scholarly journals The feasibility of targeted test-trace-isolate for the control of SARS-CoV-2 variants

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 291
Author(s):  
William Bradshaw ◽  
Jonathan Huggins ◽  
Alun Lloyd ◽  
Kevin Esvelt
Keyword(s):  
Process Model ◽  
Branching Process ◽  
Large Fraction ◽  
Contact Tracing ◽  
Rt Pcr ◽  
Health Agencies ◽  
The Common ◽  
Ancestral Strain

The SARS-CoV-2 variant B.1.1.7 reportedly exhibits substantially higher transmission than the ancestral strain and may generate a major surge of cases before vaccines become widely available, while the P.1 and B.1.351 variants may be equally transmissible and also resist vaccines. All three variants can be sensitively detected by RT-PCR due to an otherwise rare del11288-11296 mutation in orf1ab; B.1.1.7 can also be detected using the common TaqPath kit. Testing, contact tracing, and isolation programs overwhelmed by SARS-CoV-2 could slow the spread of the new variants, which are still outnumbered by tracers in most countries. However, past failures and high rates of mistrust may lead health agencies to conclude that tracing is futile, dissuading them from redirecting existing tracers to focus on the new variants. Here we apply a branching-process model to estimate the effectiveness of implementing a variant-focused testing, contact tracing, and isolation strategy with realistic levels of performance. Our model indicates that bidirectional contact tracing can substantially slow the spread of SARS-CoV-2 variants even in regions where a large fraction of the population refuses to cooperate with contact tracers or to abide by quarantine and isolation requests.

scholarly journals The feasibility of targeted test-trace-isolate for the control of SARS-CoV-2 variants

2021 ◽  
Author(s):  
William J. Bradshaw ◽  
Jonathan H. Huggins ◽  
Alun L. Lloyd ◽  
Kevin M. Esvelt
Keyword(s):  
Process Model ◽  
Branching Process ◽  
Large Fraction ◽  
Contact Tracing ◽  
Rt Pcr ◽  
Health Agencies ◽  
The Common ◽  
Ancestral Strain

AbstractThe SARS-CoV-2 variant B.1.1.7 reportedly exhibits substantially higher transmission than the ancestral strain and may generate a major surge of cases before vaccines become widely available, while the P.1 and B.1.351 variants may be equally transmissible and also resist vaccines. All three variants can be sensitively detected by RT-PCR due to an otherwise rare del11288-11296 mutation in orf1ab; B.1.1.7 can also be detected using the common TaqPath kit. Testing, contact tracing, and isolation programs overwhelmed by SARS-CoV-2 could slow the spread of the new variants, which are still outnumbered by tracers in most countries. However, past failures and high rates of mistrust may lead health agencies to conclude that tracing is futile, dissuading them from redirecting existing tracers to focus on the new variants. Here we apply a branching-process model to estimate the effectiveness of implementing a variant-focused testing, contact tracing, and isolation strategy with realistic levels of performance. Our model indicates that bidirectional contact tracing can substantially slow the spread of SARS-CoV-2 variants even in regions where a large fraction of the population refuses to cooperate with contact tracers or to abide by quarantine and isolation requests.

scholarly journals Bidirectional contact tracing dramatically improves COVID-19 control

2020 ◽  
Author(s):  
William J. Bradshaw ◽  
Ethan C. Alley ◽  
Jonathan H. Huggins ◽  
Alun L. Lloyd ◽  
Kevin M. Esvelt
Keyword(s):  
Process Model ◽  
Branching Process ◽  
Reproduction Number ◽  
Contact Tracing ◽  
Test Sensitivity ◽  
Outbreak Control ◽  
Case Ascertainment ◽  
Health Agencies

AbstractContact tracing is critical to controlling COVID-19, but most protocols only “forward-trace” to notify people who were recently exposed. Using a stochastic branching-process model, we show that “bidirectional” tracing to identify infector individuals and their other infectees robustly improves outbreak control, reducing the effective reproduction number (Reff) by at least ∼0.3 while dramatically increasing resilience to low case ascertainment and test sensitivity. Adding smartphone-based exposure notification can further reduce Reff by 0.25, but only if nearly all smartphones can detect exposure events. Our results suggest that with or without digital approaches, implementing bidirectional tracing will enable health agencies to control COVID-19 more effectively without requiring high-cost interventions.

