A synoptic review of plant disease epidemics and outbreaks was made using two complementary approaches. The first approach involved reviewing scientific literature published in 2021, in which quantitative data related to new plant disease epidemics or outbreaks were obtained via surveys or similar methodologies. The second approach involved retrieving new records added in 2021 to the CABI Distribution Database, which contains over a million global geographic records of organisms from over 50,000 species. The literature review retrieved 186 articles, describing studies in 62 categories (pathogen species/species complexes) across >40 host species on 6 continents. Pathogen species with >5 articles were: Bursaphelenchus xylophilus, Candidatus Liberibacter asiaticus, cassava mosaic viruses, citrus tristeza virus, Erwinia amylovora, Fusarium spp. complexes, Fusarium oxysporum f. sp. cubense, Magnaporthe oryzae, maize lethal necrosis co-infecting viruses, Meloidogyne spp. complexes, Pseudomonas syringae pvs, Puccinia striiformis f. sp. tritici, Xylella fastidiosa, and Zymoseptoria tritici. Automated searches of the CABI Distribution Database identified 617 distribution records new in 2021 of 283 plant pathogens. A further manual review of these records confirmed 15 pathogens reported in new locations: apple hammerhead viroid, apple rubbery wood viruses, Aphelenchoides besseyi, Biscogniauxia mediterranea, Ca. Liberibacter asiaticus, citrus tristeza virus, Colletotrichum siamense, cucurbit chlorotic yellows virus, Erwinia rhapontici, Erysiphe corylacearum, Fusarium oxysporum f. sp. cubense Tropical Race 4, Globodera rostochiensis, Nothophoma quercina, potato spindle tuber viroid, and tomato brown rugose fruit virus. Of these, 4 pathogens had at least 25% of all records reported in 2021. We assessed two of these pathogens – tomato brown rugose fruit virus and cucurbit chlorotic yellows virus – to be actively emerging in/spreading to new locations. Although three important pathogens – Ca. Liberibacter asiaticus, citrus tristeza virus and Fusarium oxysporum f. sp. cubense – were represented in the results of both our literature review and our interrogation of the CABI Distribution Database, in general our dual approaches revealed distinct sets of plant disease outbreaks and new records, with little overlap.

Epidemics are the most common natural phenomena that have occurred throughout the entire history of human society. Depending on the type of disease and the development of the collective immunity that society had acquired by then, the consequences of epidemics were usually very severe. Precisely because of this, the aim of the paper is a scientific description of the way in which the prescribed preventive measures should be applied from the epidemiological, security, economic, legal and other aspects, so that the society, through the mechanisms of the state, can defend and rehabilitate the consequences of an epidemic of an infectious disease. Eliminating the epidemic's impacts is a very difficult issue. In particular, there is an infectious illness epidemic that is spreading uncontrolled throughout society on the one hand. In order to introduce a quarantine that restricts the epidemic's progress and, if the quarantine lasts long enough, to end the epidemic, contact between members of the social group must be broken. On the other side, the cessation of communication between members of a social group also signifies the cessation of all facets of life in that society, including economic ties, education, growth of culture, scientific research, etc.

With the increasing pace of global warming, it is important to understand the role of meteorological factors in influenza virus (IV) epidemics. In this study, we investigated the impact of temperature, UV index, humidity, wind speed, atmospheric pressure, and precipitation on IV activity in Norway, Sweden, Finland, Estonia, Latvia and Lithuania during 2010-2018. Both correlation and machine learning analyses revealed that low temperature and low UV indexes were the most predictive meteorological factors for IV epidemics in the Northern European countries. Our in vitro experiments confirmed that low temperature and UV radiation preserved IV infectivity. Associations between these meteorological factors and IV activity could improve surveillance and promote development of accurate predictive models for future influenza outbreaks in Northern Europe.

