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Nascimento F.F.,University of Sydney | Nascimento F.F.,Federal University of Rio de Janeiro | Gongora J.,University of Sydney | Charleston M.,University of Sydney | And 3 more authors.
BMC Evolutionary Biology | Year: 2011

Background: Porcine endogenous retroviruses (PERVs) represent remnants of an exogenous form that have become integrated in the domestic pig (Sus scrofa) genome. Although they are usually inactive, the capacity of 1 ERVs to infect human cells in vitro has raised concerns about xenotransplantation because the viruses could cross the species barrier to humans. Here we have analyzed the evolution of 1 ERVs in ten species of Suidae (suids, pigs and hogs) from Eurasia and Africa using DNA sequences for their coding domains (gag, pro/pol and env genes). For comparison with 1 PERVs, we have also analysed 2 ERVs which in domestic pigs are known to be inactive and do not pose a risk to xenotransplantation. Results: Phylogenetic analysis using Bayesian inference showed that 1 and 2 ERVs have distinctive evolutionary histories. Firstly, two different viral lineages of 1 ERVs were found and a coevolutionary analysis demonstrated that they correspond broadly to their host phylogeny, one of Eurasian and another of African species, and show no evidence of horizontal transmission. 2 ERVs, however, show a bush-like evolution, suggesting a rapid viral radiation from a single common ancestor with no correspondence between host and viral evolutionary trees. Furthermore, though 1 ERV env genes do not possess frequent stop codons, 2 env genes do. To understand whether 1 suid ERVs may be still replicating, we have also evaluated their likely mechanism of proliferation by statistically testing internal to terminal branches using nonsynonymous versus synonymous substitution ratios. Our results suggest that 1 ERVs are increasing in copy number by reinfection, which requires the translocation of the virus from one cell to another. Conclusions: Evidence of at least two viral subpopulations was observed in 1 ERVs from Eurasian and African host species. These results should be taken into account in xenotransplantation since 1 ERVs appear to be codiverging with their host and maintaining ongoing capacity to infect somatic and germ cells. © 2011 Nascimento et al; licensee BioMed Central Ltd.

Roeber F.,University of Melbourne | Jex A.R.,University of Melbourne | Campbell A.J.D.,University of Melbourne | Nielsen R.,Veterinary Health Research Pty Ltd. | And 3 more authors.
International Journal for Parasitology | Year: 2012

The accurate diagnosis of strongylid nematode infections is central to investigating their epidemiology and for parasite control. To overcome major limitations in sensitivity or specificity of traditional methods, including faecal egg count (FEC) and/or larval culture (LC), we evaluated and established a semi-automated, high throughput multiplexed-tandem PCR (MT-PCR) platform for the diagnosis of gastrointestinal strongylid nematode infections in sheep, and established its diagnostic sensitivity (100%) and specificity (87.5%) based on the testing of 100 faecal DNA samples from helminth-free sheep and 30 samples from sheep with infections confirmed by necropsy. Subsequently, the platform was employed to test 219 faecal samples from sheep with naturally acquired infections from various geographical localities within Australia and the results compared with those from conventional LC using 139 of the 219 samples. The results obtained using both MT-PCR and LC correlated significantly for most nematodes examined, but revealed that Oesophagostomum venulosum and Chabertia ovina (parasites of the large intestine) were significantly under-represented in the LC results. The results showed that Trichostrongylus spp. (87%), Teladorsagia circumcincta (80%) and Haemonchus contortus (67%) had the highest prevalences, followed by O. venulosum (51%) and C. ovina (12%). The molecular-diagnostic platform established can be used for species- or genus-specific diagnosis of patent nematode infections within 24. h (compared with 7-10. days for LC), and is a sensitive and cost effective tool for routine application in research and service laboratories. © 2012.

Cliffe K.M.,PIC Research Laboratory | Cliffe K.M.,University of Cambridge | Day A.E.,PIC Research Laboratory | Day A.E.,Abcam | And 13 more authors.
Animal Genetics | Year: 2010

Sequences from 20 amplicons representing nine different loci and 11369bp from the short arm of the pig Y chromosome were compared using pools of DNA from different European and Chinese breeds. A total of 33 polymorphic sites were identified, including five indels and 28 single nucleotide polymorphisms (SNPs). Three high frequency SNPs within the coding regions of SRY were further analysed across 889 males representing 25 European and 25 Asian breeds or Lines, plus a European Line of Meishan. Two haplotypes seen to be associated with European or Chinese origin in the initial SNP discovery phase were found to be the most common in their respective groups of breeds in a more detailed genotyping study. Two further SRY haplotypes are relatively rare. One was found exclusively within Tamworth, at low frequency in Retinto, and in three Chinese breeds (Huai, Sahwutou and Xiaomeishan). The other uncommon haplotype is found exclusively in Bamajiang, two further Chinese breeds (Hangjiang Black and Longling) and two European rare breeds (Mangalica and Linderödssvin), but appears based on comparison with other suids to represent an ancestral sequence. © 2010 Stichting International Foundation for Animal Genetics.

do Nascimento F.F.,University of Sydney | do Nascimento F.F.,Federal University of Rio de Janeiro | Gongora J.,University of Sydney | Tristem M.,Imperial College London | And 2 more authors.
Infection, Genetics and Evolution | Year: 2011

Diversity of long terminal repeats (LTRs) from γ1 endogenous retroviruses (ERVs) was analysed by DNA sequencing in 10 species of the family Suidae (suids, pigs and hogs). Phylogenetic analysis separated LTR sequences into two groups which correlated approximately with either the previously described cluster I and III, or the clusters II, IV and V. Interestingly, a specific LTR exhibiting a novel molecular rearrangement was identified exclusively within African host species when compared to LTRs previously reported from known ERVs in the domestic pig (Sus scrofa). Furthermore, other sections of LTRs appear to be unique to African suids as suggested by phylogenetic analysis. These differences between African and Eurasian ERV lineages show that these ERVs belong to different viral sub-populations, implying coevolution of endogenous viral sequences with their host species and providing no evidence of transfer of viral sequences between African and Eurasian suids. © 2011 Elsevier B.V.

Gongora J.,University of Sydney | Cuddahee R.E.,Duke University | Nascimento F.F.D.,University of Sydney | Palgrave C.J.,Roslin Institute | And 12 more authors.
Zoologica Scripta | Year: 2011

Although African suids have been of scientific interest for over two centuries, their origin, evolution, phylogeography and phylogenetic relationships remain contentious. There has been a long-running debate concerning the evolution of pigs and hogs (Suidae), particularly regarding the phylogenetic relationships among extant Eurasian and African species of the subfamily Suinae. To investigate these issues, we analysed the mitochondrial and nuclear DNA sequences of extant genera of Suidae from Eurasia and Africa. Molecular phylogenetic analyses revealed that all extant sub-Saharan African genera form a monophyletic clade separate from Eurasian suid genera, contradicting previous attempts to resolve the Suidae phylogeny. Two major sub-Saharan African clades were identified, with Hylochoerus and Phacochoerus grouping together as a sister clade to Potamochoerus. In addition, we find that the ancestors of extant African suids may have evolved separately from the ancestors of modern day Sus and Porcula in Eurasia before they colonised Africa. Our results provide a revision of the intergeneric relationships within the family Suidae. © 2011 The Authors. Zoologica Scripta © 2011 The Norwegian Academy of Science and Letters.

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