Changes in population dynamics in mutualistic versus pathogenic viruses

Prediction and characterization of prophages of Stenotrophomonas maltophilia reveals a remarkable phylogenetic diversity of prophages

Prophages, which enables bacterial hosts to acquire novel traits, and increase genetic variation and evolutionary innovation, are considered to be one of the greatest drivers of bacterial diversity and evolution. Stenotrophomonas maltophilia is widely distributed and one of the most important multidrug resistant bacteria in hospitals. However, the distribution and genetic diversity of S. maltophilia prophages have not been elucidated. In this study, putative prophages were predicted in S. maltophilia genomes by using virus prediction tools, and the genetic diversity and phylogeny of S. maltophilia and the prophages they harbor were further analyzed. A total of 356 prophage regions were predicted from 88 S. maltophilia genomes. Among them, 144 were intact prophages, but 77.09% of the intact prophages did not match any known phage sequences in the public database. The number of prophage carried by S. maltophilia is related to its host habitat and is an important factor affecting the size of the host genome, but it is not related to the genetic diversity of the prophage. The prediction of auxiliary genes encoded by prophage showed that antibiotic resistance genes was not predicted for any of the prophages except for one questionable prophage, while 53 virulence genes and 169 carbohydrate active enzymes were predicted from 11.24 and 44.1% prophages, respectively. Most of the prophages (72.29%) mediated horizontal gene transfer of S. maltophilia genome, but only involved in 6.25% of the horizontal gene transfer events. In addition, CRISPR prediction indicated 97.75% S. maltophilia strains contained the CRISPR-Cas system containing 818 spacer sequences. However, these spacer sequences did not match any known S. maltophilia phages, and only a few S. maltophilia prophages. Comparative genomic analysis revealed a highly conserved and syntenic organization with genomic rearrangement between the prophages and the known related S. maltophilia phages. Our results indicate a high prevalence and genetic diversity of prophages in the genome of S. maltophilia, as well as the presence of a large number of uncharacterized phages. It provides an important complement to understanding the diversity and biological characteristics of phages, as well as the interactions and evolution between bacteria and phages.

Beyond pathogenesis: Detecting the full spectrum of ecological interactions in the virosphere

The public perception of viruses has historically been negative. We are now at a stage where the development of tools to study viruses is at an all-time high, but society's perception of viruses is at an all-time low. The literature regarding viral interactions has been skewed towards negative (i.e., pathogenic) symbioses, whereas viral mutualisms remain relatively underexplored. Viral interactions with their hosts are complex and some non-pathogenic viruses could have potential benefits to society. However, viral research is seldom designed to identify viral mutualists, a gap that merits considering new experimental designs. Determining whether antagonisms, mutualisms, and commensalisms are equally common ecological strategies requires more balanced research efforts that characterize the full spectrum of viral interactions.

Emerging Risk of Cross-Species Transmission of Honey Bee Viruses in the Presence of Invasive Vespid Species

The increase in invasive alien species is a concern for the environment. The establishment of some of these species may be changing the balance between pathogenicity and host factors, which could alter the defense strategies of native host species. Vespid species are among the most successful invasive animals, such as the genera Vespa, Vespula and Polistes. Bee viruses have been extensively studied as an important cause of honey bee population losses. However, knowledge about the transmission of honey bee viruses in Vespids is a relevant and under-researched aspect. The role of some mites such as Varroa in the transmission of honey bee viruses is clearer than in the case of Vespidae. This type of transmission by vectors has not yet been clarified in Vespidae, with interspecific relationships being the main hypotheses accepted for the transmission of bee viruses. A majority of studies describe the presence of viruses or their replicability, but aspects such as the symptomatology in Vespids or the ability to infect other hosts from Vespids are scarcely discussed. Highlighting the case of Vespa velutina as an invader, which is causing huge losses in European beekeeping, is of special interest. The pressure caused by V. velutina leads to weakened hives that become susceptible to pathogens. Gathering this information is necessary to promote further research on the spread of bee viruses in ecosystems invaded by invasive species of Vespids, as well as to prevent the decline of bee populations due to bee viruses.

Infectious agents and inflammation in donated hearts and dilated cardiomyopathies related to cardiovascular diseases, Chagas' heart disease, primary and secondary dilated cardiomyopathies

BACKGROUND

Clinical and experimental conflicting data have questioned the relationship between infectious agents, inflammation and dilated cardiomyopathy (DCM).

