scholarly journals Estimating the increase in reproduction number associated with the Delta variant using local area dynamics in England

Author(s):  
Sam Abbott ◽  
Adam J. Kucharski ◽  
Sebastian Funk ◽  

AbstractBackgroundLocal estimates of the time-varying effective reproduction number (Rt) of COVID-19 in England became increasingly heterogeneous during April and May 2021. This may have been attributable to the spread of the Delta SARS-CoV-2 variant. This paper documents real-time analysis that aimed to investigate the association between changes in the proportion of positive cases that were S-gene positive, an indicator of the Delta variant against a background of the previously predominant Alpha variant, and the estimated time-varying Rt at the level of upper-tier local authorities (UTLA).MethodWe explored the relationship between the proportion of samples that were S-gene positive and the Rt of test-positive cases over time from the 23 February 2021 to the 25 May 2021. Effective reproduction numbers were estimated using the EpiNow2 R package independently for each local authority using two different estimates of the generation time. We then fit a range of regression models to estimate a multiplicative relationship between S-gene positivity and weekly mean Rt estimate.ResultsWe found evidence of an association between increased mean Rt estimates and the proportion of S-gene positives across all models evaluated with the magnitude of the effect increasing as model flexibility was decreased. Models that adjusted for either national level or NHS region level time-varying residuals were found to fit the data better, suggesting potential unexplained confounding.ConclusionsOur results indicated that even after adjusting for time-varying residuals between NHS regions, S-gene positivity was associated with an increase in the effective reproduction number of COVID-19. These findings were robust across a range of models and generation time assumptions, though the specific effect size was variable depending on the assumptions used. The lower bound of the estimated effect indicated that the reproduction number of Delta was above 1 in almost all local authorities throughout the period of investigation.

BMC Medicine ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Sahamoddin Khailaie ◽  
Tanmay Mitra ◽  
Arnab Bandyopadhyay ◽  
Marta Schips ◽  
Pietro Mascheroni ◽  
...  

Abstract Background SARS-CoV-2 has induced a worldwide pandemic and subsequent non-pharmaceutical interventions (NPIs) to control the spread of the virus. As in many countries, the SARS-CoV-2 pandemic in Germany has led to a consecutive roll-out of different NPIs. As these NPIs have (largely unknown) adverse effects, targeting them precisely and monitoring their effectiveness are essential. We developed a compartmental infection dynamics model with specific features of SARS-CoV-2 that allows daily estimation of a time-varying reproduction number and published this information openly since the beginning of April 2020. Here, we present the transmission dynamics in Germany over time to understand the effect of NPIs and allow adaptive forecasts of the epidemic progression. Methods We used a data-driven estimation of the evolution of the reproduction number for viral spreading in Germany as well as in all its federal states using our model. Using parameter estimates from literature and, alternatively, with parameters derived from a fit to the initial phase of COVID-19 spread in different regions of Italy, the model was optimized to fit data from the Robert Koch Institute. Results The time-varying reproduction number (Rt) in Germany decreased to <1 in early April 2020, 2–3 weeks after the implementation of NPIs. Partial release of NPIs both nationally and on federal state level correlated with moderate increases in Rt until August 2020. Implications of state-specific Rt on other states and on national level are characterized. Retrospective evaluation of the model shows excellent agreement with the data and usage of inpatient facilities well within the healthcare limit. While short-term predictions may work for a few weeks, long-term projections are complicated by unpredictable structural changes. Conclusions The estimated fraction of immunized population by August 2020 warns of a renewed outbreak upon release of measures. A low detection rate prolongs the delay reaching a low case incidence number upon release, showing the importance of an effective testing-quarantine strategy. We show that real-time monitoring of transmission dynamics is important to evaluate the extent of the outbreak, short-term projections for the burden on the healthcare system, and their response to policy changes.


2020 ◽  
Author(s):  
Padmanaban Venkatesan

AbstractTo understand the effect of nationwide lockdown on transmissibilty of SARS-CoV-2 in India, time varying reproduction number during the first weeks of April, 2020 was estimated. The time varying reproduction number was estimated using EpiEstim package in R programming language. The reproduction number has come down significantly during the lockdown period both at national level and in most states but it wasn’t reduced to less than 1. This calls for urgent need for more effective control measures in addition to lockdown to stop the epidemic spread of the virus.


2021 ◽  
Author(s):  
Sylvia K. Ofori ◽  
Jessica S. Schwind ◽  
Kelly L. Sullivan ◽  
Benjamin J Cowling ◽  
Gerardo Chowell ◽  
...  

