scholarly journals Characterising contact in disease outbreaks via a network model of spatial-temporal proximity

Author(s):  
Ashleigh Myall ◽  
Robert L. Peach ◽  
Yu Wan ◽  
Siddharth Mookerjee ◽  
Elita Jauneikaite ◽  
...  

ABSTRACTContact tracing is a key tool in epidemiology to identify and control outbreaks of infectious diseases. Existing contact tracing methodologies produce contact maps of individuals based on a binary definition of contact which can be hampered by missing data and indirect contacts. Here, we present a Spatial-temporal Epidemiological Proximity (StEP) model to recover contact maps in disease outbreaks based on movement data. The StEP model accounts for imperfect data by considering probabilistic contacts between individuals based on spatial-temporal proximity of their movement trajectories, creating a robust movement network despite possible missing data and unseen transmission routes. Using real-world data we showcase the potential of StEP for contact tracing with outbreaks of multidrug-resistant bacteria and COVID-19 in a large hospital group in London, UK. In addition to the core structure of contacts that can be recovered using traditional methods of contact tracing, the StEP model reveals missing contacts that connect seemingly separate outbreaks. Comparison with genomic data further confirmed that these recovered contacts indeed improve characterisation of disease transmission and so highlights how the StEP framework can inform effective strategies of infection control and prevention.

Author(s):  
Joel Hellewell ◽  
Sam Abbott ◽  
Amy Gimma ◽  
Nikos I Bosse ◽  
Christopher I Jarvis ◽  
...  

AbstractBackgroundTo assess the viability of isolation and contact tracing to control onwards transmission from imported cases of 2019-nCoV.MethodsWe developed a stochastic transmission model, parameterised to the 2019-nCoV outbreak. We used the model to quantify the potential effectiveness of contact tracing and isolation of cases at controlling a 2019 nCoV-like pathogen. We considered scenarios that varied in: the number of initial cases; the basic reproduction number R0; the delay from symptom onset to isolation; the probability contacts were traced; the proportion of transmission that occurred before symptom onset, and the proportion of subclinical infections. We assumed isolation prevented all further transmission in the model. Outbreaks were deemed controlled if transmission ended within 12 weeks or before 5000 cases in total. We measured the success of controlling outbreaks using isolation and contact tracing, and quantified the weekly maximum number of cases traced to measure feasibility of public health effort.FindingsWhile simulated outbreaks starting with only 5 initial cases, R0 of 1.5 and little transmission before symptom onset could be controlled even with low contact tracing probability, the prospects of controlling an outbreak dramatically dropped with the number of initial cases, with higher R0, and with more transmission before symptom onset. Across different initial numbers of cases, the majority of scenarios with an R0 of 1.5 were controllable with under 50% of contacts successfully traced. For R0 of 2.5 and 3.5, more than 70% and 90% of contacts respectively had to be traced to control the majority of outbreaks. The delay between symptom onset and isolation played the largest role in determining whether an outbreak was controllable for lower values of R0. For higher values of R0 and a large initial number of cases, contact tracing and isolation was only potentially feasible when less than 1% of transmission occurred before symptom onset.InterpretationWe found that in most scenarios contact tracing and case isolation alone is unlikely to control a new outbreak of 2019-nCov within three months. The probability of control decreases with longer delays from symptom onset to isolation, fewer cases ascertained by contact tracing, and increasing transmission before symptoms. This model can be modified to reflect updated transmission characteristics and more specific definitions of outbreak control to assess the potential success of local response efforts.FundingWellcome Trust, Global Challenges Research Fund, and HDR UK.Research in ContextEvidence before this studyContact tracing and isolation of cases is a commonly used intervention for controlling infectious disease outbreaks. This intervention can be effective, but may require intensive public health effort and cooperation to effectively reach and monitor all contacts. When the pathogen has infectiousness before symptom onset, control of outbreaks using contact tracing and isolation is more challenging.Added value of this studyThis study uses a mathematical model to assess the feasibility of contact tracing and case isolation to control outbreaks of 2019-nCov, a newly emerged pathogen. We used disease transmission characteristics specific to the pathogen and therefore give the best available evidence if contact tracing and isolation can achieve control of outbreaks.Implications of all the available evidenceContact tracing and isolation may not contain outbreaks of 2019-nCoV unless very high levels of contact tracing are achieved. Even in this case, if there is asymptomatic transmission, or a high fraction of transmission before onset of symptoms, this strategy may not achieve control within three months.