scholarly journals Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks

2021 ◽  
Vol 5 ◽  
pp. 239
Author(s):  
Akira Endo ◽  
Quentin J. Leclerc ◽  
Gwenan M. Knight ◽  
Graham F. Medley ◽  
Katherine E. Atkins ◽  
...  
Keyword(s):  
Process Model ◽  
Branching Process ◽  
Contact Tracing ◽  
Level Variation ◽  
Primary Case ◽  
Typical Size ◽  
Individual Level ◽  
Outbreak Control ◽  
Incremental Effectiveness ◽  
Parameter Values

Introduction: Contact tracing has the potential to control outbreaks without the need for stringent physical distancing policies, e.g. civil lockdowns. Unlike forward contact tracing, backward contact tracing identifies the source of newly detected cases. This approach is particularly valuable when there is high individual-level variation in the number of secondary transmissions (overdispersion). Methods: By using a simple branching process model, we explored the potential of combining backward contact tracing with more conventional forward contact tracing for control of COVID-19. We estimated the typical size of clusters that can be reached by backward tracing and simulated the incremental effectiveness of combining backward tracing with conventional forward tracing. Results: Across ranges of parameter values consistent with dynamics of SARS-CoV-2, backward tracing is expected to identify a primary case generating 3-10 times more infections than a randomly chosen case, typically increasing the proportion of subsequent cases averted by a factor of 2-3. The estimated number of cases averted by backward tracing became greater with a higher degree of overdispersion. Conclusion: Backward contact tracing can be an effective tool for outbreak control, especially in the presence of overdispersion as is observed with SARS-CoV-2.

scholarly journals Using a household-structured branching process to analyse contact tracing in the SARS-CoV-2 pandemic

2021 ◽  
Vol 376 (1829) ◽  
pp. 20200267
Author(s):  
Martyn Fyles ◽  
Elizabeth Fearon ◽  
Christopher Overton ◽  
Tom Wingfield ◽  
Graham F. Medley ◽  
...  
Keyword(s):  
Process Model ◽  
Branching Process ◽  
Household Structure ◽  
Contact Tracing ◽  
Symptom Report ◽  
Primary Model ◽  
Imported Cases ◽  
Strategic Implementation ◽  
Household Members ◽  
The Uk

We explore strategies of contact tracing, case isolation and quarantine of exposed contacts to control the SARS-CoV-2 epidemic using a branching process model with household structure. This structure reflects higher transmission risks among household members than among non-household members. We explore strategic implementation choices that make use of household structure, and investigate strategies including two-step tracing, backwards tracing, smartphone tracing and tracing upon symptom report rather than test results. The primary model outcome is the effect of contact tracing, in combination with different levels of physical distancing, on the growth rate of the epidemic. Furthermore, we investigate epidemic extinction times to indicate the time period over which interventions must be sustained. We consider effects of non-uptake of isolation/quarantine, non-adherence, and declining recall of contacts over time. Our results find that, compared to self-isolation of cases without contact tracing, a contact tracing strategy designed to take advantage of household structure allows for some relaxation of physical distancing measures but cannot completely control the epidemic absent of other measures. Even assuming no imported cases and sustainment of moderate physical distancing, testing and tracing efforts, the time to bring the epidemic to extinction could be in the order of months to years. This article is part of the theme issue ‘Modelling that shaped the early COVID-19 pandemic response in the UK’.

scholarly journals Using a household structured branching process to analyse contact tracing in the SARS-CoV-2 pandemic

2021 ◽  
Author(s):  
Martyn Fyles ◽  
Elizabeth Fearon ◽  
Christopher Overton ◽  
Tom Wingfield ◽  
Graham F Medley ◽  
...  
Keyword(s):  
Process Model ◽  
Branching Process ◽  
Household Structure ◽  
Contact Tracing ◽  
Test Results ◽  
Symptom Report ◽  
Time Period ◽  
Primary Model ◽  
Imported Cases ◽  
Household Members

