Direct and indirect viral associations predict coexistence in wild plant virus communities

Viruses are a vastly underestimated component of biodiversity that occur as diverse communities across hierarchical scales from the landscape level to individual hosts. The integration of community ecology with disease biology is a powerful, novel approach that can yield unprecedented insights into the abiotic and biotic drivers of pathogen community assembly. Here, we sampled wild plant populations to characterize and analyze the diversity and co-occurrence structure of within-host virus communities and their predictors. Our results show that these virus communities are characterized by diverse, non-random coinfections. Using a novel graphical network modeling framework, we demonstrate how environmental heterogeneity influences the network of virus taxa and how the virus co-occurrence patterns can be attributed to non-random, direct statistical virus-virus associations. Moreover, we show that environmental heterogeneity changed virus association networks, especially through their indirect effects. Our results highlight a previously underestimated mechanism of how environmental variability can influence disease risks by changing associations between viruses that are conditional on their environment.

A Virus Is a Community: Diversity within Negative-Sense RNA Virus Populations

Negative-sense RNA virus populations are composed of diverse viral components that interact to form a community and shape the outcome of virus infections. At the genomic level, RNA virus populations consist not only of a homogeneous population of standard viral genomes but also of an extremely large number of genome variants, termed viral quasispecies, and nonstandard viral genomes, which include copy-back viral genomes, deletion viral genomes, mini viral RNAs, and hypermutated RNAs. At the particle level, RNA virus populations are composed of pleomorphic particles, particles missing or having additional genomes, and single particles or particle aggregates. As we continue discovering more about the components of negative-sense RNA virus populations and their crucial functions during virus infection, it will become more important to study RNA virus populations as a whole rather than their individual parts. In this review, we will discuss what is known about the components of negative-sense RNA virus communities, speculate how the components of the virus community interact, and summarize what vaccines and antiviral therapies are being currently developed to target or harness these components.

[Distribution Characteristics of Viruses Microorganisms in a Water Supply System with Combined Ultraviolet Chloramine Disinfection]

To study the effect of combined ultraviolet (UV) chloramine disinfection on viruses in a drinking water supply system, a full-scale experiment was conducted to analyze the distribution, variability, community structure, and hosts of viruses using metagenomics. The results showed that the combined UV chloramine process reduced the number of virus species (6.13%) and gene abundance (51.97%) but did not completely remove the viruses from the water. The United States Environmental Protection Agency (USEPA) report that virus removal efficiencies from water can reach 99%-99.99% based on culturing methods. However, in this study, metagenomic analysis indicated a total virus removal rate of only 93.46%. Therefore, the detection of viruses in water using culturing method cannot reliably detect viruses in drinking water. Caudovirales are the most abundant type of virus in water supply systems and are sensitive to chloramine disinfection. Lentivirus, as a virus that can infect humans and vertebrates, has strong resistance to UV and chloramine disinfection. The main virus hosts in the studied water supply system were bacteria (61.50%). The viruses in the raw water were mainly parasitic in Synechococcus. The dominant virus host was Pseudomonas in both the effluent water and pipe network water. The gene abundance of the Pseudomonas aeruginosa host in the pipe network increased by 342.62%, which requires further attention as a virus risk in pipe network systems. Overall, combined UV chloramine disinfection was more effective at the removal of virus hosts than single UV disinfection (51.97% compared to 0.79%).

The 'Neglected' Soil Virome - Potential Role and Impact

Bacteriophages are among the most abundant and diverse biological units in the biosphere. They have contributed to our understanding of the central dogma of biology and have been instrumental in the evolutionary success of bacterial pathogens. In contrast to our current understanding of marine viral communities, the soil virome and its function in terrestrial ecosystems has remained relatively understudied. Here, we examine, in a comparative fashion, the knowledge gathered from studies performed in soil versus marine settings. We address the information with respect to the abundance, diversity, ecological significance, and effects of, in particular, bacteriophages on their host's evolutionary trajectories. We also identify the main challenges that soil virology faces and the studies that are required to accompany the current developments in marine settings.