Arboviruses represents a real public health problem globally and in the Central African subregion in particular that represents a high risk zone for the emergence and re-emergence of arboviruses outbreaks. Furthermore, an updated review on the current arboviruses burden and associated mosquito vectors is lacking for this region. To contribute in filling this knowledge gap, the current study was designed with following objectives: (i) to systematically review data on the occurrence and distribution of arboviruses and mosquito fauna and (ii) to identify potential spillover mosquito species in Central African region in the last 30 years. Web search enabled the documentation of 2454 articles from different online databases. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and The Quality of Reporting of Meta-analyses (QUORUM) steps for a systematic review enabled the selection of 164 articles that fulfilled our selection criteria. Of the six arboviruses (Dengue Virus (DENV), Chikungunya Virus (CHIKV), Yellow Fever Virus (YFV), Zika Virus (ZIKV), Rift Valley Fever Virus (RVFV), and West Nile Virus (WNV)) of public health concern studied, the most frequently reported were Chikungunya and Dengue. The entomological records showed >248 species of mosquitoes and regrouped under 15 genera with Anopheles (n= 100 species), Culex (n= 56 species) and Aedes (n=52 species) having high species diversity. Three genera were rarely represented with only one species and included: Orthopodomyia, Lutzia, and Verrallina, but individuals of the genera Toxorhinchites and Finlayas were not identified upto the species level. We found that two Aedes species (Ae. aegypti and Ae. albopictus) colonised the same microhabitat and were involved in major epidemics of the six medically important arboviruses and other less frequently identified mosquito-genera consisted of competent species and were associated with outbreaks of medical and zoonotic arboviruses. The present study reveals high species richness of competent mosquito-vectors that could lead to the spillover of medically important arboviruses in the region. Although epidemiological studies were found, they were not regularly documented and this also applies to vector competence and transmission studies. Future studies will consider unpublished information in dissertations, technical reports from different countries to enable it more consistent. A regional project entitled: Ecology of Arboviruses (EcoVir) is underway in three countries (Gabon, Benin and Cote d’Ivoire) to generate a more comprehensive epidemiological and entomological data on this topic.

Most popular statistical models in epidemic evolution focus on the dynamics of average relevant quantities and overlooks the role of small fluctuations on the model parameters. Models for Covid-19 are no exception. In this paper we show that the role of time-correlated fluctuations, far from being negligible, can in fact determine the spreading of an epidemic and, most importantly, the resurgence of the exponential diffusion in the presence of time-limited episodes in promiscuity behaviours.

Prior to lockdown the spread of COVID-19 in UK is found to be exponential, with an exponent α=0.207 In case of COVID-19 this spreading patterns is quantitatively better described with mobility-driven SIR-SEIR model [2] rather than the homogenous mixing models Lockdown has dramatically slowed down the spread of COVID-19 in UK, and even more significantly has changed the growth in the total number of infected from exponential to quadratic. This significant change is due a transition from a mobility-driven epidemic spreading to a spatial epidemic which is dominated by slow growth of spatially isolated clusters of infected population. Our results strongly indicated that, to avoid a return to exponential growth of COVID-19 (also known as “second wave”) mobility restrictions should not be prematurely lifted. Instead mobility should be kept restricted while new measures, such as wearing mask and contact tracing, get implemented in order to allow a safe exit from lockdown.

Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3'UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3'UTR architecture among different CHIKV lineages.

Emerging infectious diseases (EIDs) continue to be a problem all across the world, but in certain areas the threat is greater than in others. The detection of new diseases will aid in the focus of surveillance efforts. Specifically, identifying a "patient zero" is critical step to help limit further transmission. In fact, several factors have been found to contribute to emerging infectious diseases emergence and transmission. Antigenic drift is an important factor that affects vaccine effectiveness and it is important for scientists and healthcare providers alike to understand how this process works in order to ensure that people receive effective vaccinations against infectious diseases. However, recent advances in biotechnology, immunology and artificial intelligence have enabled us to make progress in diagnosis, treatment, prevention and control of infectious diseases. The fight against infectious diseases will always be ongoing, but the advancement of bioscience offers a promising outlook for the near future. In the last two decades, several high impact zoonotic disease outbreaks have been linked to bat-borne viruses. These include SARS coronavirus, Hendra virus and Nipah virus. In addition, it has been suspected that ebolaviruses and MERS coronavirus are also linked to bats. It is being increasingly accepted that bats are potential reservoirs of a large number of known and unknown viruses, many of which could spillover into animal and human populations. In this article, we discuss the potential risk factors that contribute in emerging infectious diseases. Also, we discuss the management of disease prevention and control.

Most studies modelling population mobility and the spread of infectious diseases, particularly using meta-population-multi-patched models, tend to focus on theoretical properties and numerical simulations of such models. There is relatively scanty literature published on fit, inference and uncertainty quantification on epidemic models with population mobility. In this research, we have used three estimation techniques to solve an inverse problem and quantify its uncertainty on a human mobility-based multi-patched epidemic model, using mobile phone sensing data and COVID-19 confirmed positive cases in Hermosillo, Mexico. First, we have utilized a Brownian bridge model using mobile phone GPS data to estimate residence and mobility parameters of the epidemic model. In the second step, we have estimated the optimal model epidemiological parameters by deterministically inverting the model using a Darwinian inspired evolutionary algorithm (EA) known as the genetic algorithm (GA). The third part of the analysis involves performing inference and uncertainty quantification on the epidemic model using two Bayesian Monte Carlo sampling methods: t-walk and Hamiltonian Monte Carlo (HMC). The results show that the estimated model parameters and incidence adequately fit the observed daily COVID-19 incidence in Hermosillo. Moreover, the estimated parameters from HMC result into large credible intervals, improving their coverage for the observed and predicted daily incidences. We also observe improved predictions when using multi-patch model with mobility against the single-patch model.

