Epidemic risk from friendship network data: an equivalence with a non-uniform sampling of contact networks

A general framework for optimising cost-effectiveness of pandemic response under partial intervention measures

The COVID-19 pandemic created enormous public health and socioeconomic challenges. The health effects of vaccination and non-pharmaceutical interventions (NPIs) were often contrasted with significant social and economic costs. We describe a general framework aimed to derive adaptive cost-effective interventions, adequate for both recent and emerging pandemic threats. We also quantify the net health benefits and propose a reinforcement learning approach to optimise adaptive NPIs. The approach utilises an agent-based model simulating pandemic responses in Australia, and accounts for a heterogeneous population with variable levels of compliance fluctuating over time and across individuals. Our analysis shows that a significant net health benefit may be attained by adaptive NPIs formed by partial social distancing measures, coupled with moderate levels of the society's willingness to pay for health gains (health losses averted). We demonstrate that a socially acceptable balance between health effects and incurred economic costs is achievable over a long term, despite possible early setbacks.

COVID-19 digital contact tracing applications and techniques: A review post initial deployments

The coronavirus disease 2019 (COVID-19) is a severe global pandemic that has claimed millions of lives and continues to overwhelm public health systems in many countries. The spread of COVID-19 pandemic has negatively impacted the human mobility patterns such as daily transportation-related behavior of the public. There is a requirement to understand the disease spread patterns and its routes among neighboring individuals for the timely implementation of corrective measures at the required placement. To increase the effectiveness of contact tracing, countries across the globe are leveraging advancements in mobile technology and Internet of Things (IoT) to aid traditional manual contact tracing to track individuals who have come in close contact with identified COVID-19 patients. Even as the first administration of vaccines begins in 2021, the COVID-19 management strategy will continue to be multi-pronged for the foreseeable future with digital contact tracing being a vital component of the response along with the use of preventive measures such as social distancing and the use of face masks. After some months of deployment of digital contact tracing technology, deeper insights into the merits of various approaches and the usability, privacy, and ethical trade-offs involved are emerging. In this paper, we provide a comprehensive analysis of digital contact tracing solutions in terms of their methodologies and technologies in the light of the new data emerging about international experiences of deployments of digital contact tracing technology. We also provide a discussion on open challenges such as scalability, privacy, adaptability and highlight promising directions for future work.

Digital contact tracing technologies in epidemics: a rapid review

BACKGROUND

Reducing the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global priority. Contact tracing identifies people who were recently in contact with an infected individual, in order to isolate them and reduce further transmission. Digital technology could be implemented to augment and accelerate manual contact tracing. Digital tools for contact tracing may be grouped into three areas: 1) outbreak response; 2) proximity tracing; and 3) symptom tracking. We conducted a rapid review on the effectiveness of digital solutions to contact tracing during infectious disease outbreaks.

OBJECTIVES

To assess the benefits, harms, and acceptability of personal digital contact tracing solutions for identifying contacts of an identified positive case of an infectious disease.

SEARCH METHODS

An information specialist searched the literature from 1 January 2000 to 5 May 2020 in CENTRAL, MEDLINE, and Embase. Additionally, we screened the Cochrane COVID-19 Study Register.

SELECTION CRITERIA

We included randomised controlled trials (RCTs), cluster-RCTs, quasi-RCTs, cohort studies, cross-sectional studies and modelling studies, in general populations. We preferentially included studies of contact tracing during infectious disease outbreaks (including COVID-19, Ebola, tuberculosis, severe acute respiratory syndrome virus, and Middle East respiratory syndrome) as direct evidence, but considered comparative studies of contact tracing outside an outbreak as indirect evidence. The digital solutions varied but typically included software (or firmware) for users to install on their devices or to be uploaded to devices provided by governments or third parties. Control measures included traditional or manual contact tracing, self-reported diaries and surveys, interviews, other standard methods for determining close contacts, and other technologies compared to digital solutions (e.g. electronic medical records).

DATA COLLECTION AND ANALYSIS

Two review authors independently screened records and all potentially relevant full-text publications. One review author extracted data for 50% of the included studies, another extracted data for the remaining 50%; the second review author checked all the extracted data. One review author assessed quality of included studies and a second checked the assessments. Our outcomes were identification of secondary cases and close contacts, time to complete contact tracing, acceptability and accessibility issues, privacy and safety concerns, and any other ethical issue identified. Though modelling studies will predict estimates of the effects of different contact tracing solutions on outcomes of interest, cohort studies provide empirically measured estimates of the effects of different contact tracing solutions on outcomes of interest. We used GRADE-CERQual to describe certainty of evidence from qualitative data and GRADE for modelling and cohort studies.

