On the contact tracing for COVID-19: A simulation study.

BACKGROUND: Contact tracing is one of the most effective non-pharmaceutical interventions in the COVID-19 pandemic. This study uses a multi-agent model to investigate the impact of four types of contact tracing strategies to prevent the spread of COVID-19. METHODS: In order to analyse individual contact tracing in a reasonably realistic setup, we construct an agent-based model of a small municipality with about 60.000 inhabitants (nodes) and about 2.8 million social contacts (edges) in 30 different layers. Those layers reflect demographic, geographic, sociological and other patterns of the TTWA (Travel-to-work-area) Hodonín in Czechia. Various data sources such as census, land register, transport data or data reflecting the shopping behaviour, were employed to meet this purpose. On this multi-graph structure we run a modified SEIR model of the COVID-19 dynamics. The parameters of the model are calibrated on data from the outbreak in the Czech Republic in the period March to June 2020. The simplest type of contact tracing follows just the family, the second tracing version tracks the family and all the work contacts, the third type finds all contacts with the family, work contacts and friends (leisure activities). The last one is a complete (digital) tracing capable of recalling any and all contacts. We evaluate the performance of these contact tracing strategies in four different environments. First, we consider an environment without any contact restrictions (benchmark); second with strict contact restriction (replicating the stringent non-pharmaceutical interventions employed in Czechia in the spring 2020); third environment, where the measures were substantially relaxed, and, finally an environment with weak contact restrictions and superspreader events (replicating the situation in Czechia in the summer 2020). FINDINGS: There are four main findings in our paper. 1. In general, local closures are more effective than any type of tracing. 2. In an environment with strict contact restrictions there are only small differences among the four contact tracing strategies. 3. In an environment with relaxed contact restrictions the effectiveness of the tracing strategies differs substantially. 4. In the presence of superspreader events only complete contact tracing can stop the epidemic. INTERPRETATION: In situations, where many other non-pharmaceutical interventions are in place, the specific extent of contact tracing may not have a large influence on their effectiveness. In a more relaxed setting with few contact restrictions and larger events the effectiveness of contact tracing depends heavily on their extent.

Learning mitigates genetic drift.

Genetic drift is a basic evolutionary principle describing random changes in allelic frequencies, with far-reaching consequences in various topics ranging from species conservation efforts to speciation. The conventional approach assumes that genetic drift has the same effect on all populations undergoing the same changes in size, regardless of different non-reproductive behaviors and history of the populations. However, here we reason that processes leading to a systematic increase of individuals` chances of survival, such as learning or immunological memory, can mitigate loss of genetic diversity caused by genetic drift even if the overall mortality rate in the population does not change. We further test this notion in an agent-based model with overlapping generations, monitoring allele numbers in a population of prey, either able or not able to learn from successfully escaping predators' attacks. Importantly, both these populations start with the same effective size and have the same and constant overall mortality rates. Our results demonstrate that even under these conditions, learning can mitigate loss of genetic diversity caused by drift, by creating a pool of harder-to-die individuals that protect alleles they carry from extinction. Furthermore, this effect holds regardless if the population is haploid or diploid or whether it reproduces sexually or asexually. These findings may be of importance not only for basic evolutionary theory but also for other fields using the concept of genetic drift.

Protection provided by vaccination, booster doses and previous infection against covid-19 infection, hospitalisation or death over time in Czechia.

Studies demonstrating the waning of post-vaccination and post-infection immunity against covid-19 generally analyzed a limited range of vaccines or subsets of populations. Using Czech national health data from the beginning of the covid-19 pandemic till November 20, 2021 we estimated the risks of reinfection, breakthrough infection, hospitalization and death by a Cox regression adjusted for sex, age, vaccine type and vaccination status. Vaccine effectiveness against infection declined from 87% at 0-2 months after the second dose to 53% at 7-8 months for BNT162b2 vaccine, from 90% at 0-2 months to 65% at 7-8 months for mRNA-1273, and from 83% at 0-2 months to 55% at 5-6 months for the ChAdOx1-S. Effectiveness against hospitalization and deaths declined by about 15% and 10%, respectively, during the first 6-8 months. Boosters (third dose) returned the protection to the levels observed shortly after dose 2. In unvaccinated, previously infected individuals the protection against infection declined from 97% after 2 months to 72% at 18 months. Our results confirm the waning of vaccination-induced immunity against infection and a smaller decline in the protection against hospitalization and death. Boosting restores the original vaccine effectiveness. Post-infection immunity also decreases over time.

