Key epidemiological indicators and spatial autocorrelation patterns across five waves of COVID-19 in Catalonia

This research studies the evolution of COVID-19 crude incident rates, effective reproduction number R(t) and their relationship with incidence spatial autocorrelation patterns in the 19 months following the disease outbreak in Catalonia (Spain). A cross-sectional ecological panel design based on n = 371 health-care geographical units is used. Five general outbreaks are described, systematically preceded by generalized values of R(t) > 1 in the two previous weeks. No clear regularities concerning possible initial focus appear when comparing waves. As for autocorrelation, we identify a wave's baseline pattern in which global Moran's I increases rapidly in the first weeks of the outbreak to descend later. However, some waves significantly depart from the baseline. In the simulations, both baseline pattern and departures can be reproduced when measures aimed at reducing mobility and virus transmissibility are introduced. Spatial autocorrelation is inherently contingent on the outbreak phase and is also substantially modified by external interventions affecting human behavior.

Inequalities in COVID-19 inequalities research: Who had the capacity to respond?

The COVID-19 pandemic has been testing countries’ capacities and scientific preparedness to actively respond and collaborate on a common global threat. It has also heightened awareness of the urgent need to empirically describe and analyze health inequalities to be able to act effectively. In turn, this raises several important questions that need answering: What is known about the rapidly emerging COVID-19 inequalities research field? Which countries and world regions have been able to rapidly produce research on this topic? What research patterns and trends have emerged, and how to these compared to the (pre-COVID-19) global health inequalities research field? Which countries have been scientifically collaborating on this important topic? Where are the scientific knowledge gaps, and indirectly where might research capacities need to be strengthened? In order to answer these queries, we analyzed the global scientific production (2020–2021) on COVID-19 associated inequalities by conducting bibliometric and network analyses using the Scopus database. Specifically, we analyzed the volume of scientific production per country (via author affiliations), its distribution by country income groups and world regions, as well as the inter-country collaborations within this production. Our results indicate that the COVID-19 inequalities research field has been highly collaborative; however, a number of significant inequitable research practices exist. When compared to the (pre-COVID-19) global health inequalities research field, similar inequalities were identified, however, several new dynamics and partnerships have also emerged that warrant further in-depth exploration. To ensure preparedness for future crises, and effective strategies to tackle growing social inequalities in health, investment in global health inequalities research capacities must be a priority for all.

Rapid evolution of SARS-CoV-2 challenges human defenses

The race between pathogens and their hosts is a major evolutionary driver, where both reshuffle their genomes to overcome and reorganize the defenses for infection, respectively. Evolutionary theory helps formulate predictions on the future evolutionary dynamics of SARS-CoV-2, which can be monitored through unprecedented real-time tracking of SARS-CoV-2 population genomics at the global scale. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein determining infection success. We estimate that the > 820 million people that had been infected by October 5, 2021, produced up to 10²¹ copies of the virus, with 12 new effective RBD variants appearing, on average, daily. Doubling of the number of RBD variants every 89 days, followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics involving collaborative global sequencing and vaccination.

Global COVID-19 lockdown highlights humans as both threats and custodians of the environment

The global lockdown to mitigate COVID-19 pandemic health risks has altered human interactions with nature. Here, we report immediate impacts of changes in human activities on wildlife and environmental threats during the early lockdown months of 2020, based on 877 qualitative reports and 332 quantitative assessments from 89 different studies. Hundreds of reports of unusual species observations from around the world suggest that animals quickly responded to the reductions in human presence. However, negative effects of lockdown on conservation also emerged, as confinement resulted in some park officials being unable to perform conservation, restoration and enforcement tasks, resulting in local increases in illegal activities such as hunting. Overall, there is a complex mixture of positive and negative effects of the pandemic lockdown on nature, all of which have the potential to lead to cascading responses which in turn impact wildlife and nature conservation. While the net effect of the lockdown will need to be assessed over years as data becomes available and persistent effects emerge, immediate responses were detected across the world. Thus, initial qualitative and quantitative data arising from this serendipitous global quasi-experimental perturbation highlights the dual role that humans play in threatening and protecting species and ecosystems. Pathways to favorably tilt this delicate balance include reducing impacts and increasing conservation effectiveness.