The dynamical equations of the susceptible-infected-recovered/removed (SIR) epidemics model play an important role to predict and/or analyze the temporal evolution of epidemics outbreaks. Crucial input quantities are the time-dependent infection ($a(t)$) and recovery ($\mu (t)$) rates regulating the transitions between the compartments $S\to I$ and $I\to R$, respectively. Accurate analytical approximations for the temporal dependence of the rate of new infections $\dot{J}(t)=a(t)S(t)I(t)$ and the corresponding cumulative fraction of new infections $J(t)=J(t_0)+\int_{t_0}^tdx\dot{J}(x)$ are available in the literature for either stationary infection and recovery rates and for a stationary value of the ratio $k(t)=\mu (t)/a(t)$. Here a new and original accurate analytical approximation is derived for general, arbitrary and different temporal dependencies of the infection and recovery rates which is valid for not too late times after the start of the infection when the cumulative fraction $J(t)\ll 1$ is much less than unity. The comparison of the analytical approximation with the exact numerical solution of the SIR-equations for different illustrative examples proves the accuracy of the analytical approach.

The ABCDEFG Protocol provides an evolving tool for imposing structure on the flow of Covid infection information obtained from community testing, collective policy and individual compliance. ABCDEFG Protocol could not assume soundness, invariance, symmetry and completeness of the available information and relied on signaling game theory to design solutions that could evolve with the variable narratives, theories, individual utilities and pathogen variants. Thus, ABCDEFG Protocol suggests a novel and a very flexible pool-testing and badging protocol in the context of controlling contagious epidemics and tackling the far-reaching associated challenges, including understanding and evaluating individual and collective risks of returning prior infected individuals to normal society and other economic and social arrangements and interventions to protect against disease. AbCDEFG Proto uses both control theoretic and game theoretic mathematical models that may be centralized (an optimizing policy maker mandates behavior based on estimated models) or decentralized (a strategizing individual selects their behavior based on available asymmetric information). ABCDEFG protocol demonstrates how society can continue to carry out plausible economic activities in addition to controlling the prevalence of a contagious disease by keeping the number of infected people below a desired limit without compromising an individuals' privacy despite the presence of deception and selfishness among people, and limitations of available resources. Different types of badges would come with different restrictions. Badges would be reissued periodically by third-party testing centers via suitably frequent pool testing of samples of the participants. The size of the pools, frequency of tests, and allowable activities for people with a given type of badge would depend on the available resources, the prevalence of the disease, and the efficacy of the equipment used in the tests.

The sudden onset of the Covid-19 pandemic disrupted the modern multi-national interconnected society and led the countries and societies to enforce unprecedented restrictions on movement. Among myriad containment measures, the policy of trace and quarantine found universal adoption among countries; the swift adoption of the policy was soon met with widespread criticism and opposition activists who questioned the utility and the risk associated with such a large scale collection of data and infringement on the movement of individuals. Consequently, one often tends to be either pro- or anti-trace and quarantine; the ensuing polarizing and politicized left little room for nuance. In this work, we undertake a methodology study to understand the nuances of the impact of different implementations of trace and quarantine. To this end, we design a user-friendly and intuitive tool that can be employed by experts to model the disease dynamics and societal structure. We focus on the study of the cost of policy with respect to quarantine degree, which captures the distance between the person required to quarantine after a person is detected to be infected. Our study results in a surprising conclusion: the cost is not necessarily monotone with respect to the degree of quarantine. Our analysis indicates that governments must curb the urge to adopt simplistic policy and the optimal policy of trace and quarantine for a country strongly depends on its societal structure and disease dynamics.