The study characterized the transmission of COVID-19 in Ghana by estimating the time-varying reproduction number (Rt) and exploring the effect of various public health interventions at the national and regional levels. The median Rt for Ghana and six out of sixteen regions dropped from greater than 1 in March 2020 to less than 1 in September but increased above 1 in January 2021. The relaxation of movement restrictions and religious gatherings were not associated with increased Rt in the regions with lower case burdens. However, Rt increased in most regions after schools were reopened in January 2021. In a regression analysis, we estimated that the per-capita cumulative case count increased with population size. Findings indicated the public health interventions reduced the Rt at the national level while at the regional levels, the Rt fluctuated, and the extent of fluctuation varied across regions.


Author(s):  
Michelle Kendall ◽  
Luke Milsom ◽  
Lucie Abeler-Dorner ◽  
Chris Wymant ◽  
Luca Ferretti ◽  
...  

In May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Local Authorities in England, and at the National level, before and after the launch of the programme on the Isle of Wight. We used Bayesian and Maximum-Likelihood methods to estimate R, and compared the Isle of Wight to other areas using a synthetic control method. We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch. These results are robust across each of our approaches. Our results show that the sub-epidemic on the Isle of Wight was controlled significantly more effectively than the sub-epidemics of most other Upper Tier Local Authorities, changing from having the third highest reproduction number R (of 150) before the intervention to the tenth lowest afterwards. The data is not yet available to establish a causal link. However, the findings highlight the need for further research to determine the causes of this reduction, as these might translate into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination becomes available.


Author(s):  
Anatolii Petrovich Mykolaiets

It is noted that from the standpoint of sociology, “management — a function of organized systems of various nature — (technical, biological, social), which ensures the preservation of their structure, maintaining a certain state or transfer to another state, in accordance with the objective laws of the existence of this system, which implemented by a program or deliberately set aside”. Management is carried out through the influence of one subsystem-controlling, on the other-controlled, on the processes taking place in it with the help of information signals or administrative actions. It is proved that self-government allows all members of society or a separate association to fully express their will and interests, overcome alienation, effectively combat bureaucracy, and promote public self-realization of the individual. At the same time, wide direct participation in the management of insufficiently competent participants who are not responsible for their decisions, contradicts the social division of labor, reduces the effectiveness of management, complicates the rationalization of production. This can lead to the dominance of short-term interests over promising interests. Therefore, it is always important for society to find the optimal measure of a combination of self-management and professional management. It is determined that social representation acts, on the one hand, as the most important intermediary between the state and the population, the protection of social interests in a politically heterogeneous environment. On the other hand, it ensures the operation of a mechanism for correcting the political system, which makes it possible to correct previously adopted decisions in a legitimate way, without resorting to violence. It is proved that the system of social representation influences the most important political relations, promotes social integration, that is, the inclusion of various social groups and public associations in the political system. It is proposed to use the term “self-government” in relation to several levels of people’s association: the whole community — public self-government or self-government of the people, to individual regions or communities — local, to production management — production self-government. Traditionally, self-government is seen as an alternative to public administration. Ideology and practice of selfgovernment originate from the primitive, communal-tribal democracy. It is established that, in practice, centralization has become a “natural form of government”. In its pure form, centralization does not recognize the autonomy of places and even local life. It is characteristic of authoritarian regimes, but it is also widely used by democratic regimes, where they believe that political freedoms should be fixed only at the national level. It is determined that since the state has achieved certain sizes, it is impossible to abandon the admission of the existence of local authorities. Thus, deconcentration appears as one of the forms of centralization and as a cure for the excesses of the latter. Deconcentration assumes the presence of local bodies, which depend on the government functionally and in the order of subordination of their officials. The dependency of officials means that the leadership of local authorities is appointed by the central government and may be displaced.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qing Cheng ◽  
Zeyi Liu ◽  
Guangquan Cheng ◽  
Jincai Huang

AbstractBeginning on December 31, 2019, the large-scale novel coronavirus disease 2019 (COVID-19) emerged in China. Tracking and analysing the heterogeneity and effectiveness of cities’ prevention and control of the COVID-19 epidemic is essential to design and adjust epidemic prevention and control measures. The number of newly confirmed cases in 25 of China’s most-affected cities for the COVID-19 epidemic from January 11 to February 10 was collected. The heterogeneity and effectiveness of these 25 cities’ prevention and control measures for COVID-19 were analysed by using an estimated time-varying reproduction number method and a serial correlation method. The results showed that the effective reproduction number (R) in 25 cities showed a downward trend overall, but there was a significant difference in the R change trends among cities, indicating that there was heterogeneity in the spread and control of COVID-19 in cities. Moreover, the COVID-19 control in 21 of 25 cities was effective, and the risk of infection decreased because their R had dropped below 1 by February 10, 2020. In contrast, the cities of Wuhan, Tianmen, Ezhou and Enshi still had difficulty effectively controlling the COVID-19 epidemic in a short period of time because their R was greater than 1.