The global network of ports supporting high seas fishing

Fisheries in waters beyond national jurisdiction ("high seas") are difficult to monitor and manage. Their regulation for sustainability requires critical information on how fishing effort is distributed across fishing and landing areas, including possible border effects at the exclusive economic zone (EEZ) limits. We infer the global network linking harbors supporting fishing vessels to fishing areas in high seas from automatic identification system tracking data in 2014, observing a modular structure, with vessels departing from a given harbor fishing mostly in a single province. The top 16% of these harbors support 84% of fishing effort in high seas, with harbors in low- and middle-income countries ranked among the top supporters. Fishing effort concentrates along narrow strips attached to the boundaries of EEZs with productive fisheries, identifying a free-riding behavior that jeopardizes efforts by nations to sustainably manage their fisheries, perpetuating the tragedy of the commons affecting global fishery resources.

Risk of Secondary Infection Waves of COVID-19 in an Insular Region: The Case of the Balearic Islands, Spain

The Spanish government declared the lockdown on March 14th, 2020 to tackle the fast-spreading of COVID-19. As a consequence, the Balearic Islands remained almost fully isolated due to the closing of airports and ports, these isolation measures and the home-based confinement have led to a low prevalence of COVID-19 in this region. We propose a compartmental model for the spread of COVID-19 including five compartments (Susceptible, Exposed, Presymptomatic Infective, Diseased, and Recovered), and the mobility between municipalities. The model parameters are calibrated with the temporal series of confirmed cases provided by the Spanish Ministry of Health. After calibration, the proposed model captures the trend of the official confirmed cases before and after the lockdown. We show that the estimated number of cases depends strongly on the initial dates of the local outbreak onset and the number of imported cases before the lockdown. Our estimations indicate that the population has not reached the level of herd immunization necessary to prevent future outbreaks. While the low prevalence, in comparison to mainland Spain, has prevented the saturation of the health system, this low prevalence translates into low immunization rates, therefore facilitating the propagation of new outbreaks that could lead to secondary waves of COVID-19 in the region. These findings warn about scenarios regarding after-lockdown-policies and the risk of second outbreaks, emphasize the need for widespread testing, and could potentially be extrapolated to other insular and continental regions.

Robustness to extinction and plasticity derived from mutualistic bipartite ecological networks

Understanding the response of ecological networks to perturbations and disruptive events is needed to anticipate the biodiversity loss and extinction cascades. Here, we study how network plasticity reshapes the topology of mutualistic networks in response to species loss. We analyze more than one hundred empirical mutualistic networks and considered random and targeted removal as mechanisms of species extinction. Network plasticity is modeled as either random rewiring, as the most parsimonious approach, or resource affinity-driven rewiring, as a proxy for encoding the phylogenetic similarity and functional redundancy among species. This redundancy should be positively correlated with the robustness of an ecosystem, as functions can be taken by other species once one of them is extinct. We show that effective modularity, i.e. the ability of an ecosystem to adapt or restructure, increases with increasing numbers of extinctions, and with decreasing the replacement probability. Importantly, modularity is mostly affected by the extinction rather than by rewiring mechanisms. These changes in community structure are reflected in the robustness and stability due to their positive correlation with modularity. Resource affinity-driven rewiring offers an increase of modularity, robustness, and stability which could be an evolutionary favored mechanism to prevent a cascade of co-extinctions.

Incubation periods impact the spatial predictability of cholera and Ebola outbreaks in Sierra Leone

Forecasting the spatiotemporal spread of infectious diseases during an outbreak is an important component of epidemic response. However, it remains challenging both methodologically and with respect to data requirements, as disease spread is influenced by numerous factors, including the pathogen's underlying transmission parameters and epidemiological dynamics, social networks and population connectivity, and environmental conditions. Here, using data from Sierra Leone, we analyze the spatiotemporal dynamics of recent cholera and Ebola outbreaks and compare and contrast the spread of these two pathogens in the same population. We develop a simulation model of the spatial spread of an epidemic in order to examine the impact of a pathogen's incubation period on the dynamics of spread and the predictability of outbreaks. We find that differences in the incubation period alone can determine the limits of predictability for diseases with different natural history, both empirically and in our simulations. Our results show that diseases with longer incubation periods, such as Ebola, where infected individuals can travel farther before becoming infectious, result in more long-distance sparking events and less predictable disease trajectories, as compared to the more predictable wave-like spread of diseases with shorter incubation periods, such as cholera.

