Effects of life history and ecology on virus evolutionary potential

Endogenous feline leukemia virus long terminal repeat integration site diversity is highly variable in related and unrelated domestic cats

Endogenous retroviruses (ERV) are indicators of vertebrate evolutionary history and play important roles as homeostatic regulators. ERV long terminal repeat (LTR) elements may act as cis-activating promoters or trans-activating enhancer elements modifying gene transcription distant from LTR insertion sites. We previously documented that endogenous feline leukemia virus (FeLV)-LTR copy number variation in individual cats tracks inversely with susceptibility to virulent FeLV disease. To evaluate FeLV-LTR insertion characteristics, we assessed enFeLV-LTR integration site diversity in 20 cats from three genetically distinct populations using a baited linker-mediated PCR approach. We documented 765 individual integration sites unequally represented among individuals. Only three LTR integration sites were shared among all individuals, while 412 sites were unique to a single individual. When primary fibroblast cultures were challenged with exogenous FeLV, we found significantly increased expression of both exogenous and endogenous FeLV orthologs, supporting previous findings of potential exFeLV-enFeLV interactions; however, viral challenge did not elicit transcriptional changes in genes associated with the vast majority of integration sites. This study assesses FeLV-LTR integration sites in individual animals, providing unique transposome genotypes. Further, we document substantial individual variation in LTR integration site locations, even in a highly inbred population, and provide a framework for understanding potential endogenous retroviral element position influence on host gene transcription.

Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches

Numerous pathogenic viruses are endemic in humans and cause a broad variety of diseases, but what is their potential for causing new pandemics? We show that most human pathogenic RNA viruses form multiple, cocirculating lineages with low turnover rates. These lineages appear to be largely noncompeting and occupy distinct epidemiological niches that are not regionally or seasonally defined, and their persistence appears to stem from limited outbreaks in small communities so that only a small fraction of the global susceptible population is infected at any time. However, due to globalization, interaction and competition between lineages might increase, potentially leading to increased diversification and pathogenicity. Thus, endemic viruses appear to merit global attention with respect to the prevention of future pandemics.

Many pathogenic viruses are endemic among human populations and can cause a broad variety of diseases, some potentially leading to devastating pandemics. How virus populations maintain diversity and what selective pressures drive population turnover is not thoroughly understood. We conducted a large-scale phylodynamic analysis of 27 human pathogenic RNA viruses spanning diverse life history traits, in search of unifying trends that shape virus evolution. For most virus species, we identify multiple, cocirculating lineages with low turnover rates. These lineages appear to be largely noncompeting and likely occupy semiindependent epidemiological niches that are not regionally or seasonally defined. Typically, intralineage mutational signatures are similar to interlineage signatures. The principal exception are members of the family Picornaviridae, for which mutations in capsid protein genes are primarily lineage defining. Interlineage turnover is slower than expected under a neutral model, whereas intralineage turnover is faster than the neutral expectation, further supporting the existence of independent niches. The persistence of virus lineages appears to stem from limited outbreaks within small communities, so that only a small fraction of the global susceptible population is infected at any time. As disparate communities become increasingly connected through globalization, interaction and competition between lineages might increase as well, which could result in changing selective pressures and increased diversification and/or pathogenicity. Thus, in addition to zoonotic events, ongoing surveillance of familiar, endemic viruses appears to merit global attention with respect to the prevention or mitigation of future pandemics.

Man is a "Rope" Stretched Between Virosphere and Humanoid Robots: On the Urgent Need of an Ethical Code for Ecosystem Survival

In this paper we compare the strategies applied by two successful biological components of the ecosystem, the viruses and the human beings, to interact with the environment. Viruses have had and still exert deep and vast actions on the ecosystem especially at the genome level of most of its biotic components. We discuss on the importance of the human being as contraptions maker in particular of robots, hence of machines capable of automatically carrying out complex series of actions. Beside the relevance of designing and assembling these contraptions, it is of basic importance the goal for which they are assembled and future scenarios of their possible impact on the ecosystem. We can't procrastinate the development and implementation of a highly inspired and stringent "ethical code" for human beings and humanoid robots because it will be a crucial aspect for the wellbeing of the mankind and of the entire ecosystem.

