Modelling the Effect of the Interaction between Vaccination and Nonpharmaceutical Measures on COVID-19 Incidence

Since December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly from Wuhan (China) across the globe, affecting more than 200 countries by mid-2021, with over 190M reported cases and around 4M fatalities. During the first year of the pandemic, affected countries implemented a variety of nonpharmaceutical interventions to control virus transmission. In December 2020, countries started administering several authorised vaccines under a limited supply scenario. In this context, the aim of this study was to develop a SEIR-type continuous-time deterministic disease model, to determine the impact of interaction between different vaccination scenarios and levels of protection measures on disease incidence. For this, the model incorporates (i) a protection measure including low (self-protection), medium (mobility limitation), high (closure of indoor facilities), and very high (lockdown) protection levels, (ii) quarantine for confirmed cases, and (iii) vaccination rate and efficacy of four types of vaccines (Pfizer, Moderna, Astra Zeneca, and Janssen). The model was verified and evaluated using the response timeline and vaccination strategies and rates in the Basque Country (N. Spain). Once the model performance was validated, different initial phase (when 30% of the population is vaccinated) vaccination scenarios were simulated, including (i) a realistic vaccine limited supply scenario and (ii) four potential full vaccine supply scenarios where a unique vaccine type is administered. Significant differences in disease prevalence and cumulative mortality were found between vaccination scenarios for low and medium-level protection measures. For high-level protection measures, any vaccine scenario is effective at limiting the virus transmission and disease mortality. The results obtained here may vary in further studies since there may be some unpredictable factors/covariates. With this in mind, the model here could be easily applied to other regions or countries, modifying the strategies implemented and initial conditions

Does expansion of the introduced Manila clam Ruditapes philippinarum cause competitive displacement of the European native clam Ruditapes decussatus?

In several estuaries or lagoons of Europe the introduced Manila clam Ruditapes philippinarum has supplanted the native grooved carpet shell clam Ruditapes decussatus by occupying almost entirely its ecological niche and relegating it to restricted areas. However, it is not clear if the nonindigenous clam is the one directly responsible for these predominance patterns. Within this context, the main goal of the present study was to analyze the competitive interaction between the nonindigenous Manila clam and the native carpet shell clam to determine whether this interaction could impact directly growth and mortality of the native clam populations. The effect of exposure to predators on both species was also examined. For this purpose, between May 2010 and May 2011 a field experiment was conducted on an intertidal area in the Bay of Santander (N Spain) where both species coexist without an extreme predominance of the introduced species. Relative density of clam species was manipulated in a randomized block experimental design. The results obtained show that (i) the increased density of Manila clam simulating species expansion scenario does not affect growth or mortality of the native clam; and (ii) for densities of Manila clam substantially higher than observed in the field, predation plays an essential role in regulating both species populations, limiting their density increase. Moreover, Manila clam appears to be more negatively impacted by predation compared to the native clam. Overall, our results indicate that predation has a more significant effect on both populations when compared to competitive interaction

Predicting the Growth of Vibrio parahaemolyticus in Oysters under Varying Ambient Temperature

Temperature is a critical factor that influences the proliferation of pathogens in hosts. One example of this is the human pathogen Vibrio parahaemolyticus (V. parahaemolyticus) in oysters. Here, a continuous time model was developed for predicting the growth of Vibrio parahaemolyticus in oysters under varying ambient temperature. The model was fit and evaluated against data from previous experiments. Once evaluated, the V. parahaemolyticus dynamics in oysters were estimated at different post-harvest varying temperature scenarios affected by water and air temperature and different ice treatment timing. The model performed adequately under varying temperature, reflecting that (i) increasing temperature, particularly in hot summers, favors a rapid V. parahaemolyticus growth in oysters, resulting in a very high risk of gastroenteritis in humans after consumption of a serving of raw oysters, (ii) pathogen inactivation due to day/night oscillations and, more evidently, due to ice treatments, and (iii) ice treatment is much more effective, limiting the risk of illness when applied immediately onboard compared to dockside. The model resulted in being a promising tool for improving the understanding of the V. parahaemolyticus–oyster system and supporting studies on the public health impact of pathogenic V. parahaemolyticus associated with raw oyster consumption. Although robust validation of the model predictions is needed, the initial results and evaluation showed the potential of the model to be easily modified to match similar systems where the temperature is a critical factor shaping the proliferation of pathogens in hosts.This research was funded by the Basque Government (GIC21/82