Scaling of species distribution explains the vast potential marine prokaryote diversity

Global ocean expeditions have provided minimum estimates of ocean’s prokaryote diversity, supported by apparent asymptotes in the number of prokaryotes with sampling effort, of about 40,000 species, representing <1% of the species cataloged in the Earth Microbiome Project, despite being the largest habitat in the biosphere. Here we demonstrate that the abundance of prokaryote OTUs follows a scaling that can be represented by a power-law distribution, and as a consequence, we demonstrate, mathematically and through simulations, that the asymptote of rarefaction curves is an apparent one, which is only reached with sample sizes approaching the entire ecosystem. We experimentally confirm these findings using exhaustive repeated sampling of a prokaryote community in the Red Sea and the exploration of global assessments of prokaryote diversity in the ocean. Our findings indicate that, far from having achieved a thorough sampling of prokaryote species abundance in the ocean, global expeditions provide just a start for this quest as the richness in the global ocean is much larger than estimated.

Flexible model of network embedding

There has lately been increased interest in describing complex systems not merely as single networks but rather as collections of networks that are coupled to one another. We introduce an analytically tractable model that enables one to connect two layers in a multilayer network by controlling the locality of coupling. In particular we introduce a tractable model for embedding one network (A) into another (B), focusing on the case where network A has many more nodes than network B. In our model, nodes in network A are assigned, or embedded, to the nodes in network B using an assignment rule where the extent of node localization is controlled by a single parameter. We start by mapping an unassigned "source" node in network A to a randomly chosen "target" node in network B. We then assign the neighbors of the source node to the neighborhood of the target node using a random walk starting at the target node and with a per-step stopping probability q. By varying the parameter q, we are able to produce a range of embeddings from local (q = 1) to global (q → 0). The simplicity of the model allows us to calculate key quantities, making it a useful starting point for more realistic models.

Election Forensics: Quantitative methods for electoral fraud detection

The last decade has witnessed an explosion on the computational power and a parallel increase of the access to large sets of data - the so called Big Data paradigm - which is enabling to develop brand new quantitative strategies underpinning description, understanding and control of complex scenarios. One interesting area of application concerns fraud detection from online data, and more particularly extracting meaningful information from massive digital fingerprints of electoral activity to detect, a posteriori, evidence of fraudulent behavior. In this short article we discuss a few quantitative methodologies that have emerged in recent years on this respect, which altogether form the nascent interdisciplinary field of election forensics. Aiming to foster discussion and raise awareness on this interdisciplinary area, we hereby enumerate a few of the most relevant approaches and methods.

Joint effect of ageing and multilayer structure prevents ordering in the voter model

The voter model rules are simple, with agents copying the state of a random neighbor, but they lead to non-trivial dynamics. Besides opinion processes, the model has also applications for catalysis and species competition. Inspired by the temporal inhomogeneities found in human interactions, one can introduce ageing in the agents: the probability to update their state decreases with the time elapsed since the last change. This modified dynamics induces an approach to consensus via coarsening in single-layer complex networks. In this work, we investigate how a multilayer structure affects the dynamics of the ageing voter model. The system is studied as a function of the fraction of nodes sharing states across layers (multiplexity parameter q). We find that the dynamics of the system suffers a notable change at an intermediate value q*. Above it, the voter model always orders to an absorbing configuration. While below it a fraction of the realizations falls into dynamical traps associated to a spontaneous symmetry breaking. In this latter case, the majority opinion in the different layers takes opposite signs and the arrival at the absorbing state is indefinitely delayed due to ageing.

Influence of a patient transfer network of US inpatient facilities on the incidence of nosocomial infections

Antibiotic-resistant bacterial infections are a substantial source of morbidity and mortality and have a common reservoir in inpatient settings. Transferring patients between facilities could be a mechanism for the spread of these infections. We wanted to assess whether a network of hospitals, linked by inpatient transfers, contributes to the spread of nosocomial infections and investigate how network structure may be leveraged to design efficient surveillance systems. We construct a network defined by the transfer of Medicare patients across US inpatient facilities using a 100% sample of inpatient discharge claims from 2006-2007. We show the association between network structure and C. difficile incidence, with a 1% increase in a facility's C. difficile incidence being associated with a 0.53% increase in C. difficile incidence of neighboring facilities. Finally, we used network science methods to determine the facilities to monitor to maximize surveillance efficiency. An optimal surveillance strategy for selecting "sensor" hospitals, based on their network position, detects 80% of the C. difficile infections using only 2% of hospitals as sensors. Selecting a small fraction of facilities as "sensors" could be a cost-effective mechanism to monitor emerging nosocomial infections.

