Population viscosity suppresses disease emergence by preserving local herd immunity

Animal reservoirs for infectious diseases pose ongoing risks to human populations. In this theory of zoonoses, the introduction event that starts an epidemic is assumed to be independent of all preceding events. However, introductions are often concentrated in communities that bridge the ecological interfaces between reservoirs and the general population. In this paper, we explore how the risks of disease emergence are altered by the aggregation of introduction events within bridge communities. In viscous bridge communities, repeated introductions can elevate the local prevalence of immunity. This local herd immunity can form a barrier reducing the opportunities for disease emergence. In some situations, reducing exposure rates counterintuitively increases the emergence hazards because of off-setting reductions in local immunity. Increases in population mixing can also increase emergence hazards, even when average contact rates are conserved. Our theory of bridge communities may help guide prevention and explain historical emergence events, where disruption of stable economic, political or demographic processes reduced population viscosity at ecological interfaces.

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Age-targeted dose allocation can halve COVID-19 vaccine requirements

10.1101/2020.10.08.20208108 ◽

2020 ◽

Author(s):

Michael T. Meehan ◽

Daniel G. Cocks ◽

Jamie M. Caldwell ◽

James M. Trauer ◽

Adeshina I. Adekunle ◽

...

Keyword(s):

Mathematical Model ◽

Severe Disease ◽

Herd Immunity ◽

Population Level ◽

Morbidity And Mortality ◽

Effective Strategy ◽

Risk Of Infection ◽

Middle Aged ◽

Contact Rates ◽

Age Structured

ABSTRACTIn anticipation of COVID-19 vaccine deployment, we use an age-structured mathematical model to investigate the benefits of optimizing age-specific dose allocation to suppress the transmission, morbidity and mortality of SARS-CoV-2 and the associated disease, COVID-19. To minimize transmission, we find that the highest priority individuals across 179 countries are typically those between 30 and 59 years of age because of their high contact rates and higher risk of infection and disease. Conversely, morbidity and mortality are initially most effectively reduced by targeting 60+ year olds who are more likely to experience severe disease. However, when population-level coverage is sufficient — such that herd immunity can be achieved through targeted dose allocation — prioritizing middle-aged individuals becomes the most effective strategy to minimize hospitalizations and deaths. For each metric considered, we show that optimizing the allocation of vaccine doses can more than double their effectiveness.

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Mathematical Epidemiological Model of the Propagation and Prevention of Infectious Diseases Considering COVID-19 Vaccination

10.21203/rs.3.rs-709496/v1 ◽

2021 ◽

Author(s):

Kazumi Omata ◽

Hiroaki Mitsuya

Keyword(s):

Infectious Diseases ◽

Time Scale ◽

Reproduction Number ◽

Herd Immunity ◽

Epidemiological Studies ◽

Human Populations ◽

Future Scenarios ◽

Vaccination Programs ◽

Asymptotic Nature ◽

Alternative Approach

Abstract The duration of the necessity of current restrictions and preventive countermeasures against the COVID-19 pandemic is of great concern. While several previous epidemiological studies have discussed controlling the course of the epidemic with regard to social distancing, vaccination, care capacities, and future scenarios, we adopt an alternative approach to provide insights into the time scale of epidemic propagation in human populations. We show that the reproduction number modified by preventive countermeasures Rm implies a threshold R~m to reach the herd immunity level at time Th. While Th varies moderately for large Rm, it increases sharply around Rm=R~m, and Th is infinite below Rm=R~m. The transition region for this increase is minute, demonstrating that prevention of infectious diseases must consider the relatively asymptotic nature of their propagation, which varies unpredictably between steady transmission and explosive outbreaks. These results suggest the continuation of preventive countermeasures to suppress the transmission of COVID-19 for many years; if they were discontinued or reduced such that Rm exceeded R~m, the disease would be transmitted throughout the considered community, and the required herd immunity level would be reached within 250 days if Rm > 1.6. However, the implementation of vaccination programs could drastically alter this dynamic.

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Population-based seroprevalence of SARS-CoV-2 and the herd immunity threshold in Maranhão

Revista de Saúde Pública ◽

10.11606/s1518-8787.2020054003278 ◽

2020 ◽

Vol 54 ◽

pp. 131

Author(s):

Antônio Augusto Moura da Silva ◽

Lídio Gonçalves Lima-Neto ◽

Conceição de Maria Pedrozo e Silva de Azevedo ◽

Léa Márcia Melo da Costa ◽

Maylla Luanna Barbosa Martins Bragança ◽

...

