Matthew Walters

Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera)

Dragonfly cyclovirus (DfCyV), a new species of ssDNA virus discovered using viral metagenomics in dragonflies (family Libellulidae) from the Kingdom of Tonga. Metagenomic sequences of DfCyV were similar to viruses of the recently proposed genus Cyclovirus within the family Circoviridae. Specific PCRs resulted in the recovery of 21 DfCyV genomes from three dragonfly species (Pantala flavescens, Tholymis tillarga and Diplacodes bipunctata). The 1741 nt DfCyV genomes share >95 % nucleotide identity and are classified into 11 subtypes representing a single strain. The DfCyV genomes share 48-63 % genome-wide nucleotide identity with cycloviruses identified in human faecal samples. Recombination analysis revealed three recombinant DfCyV genomes, suggesting that recombination plays an important role in cyclovirus evolution. To our knowledge, this is the first report of a circular ssDNA virus identified in insects, and the data may help elucidate evolutionary links among novel Circoviridae recently identified in animals and environmental samples.

Extensive recombination detected among beak and feather disease virus isolates from breeding facilities in Poland.

Beak and feather disease virus (BFDV) causes the highly contagious, in some cases fatal, psittacine beak and feather disease in parrots. The European continent has no native parrots, yet in the past has been one of the worlds biggest importers of wild-caught exotic parrot species. Following the banning of this practice in 2007, the demand for exotic pet parrots has largely been met by established European breeding facilities, which can also supply buyers outside Europe. However, the years of unregulated importation have provided numerous opportunities for BFDV to enter Europe, meaning the likelihood of birds within captive breeding facilities being BFDV positive is high. This study examined the BFDV status of such facilities in Poland, a country previously shown to have BFDV among captive birds. A total of 209 birds from over 50 captive breeding facilities across Poland were tested, and 43 birds from 18 different facilities tested positive for BFDV. The full BFDV genomes from these 43 positive birds were determined, and phylogenetic analysis revealed that these samples harboured a relatively high degree of diversity and that they were highly recombinant. It is evident that there have been multiple introductions of BFDV into Poland over a long period of time, and the close association of different species of birds in the captive environment has probably facilitated the evolution of new BFDV strains through recombination.

Evidence of multiple introductions of beak and feather disease virus into the Pacific islands of Nouvelle-Caledonie (New Caledonia).

Beak and feather disease virus (BFDV) is a circular ssDNA virus that causes psittacine beak and feather disease and has almost global presence. Here, we report for the first time the presence of in Nouvelle-Calédonie (New Caledonia). One hundred and sixty-eight exotic and 79 endemic birds were sampled in Nouvelle-Calédonie, 26 were found to be positive for BFDV. We characterized the full genomes of 26 isolates and phylogenetic analysis placed nine of the isolates into the BFDV-J strain, with the remaining 17 isolates from Deplanches Rainbow Lorikeet (Trichoglossus haematodus deplanchii) forming a novel strain, BFDV-P. Of more concern was the discovery of an infected bird from the vulnerable and endemic New Caledonian Parakeet (Cyanoramphus saisseti). Our results reveal that there have been at least two introductions of BFDV into Nouvelle-Calédonie.

Australian monocot-infecting mastrevirus diversity rivals that in Africa

Monocotyledonous plant infecting mastreviruses (family Geminiviridae) have been found in the Old World. The greatest diversity of these viruses has been found in Africa but this may simply reflect the more extensive sampling that has been done there. To provide a better understanding of mastrevirus diversity in Australia, we have sequenced the genomes of 41 virus isolates found in naturalised and native grasses and identified four new species in addition to the four previously characterised species. Two of these species, which were recovered from a single Sporobolus plant, are highly divergent and are most closely related to the African streak viruses. This, coupled with the discovery of divergent dicotyledonous plant infecting mastreviruses in Australia brings into question the hypothesis that mastreviruses may have originated in Africa. We found that the patterns of inter- and intra-species recombination and the recombination hotspots mirror those found in both their African monocot-infecting counterparts and dicot-infecting mastrevirus.

Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar

BackgroundCassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands.ResultsThe isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar.ConclusionsOur study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region of the world, the risks of recombinant CMG variants emerging on this island are likely to be higher than elsewhere. Evidence of an epidemiological link between Madagascan and mainland African CMGs suggests that the consequences of such emergence events could reach far beyond the shores of this island.

Novel mastreviruses identified in Australian wild rice

Most known mastreviruses (family Geminiviridae) infect members of the grass family, Poaceae. Although the greatest number of grass-infecting mastrevirus species have been discovered in Africa, it is apparent that the ten grass-infecting mastrevirus species that have so far only been discovered in south-east Queensland have a degree of diversity that rivals that observed in Africa. In this study, we have used a deep sequencing approach to identify two new mastrevirus species, tentatively named rice latent virus 1 and 2 (RLV 1 and 2), from two, undescribed wild rice species (Oryza AA genome group) in Cape York Peninsula, Queensland. The sequences of these new viruses had less than 70% identity with any previously identified mastrevirus, and therefore their discovery vastly expands the known diversity of monocot-infecting mastreviruses in Australia. This study also highlights the potential risks of novel crop pathogens emerging from uncultivated grass species, as the wild rice hosts are very closely related to domesticated rice.

Molecular diversity, geographic distribution and host range of monocot-infecting mastreviruses in Africa and surrounding islands

Maize streak virus (MSV), an important pathogen of maize in Africa, is the most extensively studied member of the Mastrevirus genus in the family Geminiviridae. Comparatively little is known about other monocot-infecting African mastreviruses, most of which infect uncultivated grasses. Here we determine the complete sequences of 134 full African mastrevirus genomes from predominantly uncultivated Poaceae species. Based on established taxonomic guidelines for the genus Mastrevirus, these genomes could be classified as belonging to the species Maize streak virus, Eragrostis minor streak virus, Maize streak Reunion virus, Panicum streak virus, Sugarcane streak Reunion virus and Sugarcane streak virus. Together with all other publicly available African monocot-infecting mastreviruses, the 134 new isolates extend the known geographical distributions of many of these species, including MSV which we found infecting Digitaria sp. on the island of Grand Canaria: the first definitive discovery of any African monocot-infecting mastreviruses north-west of the Saharan desert. These new isolates also extend the known host ranges of both African mastrevirus species and the strains within these. Most notable was the discovery of MSV-C isolates infecting maize which suggests that this MSV strain, which had previously only ever been found infecting uncultivated species, may be in the process of becoming adapted to this important staple crop.

Novel Single-Stranded DNA Virus Genomes Recovered from Chimpanzee Feces Sampled from the Mambilla Plateau in Nigeria

ABSTRACT Metagenomic approaches are rapidly expanding our knowledge of the diversity of viruses. In the fecal matter of Nigerian chimpanzees we recovered three gokushovirus genomes, one circular replication-associated protein encoding single-stranded DNA virus (CRESS), and a CRESS DNA molecule.