2021 ◽  
Author(s):  
Christopher M Baker ◽  
Iadine Chades ◽  
Jodie McVernon ◽  
Andrew Robinson ◽  
Howard Bondell

PCR testing is a crucial capability for managing disease outbreaks, but it is also a limited resource and must be used carefully to ensure the information gain from testing is valuable. Testing has two broad uses, namely to track epidemic dynamics and to reduce transmission by identifying and managing cases. In this work we develop a modelling framework to examine the effects of test allocation in an epidemic, with a focus on using testing to minimise transmission. Using the COVID-19 pandemic as an example, we examine how the number of tests conducted per day relates to reduction in disease transmission, in the context of logistical constraints on the testing system. We show that if daily testing is above the routine capacity of a testing system, which can cause delays, then those delays can undermine efforts to reduce transmission through contact tracing and quarantine. This work highlights that the two goals of aiming to reduce transmission and aiming to identify all cases are different, and it is possible that focusing on one may undermine achieving the other. To develop an effective strategy, the goals must be clear and performance metrics must match the goals of the testing strategy. If metrics do not match the objectives of the strategy, then those metrics may incentivise actions that undermine achieving the objectives.


2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Frank Schlosser ◽  
Dirk Brockmann

AbstractFinding the origin location of an infectious disease outbreak quickly is crucial in mitigating its further dissemination. Current methods to identify outbreak locations early on rely on interviewing affected individuals and correlating their movements, which is a manual, time-consuming, and error-prone process. Other methods such as contact tracing, genomic sequencing or theoretical models of epidemic spread offer help, but they are not applicable at the onset of an outbreak as they require highly processed information or established transmission chains. Digital data sources such as mobile phones offer new ways to find outbreak sources in an automated way. Here, we propose a novel method to determine outbreak origins from geolocated movement data of individuals affected by the outbreak. Our algorithm scans movement trajectories for shared locations and identifies the outbreak origin as the most dominant among them. We test the method using various empirical and synthetic datasets, and demonstrate that it is able to single out the true outbreak location with high accuracy, requiring only data of $N=4$ N = 4 individuals. The method can be applied to scenarios with multiple outbreak locations, and is even able to estimate the number of outbreak sources if unknown, while being robust to noise. Our method is the first to offer a reliable, accurate out-of-the-box approach to identify outbreak locations in the initial phase of an outbreak. It can be easily and quickly applied in a crisis situation, improving on previous manual approaches. The method is not only applicable in the context of disease outbreaks, but can be used to find shared locations in movement data in other contexts as well.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
G. Cencetti ◽  
G. Santin ◽  
A. Longa ◽  
E. Pigani ◽  
A. Barrat ◽  
...  

AbstractDigital contact tracing is a relevant tool to control infectious disease outbreaks, including the COVID-19 epidemic. Early work evaluating digital contact tracing omitted important features and heterogeneities of real-world contact patterns influencing contagion dynamics. We fill this gap with a modeling framework informed by empirical high-resolution contact data to analyze the impact of digital contact tracing in the COVID-19 pandemic. We investigate how well contact tracing apps, coupled with the quarantine of identified contacts, can mitigate the spread in real environments. We find that restrictive policies are more effective in containing the epidemic but come at the cost of unnecessary large-scale quarantines. Policy evaluation through their efficiency and cost results in optimized solutions which only consider contacts longer than 15–20 minutes and closer than 2–3 meters to be at risk. Our results show that isolation and tracing can help control re-emerging outbreaks when some conditions are met: (i) a reduction of the reproductive number through masks and physical distance; (ii) a low-delay isolation of infected individuals; (iii) a high compliance. Finally, we observe the inefficacy of a less privacy-preserving tracing involving second order contacts. Our results may inform digital contact tracing efforts currently being implemented across several countries worldwide.


2021 ◽  
Author(s):  
Marcelo Eduardo Borges ◽  
Leonardo Souto Ferreira ◽  
Silas Poloni ◽  
Ângela Maria Bagattini ◽  
Caroline Franco ◽  
...  

Among the various non–pharmaceutical interventions implemented in response to the Covid–19 pandemic during 2020, school closures have been in place in several countries to reduce infection transmission. Nonetheless, the significant short and long–term impacts of prolonged suspension of in–person classes is a major concern. There is still considerable debate around the best timing for school closure and reopening, its impact on the dynamics of disease transmission, and its effectiveness when considered in association with other mitigation measures. Despite the erratic implementation of mitigation measures in Brazil, school closures were among the first measures taken early in the pandemic in most of the 27 states in the country. Further, Brazil delayed the reopening of schools and stands among the countries in which schools remained closed for the most prolonged period in 2020. To assess the impact of school reopening and the effect of contact tracing strategies in rates of Covid–19 cases and deaths, we model the epidemiological dynamics of disease transmission in 3 large urban centers in Brazil under different epidemiological contexts. We implement an extended SEIR model stratified by age and considering contact networks in different settings – school, home, work, and elsewhere, in which the infection transmission rate is affected by various intervention measures. After fitting epidemiological and demographic data, we simulate scenarios with increasing school transmission due to school reopening. Our model shows that reopening schools results in a non–linear increase of reported Covid-19 cases and deaths, which is highly dependent on infection and disease incidence at the time of reopening. While low rates of within[&ndash]school transmission resulted in small effects on disease incidence (cases/100,000 pop), intermediate or high rates can severely impact disease trends resulting in escalating rates of new cases even if other interventions remain unchanged. When contact tracing and quarantining are restricted to school and home settings, a large number of daily tests is required to produce significant effects of reducing the total number of hospitalizations and deaths. Our results suggest that policymakers should carefully consider the epidemiological context and timing regarding the implementation of school closure and return of in-person school activities. Also, although contact tracing strategies are essential to prevent new infections and outbreaks within school environments, our data suggest that they are alone not sufficient to avoid significant impacts on community transmission in the context of school reopening in settings with high and sustained transmission rates.


Author(s):  
Asma A. Rahim ◽  
Sujina C. Muthukutty ◽  
Sabitha R. Jacob ◽  
Rini Ravindran ◽  
Jayakrishnan Thayyil ◽  
...  

Kozhikode district of North Kerala, India witnessed an outbreak of Nipah virus (NiV) in the month of May 2018. Two adjacent districts were affected leaving 17 patients dead out of the 19 confirmed. United Nations and WHO lauded the expeditious response of the state’s health system in the diagnosis and containment of the outbreak which was unprecedented. The authors being in the contact tracing and surveillance operation district team, had kept a record of timeline of events and actions at the state level, compiled the news clippings and tracked events. In the absence of an end‑of‑epidemic report for reference, these records served as a valuable tool for the present review. We used the Management science for health frame work tool (MSH framework) to evaluate the district and state coordinated actions which helped in curbing the outbreak. Though NiV outbreak in South India (2018) had similar epidemiological features to previous disease outbreaks, it stands out as the one to be detected and contained in a short span of time. As health personnel working in the government medical college of an affected district and directly involved in contact tracing operations and containment measures, exploring and sharing, what worked and how, in the context of multidisciplinary response and recovery attempts of the outbreak in the state may be beneficial to public health personnel and policy makers. This management framework may be replicated in the national and international context, particularly in South East Asian region under threat of emerging viral infections like COVID-19, lacking specific epidemic management frameworks for outbreak response and containment.


2021 ◽  
Author(s):  
Dionne M. Aleman ◽  
Benjamin Z. Tham ◽  
Sean J. Wagner ◽  
Justin Semelhago ◽  
Asghar Mohammadi ◽  
...  

AbstractBackgroundTo prevent the spread of COVID-19 in Newfoundland & Labrador (NL), NL implemented a wide travel ban in May 2020. We estimate the effectiveness of this travel ban using a customized agent-based simulation (ABS).MethodsWe built an individual-level ABS to simulate the movements and behaviors of every member of the NL population, including arriving and departing travellers. The model considers individual properties (spatial location, age, comorbidities) and movements between environments, as well as age-based disease transmission with pre-symptomatic, symptomatic, and asymptomatic transmission rates. We examine low, medium, and high travel volume, traveller infection rates, and traveller quarantine compliance rates to determine the effect of travellers on COVID spread, and the ability of contact tracing to contain outbreaks.ResultsInfected travellers increased COVID cases by 2-52x (8-96x) times and peak hospitalizations by 2-49x (8-94x), with (without) contact tracing. Although contact tracing was highly effective at reducing spread, it was insufficient to stop outbreaks caused by travellers in even the best-case scenario, and the likelihood of exceeding contact tracing capacity was a concern in most scenarios. Quarantine compliance had only a small impact on COVID spread; travel volume and infection rate drove spread.InterpretationNL’s travel ban was likely a critically important intervention to prevent COVID spread. Even a small number of infected travellers can play a significant role in introducing new chains of transmission, resulting in exponential community spread and significant increases in hospitalizations, while outpacing contact tracing capabilities. With the presence of more transmissible variants, e.g., the UK variant, prevention of imported cases is even more critical.