Delays, Masks, the Elderly, and Schools: First Covid-19 Wave in the Czech Republic.

Running across the globe for nearly 2 years, the Covid-19 pandemic keeps demonstrating its strength. Despite a lot of understanding, uncertainty regarding the efficiency of interventions still persists. We developed an age-structured epidemic model parameterized with epidemiological and sociological data for the first Covid-19 wave in the Czech Republic and found that (1) starting the spring 2020 lockdown 4 days earlier might prevent half of the confirmed cases by the end of lockdown period, (2) personal protective measures such as face masks appear more effective than just a realized reduction in social contacts, (3) the strategy of sheltering just the elderly is not at all effective, and (4) leaving schools open is a risky strategy. Despite vaccination programs, evidence-based choice and timing of non-pharmaceutical interventions remains an effective weapon against the Covid-19 pandemic.

Importance of vaccine action and availability and epidemic severity for delaying the second vaccine dose.

Following initial optimism regarding potentially rapid vaccination, delays and shortages in vaccine supplies occurred in many countries during spring 2021. Various strategies to counter this gloomy reality and speed up vaccination have been set forth, of which the most popular has been to delay the second vaccine dose for a longer period than originally recommended by the manufacturers. Controversy has surrounded this strategy, and overly simplistic models have been developed to shed light on this issue. Here we use three different epidemic models, all accounting for then actual COVID-19 epidemic in the Czech Republic, including the real vaccination rollout, to explore when delaying the second vaccine dose by another 3 weeks from 21 to 42 days is advantageous. Using COVID-19-related deaths as a quantity to compare various model scenarios, we find that the way of vaccine action at the beginning of the infection course (preventing infection and symptoms appearance), mild epidemic and sufficient vaccine supply rate call for the original inter-dose period of 21 days regardless of vaccine efficacy. On the contrary, for the vaccine action at the end of infection course (preventing severe symptoms and death), severe epidemic and low vaccine supply rate, the 42-day inter-dose period is preferable, at any plausible vaccine efficacy.

Protection by Vaccines and Previous Infection Against the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2.

BACKGROUND: The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades immunity conferred by vaccines and previous infections. METHODS: We used a Cox proportional hazards model and a logistic regression on individual-level population-wide data from the Czech Republic to estimate risks of infection and hospitalization, including severe states. RESULTS: A recent (≤2 months) full vaccination reached vaccine effectiveness (VE) of 43% (95% confidence interval [CI], 42%-44%) against infection by Omicron compared to 73% (95% CI, 72%-74%) against Delta. A recent booster increased VE to 56% (95% CI, 55%-56%) against Omicron infection compared to 90% (95% CI, 90%-91%) for Delta. The VE against Omicron hospitalization of a recent full vaccination was 45% (95% 95% CI, 29%-57%), with a recent booster 87% (95% CI, 84%-88%). The VE against the need for oxygen therapy due to Omicron was 57% (95% CI, 32%-72%) for recent vaccination, 90% (95% CI, 87%-92%) for a recent booster. Postinfection protection against Omicron hospitalization declined from 68% (95% CI, 68%-69%) at ≤6 months to 13% (95% CI, 11%-14%) at >6 months after a previous infection. The odds ratios for Omicron relative to Delta were 0.36 (95% CI, .34-.38) for hospitalization, 0.24 (95% CI, .22-.26) for oxygen, and 0.24 (95% CI, .21-.28) for intensive care unit admission. CONCLUSIONS: Recent vaccination still brings substantial protection against severe outcome for Omicron.

Predation has small, short-term, and in certain conditions random effects on the evolution of aging.

