Varsani, A. | bioRxiv Science

bioRxiv2019

Genetic characterization of a recombinant myxoma virus leap into the Iberian hare (Lepus granatensis)

Myxomatosis is a lethal disease of wild European and domestic rabbits (Oryctolagus cuniculus) caused by a Myxoma virus (MYXV) infection, a leporipoxvirus that is found naturally in some Sylvilagus rabbit species in South America and California. The introduction of MYXV in the early 1950s into feral European rabbit populations in Australia and Europe demonstrate the best documented field example of host-virus coevolution following a cross-species transmission. Recently, a new cross-species jump of MYXV has been suggested in both Great Britain and Spain, where European brown hares (Lepus europaeus) and Iberian hares (Lepus granatensis) were found dead with lesions consistent with those observed in myxomatosis. To investigate the possibility of a new cross-species transmission event by MYXV, tissue samples collected from a wild Iberian hare found dead in Spain (Toledo region) were analyzed and deep sequenced. Our results report a new MYXV strain (MYXV Toledo) in the tissues of this species. The genome of this new strain encodes three disrupted genes (M009L, M036L and M152R) and a novel 2.8 KB recombinant region that resulted from an insertion of four novel poxviral genes towards the 5 end of its genome. From the open reading frames inserted into the MYXV Toledo strain, a new orthologue of a poxvirus host range gene family member was identified which is related to the MYXV gene M064R. Overall, we confirmed the identity of a new MYXV strain in Iberian hares that we hypothesize was able to more effectively counteract the host defenses in hares and start an infectious process in this new host.

microbiology↗

bioRxiv2019

crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyads

crAssphages are a class of bacteriophages that are highly abundant in the human gastrointestinal tract. Accordingly, crAssphage genomes have been identified in most human fecal viral metagenome studies. However, we currently have an incomplete understanding of factors impacting the transmission frequencies of these phages between mothers and infants, and the evolutionary pressures associated with such transmissions. Here, we use metagenome sequencing of stool-associated virus-like particles to identify the prevalence of crAssphage across ten South African mother-infant dyads that are discordant for HIV infection. We report the identification of a complete 97kb crAssphage genome, parts of which are detected at variable levels across each mother-infant dyad. We observed average nucleotide sequence identities of >99% for crAssphages from related mother-infant pairs but [~]97% identities between crAssphages from unrelated mothers and infants: a finding strongly suggestive of vertical mother to infant transmission. We further analyzed patterns of nucleotide diversity across the crAssphage sequences described here, identifying particularly elevated positive selection in RNA polymerase and phage tail protein encoding genes, which we validated against a crAssphage genome from previous studies. Using 16S rRNA gene sequencing, we found that the relative abundances of Bacteroides thetaiotaomicron and Parabacteroides merdae (Order: Bacteroidales) were differentially correlated with crAssphage abundance. Together, our results reveal that crAssphages may be vertically transmitted from mothers to their infants and that hotspots of selection within crAssphage RNA polymerase and phage tail protein encoding genes are potentially mediated by interactions between crAssphages and their bacterial partners.\n\nImportancecrAssphages are an ubiquitous member of the human gut microbiome and modulate interactions with key bacterial associates within the order Bacteroidales. However, the role of this interaction in the genomic evolution of crAssphage remains unclear. Across a longitudinally sampled cohort of ten South African mother-infant dyads, we use metagenome sequencing of the fecal virome and 16S rRNA gene sequencing of the fecal bacterial microbiota to elucidate the ecological and evolutionary dynamics of these interactions. Here, we demonstrate elevated levels of crAssphage average nucleotide identity between related mother-infant dyads as compared to unrelated individuals, suggesting vertical transmission. We report strong positive selection in crAssphage RNA polymerase and phage tail protein genes. Finally, we demonstrate that crAssphage abundance is linearly correlated (P < 0.014) with the abundance of two bacterial taxa, Bacteroides thetaiotaomicron and Parabacteroides merdae. These results suggest that phage-bacterial interactions may help shape ecological and evolutionary dynamics in the gut.

microbiology↗

bioRxiv2019

Discovery of several thousand highly diverse circular DNA viruses

Although it is suspected that there are millions of distinct viral species, fewer than 9,000 are catalogued in GenBanks RefSeq database. We selectively enriched for and amplified the genomes of circular DNA viruses in over 70 animal samples, ranging from cultured soil nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2,500 circular genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA viruses and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these "dark matter" sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere.

microbiology↗