Viruses have established symbiotic relationships with almost every other living organism on Earth and at all levels of biological organisation, from other viruses up to entire ecosystems. In most cases, peacefully coexisting with their hosts, but in most relevant cases, parasitising them and inducing diseases. Viruses are playing an essential role in shaping the eco-evolutionary dynamics of their hosts, and have been also involved in some of the major evolutionary innovations either by working as vectors of genetic information or by being themselves coopted by the host into their genomes. Viruses can be studied at different levels of biological organisation, from the molecular mechanisms of genome replication, gene expression and encapsidation, to global pandemics. All these levels are different and yet connected through the presence of threshold conditions allowing for the formation of a capsid, the loss of genetic information or epidemic spreading. These thresholds, as it occurs with temperatures separating phases in a liquid, define sharp qualitative types of behaviour. These {\em phase transitions} are very well known in Physics. They have been studied by means of simple, but powerful models able to capture their essential properties, allowing to understand them. Can the physics of phase transitions be an inspiration for our understanding of viral dynamics at different scales? Here we review well-known examples of transition phenomena in virology and their simplest mathematical modelling approaches. We suggest that the advantages of abstract, simplified pictures used in Physics are also the key to properly understand the origins and evolution of complexity in viruses. By means of several examples, we explore this multilevel landscape and how minimal models provide deep insights into a diverse array of problems. The relevance of these transitions in connecting dynamical patterns across levels and their evolutionary and clinical implications are outlined.

The semi-logarithmic plot of the cumulative number of cases of epidemics resembles the response of a first-order systems for a step load. This similarity was utilized to develop a first order model that can be used for extracting information about the dynamics of infectious disease epidemics. The developed model was validated using COVID-19 data of China. It was also heuristically fitted to other 13 countries. Obtained results indicated that the model can reliably forecasts the number of infected person, epidemic growth speed towards steady-state condition (process time constant, T), and time to reach steady-state condition (4T). The developed model will help public health authorities in developing more effective control strategies of epidemics.

It is known for decades that viruses from the Coronoviridae family can adapt to human-to-human transmission. In 2020, SARS-CoV-2 caused a global pandemic of unprecedented scale imposing the loss of millions of human lives and being at the heart of a global economic crisis. Thus, we overviewed key research advances generated from the identification of the etiological agent to a better understanding of its origin, evolution and factors underlying global spread. Furthermore, we analyze the scientific productivity using the PubMed database. We found that the total number of publications increased more than 8% in 2020 when compared with 2019 or the average publications per year in the previous quinquennial. Remarkably, 86,638 publications related with COVID-19 and SARS-CoV-2 were published in 2020. Furthermore, there was also an increase in 2020 of publications in other major infectious diseases, such as AIDS, tuberculosis, or malaria. This success is likely the result from the vigorous, international, collaborative, and multidisciplinary response by the research community. During 2020 it was demonstrated, that with adequate support, it is possible to boost the rate of scientific progress in infectious diseases. Sustained investment in science will be key to address existing and future pandemics as the human population increases.

The coronavirus (COVID-19) pandemic was particularly invasive in Italy during the period between March and late April 2020 then decreased in both in the number of infections and in the seriousness of the illness throughout the summer of 2020. In this discussion, we measure the severity of the disease by the ratio of Intensive Care Units (ICU) spaces occupied by COVID-19 patients and the number of Active Cases (AC) each month from April to October 2020. We also use the ratio of the number of Deaths (D) to the number of Active Cases. What clearly emerges, from rigorous statistical analysis, is a progressive decrease in both ratios until August, indicating progressive mitigation of the disease. This is particularly evident when comparing March-April with July-August; during the summer period the two ratios became roughly 18 times lower. We test such sharp decreases against possible bias in counting active cases and we confirm their statistical significance. We then interpret such evidence in terms of the well-known seasonality of the human immune system and the virus-inactivating effect of stronger UV rays in the summer. Both ratios, however, increased again in October as ICU/AC began to increase in September 2020. These ratios and the exponential growth of infections in October indicate that the virus - if not contained by strict measures - will lead to unsustainable challenges for the Italian health system in the winter of 2020-2021 .

Our aim is to provide an insight of the procedures and the dynamics that lead the spread of contagious diseases through populations. Our simulation tool can increase our understanding on the spatial parameters which affect the diffusion of a virus. SIR models are based on the hypothesis that populations are “well mixed”. Our model constitutes an attempt to focus on the effects of the specific distribution of the initially infected individuals through the population and provide insights, considering the stochasticity of the transmission process. For this purpose, we represent the population using a square lattice of nodes. Each node represents an individual that may or may not carry the virus. Nodes that carry the virus can only transfer it to susceptible neighboring nodes. This important revision of the common SIR model provides a very realistic property: the same number of initially infected individuals can lead to multiple paths, depending on their initial distribution in the lattice. This property creates better predictions and probable scenarios to construct a probability function and appropriate confidence intervals. Finally, this structure permits realistic visualizations of the results to understand the procedure of contagion and spread of a disease and the effects of any measures applied.

