Genome scale evolution of myxoma virus reveals host-pathogen adaptation and rapid geographic spread

The evolutionary interplay between myxoma virus (MYXV) and the European rabbit (Oryctolagus cuniculus) following release of the virus in Australia in 1950 as a biological control is a classic example of host-pathogen coevolution. We present a detailed genomic and phylogeographic analysis of 30 strains of MYXV, including the Australian progenitor strain Standard Laboratory Strain (SLS), 24 Australian viruses isolated from 1951 to 1999, and three isolates from the early radiation in Britain from 1954 and 1955. We show that in Australia MYXV has spread rapidly on a spatial scale, with multiple lineages cocirculating within individual localities, and that both highly virulent and attenuated viruses were still present in the field through the 1990s. In addition, the detection of closely related virus lineages at sites 1,000 km apart suggests that MYXV moves freely in geographic space, with mosquitoes, fleas, and rabbit migration all providing means of transport. Strikingly, despite multiple introductions, all modern viruses appear to be ultimately derived from the original introductions of SLS. The rapidity of MYXV evolution was also apparent at the genomic scale, with gene duplications documented in a number of viruses. Duplication of potential virulence genes may be important in increasing the expression of virulence proteins and provides the basis for the evolution of novel functions. Mutations leading to loss of open reading frames were surprisingly frequent and in some cases may explain attenuation, but no common mutations that correlated with virulence or attenuation were identified.This work was funded in part by grant R01 AI093804 from the National Institute of Allergy and Infectious Diseases, National Institutes of Health. E.C.H. is funded by an NHMRC Australia Fellowship. D.C.T. is funded by an ARC Future Fellowship

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome

Defining <i>Brugia malayi</i> and <i>Wolbachia</i> symbiosis by stage-specific dual RNA-seq

<div><p>Background</p><p>Filarial nematodes currently infect up to 54 million people worldwide, with millions more at risk for infection, representing the leading cause of disability in the developing world. <i>Brugia malayi</i> is one of the causative agents of lymphatic filariasis and remains the only human filarial parasite that can be maintained in small laboratory animals. Many filarial nematode species, including <i>B</i>. <i>malayi</i>, carry an obligate endosymbiont, the alpha-proteobacteria <i>Wolbachia</i>, which can be eliminated through antibiotic treatment. Elimination of the endosymbiont interferes with development, reproduction, and survival of the worms within the mamalian host, a clear indicator that the <i>Wolbachia</i> are crucial for survival of the parasite. Little is understood about the mechanism underlying this symbiosis.</p><p>Methodology/ Principle findings</p><p>To better understand the molecular interplay between these two organisms we profiled the transcriptomes of <i>B</i>. <i>malayi</i> and <i>Wolbachia</i> by dual RNA-seq across the life cycle of the parasite. This helped identify functional pathways involved in this essential symbiotic relationship provided by the co-expression of nematode and bacterial genes. We have identified significant stage-specific and gender-specific differential expression in <i>Wolbachia</i> during the nematode’s development. For example, during female worm development we find that <i>Wolbachia</i> upregulate genes involved in ATP production and purine biosynthesis, as well as genes involved in the oxidative stress response.</p><p>Conclusions/ Significance</p><p>This global transcriptional analysis has highlighted specific pathways to which both <i>Wolbachia</i> and <i>B</i>. <i>malayi</i> contribute concurrently over the life cycle of the parasite, paving the way for the development of novel intervention strategies.</p></div

Circos plots of stage-specific <i>Wolbachia</i> gene expression.

<p><i>Wolbachia</i> expression profiles using normalized FPKMs over development of male and female worms from L4 to 120 days post infection (dpi); genomic location is shown around the perimeter, and the black rectangles represent the CDS.</p

The co-expression network for <i>B</i>. <i>malayi</i> and <i>Wolbachia</i>.

<p>The network heatmap plot of network connectivity for <i>B</i>. <i>malayi</i> and <i>Wolbachia</i> calculated using weighted gene correlation network analysis (WGCNA). The black branches show the hierarchical clustering dendrograms, which were assigned to clusters using dynamic tree cutting to identify modules of co-expressed genes, shown as colored bars. High co-expression interconnectedness is indicated by increasingly saturated orange and red coloring. Modules correspond to groups of highly interconnected genes.</p

Dual RNA-seq sequencing summary.

<p>The table shows the total reads sequenced and mapped in each biological replicate at each developmental stage, L4 to 120 days post infection (dpi) males (M) and females (F), lower case a and b refer to separate biological replicates.</p

Heatmap of gene expression of pathways of interest.

<p>Expression, in log FPKMs, is plotted over the development of the nematode, L4 to 120 days post infection (dpi) male (M) and female (F), by pathway for heme, riboflavin, FAD, peptidoglycan, and isoprenoid biosynthesis as well as expression of the main secretion systems in <i>Wolbachia</i> including Sec translocase, Type IV secretion system, and ABC transporters.</p

Clustering of stages based on <i>B</i>. <i>malayi</i> gene expression.

<p>Clustering of <i>B</i>. <i>malayi</i> genes and developmental stages, L4 to 120 days post infection (dpi) Male (M) and Female (F), based on gene expression in normalized FPKMs. Expression was scaled using Z score prior to clustering, with red representing high expression and blue representing low expression. Biological replicates were combined prior to analysis.</p

Clustering of stages and <i>Wolbachia</i> DE genes.

<p>Hierarchical clustering of <i>Wolbachia</i> DE genes and developmental stages, L4 through 120 days post infection (dpi) male (M) and female (F), based on gene expression in normalized FPKMs. Expression values were scaled prior to clustering using a Z score calculation, with red representing high expression and blue representing low expression. Biological replicates were combined prior to clustering.</p