AbstractWe explore strategies of contact tracing, case isolation and quarantine of exposed contacts to control the SARS-CoV-2 epidemic using a branching process model with household structure. This structure reflects higher transmission risks among household members than among non-household members, and is also the level at which physical distancing policies have been applied. We explore implementation choices that make use of household structure, and investigate strategies including two-step tracing, backwards tracing, smartphone tracing and tracing upon symptom report rather than test results. The primary model outcome is the effect on the growth rate of the epidemic under contact tracing in combination with different levels of physical distancing, and we investigate epidemic extinction times to indicate the time period over which interventions must be sustained. We consider effects of non-uptake of isolation/quarantine, non-adherence, and declining recall of contacts over time. We find that compared to self-isolation of cases but no contact tracing, a household-based contact tracing strategy allows for some relaxation of physical distancing measures; however, it is unable to completely control the epidemic in the absence of other measures. Even assuming no imported cases and sustainment of moderate distancing, testing and tracing efforts, the time to bring the epidemic to extinction could be in the order of months to years.

scholarly journals Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks

2020 ◽  
Vol 5 ◽  
pp. 239 ◽  
Author(s):  
Akira Endo ◽  
Quentin J. Leclerc ◽  
Gwenan M. Knight ◽  
Graham F. Medley ◽  
Katherine E. Atkins ◽  
...  
Keyword(s):  
Process Model ◽  
Branching Process ◽  
Contact Tracing ◽  
Level Variation ◽  
Primary Case ◽  
Typical Size ◽  
Individual Level ◽  
Outbreak Control ◽  
Incremental Effectiveness ◽  
Parameter Values

Introduction: Contact tracing has the potential to control outbreaks without the need for stringent physical distancing policies, e.g. civil lockdowns. Unlike forward contact tracing, backward contact tracing identifies the source of newly detected cases. This approach is particularly valuable when there is high individual-level variation in the number of secondary transmissions (overdispersion). Methods: By using a simple branching process model, we explored the potential of combining backward contact tracing with more conventional forward contact tracing for control of COVID-19. We estimated the typical size of clusters that can be reached by backward tracing and simulated the incremental effectiveness of combining backward tracing with conventional forward tracing. Results: Across ranges of parameter values consistent with dynamics of SARS-CoV-2, backward tracing is expected to identify a primary case generating 3-10 times more infections than average, typically increasing the proportion of subsequent cases averted by a factor of 2-3. The estimated number of cases averted by backward tracing became greater with a higher degree of overdispersion. Conclusion: Backward contact tracing can be an effective tool for outbreak control, especially in the presence of overdispersion as was observed with SARS-CoV-2.

scholarly journals Potential reduction in transmission of COVID-19 by digital contact tracing systems

2020 ◽  
Author(s):  
Michael J Plank ◽  
Alex James ◽  
Audrey Lustig ◽  
Nicholas Steyn ◽  
Rachelle N Binny ◽  
...  
Keyword(s):  
Uptake Rate ◽  
Process Model ◽  
Reproduction Number ◽  
Contact Tracing ◽  
Location Tracking ◽  
Public Health Agencies ◽  
Proximity Detection ◽  
Health Agencies ◽  
Alternative Approaches ◽  
Age Structured

Digital tools are being developed to support contact tracing as part of the global effort to control the spread of COVID-19. These include smartphone apps, Bluetooth-based proximity detection, location tracking, and automatic exposure notification features. Evidence on the effectiveness of alternative approaches to digital contact tracing is so far limited. We use an age-structured branching process model of the transmission of COVID-19 in different settings to estimate the potential of manual contact tracing and digital tracing systems to help control the epidemic. We investigate the effect of the uptake rate and proportion of contacts recorded by the digital system on key model outputs: the effective reproduction number, the mean outbreak size after 30 days, and the probability of elimination. We show that effective manual contact tracing can reduce the effective reproduction number from 2.4 to around 1.5. The addition of a digital tracing system with a high uptake rate over 75% could further reduce the effective reproduction number to around 1.1. Fully automated digital tracing without manual contact tracing is predicted to be much less effective. We conclude that, for digital tracing systems to make a significant contribution to the control of COVID-19, they need be designed in close conjunction with public health agencies to support and complement manual contact tracing by trained professionals.

scholarly journals Engagement and adherence trade-offs for SARS-CoV-2 contact tracing