Predicting coexistence and predominance patterns between the introduced Manila clam (Ruditapes philippinarum) and the European native clam (Ruditapes decussatus)

In several European estuaries, the introduced Manila clam (Ruditapes philippinarum) has become a widespread and predominating species supplanting the native carpet shell clam (Ruditapes decussatus) whereas in other estuaries such as the Bay of Santander (Gulf of Biscay) this pattern has not been detected. Using this estuary as a case study, the potential coexistence/predominance patterns between these two species were explored with the objective of providing insight into the capacity of expansion of R. philippinarum. Firstly, the Ecological Niche Factor Analysis (ENFA) was applied to determine the niches of both species, using seven contemporary environmental variables, i.e. salinity, water depth, current velocity, and sediment sand, gravel, silt and organic matter content. Secondly, ENFA-derived habitat-suitability (HS) maps were simultaneously treated, using geospatial techniques and following HS index-based criteria, to determine the potential distribution patterns. Both species models performed well according to the cross-validation evaluation method. The environmental variables that most determined the presence of both clams were depth, current velocity and salinity. ENFA factors showed that R. philippinarum habitat differs more from the mean environmental conditions over the estuary (i.e. higher marginality) and has less narrow requirements (i.e. lower specialization). R. philippinarum dominated areas, determined by relatively lower current velocities and percentages of sand, higher organic matter contents and slightly shallower depths, were very reduced (i.e. 2.0% of the bay surface) compared to coexistence (47%) and R. decussatus predominance areas (7.4%). These results suggest that HS may regulate the expansion of R. philippinarum. ENFA, together with geospatial analysis of HS index, seems to be a valuable approach to explore the expansion potential of estuarine invasive or introduced species and thus support conservation decisions regarding native species

LARVAHS: Predicting clam larval dispersal and recruitment using habitat suitability-based particle tracking model

We herein explore the potential larval dispersal and recruitment patterns of Ruditapes decussatus and Ruditapes philippinarum clams, influenced by larval behavior and hydrodynamics, by means of a particle-tracking model coupled to a hydrodynamic model. The main contribution of this study is that a habitat suitability-based (ENFA, Environmental Niche Factor Analysis) settlement–recruitment submodel was incorporated into the larval dispersal model to simulate settlement behavior and post-settlement mortality. For this purpose, a specific study was carried out in the Bay of Santander (Northern Spain), a well-mixed shallow water estuary where shellfishery of both species is carried out. The model was fed with observed winds, freshwater flows and astronomical tides to obtain predictions during the clams spawning period. Dispersion of larvae from seven spawning zones was tracked, subjected to three-dimensional advection, vertical turbulent diffusion and imposed vertical migration behavior parameterized from existing literature. Three simulation periods (Spring, Summer and Autumn) and two initial releases (spring/neap tide) were combined in six different modeling scenarios. The LARVAHS model proved to be a powerful approach to estimating recruitment success, highlighting the role of habitat suitability, larval swimming behavior, planktonic duration, season (i.e. predominating winds) and spawning ground location on recruitment success together with the effect of the tidal phase at spawning. Moreover, it has proven to be a valuable tool for determining major spawning and nursery grounds and to explore the connectivity between them, having important implications for restoration strategies and shellfisheries as well as aquaculture management

Marine infectious disease dynamics and outbreak thresholds: contact transmission, pandemic infection, and the potential role of filter feeders