Keyword(s):

Herd Immunity ◽

Household Survey ◽

Population Based ◽

Igg Antibodies ◽

Infection Rates ◽

Qualitative Detection ◽

Roche Diagnostics ◽

Local Herd ◽

Pharmaceutical Interventions ◽

Population Based Survey

OBJECTIVE: To estimate the seroprevalence of SARS-CoV-2 in the state of Maranhão, Brazil. METHODS: A population-based household survey was performed, from July 27, 2020 to August 8, 2020. The estimates considered clustering, stratification and non-response. Qualitative detection of IgM and IgG antibodies was performed in a fully-automated Elecsys® Anti-SARS-CoV-2 electrochemiluminescence immunoassay on the Cobas® e601 analyzer (Roche Diagnostics). RESULTS: In total, 3,156 individuals were interviewed. Seroprevalence of total antibodies against SARS-CoV-2 was 40.4% (95%CI 35.6-45.3). Population adherence to non-pharmaceutical interventions was higher at the beginning of the pandemic than in the last month. SARS-CoV-2 infection rates were significantly lower among mask wearers and among those who maintained social and physical distancing in the last month compared to their counterparts. Among the infected, 26.0% were asymptomatic. The infection fatality rate (IFR) was 0.14%, higher for men and older adults. The IFR based on excess deaths was 0.28%. The ratio of estimated infections to reported cases was 22.2. CONCLUSIONS: To the best of our knowledge, the seroprevalence of SARS-CoV-2 estimated in this population-based survey is one of the highest reported. The local herd immunity threshold may have been reached or might be reached soon.

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Global demographic history of human populations inferred from whole mitochondrial genomes

Royal Society Open Science ◽

10.1098/rsos.180543 ◽

2018 ◽

Vol 5 (8) ◽

pp. 180543 ◽

Cited By ~ 3

Author(s):

Eleanor F. Miller ◽

Andrea Manica ◽

William Amos

Keyword(s):

Demographic History ◽

Population Expansion ◽

Human Populations ◽

Population Mixing ◽

Neolithic Transition ◽

Current Location ◽

Geographical Regions ◽

Population Sizes ◽

History Of ◽

Complete Mtdna

The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from the 1000 Genomes Project Phase 3, to explore changes in populations sizes in five populations for each of four major geographical regions, using a sophisticated coalescent-based Bayesian method (extended Bayesian skyline plots) and mutation rates calibrated with ancient DNA. Despite the power and sophistication of our analysis, we fail to find size changes that correspond to the Neolithic transitions of the study populations. However, we do detect a number of size changes, which tend to be replicated in most populations within each region. These changes are mostly much older than the Neolithic transition and could reflect either population expansion or changes in population structure. Given the amount of migration and population mixing that occurred after these ancient signals were generated, we caution that modern populations will often carry ghost signals of demographic events that occurred far away from their current location.

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Vaccination and herd immunity thresholds in heterogeneous populations

10.1101/2021.02.26.21252553 ◽

2021 ◽

Author(s):

Elamin H. Elbasha ◽

Abba B. Gumel

Keyword(s):

Vaccine Efficacy ◽

Reproduction Number ◽

Herd Immunity ◽

Heterogeneous Population ◽

Relative Population ◽

Homogeneous Population ◽

Heterogeneous Populations ◽

Contact Rates ◽

Per Capita ◽

Rigorous Mathematical Analysis

AbstractIt has been suggested, without rigorous mathematical analysis, that the classical vaccine-induced herd immunity threshold (HIT) assuming a homogeneous population can be substantially higher than the minimum HIT obtained when considering population heterogeneities. We investigated this claim by developing, and rigorously analyzing, a vaccination model that incorporates various forms of heterogeneity and compared it with a model of a homogeneous population. By employing a two-group vaccination model in heterogeneous populations, we theoretically established conditions under which heterogeneity leads to different HIT values, depending on the relative values of the contact rates for each group, the type of mixing between groups, relative vaccine efficacy, and the relative population size of each group. For example, under biased random mixing and when vaccinating a given group results in disproportionate prevention of higher transmission per capita, it is optimal to vaccinate that group before vaccinating other groups. We also found situations, under biased assortative mixing assumption, where it is optimal to vaccinate more than one group. We show that regardless of the form of mixing between groups, the HIT values assuming a heterogeneous population are always lower than the HIT values obtained from a corresponding model with a homogeneous population. Using realistic numerical examples and parametrization (e.g., assuming assortative mixing together with vaccine efficacy of 95% and basic reproduction number of 2.5), we demonstrate that the HIT value considering heterogeneity (e.g., biased assortative mixing) is significantly lower (40%) compared with a HIT value of (63%) assuming a homogeneous population.