MAIN RESULTS

We identified six cohort studies reporting quantitative data and six modelling studies reporting simulations of digital solutions for contact tracing. Two cohort studies also provided qualitative data. Three cohort studies looked at contact tracing during an outbreak, whilst three emulated an outbreak in non-outbreak settings (schools). Of the six modelling studies, four evaluated digital solutions for contact tracing in simulated COVID-19 scenarios, while two simulated close contacts in non-specific outbreak settings. Modelling studies Two modelling studies provided low-certainty evidence of a reduction in secondary cases using digital contact tracing (measured as average number of secondary cases per index case - effective reproductive number (R eff)). One study estimated an 18% reduction in R eff with digital contact tracing compared to self-isolation alone, and a 35% reduction with manual contact-tracing. Another found a reduction in R eff for digital contact tracing compared to self-isolation alone (26% reduction) and a reduction in R eff for manual contact tracing compared to self-isolation alone (53% reduction). However, the certainty of evidence was reduced by unclear specifications of their models, and assumptions about the effectiveness of manual contact tracing (assumed 95% to 100% of contacts traced), and the proportion of the population who would have the app (53%). Cohort studies Two cohort studies provided very low-certainty evidence of a benefit of digital over manual contact tracing. During an Ebola outbreak, contact tracers using an app found twice as many close contacts per case on average than those using paper forms. Similarly, after a pertussis outbreak in a US hospital, researchers found that radio-frequency identification identified 45 close contacts but searches of electronic medical records found 13. The certainty of evidence was reduced by concerns about imprecision, and serious risk of bias due to the inability of contact tracing study designs to identify the true number of close contacts. One cohort study provided very low-certainty evidence that an app could reduce the time to complete a set of close contacts. The certainty of evidence for this outcome was affected by imprecision and serious risk of bias. Contact tracing teams reported that digital data entry and management systems were faster to use than paper systems and possibly less prone to data loss. Two studies from lower- or middle-income countries, reported that contact tracing teams found digital systems simpler to use and generally preferred them over paper systems; they saved personnel time, reportedly improved accuracy with large data sets, and were easier to transport compared with paper forms. However, personnel faced increased costs and internet access problems with digital compared to paper systems. Devices in the cohort studies appeared to have privacy from contacts regarding the exposed or diagnosed users. However, there were risks of privacy breaches from snoopers if linkage attacks occurred, particularly for wearable devices.

AUTHORS' CONCLUSIONS

The effectiveness of digital solutions is largely unproven as there are very few published data in real-world outbreak settings. Modelling studies provide low-certainty evidence of a reduction in secondary cases if digital contact tracing is used together with other public health measures such as self-isolation. Cohort studies provide very low-certainty evidence that digital contact tracing may produce more reliable counts of contacts and reduce time to complete contact tracing. Digital solutions may have equity implications for at-risk populations with poor internet access and poor access to digital technology. Stronger primary research on the effectiveness of contact tracing technologies is needed, including research into use of digital solutions in conjunction with manual systems, as digital solutions are unlikely to be used alone in real-world settings. Future studies should consider access to and acceptability of digital solutions, and the resultant impact on equity. Studies should also make acceptability and uptake a primary research question, as privacy concerns can prevent uptake and effectiveness of these technologies.

Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling

In January 2020, a novel betacoronavirus (family Coronaviridae), named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of a cluster of pneumonia cases occurring in Wuhan City, Hubei Province, China^1,2. The disease arising from SARS-CoV-2 infection, coronavirus disease 2019 (COVID-19), subsequently spread rapidly causing a worldwide pandemic. Here we examine the added value of near real-time genome sequencing of SARS-CoV-2 in a subpopulation of infected patients during the first 10 weeks of COVID-19 containment in Australia and compare findings from genomic surveillance with predictions of a computational agent-based model (ABM). Using the Australian census data, the ABM generates over 24 million software agents representing the population of Australia, each with demographic attributes of an anonymous individual. It then simulates transmission of the disease over time, spreading from specific infection sources, using contact rates of individuals within different social contexts. We report that the prospective sequencing of SARS-CoV-2 clarified the probable source of infection in cases where epidemiological links could not be determined, significantly decreased the proportion of COVID-19 cases with contentious links, documented genomically similar cases associated with concurrent transmission in several institutions and identified previously unsuspected links. Only a quarter of sequenced cases appeared to be locally acquired and were concordant with predictions from the ABM. These high-resolution genomic data are crucial to track cases with locally acquired COVID-19 and for timely recognition of independent importations once border restrictions are lifted and trade and travel resume.