Disease-causing organisms can have significant impacts on marine species and communities. However, the dynamics that underlie the emergence of disease outbreaks in marine ecosystems still lack the equivalent level of description, conceptual understanding, and modeling context routinely present in the terrestrial systems. Here, we propose a theoretical basis for modeling the transmission of marine infectious diseases (MIDs) developed from simple models of the spread of infectious disease. The models represent the dynamics of a variety of host–pathogen systems including those unique to marine systems where transmission of disease is by contact with waterborne pathogens both directly and through filter-feeding processes. Overall, the analysis of the epizootiological models focused on the most relevant processes that interact to drive the initiation and termination of epizootics. A priori, systems with multi-step disease infections (e.g., infection-death-particle release-filtration-transmission) reduced dependence on individual parameters resulting in inherently slower transmissions rates. This is demonstrably not the case; thus, these alternative transmission pathways must also considerably increase the rates of processes involved in transmission. Scavengers removing dead infected animals may inhibit disease spread in both contact-based and waterborne pathogen-based diseases. The capacity of highly infected animals, both alive and dead, to release a substantial number of infective elements into the water column, making them available to suspension feeders results in such diseases being highly infective with a very small “low-abundance refuge”. In these systems, the body burden of pathogens and the relative importance between the release and the removal rate of pathogens in the host tissue or water column becomes paramount. Two processes are of potential consequence inhibiting epizootics. First, large water volumes above the benthic susceptible populations can function as a sink for pathogens. Second, unlike contact-based disease models in which an increase in the number of susceptible individuals in the population increases the likelihood of transmission and epizootic development, large populations of filter feeders can reduce this likelihood through the overfiltration of infective particles.This investigation was funded by the NSF Evolution and Ecology of Infectious Diseases (EEID) Program Grant # OCE-1216220. We appreciate this support

Distribution patterns of the gooseneck barnacle (Pollicipes Pollicipes [GMELINn, 1789]) in the Cantabria region (N Spain): exploring different population assessment methods

The gooseneck barnacle Pollicipes pollicipes is a very valuable marine resource on the coasts of Spain and Portugal. To maintain the sustainable exploitation of this species, periodical large-scale population assessments are essential. Because of the heterogeneous distribution of these populations in aggregates, together with the difficulties associated with sampling (i.e., access to rocky reefs, wave exposure, high tides, etc.), there is a lack of studies in this regard. In light of these constraints, the coverage, biomass, and available stock of gooseneck barnacle were first estimated using a novel semiquantitative method along a 215-km long coast at 10 fishing zones and three tidal levels. This study contributed to the first assessment of the distribution variability of gooseneck barnacle in the Cantabria region (N Spain), as the first step toward a long-term monitoring goal. The proposed method is based on a general coverage (GC) estimation, by means of (1) quantitative coverage measurements on quadrats (50 cm350 cm) located along vertical transects covering the intertidal bandwidth and corrected by tidal level bandwidths, (2) semiquantitative coverage estimates in larger areas, including 5 m on either side of the quadrats along the transect. Biomass samples were collected at each sampling point by scraping the 50 cm350 cm quadrat and fresh weight of the samples was measured. This method arrives at the biomass estimates by means of a power regression model for the coverage?biomass relationship. The population distribution pattern along the coast was also explored separately, by commonly used (1) quantitative coverage estimates in quadrats with no bandwidth correction (sample coverage, SC) and (2) semiquantitative estimates, as in the proposed method (transect coverage, TC), both of which included biomass sampling. Biomass and standing stocks values obtained using GC were lower and consumed less sampling time than those obtained by TC, and particularly SC. The results suggest that the proposed method might be suitable for the assessment of P. pollicipes populations in large coastal areas, as it potentially avoids stock overestimation by detecting the spatial distribution heterogeneity and reduces the sampling time.The main Directorate of Fisheries of Cantabria (DFC) funded this work. We wish to thank DFC technicians, fishery guards and shell-fishermen for the specific support during the fieldwork, and the colleagues from DFC, who helped us in the laboratory works

The Role of Microplastics in Marine Pathogen Transmission: Retrospective Regression Analysis, Experimental Design, and Disease Modelling