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Assessing Targeted Containment Policies to Fight COVID-19

IMF Working Papers ◽

10.5089/9781513560915.001 ◽

2020 ◽

Vol 20 (277) ◽

Author(s):

Ariadne Checo ◽

Francesco Grigoli ◽

José Mota

Keyword(s):

Herd Immunity ◽

Age Groups ◽

Mortality Rates ◽

Economic Costs ◽

Contact Rates ◽

Containment Measures ◽

Containment Policy ◽

The Government ◽

Death Count ◽

Targeted Approach

The large economic costs of full-blown lockdowns in response to COVID-19 outbreaks, coupled with heterogeneous mortality rates across age groups, led to question non-discriminatory containment measures. In this paper we provide an assessment of the targeted approach to containment. We propose a SIR-macro model that allows for heterogeneous agents in terms of mortality rates and contact rates, and in which the government optimally bans people from working. We find that under a targeted policy, the optimal containment reaches a larger portion of the population than under a blanket policy and is held in place for longer. Compared to a blanket policy, a targeted approach results in a smaller death count. Yet, it is not a panacea: the recession is larger under such approach as the containment policy applies to a larger fraction of people, remains in place for longer, and herd immunity is achieved later. Moreover, we find that increased interactions between low- and high-risk individuals effectively reduce the benefits of a targeted approach to containment.

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Spatial Clustering of Vaccine Exemptions on the Risk of a Measles Outbreak

PEDIATRICS ◽

10.1542/peds.2021-050971 ◽

2021 ◽

Vol 149 (1) ◽

Cited By ~ 1

Author(s):

Ashley Gromis ◽

Ka-Yuet Liu

Keyword(s):

Large Scale ◽

Spatial Clustering ◽

Vaccine Coverage ◽

Herd Immunity ◽

The United States ◽

Vaccine Preventable Diseases ◽

Measles Outbreak ◽

Measles Outbreaks ◽

Lower Population ◽

Local Herd

OBJECTIVES Areas of increased school-entry vaccination exemptions play a key role in epidemics of vaccine-preventable diseases in the United States. California eliminated nonmedical exemptions in 2016, which increased overall vaccine coverage but also rates of medical exemptions. We examine how spatial clustering of exemptions contributed to measles outbreak potential pre- and postpolicy change. METHODS We modeled measles transmission in an empirically calibrated hypothetical population of youth aged 0 to 17 years in California and compared outbreak sizes under the observed spatial clustering of exemptions in schools pre- and postpolicy change with counterfactual scenarios of no postpolicy change increase in medical exemptions, no clustering of exemptions, and lower population immunization levels. RESULTS The elimination of nonmedical exemptions significantly reduced both average and maximal outbreak sizes, although increases in medical exemptions resulted in more than twice as many infections, on average, than if medical exemptions were maintained at prepolicy change levels. Spatial clustering of nonmedical exemptions provided some initial protection against random introduction of measles infections; however, it ultimately allowed outbreaks with thousands more infections than when exemptions were randomly distributed. The large-scale outbreaks produced by exemption clusters could not be reproduced when exemptions were distributed randomly until population vaccination was lowered by >6 percentage points. CONCLUSIONS Despite the high overall vaccinate rate, the spatial clustering of exemptions in schools was sufficient to threaten local herd immunity and reduce protection from measles outbreaks. Policies strengthening vaccine requirements may be less effective if alternative forms of exemptions (eg, medical) are concentrated in existing low-immunization areas.

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Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures

Nature Communications ◽

10.1038/s41467-021-25524-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Moisès Coll Macià ◽

Laurits Skov ◽

Benjamin Marco Peter ◽

Mikkel Heide Schierup

Keyword(s):

Fragment Length ◽

Human Populations ◽

Female Age ◽

Generation Interval ◽

The Past ◽

Neanderthal Admixture ◽

Demographic Processes ◽

Out Of Africa ◽

Rates Of Decay ◽

Insight Into

AbstractAfter the main Out-of-Africa event, humans interbred with Neanderthals leaving 1–2% of Neanderthal DNA scattered in small fragments in all non-African genomes today. Here we investigate what can be learned about human demographic processes from the size distribution of these fragments. We observe differences in fragment length across Eurasia with 12% longer fragments in East Asians than West Eurasians. Comparisons between extant populations with ancient samples show that these differences are caused by different rates of decay in length by recombination since the Neanderthal admixture. In concordance, we observe a strong correlation between the average fragment length and the mutation accumulation, similar to what is expected by changing the ages at reproduction as estimated from trio studies. Altogether, our results suggest differences in the generation interval across Eurasia, by up 10–20%, over the past 40,000 years. We use sex-specific mutation signatures to infer whether these changes were driven by shifts in either male or female age at reproduction, or both. We also find that previously reported variation in the mutational spectrum may be largely explained by changes to the generation interval. We conclude that Neanderthal fragment lengths provide unique insight into differences among human populations over recent history.

