On March 22nd, Re for P1 and P2 are estimated at 1·13 (1·07-1·17) and 1·38 (1·25-1·63) respectively. After the curfew had taken effect, Re for P1 dropped modestly to 1·04 (1·02-1·06) but almost doubled for P2 to 2·47 (1·98-3·45). Our simulated epidemic trajectories show that the partial curfew measure modestly reduced and delayed the height of the peak in P1, yet significantly elevated and hastened the peak in P2. Modest cross-transmission from P2 to P1 elevated the height of the peak in P1 and brought it forward in time closer to the peak of P2. Conclusion: Our results demonstrate that a lockdown can reduce SARS-CoV2 transmission in one subpopulation but accelerate it in another. At the population level, the consequences of lockdowns may vary across the socioeconomic spectrum. Any public health intervention needs to be sensitive to disparities within populations.

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Assessing the impact of adherence to Non-pharmaceutical interventions and indirect transmission on the dynamics of COVID-19: a mathematical modelling study

10.1101/2021.08.16.21262135 ◽

2021 ◽

Author(s):

Sarafa A. Iyaniwura ◽

Musa Rabiu ◽

Jummy F. David ◽

Jude D. Kong

Keyword(s):

Public Health ◽

Reproduction Number ◽

Health Policies ◽

Public Health Policies ◽

Indirect Transmission ◽

Epidemic Size ◽

Final Epidemic Size ◽

The Impact ◽

Size Relation ◽

Pharmaceutical Interventions

AbstractAdherence to public health policies such as the non-pharmaceutical interventions implemented against COVID-19 plays a major role in reducing infections and controlling the spread of the diseases. In addition, understanding the transmission dynamics of the disease is also important in order to make and implement efficient public health policies. In this paper, we developed an SEIR-type compartmental model to assess the impact of adherence to COVID-19 non-pharmaceutical interventions and indirect transmission on the dynamics of the disease. Our model considers both direct and indirect transmission routes and stratifies the population into two groups: those that adhere to COVID-19 non-pharmaceutical interventions (NPIs) and those that do not adhere to the NPIs. We compute the control reproduction number and the final epidemic size relation for our model and study the effect of different parameters of the model on these quantities. Our results show that direct transmission has more effect on the reproduction number and final epidemic size, relative to indirect transmission. In addition, we showed that there is a significant benefit in adhering to the COVID-19 NPIs.

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A viral perspective on worldwide non-pharmaceutical interventions against COVID-19

10.1101/2020.08.24.20180927 ◽

2020 ◽

Cited By ~ 1

Author(s):

Jean-Philippe Rasigade ◽

Anaïs Barray ◽

Julie Teresa Shapiro ◽

Charlène Coquisart ◽

Yoann Vigouroux ◽

...

Keyword(s):

Large Scale ◽

Reproduction Number ◽

Cumulative Effect ◽

Epidemiological Data ◽

Time And Space ◽

Minimal Set ◽

Genomic Divergence ◽

The Impact ◽

Pharmaceutical Interventions

AbstractQuantifying the effectiveness of large-scale non-pharmaceutical interventions (NPIs) against COVID-19 is critical to adapting responses against future waves of the pandemic. Most studies of NPIs thus far have relied on epidemiological data. Here, we report the impact of NPIs on the evolution of SARS-CoV-2, taking the perspective of the virus. We examined how variations through time and space of SARS-CoV-2 genomic divergence rates, which reflect variations of the epidemic reproduction number Rt, can be explained by NPIs and combinations thereof. Based on the analysis of 5,198 SARS-CoV-2 genomes from 57 countries along with a detailed chronology of 9 non-pharmaceutical interventions during the early epidemic phase up to May 2020, we find that home containment (35% Rt reduction) and education lockdown (26%) had the strongest predicted effectiveness. To estimate the cumulative effect of NPIs, we modelled the probability of reducing Rt below 1, which is required to stop the epidemic, for various intervention combinations and initial Rt values. In these models, no intervention implemented alone was sufficient to stop the epidemic for Rt’s above 2 and all interventions combined were required for Rt’s above 3. Our approach can help inform decisions on the minimal set of NPIs required to control the epidemic depending on the current Rt value.