Make it clean, make it safe: A review on virus elimination via adsorption

Recently, the potential dangers of viral infection transmission through water and air have become the focus of worldwide attention, via the spread of COVID-19 pandemic. The occurrence of large-scale outbreaks of dangerous infections caused by unknown pathogens and the isolation of new pandemic strains require the development of improved methods of viruses' inactivation. Viruses are not stable self-sustaining living organisms and are rapidly inactivated on isolated surfaces. However, water resources and air can participate in the pathogens' diffusion, stabilization, and transmission. Viruses inactivation and elimination by adsorption are relevant since they can represent an effective and low-cost method to treat fluids, and hence limit the spread of pathogen agents. This review analyzed the interaction between viruses and carbon-based, oxide-based, porous materials and biological materials (e.g., sulfated polysaccharides and cyclodextrins). It will be shown that these adsorbents can play a relevant role in the viruses removal where water and air purification mostly occurring via electrostatic interactions. However, a clear systematic vision of the correlation between the surface potential and the adsorption capacity of the different filters is still lacking and should be provided to achieve a better comprehension of the global phenomenon. The rationalization of the adsorption capacity may be achieved through a proper physico-chemical characterization of new adsorbents, including molecular modeling and simulations, also considering the adsorption of virus-like particles on their surface. As a most timely perspective, the results on this review present potential solutions to investigate coronaviruses and specifically SARS-CoV-2, responsible of the COVID-19 pandemic, whose spread can be limited by the efficient disinfection and purification of closed-spaces air and urban waters.

GESS: a database of global evaluation of SARS-CoV-2/hCoV-19 sequences

The COVID-19 outbreak has become a global emergency since December 2019. Analysis of SARS-CoV-2 sequences can uncover single nucleotide variants (SNVs) and corresponding evolution patterns. The Global Evaluation of SARS-CoV-2/hCoV-19 Sequences (GESS, https://wan-bioinfo.shinyapps.io/GESS/) is a resource to provide comprehensive analysis results based on tens of thousands of high-coverage and high-quality SARS-CoV-2 complete genomes. The database allows user to browse, search and download SNVs at any individual or multiple SARS-CoV-2 genomic positions, or within a chosen genomic region or protein, or in certain country/area of interest. GESS reveals geographical distributions of SNVs around the world and across the states of USA, while exhibiting time-dependent patterns for SNV occurrences which reflect development of SARS-CoV-2 genomes. For each month, the top 100 SNVs that were firstly identified world-widely can be retrieved. GESS also explores SNVs occurring simultaneously with specific SNVs of user's interests. Furthermore, the database can be of great help to calibrate mutation rates and identify conserved genome regions. Taken together, GESS is a powerful resource and tool to monitor SARS-CoV-2 migration and evolution according to featured genomic variations. It provides potential directive information for prevalence prediction, related public health policy making, and vaccine designs.

The Epidemiology of Plant Virus Disease: Towards a New Synthesis

Epidemiology is the science of how disease develops in populations, with applications in human, animal and plant diseases. For plant diseases, epidemiology has developed as a quantitative science with the aims of describing, understanding and predicting epidemics, and intervening to mitigate their consequences in plant populations. Although the central focus of epidemiology is at the population level, it is often necessary to recognise the system hierarchies present by scaling down to the individual plant/cellular level and scaling up to the community/landscape level. This is particularly important for diseases caused by plant viruses, which in most cases are transmitted by arthropod vectors. This leads to range of virus-plant, virus-vector and vector-plant interactions giving a distinctive character to plant virus epidemiology (whilst recognising that some fungal, oomycete and bacterial pathogens are also vector-borne). These interactions have epidemiological, ecological and evolutionary consequences with implications for agronomic practices, pest and disease management, host resistance deployment, and the health of wild plant communities. Over the last two decades, there have been attempts to bring together these differing standpoints into a new synthesis, although this is more apparent for evolutionary and ecological approaches, perhaps reflecting the greater emphasis on shorter often annual time scales in epidemiological studies. It is argued here that incorporating an epidemiological perspective, specifically quantitative, into this developing synthesis will lead to new directions in plant virus research and disease management. This synthesis can serve to further consolidate and transform epidemiology as a key element in plant virus research.

Viral genomics in Ebola virus research

Filoviruses such as Ebola virus continue to pose a substantial health risk to humans. Advances in the sequencing and functional characterization of both pathogen and host genomes have provided a wealth of knowledge to clinicians, epidemiologists and public health responders during outbreaks of high-consequence viral disease. Here, we describe how genomics has been historically used to investigate Ebola virus disease outbreaks and how new technologies allow for rapid, large-scale data generation at the point of care. We highlight how genomics extends beyond consensus-level sequencing of the virus to include intra-host viral transcriptomics and the characterization of host responses in acute and persistently infected patients. Similar genomics techniques can also be applied to the characterization of non-human primate animal models and to known natural reservoirs of filoviruses, and metagenomic sequencing can be the key to the discovery of novel filoviruses. Finally, we outline the importance of reverse genetics systems that can swiftly characterize filoviruses as soon as their genome sequences are available.