BACKGROUND: The pace of aging varies considerably in nature. The best-known explanation of the evolution of specific rates of aging is the Williams' hypothesis suggesting that the aging rate should correlate with the level of extrinsic mortality. However, the current evidence is inconclusive with various examples where the Williams' hypothesis seems to be correct and where it doesn't. Here we explore the relationship between extrinsic mortality and aging rate by developing a simulation model of the evolution of aging rate in prey subject to predation. RESULTS: Our results suggest that more intense predation leads to the evolution of faster pace of aging in prey. However, this effect slowly vanishes when the predator diet breadth is allowed to evolve, too. Furthermore, in our model, the evolution of a specific aging rate is driven mainly by a single parameter, the strength of a trade-off between aging and fecundity. Indeed, in the absence of this trade-off the evolutionary impacts of predation on the prey aging rate appear random. CONCLUSIONS: We show that the William's hypothesis appears valid when there is a trade-off between aging and fecundity and predators and prey do not coevolve. However, we also show that when the prey and predators coevolve or if there is no trade-off between aging and fecundity the William`s hypothesis is no longer applicable.

Delays, masks, the elderly, and schools: first COVID-19 wave in the Czech Republic.

Running across the globe for more than a year, the COVID-19 pandemic keeps demonstrating its strength. Despite a lot of understanding, uncertainty regarding the efficiency of interventions still persists. We developed an age-structured epidemic model parameterized with sociological data for the Czech Republic and found that (1) delaying the spring 2020 lockdown by four days produced twice as many confirmed cases by the end of the lockdown period, (2) personal protective measures such as face masks appear more effective than just a reduction of social contacts, (3) only sheltering the elderly is by no means effective, and (4) leaving schools open is a risky strategy. Despite the onset of vaccination, an evidence-based choice and timing of non-pharmaceutical interventions still remains the most important weapon against the COVID-19 pandemic.

Fecundity-Longevity Trade-Off, Vertical Transmission, and Evolution of Virulence in Sterilizing Pathogens.

Sterilizing pathogens are common, yet studies focused on how such pathogens respond adaptively to fecundity reductions caused in their hosts are rare. Here we assume that the infected hosts, as a result of redistributing energy resources saved by reduced fecundity, have increased longevity and focus on exploring the consequences of such a fecundity-longevity trade-off on sterility virulence evolution in the pathogens. We find that the trade-off itself cannot prevent the evolution of full sterilization. Therefore, we allow for vertical transmission and reveal that the fecundity-longevity trade-off strongly determines the threshold efficiency of vertical transmission above which partial host sterilization evolves. Partial sterilization may appear as an intermediate level of sterility virulence or as a stable dimorphism at which avirulent and highly virulent strains coexist. The fecundity-longevity trade-off significantly contributes to determining the actual outcome, in many cases countering predictions made in the absence of this trade-off. It is known that in well-mixed populations, partial sterilization may evolve in pathogens under a combination of horizontal and vertical transmission. Our study highlights that this is independent of the form of horizontal transmission and the type of density dependence in host demography and that the fecundity-longevity trade-off is an important player in sterility virulence evolution.

Evolution favours aging in populations with assortative mating and in sexually dimorphic populations.

Since aging seems omnipresent, many authors regard it as an inevitable consequence of the laws of physics. However, recent research has conclusively shown that some organisms do not age, or at least do not age on a scale comparable with other aging organisms. This begets the question why aging evolved in some organisms yet not in others. Here we present a simulation model of competition between aging and non-aging individuals in a sexually reproducing population. We find that the aging individuals may outcompete the non-aging ones if they have a sufficiently but not excessively higher initial fecundity or if individuals mate assortatively with respect to their own phenotype. Furthermore, the aging phenotype outcompetes the non-aging one or resists dominance of the latter for a longer period in populations composed of genuine males and females compared to populations of simultaneous hermaphrodites. Finally, whereas sterilizing parasites promote non-aging, the effect of mortality-enhancing parasites is to enable longer persistence of the aging phenotype relative to when parasites are absent. Since the aging individuals replace the non-aging ones in diverse scenarios commonly found in nature, our study provides important insights into why aging has evolved in most, but not all organisms.