The Ecology of Human Mobility

Mobile phones and other geolocated devices have produced unprecedented volumes of data on human movement. Analysis of pooled individual human trajectories using big data approaches has revealed a wealth of emergent features that have ecological parallels in animals across a diverse array of phenomena including commuting, epidemics, the spread of innovations and culture, and collective behaviour. Movement ecology, which explores how animals cope with and optimize variability in resources, has the potential to provide a theoretical framework to aid an understanding of human mobility and its impacts on ecosystems. In turn, big data on human movement can be explored in the context of animal movement ecology to provide solutions for urgent conservation problems and management challenges.

Is the voter model a model for voters?

The voter model has been studied extensively as a paradigmatic opinion dynamics model. However, its ability to model real opinion dynamics has not been addressed. We introduce a noisy voter model (accounting for social influence) with recurrent mobility of agents (as a proxy for social context), where the spatial and population diversity are taken as inputs to the model. We show that the dynamics can be described as a noisy diffusive process that contains the proper anisotropic coupling topology given by population and mobility heterogeneity. The model captures statistical features of U.S. presidential elections as the stationary vote-share fluctuations across counties and the long-range spatial correlations that decay logarithmically with the distance. Furthermore, it recovers the behavior of these properties when the geographical space is coarse grained at different scales-from the county level through congressional districts, and up to states. Finally, we analyze the role of the mobility range and the randomness in decision making, which are consistent with the empirical observations.

Dynamics of link states in complex networks: the case of a majority rule

Motivated by the idea that some characteristics are specific to the relations between individuals and not to the individuals themselves, we study a prototype model for the dynamics of the states of the links in a fixed network of interacting units. Each link in the network can be in one of two equivalent states. A majority link-dynamics rule is implemented, so that in each dynamical step the state of a randomly chosen link is updated to the state of the majority of neighboring links. Nodes can be characterized by a link heterogeneity index, giving a measure of the likelihood of a node to have a link in one of the two states. We consider this link-dynamics model in fully connected networks, square lattices, and Erdös-Renyi random networks. In each case we find and characterize a number of nontrivial asymptotic configurations, as well as some of the mechanisms leading to them and the time evolution of the link heterogeneity index distribution. For a fully connected network and random networks there is a broad distribution of possible asymptotic configurations. Most asymptotic configurations that result from link dynamics have no counterpart under traditional node dynamics in the same topologies.

Update rules and interevent time distributions: slow ordering versus no ordering in the voter model

We introduce a general methodology of update rules accounting for arbitrary interevent time (IET) distributions in simulations of interacting agents. We consider in particular update rules that depend on the state of the agent, so that the update becomes part of the dynamical model. As an illustration we consider the voter model in fully connected, random, and scale-free networks with an activation probability inversely proportional to the time since the last action, where an action can be an update attempt (an exogenous update) or a change of state (an endogenous update). We find that in the thermodynamic limit, at variance with standard updates and the exogenous update, the system orders slowly for the endogenous update. The approach to the absorbing state is characterized by a power-law decay of the density of interfaces, observing that the mean time to reach the absorbing state might be not well defined. The IET distributions resulting from both update schemes show power-law tails.

The effect of completeness of medical records on the determination of appropriateness of hospital days

Although the Appropriateness Evaluation Protocol (AEP) has been widely used during the past decade, several methodological concerns have not yet been properly resolved, including the possible influence of low completeness of the medical records on the results yielded by the AEP in retrospective studies. We examined medical records for a random sample of 345 patient-days with the AEP, according to a protocol that included several variables potentially related to inappropriateness. The completeness of physician and nursing notes was also assessed. The proportion of inappropriate days of hospitalization was 36.2%. In the crude analysis, significantly higher proportions of inappropriateness were found for lower values of completeness. Factors related to the inappropriateness of stay were summer season, elective admission, no previous admissions, surgical and medical-surgical service in charge, and the day sampled falling within the last third of the hospital stay. Adjustment for the completeness level of medical records did not substantially change the strength of the association between these factors and the inappropriateness of hospital stay. Completeness level itself did not show any significant association with the proportion of inappropriate days in the adjusted analysis.