OBJECTIVES

The aim of this study was to determine the frequency of infectious agents and inflammation in endomyocardial biopsy (EMB) specimens from patients with idiopathic DCM, explanted hearts from different etiologies, including Chagas' disease, compared to donated hearts.

METHODS

From 2008 to 2011, myocardial samples from 29 heart donors and 55 patients with DCMs from different etiologies were studied (32 idiopathic, 9 chagasic, 6 ischemic and 8 other specific etiologies). Inflammation was investigated by immunohistochemistry and infectious agents by immunohistochemistry, molecular biology, in situ hybridization and electron microscopy.

RESULTS

There were no differences regarding the presence of macrophages, expression of HLA class II and ICAM-I in donors and DCM. Inflammation in Chagas' disease was predominant. By immunohistochemistry, in donors, there was a higher expression of antigens of enterovirus and Borrelia, hepatitis B and C in DCMs. By molecular biology, in all groups, the positivity was elevated to microorganisms, including co-infections, with a higher positivity to adenovirus and HHV6 in donors towards DCMs. This study was the first to demonstrate the presence of virus in the heart tissue of chagasic DCM.

CONCLUSIONS

The presence of inflammation and infectious agents is frequent in donated hearts, in the myocardium of patients with idiopathic DCM, myocardial dysfunction related to cardiovascular diseases, and primary and secondary cardiomyopathies, including Chagas' disease. The role of co-infection in Chagas' heart disease physiopathology deserves to be investigated in future studies.

Genome sequence of two isolates of Yellow oatgrass mosaic virus, a new grass-infecting Tritimovirus

Complete genome sequences of two Yellow oatgrass mosaic virus (YOgMV) isolates have been determined to be 9,292 nucleotides excluding the 3' polyadenylated tail. The viral RNA encodes a large putative open reading frame (ORF) of a single polyprotein consisting of 3,002 amino acids with typical genome organization of monopartite potyvirids. A small overlapping ORF encoding a pretty interesting Potyviridae ORF of 122 amino acids is found in the P3 cistron of both YOgMV isolates. The nucleotide and amino acid identities between the two YOgMV isolates are 90 and 97 %, respectively. Pairwise comparison of YOgMV putative mature proteins and proteinase cleavage sites with those of representative members of the family Potyviridae indicated that YOgMV is more closely related to members of the genus Tritimovirus. In phylogenetic trees constructed with sequences of putative polyprotein, YOgMV consistently groups with members of the genus Tritimovirus. These results suggest that YOgMV should be classified as a distinct species in the genus Tritimovirus in the family Potyviridae.

Multiplexed interactions: viruses of endophytic fungi

Mycoviruses have been detected from all four classes of fungal endophytes. The virus species richness is probably extremely high in endophytes. The incidence and diversity of mycoviruses may be affected by transmission modes, virus-fungus-plant interactions, and endophyte population structures. Endophyte viruses are unlikely to be strong antagonists to their fungal hosts and can clearly play mutualistic roles in the multiplex symbioses with endophytes and plants under some environmental conditions. A better understanding of fungal endophyte viruses will help prospects of future applications for sustainable agriculture.

Alphaherpesvirus axon-to-cell spread involves limited virion transmission

The spread of viral infection within a host can be restricted by bottlenecks that limit the size and diversity of the viral population. An essential process for alphaherpesvirus infection is spread from axons of peripheral nervous system neurons to cells in peripheral epithelia (anterograde-directed spread, ADS). ADS is necessary for the formation of vesicular lesions characteristic of reactivated herpesvirus infections; however, the number of virions transmitted is unknown. We have developed two methods to quantitate ADS events using a compartmentalized neuronal culture system. The first method uses HSV-1 and pseudorabies virus recombinants that express one of three different fluorescent proteins. The fluorescence profiles of cells infected with the virus mixtures are used to quantify the number of expressed viral genomes. Strikingly, although epithelial or neuronal cells express 3-10 viral genomes after infection by free virions, epithelial cells infected by HSV-1 or pseudorabies virus following ADS express fewer than two viral genomes. The second method uses live-cell fluorescence microscopy to track individual capsids involved in ADS. We observed that most ADS events involve a single capsid infecting a target epithelial cell. Together, these complementary analyses reveal that ADS events are restricted to small numbers of viral particles, most often a single virion, resulting in a single viral genome initiating infection.

Going viral: next-generation sequencing applied to phage populations in the human gut

Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere. Here, we briefly review the incipient rise of a phage biology renaissance, which has been catalysed by advances in next-generation sequencing. We explore how work characterizing phage diversity and lifestyles in the human gut is changing our view of ourselves as supra-organisms. Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes.