Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment

Published on Jan 14, 2021
· DOI :10.1038/S41746-020-00374-4
Alberto Ferrari2
Estimated H-index: 2
Enrico Santus16
Estimated H-index: 16
+ 6 AuthorsAlfonso Valencia115
Estimated H-index: 115
(Barcelona Supercomputing Center)
Targeted contact-tracing through mobile phone apps has been proposed as an instrument to help contain the spread of COVID-19 and manage the lifting of nation-wide lock-downs currently in place in USA and Europe. However, there is an ongoing debate on its potential efficacy, especially in light of region-specific demographics. We built an expanded SIR model of COVID-19 epidemics that accounts for region-specific population densities, and we used it to test the impact of a contact-tracing app in a number of scenarios. Using demographic and mobility data from Italy and Spain, we used the model to simulate scenarios that vary in baseline contact rates, population densities, and fraction of app users in the population. Our results show that, in support of efficient isolation of symptomatic cases, app-mediated contact-tracing can successfully mitigate the epidemic even with a relatively small fraction of users, and even suppress altogether with a larger fraction of users. However, when regional differences in population density are taken into consideration, the epidemic can be significantly harder to contain in higher density areas, highlighting potential limitations of this intervention in specific contexts. This work corroborates previous results in favor of app-mediated contact-tracing as mitigation measure for COVID-19, and draws attention on the importance of region-specific demographic and mobility factors to achieve maximum efficacy in containment policies.
#1Wee Chian KohH-Index: 8
#2Lin Naing (UBD: Universiti Brunei Darussalam)H-Index: 23
Last. Justin J.-L. WongH-Index: 24
view all 12 authors...
Introduction Current SARS-CoV-2 containment measures rely on controlling viral transmission. Effective prioritization can be determined by understanding SARS-CoV-2 transmission dynamics. We conducted a systematic review and meta-analyses of the secondary attack rate (SAR) in household and healthcare settings. We also examined whether household transmission differed by symptom status of index case, adult and children, and relationship to index case. Methods We searched PubMed, medRxiv, and bioRxi...
68 CitationsSource
#1Qifang Bi (Johns Hopkins University)H-Index: 12
#2Yongsheng WuH-Index: 3
Last. Tiejian Feng (CDC: Centers for Disease Control and Prevention)H-Index: 4
view all 22 authors...
Summary Background Rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, prompted heightened surveillance in Shenzhen, China. The resulting data provide a rare opportunity to measure key metrics of disease course, transmission, and the impact of control measures. Methods From Jan 14 to Feb 12, 2020, the Shenzhen Center for Disease Control and Prevention identified 391 SARS-CoV-2 cases and 1286 close contacts. We compared cases identified through symptomati...
974 CitationsSource
#1Jing Qin (NIH: National Institutes of Health)H-Index: 2
#1Jing Qin (NIH: National Institutes of Health)H-Index: 23
Last. Xiao-Hua Zhou (PKU: Peking University)H-Index: 59
view all 6 authors...
Abstract We propose a novel low-cost and accurate method to estimate the incubation distribution of COVID-19. We have conducted a cross-sectional and forward follow-up study by identifying those pre-symptomatic individuals at their time of departure from Wuhan and then following them until their symptoms developed. The renewal process is adopted by considering the incubation period as a renewal and the duration between departure and symptoms onset as a forward time. Such a method enhances the ac...
97 CitationsSource
#1Nadeem Ahmed (CRCs: Cooperative Research Centre)H-Index: 14
#2Regio A. Michelin (UNSW: University of New South Wales)H-Index: 8
Last. Sanjay Jha (UNSW: University of New South Wales)H-Index: 38
view all 10 authors...
The recent outbreak of COVID-19 has taken the world by surprise, forcing lockdowns and straining public health care systems. COVID-19 is known to be a highly infectious virus, and infected individuals do not initially exhibit symptoms, while some remain asymptomatic. Thus, a non-negligible fraction of the population can, at any given time, be a hidden source of transmissions. In response, many governments have shown great interest in smartphone contact tracing apps that help automate the difficu...
171 CitationsSource
#1Enrico Lavezzo (UNIPD: University of Padua)H-Index: 29
#2Elisa Franchin (UNIPD: University of Padua)H-Index: 28
Last. Andrea Crisanti (Imperial College London)H-Index: 76
view all 44 authors...
On the 21st of February 2020 a resident of the municipality of Vo', a small town near Padua, died of pneumonia due to SARS-CoV-2 infection1. This was the first COVID-19 death detected in Italy since the emergence of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. We collected information on the demography, clinical presentation, hospitalization, contact network and presence of SARS-CoV-2 ...
533 CitationsSource
#1Jessica MorleyH-Index: 12
#2Josh CowlsH-Index: 12
Last. Luciano FloridiH-Index: 71
view all 4 authors...
Protect privacy, equality and fairness in digital contact tracing with these key questions. Protect privacy, equality and fairness in digital contact tracing with these key questions.
90 CitationsSource
#1Wee Chian KohH-Index: 8
#2Lin Naing (UBD: Universiti Brunei Darussalam)H-Index: 23
Last. Justin J.-L. WongH-Index: 24
view all 8 authors...
Background Current SARS-CoV-2 containment measures rely on the capacity to control person-to-person viral transmission. Effective prioritization of these measures can be determined by understanding SARS-CoV-2 transmission dynamics. We conducted a systematic review and meta-analyses of three parameters: (i) secondary attack rate (SAR) in various settings, (ii) clinical onset serial interval (SI), and (iii) the proportion of asymptomatic infection. Methods and Findings We searched PubMed, medRxiv,...
24 CitationsSource
#1Joacim Rocklöv (Umeå University)H-Index: 45
#2Henrik Sjödin (Umeå University)H-Index: 6
Last. Annelies Wilder-Smith (Umeå University)H-Index: 65
view all 3 authors...
Cruise ships carry a large number of people in confined spaces with relative homogeneous mixing. On 3 February, 2020, an outbreak of COVID-19 on cruise ship Diamond Princess was reported with 10 initial cases, following an index case on board around 21-25 January. By 4 February, public health measures such as removal and isolation of ill passengers and quarantine of non-ill passengers were implemented. By 20 February, 619 of 3,700 passengers and crew (17%) were tested positive.We estimated the b...
264 CitationsSource
#1Yun LingH-Index: 1
#1Yun LingH-Index: 21
Last. Hong Zhou LuH-Index: 1
view all 16 authors...
Background: A patient’s infectivity is determined by the presence of the virus in different body fluids, secretions, and excreta. The persistence and clearance of viral RNA from different specimens of patients with 2019 novel coronavirus disease (COVID-19) remain unclear. This study analyzed the clearance time and factors influencing 2019 novel coronavirus (2019-nCoV) RNA in different samples from patients with COVID-19, providing further evidence to improve the management of patients during con...
480 CitationsSource
#1Marcos Matabuena (University of Santiago de Compostela)H-Index: 4
Last. LeboránH-Index: 1
view all 4 authors...
We introduce a new probabilistic model to estimate the real spread of the novel SARS-CoV-2 virus along regions or countries. Our model simulates the behavior of each individual in a population according to a probabilistic model through an inverse problem; we estimate the real number of recovered and infected people using mortality records. In addition, the model is dynamic in the sense that it takes into account the policy measures introduced when we solve the inverse problem. The results obtain...
3 Citations
Cited By8
#1Ewoud Schuit (UU: Utrecht University)H-Index: 24
Last. Robin C. Huisman (EUR: Erasmus University Rotterdam)H-Index: 10
view all 18 authors...
Abstract null Objective null To assess the diagnostic test accuracy of two rapid antigen tests in asymptomatic and presymptomatic close contacts of people with SARS-CoV-2 infection on day 5 after exposure. null Design null Prospective cross sectional study. null Setting null Four public health service covid-19 test sites in the Netherlands. null Participants null 4274 consecutively included close contacts (identified through test-and-trace programme or contact tracing app) aged 16 years or older...
#1Kevin JenniskensH-Index: 5
Last. Lotty HooftH-Index: 29
view all 9 authors...
Objective null To systematically review evidence on effectiveness of contact tracing apps (CTAs) for SARS-CoV-2 on epidemiological and clinical outcomes. null Design null Rapid systematic review. null Data sources null EMBASE (OVID), MEDLINE (PubMed), BioRxiv and MedRxiv were searched up to 28 October 2020. null Study selection null Studies, both empirical and model-based, assessing effect of CTAs for SARS-CoV-2 on reproduction number (R), total number of infections, hospitalisation rate, mortal...
Background null Availability of SARS-CoV-2 testing in the United States (U.S.) has fluctuated through the course of the COVID-19 pandemic, including in the U.S. state of Illinois. Despite substantial ramp-up in test volume, access to SARS-CoV-2 testing remains limited, heterogeneous, and insufficient to control spread. null Methods null We compared SARS-CoV-2 testing rates across geographic regions, over time, and by demographic characteristics (i.e., age and racial/ethnic groups) in Illinois du...
1 CitationsSource
#1Ewoud Schuit (UU: Utrecht University)H-Index: 24
#2I K VeldhuijzenH-Index: 1
Last. K. G. M. Moons (UU: Utrecht University)H-Index: 9
view all 18 authors...
BackgroundPre-/asymptomatic close contacts of SARS-CoV-2 infected individuals were tested at day 5 after contact by real-time reverse transcriptase polymerase chain reaction (RT-PCR). Diagnostic accuracy of antigen-detecting rapid diagnostic tests (Ag-RDT) in pre-/asymptomatic close contacts was up till now unknown. MethodsWe performed a prospective cross-sectional diagnostic test accuracy study. Close contacts (e.g. selected via the test-and-trace program or contact tracing app) aged [≥]16 year...
2 CitationsSource
#1Mehak Nanda (DCE: Delhi Technological University)
#2Aashima (DCE: Delhi Technological University)
Last. Rajesh Sharma (DCE: Delhi Technological University)H-Index: 9
view all 2 authors...
This paper investigates the epidemiology and public health response of novel coronavirus infection (COVID-19) in the Nordic region. The data on cases and deaths due to COVID-19 were drawn from the ...
#1Muhammad ShahrozH-Index: 1
#2Farooq AhmadH-Index: 9
Last. Junaid Qadir (Information Technology University)H-Index: 8
view all 7 authors...
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 place...
2 CitationsSource
#1Dounia MarbouhH-Index: 1
#2Tayaba Abbasi (Khalifa University)H-Index: 2
Last. Samer EllahhamH-Index: 6
view all 8 authors...
The sudden development of the COVID-19 pandemic exposed the limitations in modern healthcare systems to handle public health emergencies. It is evident that adopting innovative technologies such as blockchain can help in effective planning operations and resource deployments. Blockchain technology can play an important role in the healthcare sector such as improved clinical trial data management by reducing delays in regulatory approvals, streamline the communication between diverse stakeholders...
33 CitationsSource