Winter is coming: pathogen emergence in seasonal environments

Carmona, Philippe; Gandon, Sylvain

doi:10.1101/753442

Cited by 5 publications

(7 citation statements)

References 34 publications

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“…The COR is an extension of the IOR, accounting for changes in population susceptibility due to vaccination over the initial phase of the potential outbreak. The COR has previously been used to assess outbreak risks using branching processes for models in which pathogen transmission varies periodically [30,[34][35][36]. Its calculation involves solving the differential equation…”

Section: Outbreak Risk Metricsmentioning

confidence: 99%

The risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions

Sachak-Patwa

Byrne

Dyson

et al. 2021

Preprint

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Countries around the world have introduced travel restrictions to reduce SARS-CoV-2 transmission. As vaccines are gradually rolled out, attention has turned to when travel restrictions and other non-pharmaceutical interventions (NPIs) can be relaxed. Here, using SARS-CoV-2 as a case study, we develop a mathematical branching process model to assess the risk that, following the removal of NPIs, cases introduced into new locations initiate a local outbreak. Our model accounts for changes in background population immunity due to vaccination. We consider two locations in which the vaccine rollout has progressed quickly – specifically, the Isle of Man (a British crown dependency in the Irish Sea) and the country of Israel. We show that the outbreak risk is unlikely to be eliminated completely when travel restrictions and other NPIs are removed, even once the vaccine programmes in these locations are complete. Specifically, the risk that an imported case initiates an outbreak following the vaccine rollout and removal of NPIs is projected to be 0.373 (0.223,0.477) for the Isle of Man and 0.506 (0.387,0.588) for Israel. Key factors underlying these risks are the potential for transmission even following vaccination, incomplete vaccine uptake, and the recent emergence of SARS-CoV-2 variants with increased transmissibility. Combined, these factors suggest that when travel restrictions are relaxed, it will still be necessary to implement surveillance of incoming passengers to identify infected individuals quickly. This measure, as well as tracing and isolating contacts of detected infected passengers, should remain in place to suppress potential outbreaks until case numbers globally are reduced.

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Section: Outbreak Risk Metricsmentioning

confidence: 99%

The risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions

Sachak-Patwa

Byrne

Dyson

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…To cause disease, the pathogen must be able to infect and replicate in humans. Pathogen emergence-sustained human-tohuman transmission-further requires that the pathogen be sufficiently transmissible in humans, with basic reproductive number R 0 > 1 [3,4]. A pathogen with an initial R 0 < 1 in the human population could emerge as a result of adaptive evolution if genetic changes increase R 0 to a value greater than one before short transient chains of transmission stutter to extinction [5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Reservoir population dynamics and pathogen epidemiology drive pathogen genetic diversity, spillover, and emergence

Remien

Nuismer

2020

Preprint

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When several factors align, pathogens that normally infect wildlife can spill over into the human population. If pathogen transmission within the human population is self-sustaining, or rapidly evolves to be self sustaining, novel human pathogens can emerge. Although many factors influence the likelihood of spillover and emergence, the rate of contact between humans and wildlife is critical. Thus, for those pathogens inhabiting wildlife reservoirs with pronounced seasonal fluctuations in population density, it is broadly recognized that spillover risk also varies with season. What remains unknown, however, is the extent to which seasonal fluctuations in reservoir populations influence the evolutionary dynamics of pathogens in ways that affect the likelihood of emergence. Here, we use mathematical models and stochastic simulations to show that seasonal fluctuations in reservoir population densities lead to seasonal increases in genetic variation within pathogen populations and thus influence the waiting time for mutations capable of sustained human-to-human transmission. These seasonal increases in genetic variation also lead to elevated risk of emergence at predictable times of year.

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“…The COR is an extension of the IOR, accounting for changes in population susceptibility due to vaccination over the initial phase of the potential outbreak. The COR has previously been used to assess outbreak risks using branching processes for models in which pathogen transmission varies periodically [28,[32][33][34]. Its calculation involves solving the differential equation…”

Section: Outbreak Risk Metricsmentioning

confidence: 99%

The risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions

Sachak-Patwa

Byrne

Dyson

et al. 2021

Preprint

View full text Add to dashboard Cite

Countries around the world have introduced travel restrictions to reduce SARS−CoV−2 transmission. As vaccines are gradually rolled out, attention has turned to when travel restrictions and other non-pharmaceutical interventions (NPIs) can be relaxed. Here, using SARS−CoV−2 as a case study, we develop a mathematical branching process model to assess the risk that, following the removal of NPIs, cases introduced into new locations initiate a local outbreak. Our model accounts for changes in background population immunity due to vaccination. We consider two locations in which the vaccine rollout has progressed quickly − specifically, the Isle of Man (a British crown dependency in the Irish Sea) and the country of Israel. We show that the outbreak risk is unlikely to be eliminated completely when travel restrictions and other NPIs are removed, even once the vaccine programmes in these locations are complete. Specifically, the risk that an imported case initiates an outbreak following the vaccine rollout and removal of NPIs is projected to be 0.373 (0.223,0.477) for the Isle of Man and 0.506 (0.387,0.588) for Israel. Key factors underlying these risks are the potential for transmission even following vaccination, incomplete vaccine uptake, and the recent emergence of SARS−CoV−2 variants with increased transmissibility. Combined, these factors suggest that when travel restrictions are relaxed, it will still be necessary to implement surveillance of incoming passengers to identify infected individuals quickly. This measure, as well as tracing and isolating contacts of detected infected passengers, should remain in place to suppress potential outbreaks until case numbers globally are reduced.

show abstract

Winter is coming: pathogen emergence in seasonal environments

Cited by 5 publications

References 34 publications

The risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions

The risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions

Reservoir population dynamics and pathogen epidemiology drive pathogen genetic diversity, spillover, and emergence

The risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions

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