Use of social network analysis and global sensitivity and uncertainty analyses to better understand an influenza outbreak

In the summer of 2014, an influenza A(H3N2) outbreak occurred in Yichang city, Hubei province, China. A retrospective study was conducted to collect and interpret hospital and epidemiological data on it using social network analysis and global sensitivity and uncertainty analyses. Results for degree (χ²=17.6619, P<0.0001) and betweenness(χ²=21.4186, P<0.0001) centrality suggested that the selection of sampling objects were different between traditional epidemiological methods and newer statistical approaches. Clique and network diagrams demonstrated that the outbreak actually consisted of two independent transmission networks. Sensitivity analysis showed that the contact coefficient (k) was the most important factor in the dynamic model. Using uncertainty analysis, we were able to better understand the properties and variations over space and time on the outbreak. We concluded that use of newer approaches were significantly more efficient for managing and controlling infectious diseases outbreaks, as well as saving time and public health resources, and could be widely applied on similar local outbreaks.

A geo-computational algorithm for exploring the structure of diffusion progression in time and space

A diffusion process can be considered as the movement of linked events through space and time. Therefore, space-time locations of events are key to identify any diffusion process. However, previous clustering analysis methods have focused only on space-time proximity characteristics, neglecting the temporal lag of the movement of events. We argue that the temporal lag between events is a key to understand the process of diffusion movement. Using the temporal lag could help to clarify the types of close relationships. This study aims to develop a data exploration algorithm, namely the TrAcking Progression In Time And Space (TaPiTaS) algorithm, for understanding diffusion processes. Based on the spatial distance and temporal interval between cases, TaPiTaS detects sub-clusters, a group of events that have high probability of having common sources, identifies progression links, the relationships between sub-clusters, and tracks progression chains, the connected components of sub-clusters. Dengue Fever cases data was used as an illustrative case study. The location and temporal range of sub-clusters are presented, along with the progression links. TaPiTaS algorithm contributes a more detailed and in-depth understanding of the development of progression chains, namely the geographic diffusion process.

Estimating the epidemic risk using non-uniformly sampled contact data

Many datasets describing contacts in a population suffer from incompleteness due to population sampling and underreporting of contacts. Data-driven simulations of spreading processes using such incomplete data lead to an underestimation of the epidemic risk, and it is therefore important to devise methods to correct this bias. We focus here on a non-uniform sampling of the contacts between individuals, aimed at mimicking the results of diaries or surveys, and consider as case studies two datasets collected in different contexts. We show that using surrogate data built using a method developed in the case of uniform population sampling yields an improvement with respect to the use of the sampled data but is strongly limited by the underestimation of the link density in the sampled network. We put forward a second method to build surrogate data that assumes knowledge of the density of links within one of the groups forming the population. We show that it gives very good results when the population is strongly structured, and discuss its limitations in the case of a population with a weaker group structure. These limitations highlight the interest of measurements using wearable sensors able to yield accurate information on the structure and durations of contacts.

Disease Spreading in Time-Evolving Networked Communities

Human communities are organized in complex webs of contacts that may be represented by a graph or network. In this graph, vertices identify individuals and edges establish the existence of some type of relations between them. In real communities, the possible edges may be active or not for variable periods of time. These so-called temporal networks typically result from an endogenous social dynamics, usually coupled to the process under study taking place in the community. For instance, disease spreading may be affected by local information that makes individuals aware of the health status of their social contacts, allowing them to reconsider maintaining or not their social contacts. Here we investigate the impact of such a dynamical network structure on disease dynamics, where infection occurs along the edges of the network. To this end, we define an endogenous network dynamics coupled with disease spreading. We show that the effective infectiousness of a disease taking place along the edges of this temporal network depends on the population size, the number of infected individuals in the population and the capacity of healthy individuals to sever contacts with the infected, ultimately dictated by availability of information regarding each individual’s health status. Importantly, we also show how dynamical networks strongly decrease the average time required to eradicate a disease.