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The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases

EcoHealth ◽

10.1007/s10393-015-1061-0 ◽

2015 ◽

Vol 12 (4) ◽

pp. 726-735 ◽

Cited By ~ 34

Author(s):

Maia A. Rabaa ◽

Ngo Tri Tue ◽

Tran My Phuc ◽

Juan Carrique-Mas ◽

Karen Saylors ◽

...

Keyword(s):

Infectious Diseases ◽

Large Scale ◽

High Throughput Sequencing ◽

Integrated Approach ◽

Current Status ◽

Human Populations ◽

Disease Emergence ◽

Major Step ◽

Zoonotic Infections ◽

Animal Populations

Abstract The effect of newly emerging or re-emerging infectious diseases of zoonotic origin in human populations can be potentially catastrophic, and large-scale investigations of such diseases are highly challenging. The monitoring of emergence events is subject to ascertainment bias, whether at the level of species discovery, emerging disease events, or disease outbreaks in human populations. Disease surveillance is generally performed post hoc, driven by a response to recent events and by the availability of detection and identification technologies. Additionally, the inventory of pathogens that exist in mammalian and other reservoirs is incomplete, and identifying those with the potential to cause disease in humans is rarely possible in advance. A major step in understanding the burden and diversity of zoonotic infections, the local behavioral and demographic risks of infection, and the risk of emergence of these pathogens in human populations is to establish surveillance networks in populations that maintain regular contact with diverse animal populations, and to simultaneously characterize pathogen diversity in human and animal populations. Vietnam has been an epicenter of disease emergence over the last decade, and practices at the human/animal interface may facilitate the likelihood of spillover of zoonotic pathogens into humans. To tackle the scientific issues surrounding the origins and emergence of zoonotic infections in Vietnam, we have established The Vietnam Initiative on Zoonotic Infections (VIZIONS). This countrywide project, in which several international institutions collaborate with Vietnamese organizations, is combining clinical data, epidemiology, high-throughput sequencing, and social sciences to address relevant one-health questions. Here, we describe the primary aims of the project, the infrastructure established to address our scientific questions, and the current status of the project. Our principal objective is to develop an integrated approach to the surveillance of pathogens circulating in both human and animal populations and assess how frequently they are exchanged. This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance understanding of viral cross-species transmission events, and identify relevant risk factors and drivers of zoonotic disease emergence.

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A call to action: Understanding land use-induced zoonotic spillover to protect environmental, animal, and human health

10.32942/osf.io/cru9w ◽

2020 ◽

Author(s):

Raina Plowright ◽

Jamie Reaser ◽

Harvey Locke ◽

Stephen J. Woodley ◽

Jonathan A. Patz ◽

...

Keyword(s):

Land Use ◽

Human Health ◽

Relevant Literature ◽

Zoonotic Disease ◽

Human Populations ◽

Disease Emergence ◽

Call To Action ◽

Zoonotic Pathogen ◽

Wide Range ◽

Management Issues

The rapid, global spread and human health impacts of SARS-CoV-2, the agent of COVID-19 disease, demonstrates humanity’s vulnerability to zoonotic disease pandemics. Although anthropogenic land use change is known to be the major driver of zoonotic pathogen spillover from wildlife to human populations, the scientific underpinnings of land use-induced zoonotic spillover have rarely been investigated from the macro-ecology perspective. We call on colleagues to advance our knowledge of land use implications for zoonotic disease emergence. A wide range of disciplinary cosmologies, approaches, and tools are needed to identify the environmental triggers of spillover and inform the decisions needed to protect public health by reducing spillover risk as a biosecurity priority. We call for a mechanistic focus on the zoonotic pathogen “infect-shed-spill-spread” cascade and review the relevant literature, elucidating the current biases and information gaps. We also consider the opportunities for better instituting the necessary scientific collaboration, primary technical challenges, and policy and management issues that warrant particular attention.

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