2020 ◽  
Author(s):  
Tim C D Lucas ◽  
Emma L Davis ◽  
Diepreye Ayabina ◽  
Anna Borlase ◽  
Thomas Crellen ◽  
...  
Keyword(s):  
Process Model ◽  
Branching Process ◽  
Reporting Rate ◽  
Self Report ◽  
Contact Tracing ◽  
Legal Enforcement ◽  
Trade Offs ◽  
Large Outbreak ◽  
The Cost ◽  
Reporting Rates

Contact tracing is an important tool for allowing countries to ease lockdown policies introduced to combat SARS-CoV-2. For contact tracing to be effective, those with symptoms must self-report themselves while their contacts must self-isolate when asked. However, policies such as legal enforcement of self-isolation can create trade-offs by dissuading individuals from self-reporting. We use an existing branching process model to examine which aspects of contact tracing adherence should be prioritised. We consider an inverse relationship between self-isolation adherence and self-reporting engagement, assuming that increasingly strict self-isolation policies will result in fewer individuals self-reporting to the programme. We find that policies that increase the verage duration of self-isolation, or that increase the probability that people self-isolate at all, at the expense of reduced self-reporting rate, will not decrease the risk of a large outbreak and may increase the risk, depending on the strength of the trade-off. These results suggest that policies to increase self-isolation adherence should be implemented carefully. Policies that increase self-isolation adherence at the cost of self-reporting rates should be avoided.

scholarly journals Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks

2021 ◽  
Vol 5 ◽  
pp. 239 ◽  
Author(s):  
Akira Endo ◽  
Quentin J. Leclerc ◽  
Gwenan M. Knight ◽  
Graham F. Medley ◽  
Katherine E. Atkins ◽  
...  
Keyword(s):  
Process Model ◽  
Branching Process ◽  
Contact Tracing ◽  
Level Variation ◽  
Primary Case ◽  
Typical Size ◽  
Individual Level ◽  
Outbreak Control ◽  
Incremental Effectiveness ◽  
Parameter Values

Introduction: Contact tracing has the potential to control outbreaks without the need for stringent physical distancing policies, e.g. civil lockdowns. Unlike forward contact tracing, backward contact tracing identifies the source of newly detected cases. This approach is particularly valuable when there is high individual-level variation in the number of secondary transmissions (overdispersion). Methods: By using a simple branching process model, we explored the potential of combining backward contact tracing with more conventional forward contact tracing for control of COVID-19. We estimated the typical size of clusters that can be reached by backward tracing and simulated the incremental effectiveness of combining backward tracing with conventional forward tracing. Results: Across ranges of parameter values consistent with dynamics of SARS-CoV-2, backward tracing is expected to identify a primary case generating 3-10 times more infections than a randomly chosen case, typically increasing the proportion of subsequent cases averted by a factor of 2-3. The estimated number of cases averted by backward tracing became greater with a higher degree of overdispersion. Conclusion: Backward contact tracing can be an effective tool for outbreak control, especially in the presence of overdispersion as is observed with SARS-CoV-2.

scholarly journals Digital Herd Immunity and COVID-19

2020 ◽  
Author(s):  
Vir B. Bulchandani ◽  
Saumya Shivam ◽  
Sanjay Moudgalya ◽  
S. L. Sondhi
Keyword(s):  
Phase Transition ◽  
Process Model ◽  
Branching Process ◽  
Herd Immunity ◽  
Contact Tracing ◽  
Highly Efficient ◽  
Traditional Notion ◽  
Infected Population ◽  
Disease Characteristics ◽  
Promising Strategy

A population can be immune to epidemics even if not all of its individual members are immune to the disease, just as long as sufficiently many are immune—this is the traditional notion of herd immunity. In the smartphone era a population can be immune to epidemics even if not a single one of its members is immune to the disease—a notion we propose to call “digital herd immunity”, which is similarly an emergent characteristic of the population. This immunity arises because contact-tracing protocols based on smartphone capabilities can lead to highly efficient quarantining of infected population members and thus the extinguishing of nascent epidemics. When the disease characteristics are favorable and smartphone usage is high enough, the population is in this immune phase. As usage decreases there is a novel “contact tracing” phase transition to an epidemic phase. We present and study a simple branching-process model for COVID-19 and show that digital immunity is possible regardless of the proportion of non-symptomatic transmission. We believe this is a promising strategy for dealing with COVID-19 in many countries such as India, whose challenges of scale motivated us to undertake this study in the first place and whose case we discuss briefly.

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