Impacts of infection avoidance for populations affected by sexually transmitted infections.

Sexually transmitted infections are ubiquitous in nature and affect many populations. The key process for their transmission is mating, usually preceded by mate choice. Susceptible individuals may avoid mating with infected individuals to prevent infection provided it is recognizable. We show that accounting for infection avoidance significantly alters host population dynamics. We observe bistability between the disease-free and endemic or disease-induced extinction equilibria, significant abrupt reduction in the host population size and disease-induced host extinction. From the population persistence perspective, the best strategy is either not to avoid mating with the infected individuals, to prevent disease-induced host extinction, or to completely avoid mating with the infected individuals, to prevent pathogen invasion. Increasing sterilization efficiency of the infection leads to lower population sizes and reduced effect of mating avoidance. We also find that the disease-free state is more often attained by populations with strong polyandry, whereas a high-density endemic state is more often observed for populations with strong polygyny, suggesting that polygamy rather than monogamy may be promoted in denser host populations.

Host-pathogen dynamics under sterilizing pathogens and fecundity-longevity trade-off in hosts.

Infectious diseases are known to regulate population dynamics, an observation that underlies the use of pathogens as control agents of unwanted populations. Sterilizing rather than lethal pathogens are often suggested so as to avoid unnecessary suffering of the infected hosts. Until recently, models used to assess plausibility of pathogens as potential pest control agents have not included a possibility that reduced fecundity of the infected individuals may save their energy expenditure on reproduction and thus increase their longevity relative to the susceptible ones. Here, we develop a model of host-pathogen interaction that builds on this idea. We analyze the model for a variety of infection transmission functions, revealing that the indirect effect of sterilizing pathogens on mortality of the infected hosts, mediated by a fecundity-longevity trade-off, may cause hosts at endemic equilibria to attain densities higher than when there is no effect of pathogens on host mortality. On the other hand, an opposite outcome occurs when the fecundity-longevity trade-off is concave or when the degree of fecundity reduction by the pathogen is high enough. This points to a possibility that using sterilizing pathogens as agents of pest control may actually be less effective than previously thought, the more so since we also suggest that if sexual selection acts on the host species then the presence of sterilizing pathogens may even enhance host densities above the levels achieved without infection.

Density-dependent selection on mate search and evolution of Allee effects.

Sexually reproducing organisms require males and females to find each other. Increased difficulty of females finding mates as male density declines is the most frequently reported mechanism of Allee effects in animals. Evolving more effective mate search may alleviate Allee effects, but may depend on density regimes a population experiences. In particular, high-density populations may evolve mechanisms that induce Allee effects which become detrimental when populations are reduced and maintained at a low density. We develop an individual-based, eco-genetic model to study how mating systems and fitness trade-offs interact with changes in population density to drive evolution of the rate at which males or females search for mates. Finite mate search rate triggers Allee effects in our model and we explore how these Allee effects respond to such evolution. We allow a population to adapt to several population density regimes and examine whether high-density populations are likely to reverse adaptations attained at low densities. We find density-dependent selection in most of scenarios, leading to search rates that result in lower Allee thresholds in populations kept at lower densities. This mainly occurs when fecundity costs are imposed on mate search, and provides an explanation for why Allee effects are often observed in anthropogenically rare species. Optimizing selection, where the attained trait value minimizes the Allee threshold independent of population density, depended on the trade-off between search and survival, combined with monogamy when females were searching. Other scenarios led to runaway selection on the mate search rate, including evolutionary suicide. Trade-offs involved in mate search may thus be crucial to determining how density influences the evolution of Allee effects. Previous studies did not examine evolution of a trait related to the strength of Allee effects under density variation. We emphasize the crucial role that mating systems, fitness trade-offs and the evolving sex have in determining the density threshold for population persistence, in particular since evolution need not always take the Allee threshold to its minimum value.

Review: Allee effects in social species.