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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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Synergetic measures needed to control infection waves and contain SARS-CoV-2 transmission

10.1101/2021.11.24.21266824 ◽

2021 ◽

Author(s):

Hang Su ◽

Yafang Cheng ◽

Ulrich Poeschl

Keyword(s):

Basic Reproduction Number ◽

Reproduction Number ◽

Scientific Discourse ◽

Protective Measure ◽

Protective Measures ◽

Vaccination Rates ◽

The Public ◽

Individual Measure ◽

The Impact ◽

Pharmaceutical Interventions

The public and scientific discourse on how to mitigate the COVID-19 pandemic is often focused on the impact of individual protective measures, in particular on immunization by vaccination. In view of changing virus variants and conditions, however, it seems not clear if vaccination or any other single protective measure alone may suffice to contain the transmission of SARS-CoV-2. Here, we investigate the effectiveness and synergies of vaccination and different non-pharmaceutical interventions such as universal masking (surgical, N95/FFP2), distancing & ventilation, contact reduction, and testing & isolation as a function of compliance in the population. We find that it would be difficult to contain SARS-CoV-2 transmission by any individual measure as currently available under realistic conditions. Instead, we show how multiple synergetic measures can be and have to be combined to decrease and keep the effective reproduction number (Re) below unity, even for virus variants with increased basic reproduction number (R0). We suggest that the presented approach and results can be used to design and communicate efficient strategies for mitigating the COVID-19 pandemic, depending on R0 as well as the efficacy and compliance achieved with each protective measure. At vaccination rates around 70%, the combination and synergies of universal masking, distancing & ventilation, and testing & isolation with moderate compliances around 30% appear well suited to keep Re below 1 and prevent or suppress infection waves. Higher compliance or additional measures like contact reductions (confinement/lockdown) are required to effectively and swiftly break intense waves of infection. For schools, we find that the transmission of SARS-CoV-2 can be contained by 2-3 tests per week combined with distancing & ventilation and masking.

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Can a COVID-19 vaccination program guarantee the return to a pre-pandemic lifestyle?

10.1101/2021.02.03.21251108 ◽

2021 ◽

Author(s):

Juan Yang ◽

Valentina Marziano ◽

Xiaowei Deng ◽

Giorgio Guzzetta ◽

Juanjuan Zhang ◽

...

Keyword(s):

Reproduction Number ◽

Data Driven ◽

Vaccination Program ◽

Transmission Model ◽

Natural Immunity ◽

Epidemic Threshold ◽

Large Populations ◽

One Year ◽

Pharmaceutical Interventions ◽

Key Questions

AbstractCOVID-19 vaccination has been initiated in several countries to control SARS-CoV-2 transmission. Whether and when non-pharmaceutical interventions (NPIs) can be lifted as vaccination builds up remains key questions. To address them, we built a data-driven SARS-CoV-2 transmission model for China. We estimated that, to prevent local outbreaks to escalate to major widespread epidemics, stringent NPIs need to remain in place at least one year after the start of vaccination. Should NPIs be capable to keep the reproduction number (Rt) around 1.3, vaccination could reduce up to 99% of COVID-19 burden and bring Rt below the epidemic threshold in 9 months. Maintaining strict NPIs throughout 2021 is of paramount importance to reduce COVID-19 burden while vaccines are distributed, especially in large populations with little natural immunity.

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Modeling analysis of a SEIQR epidemic model to assess the impact of undetected cases , and predict the early peack of the COVID-19 outbreak in Cameroon

10.21203/rs.3.rs-64201/v1 ◽

2020 ◽

Author(s):

NKAGUE NKAMBA LEONTINE ◽

MAYOMBE MANN MARTIN LUTHER ◽

MANGA THOMAS TIMOTHEE ◽

J. Mbang

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Lyapunov Functions ◽

Reproduction Number ◽

Benign Diseases ◽

Infected People ◽

Modeling Analysis ◽

Containment Measures ◽

The Impact ◽

Case Data ◽

Disease Free

Abstract COVID-19 is a highly contagious disease, and the strain is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It belongs to the coronavirus family, which can result in benign diseases in humans, such as a cold, and can also cause serious pathologies such as Severe Acute Respiratory Syndrome (SARS). In this study, we have modeled the COVID-19 epidemic in Cameroon. We used early reported case data to predict the peak, assess the impact of containment measures, and the impact of undetected infected people on the epidemic trend and characteristics of COVID-19. The basic reproduction number is computed using Lyapunov functions, and the global stability of disease-free and endemic equilibrium are demonstrated.

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