2021 ◽  
Vol 11 (3) ◽  
pp. 263-266
Author(s):  
Emery Manirambona ◽  
Laura Wilkins ◽  
Don Eliseo Lucero-Prisno III

Although it is widely accepted that coronavirus disease 2019 (COVID-19) has adversely affected the Global South’s most vulnerable refugee communities, they have received little attention. There have been gaps in testing, which is fundamental to treat and isolate patients and make data-driven decisions to protect the refugee community. Therefore, it is imperative to holistically implement policies to curtail COVID-19 in refugee camps to ensure that refugees are safe and protected from the pandemic. Processes for timely diagnosis and treatment, quick isolation and contact tracing are essential to keep refugees safe. Furthermore, it is crucial to encourage protective behaviours and raise awareness about hygiene and social prevention to dampen disease transmission. Refugees in the Global South have been disproportionately affected by the consequences of the COVID-19 pandemic, facing financial hardship and social injustice throughout. Refugees in Africa have also faced threats to their security, being subjected to torture, disappearance, or even killings in their host countries. The pandemic has exposed gender inequalities, with females being the most affected, and health inequities in the refugee community in Africa. There is a need for international organizations like the African Union, United Nations (UN) agencies, non-governmental organizations (NGOs), and other stakeholders to take serious action regarding the refugee situation in Africa. Food aid for refugees in Africa should be increased as quickly as possible and refugees’ security must be guaranteed. Of equal importance, there must be justice for the death or disappearance of refugees. It is imperative to end discrimination against refugees and support the promotion of gender equity.


Author(s):  
Isao Yokota ◽  
Peter Y Shane ◽  
Kazufumi Okada ◽  
Yoko Unoki ◽  
Yichi Yang ◽  
...  

Abstract Background COVID-19 has rapidly evolved to become a global pandemic due largely to the transmission of its causative virus through asymptomatic carriers. Detection of SARS-CoV-2 in asymptomatic people is an urgent priority for the prevention and containment of disease outbreaks in communities. However, few data are available in asymptomatic persons regarding the accuracy of PCR testing. Additionally, although self-collected saliva has significant logistical advantages in mass screening, its utility as an alternative specimen in asymptomatic persons is yet to be determined. Methods We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using nasopharyngeal swabs (NPS) and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. Results In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence at 0.3%. In positive individuals, viral load was highly correlated between NPS and saliva. Conclusion Both nasopharyngeal and saliva specimens had high sensitivity and specificity. Self-collected saliva is a valuable specimen to detect SARS-CoV-2 in mass screening of asymptomatic persons.


2020 ◽  
Vol 46 (7) ◽  
pp. 427-431 ◽  
Author(s):  
Michael J Parker ◽  
Christophe Fraser ◽  
Lucie Abeler-Dörner ◽  
David Bonsall

In this paper we discuss ethical implications of the use of mobile phone apps in the control of the COVID-19 pandemic. Contact tracing is a well-established feature of public health practice during infectious disease outbreaks and epidemics. However, the high proportion of pre-symptomatic transmission in COVID-19 means that standard contact tracing methods are too slow to stop the progression of infection through the population. To address this problem, many countries around the world have deployed or are developing mobile phone apps capable of supporting instantaneous contact tracing. Informed by the on-going mapping of ‘proximity events’ these apps are intended both to inform public health policy and to provide alerts to individuals who have been in contact with a person with the infection. The proposed use of mobile phone data for ‘intelligent physical distancing’ in such contexts raises a number of important ethical questions. In our paper, we outline some ethical considerations that need to be addressed in any deployment of this kind of approach as part of a multidimensional public health response. We also, briefly, explore the implications for its use in future infectious disease outbreaks.


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