Allee effects have important implications for many aspects of basic and applied ecology. The benefits of aggregation of conspecific individuals are central to Allee effects, which have led to the widely held assumption that social species are more prone to Allee effects. Robust evidence for this assumption, however, remains rare. Furthermore, previous research on Allee effects has failed to adequately address the consequences of the different levels of organisation within social species' populations. Here, we review available evidence of Allee effects and model the role of demographic and behavioural factors that may combine to dampen or strengthen Allee effects in social species. We use examples across various species with contrasting social structure, including carnivores, bats, primates and eusocial insects. Building on this, we provide a conceptual framework that allows for the integration of different Allee effects in social species. Social species are characterised by nested levels of organisation. The benefits of cooperation, measured by mean individual fitness, can be observed at both the population and group levels, giving rise to "population level" and "group level" Allee effects respectively. We also speculate on the possibility of a third level, reporting per capita benefits for different individuals within a group (e.g. castes in social insects). We show that group size heterogeneity and intergroup interactions affect the strength of population-level demographic Allee effects. Populations with higher group size heterogeneity and in which individual social groups cooperate demonstrate the weakest Allee effects and may thus provide an explanation for why extinctions due to Allee effects are rare in social species. More adequately accounting for Allee effects in social species will improve our understanding of the ecological and evolutionary implications of cooperation in social species.

Evolution of mate-finding Allee effect in prey.

The search for mates is often accompanied with conspicuous behaviour or morphology that can be exploited by predators. Here we explore the evolutionary consequences of a trade-off that arises naturally between mate acquisition and risk of predation and study evolution of the rate at which male prey search for mates in a population subject to a mate-finding Allee effect and exposed to either generalist or specialist predators. Since we show that the mate search rate determines the strength of the mate-finding Allee effect, we can alternatively view this as evolution of the mate-finding Allee effect in prey. We contrast two different life histories and find that, predominantly, male prey either evolve towards the maximal mate search rate yielding the weakest possible mate-finding Allee effect (thus showing no adaptive response in mating behaviour to predation risk) or evolutionary bi-stability occurs. In the latter case, males evolve a relatively low mate search rate (hence a relatively strong mate-finding Allee effect, interpreted as an adaptive response of male prey to predation) when initially slow or the maximal mate search rate when initially fast. Disruptive selection does not occur in populations exposed to generalist predators but is possible when predators are specialists. The dimorphic phase, in which fast and conspicuous male prey coexist with slow and cryptic ones, is however but a transient in evolutionary dynamics as one branch goes extinct while the other evolves towards the maximal mate search rate.

Sexually transmitted infections and mate-finding Allee effects.

Infectious diseases can seriously impact dynamics of their host species. In this study, we model and analyze an interaction between a sexually transmitted infection and its animal host population affected by a mate-finding Allee effect. Since mating drives both host reproduction and infection transmission, the Allee effect shapes the transmission rate of the infection which we show takes a saturating form. Our model combining sexually transmitted infections with the mate-finding Allee effect in the host produces quite rich dynamics, including oscillations, several multistability regimes, and infection-induced host extinction. However, many of these complex patterns are restricted to a relatively narrow parameter range. We find that the host extinction occurs at intermediate levels of infection virulence, as well as for Allee effect strengths much lower than when the infection is absent. In both cases, a sequence of events comprising destabilization of an endemic equilibrium, growth of oscillation amplitude, and a heteroclinic bifurcation forms an underlying mechanism. We apply our model to the feline immunodeficiency virus (FIV) in domestic cats.

Eradication of Invading Insect Populations: From Concepts to Applications.

Eradication is the deliberate elimination of a species from an area. Given that international quarantine measures can never be 100% effective, surveillance for newly arrived populations of nonnative species coupled with their eradication represents an important strategy for excluding potentially damaging insect species. Historically, eradication efforts have not always been successful and have sometimes been met with public opposition. But new developments in our understanding of the dynamics of low-density populations, the availability of highly effective treatment tactics, and bioeconomic analyses of eradication strategies offer new opportunities for developing more effective surveillance and eradication programs. A key component that connects these new developments is the harnessing of Allee effects, which naturally promote localized species extinction. Here we review these developments and suggest how research might enhance eradication strategies.