COVID-19 severity is heterogeneously distributed over age strata, but current mitigation strategies are homogeneously applied to all population. Social-distancing and stay-home are effective conservative approaches but lack economic sustainability on long term. Conversely, herd-immunity is a nonrestrictive strategy which can cost remarkable number of human lives and can melt the healthcare system down. Here I propose an Age Adaptive Social Distancing (AASD) engineering strategy to mitigate COVID-19 outbreak. AASD is based on the scientific evidence that the fatality rate grows nonlinearly with age, hence also the containing strategy should adapt nonlinearly. Essentially, AASD suggests that ‘silent spreaders’ (age 0-39) should avoid/minimize direct and indirect contacts with individuals in ‘dangerous zone’ (age 40+). The rationale is: 0-19 should follow parents strategy, healthy 20-39 (low fatality rate) might conduct screened life under active surveillance, to sustain economy and acquire rational immunity; 40-59 should respect social distancing (waiting a therapy); 60+ should stay at home (waiting a vaccine). This might save human lives, reduce healthcare demand and improve economic sustainability. The final take-home message is that future studies should design precision and personalized strategies for specific contagious diseases that integrate different social constrains, active surveillance and contact tracing.

Climate change is a global phenomenon that exerts significant impacts on ecosystems. Estuaries, as critical aquatic habitats, are susceptible to these changes; however, our comprehension of their specific responses to climate change remains limited. Beyond temperature rise and alterations in precipitation patterns, climate change induces indirect effects, influencing a multitude of biotic and abiotic variables within aquatic ecosystems. In this study, we assess seagrass health as an indicator of estuary well-being in three estuaries located in northern to central California, USA. Our investigation focuses on the marine angiosperm Zostera marina (commonly known as eelgrass) and its associated parasite, Labyrinthula zosterae. Z. marina, a temperate marine plant, faces the threat of eelgrass wasting disease (EWD) caused by the protist L. zosterae. Notably, this pathogen demonstrates sensitivity to warming ocean temperatures, underscoring the imperative to comprehend its impacts on host health amidst climate change. Our study assessed EWD prevalence with relation to spatial and temporal patterns, the relationship, if any, between disease prevalence and eelgrass percent cover, the spatial patterns, if any, of eelgrass percent cover, and what climatic variables were most strongly correlated with EWD and eelgrass percent cover.

There are potentially promising mitigation activities for epidemic and pandemic scenarios that are not currently the subject of significant research effort. Large epidemics and pandemics pose risks that are important to mitigate, even if the likelihood of the events is low and uncertain. While some efforts are the subject of extensive funding and consideration, other approaches are neglected. Here, we consider such neglected interventions which could significantly reduce the impact of such an epidemic or large-scale pandemic. These are identified via a narrative literature review of extant literature reviews and overviews of mitigations in epidemic and pandemic situations, followed by consideration of the economic value of information of further study of heretofore neglected interventions and approaches.Based on that analysis, we considered several classes of mitigations, and conducted more exploratory reviews of each. Those discussed include mitigations for (1) reducing transmission, such as personal protective equipment and encouraging improved hygiene, (2) reducing exposure by changing norms and targeted changes for high-risk or critical professions and activities, (3) reducing impact for those infected, and (4) increasing large scale resilience using disaster and infrastructure continuity planning.Some proposed mitigations are found to be of low marginal value. Other mitigations are likely to be valuable, but the concepts or applications are underdeveloped. In those cases, further research, resources, or preparation are valuable for mitigating both routine and extreme disease outbreak events. Still more areas of research are identified as having uncertain value based on specific but resolvable uncertainties. In both of the latter cases, there is no guarantee that mitigations identified as worthy of further consideration will be valuable, but the argument for further research is clear.

At the end of 2019, while the world was being hit by the COVID-19 virus and, consequently, was living a global health crisis, many other pandemics were putting humankind in danger. The role of social media is of paramount importance in these kinds of contexts since they help health systems to cope with emergencies by contributing to conducting some activities such as the identification of public concerns, the detection of infections’ symptoms, and the traceability of the virus diffusion. In this paper, we have analyzed comments on events related to cholera, ebola, HIV/AIDS, influenza, malaria, Spanish influenza, swine flu, tuberculosis, typhus, yellow fever, and zika, collecting 369,472 tweets from the 3rd of March to the 15th of September, 2022. Our analysis has started with the collection of comments composed of unstructured texts on which we have applied natural language processing solutions. Afterward, we have employed topic modelling and sentiment analysis techniques to obtain a collection of people’s concerns and attitudes toward these pandemics. According to our findings, people's discussions were mostly about malaria, influenza, and tuberculosis and the focus was on the diseases themselves. As regards emotions, the most popular were fear, trust, and disgust where trust is mainly regarding HIV/AIDS tweets.