2006 ◽  
Vol 31 (1) ◽  
pp. 106-115
Author(s):  
Mathias Spaliviero

Due to its location, Mozambique suffers from cyclical flooding associated with heavy rains and cyclones. In recent years, extreme flood events affected millions of people, disrupting the economic recovery process that followed the peace agreement in 1992. Despite this natural threat, most of the population continues to live in flood prone areas both in rural environment, due to the dependency on agricultural activities, and in urban environment, since unsafe zones are often the only affordable option for new settlers. This paper presents a brief analytical review on different issues related with urban informal settlements, or slums, based on different project activities developed by the United Nations Human Settlements Programme (UN-HABITAT) in Mozambique. The aim is to identify applicable strategies to reduce vulnerability in urban slums, where approximately 70 percent of the urban population live. The implemented project activities target different organisational levels in an integrated manner, seeking for active involvement of the Government, local authorities and communities at each implementation stage, from decision-making to practical implementation. They consist of three main components: 1) supporting policy-making in order to ensure sustainable urban development, 2) delivering a comprehensive training and capacity building based on the mainstreaming concept of “Learning How to Live with Floods” as valid alternative to resettlement, and 3) facilitating participatory land use planning coupled with physical upgrading interventions at the local level. In the long-term, the intention of UN-HABITAT is to progressively focus on community-based slum upgrading and vulnerability reduction activities, coordinated by local authorities and actively monitored by central institutions, in improving and managing basic services and infrastructures (i.e. water supply, drainage, sanitation, waste management, road network, etc). This type of bottom-up experiences should then represent a basis for setting up a slum upgrading intervention strategy to be applied at the national level.


2022 ◽  
Author(s):  
Sam Abbott ◽  
Katharine Sherratt ◽  
Moritz Gerstung ◽  
Sebastian Funk

Background Early estimates from South Africa indicated that the Omicron COVID-19 variant may be both more transmissible and have greater immune escape than the previously dominant Delta variant. The rapid turnover of the latest epidemic wave in South Africa as well as initial evidence from contact tracing and household infection studies has prompted speculation that the generation time of the Omicron variant may be shorter in comparable settings than the generation time of the Delta variant. Methods We estimated daily growth rates for the Omicron and Delta variants in each UKHSA region from the 23rd of November to the 23rd of December 2021 using surveillance case counts by date of specimen and S-gene target failure status with an autoregressive model that allowed for time-varying differences in the transmission advantage of the Delta variant where the evidence supported this. By assuming a gamma distributed generation distribution we then estimated the generation time distribution and transmission advantage of the Omicron variant that would be required to explain this time varying advantage. We repeated this estimation process using two different prior estimates for the generation time of the Delta variant first based on household transmission and then based on its intrinsic generation time. Results Visualising our growth rate estimates provided initial evidence for a difference in generation time distributions. Assuming a generation time distribution for Delta with a mean of 2.5-4 days (90% credible interval) and a standard deviation of 1.9-3 days we estimated a shorter generation time distribution for Omicron with a mean of 1.5-3.2 days and a standard deviation of 1.3-4.6 days. This implied a transmission advantage for Omicron in this setting of 160%-210% compared to Delta. We found similar relative results using an estimate of the intrinsic generation time for Delta though all estimates increased in magnitude due to the longer assumed generation time. Conclusions We found that a reduction in the generation time of Omicron compared to Delta was able to explain the observed variation over time in the transmission advantage of the Omicron variant. However, this analysis cannot rule out the role of other factors such as differences in the populations the variants were mixing in, differences in immune escape between variants or bias due to using the test to test distribution as a proxy for the generation time distribution.


Author(s):  
Chris O’Leary ◽  
Chris Fox

This chapter argues that local authorities can and should use their purchasing power strategically to address the social determinants of health that affect their local area. It examines commissioning and procurement as local authority functions, defining these concepts and exploring the conceptual confusion between the two. The chapter then looks at the evidence of current practice of local authorities (with a particular focus on local authorities in the UK) in strategic use of their purchasing power. Core to the argument is the role of local voluntary organisations and small and medium-sized enterprises (SMEs), so there is a particular focus on the commissioning experience of these types of organisations. Finally, the chapter makes the case for the role that voluntary sector organisations can play in addressing social determinants of health, before drawing some broad conclusions about the way forward.


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