Marine wildlife and aquaculture species can accumulate large amounts of marine microplastic debris (MMD) (<1 mm) carrying pathogens, thus threatening the health of marine ecosystems and posing a risk to food safety and human health. Here, we outline a theoretical three-perspective approach for studying the relationship between MMD and disease. First, we provide a framework for retrospective analysis of MMD and pathogen loads in marine animal tissues to assess the relationship between these and other environmental variables in order to decide whether a compound or pathogen should be considered an emerging substance or organism. Second, we describe an experimental design for testing the effects of a variety of microplastics on infection intensity in two model species (oysters and zebrafish). Finally, we create a theoretical susceptible–infected microplastic particle and pathogen transmission model for bivalves and fish. Overall, the experiments and models we propose will pave the way for future research designed to assess the role of MMD as a vector for marine and human pathogens. This multi-faceted approach needs to be an urgent priority of the EU Strategic Research Innovation Agenda for addressing marine disease challenges related to MMD.This work was conceived under the research framework outlined by the National Science Foundation Evolution and Ecology of Infectious Diseases (EEID) Program, grant OCE-1216220. Funding was provided by the University of the Basque Country (UPV/EHU, GIU19/059) and the Basque Government (PIBA2020-1-0028). We appreciate this support

Gamifying Physics Laboratory Work Increases Motivation and Enhances Acquisition of the Skills Required for Application of the Scientific Method

Although increasing student motivation is widely accepted to enhance learning outcomes, this relationship has scarcely been studied quantitatively. Therefore, this study aimed to address this knowledge gap by exploring the effects of gamification on students’ motivation and consequently their learning performance, regarding the proper application of the scientific method. To motivate students and enhance their acquisition of new skills, we developed a gamification framework for the laboratory sessions of first-year physics in an engineering degree. Data regarding student motivation were collected through a Likert-scale-type satisfaction questionnaire. The inter-item correlations and Cronbach’s alpha confirmed the internal consistency of the questionnaire. In addition, the learning outcome was assessed based on the students’ laboratory reports. Students participating in gamified activities were more motivated than those participating in non-gamified activities and obtained better learning results overall. Our findings suggest that gamified laboratory sessions boost students´ extrinsic motivation, and consequently inspire their intrinsic motivation and increase their learning performance. Finally, we discuss our results, with a focus on specific skills and the short- and long-term effects of gamification.This work was funded by the vice-rectorate for Innovation, Social Commitment and Cultural Action of the University of the Basque Country through SAE-HELAZ (PIE 2019-20, 83)

Differential distribution pattern of native Ruditapes decussatus and introduced Ruditapes philippinarum clam populations in the Bay of Santander

The aim of the present study is to provide a first characterization of the grooved carpet shell clam Ruditapes decussatus (native) and the Manila clam Ruditapes phillippinarum (nonindigenous) populations in the Bay of Santander in order to improve the management of these commercially exploited resources. For this purpose a field survey was carried out in different fishing areas where samples were taken on transects, following artisanal shellfisher exploitation techniques. Biometric relationships, size frequency distributions, densities and stocks were evaluated for different fishing zones. In addition, a hydrodynamic model was applied in order to understand larval transport and recruitment patterns associated to the tidal currents and water flow. Within this context, the first evaluation of the clam populations in the Bay of Santander showed: (a) that fishing activity is performed on individuals under the minimum legal size (40 mm) and in closed areas, (b) a significant differences on density by zone (c) a distribution pattern with areas where both species coexist and areas where one of them dominates, (d) R. decussatus occurs at relatively low density in stations near the culture parks and (e) a limited recruitment in the inner parts of Cubas tidal fresh for R. phillippinarum and in the southern zones for R. decussatus. Based on this study, some managing guidelines are presented mainly focused on avoiding the overfishing of the native clam R. decussatus.The work described in this paper was partially supported by the Department of Livestock, Agriculture and Fisheries from the Regional Government of Cantabria, through the Regional Fisheries and Food Administration and by the VI National Plan (2008–2011) for Research in Science & Technological Innovation of the Spanish Government (Project CGL2009-10620)