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      Crocodilepox Virus Evolutionary Genomics Supports Observed Poxvirus Infection Dynamics on Saltwater Crocodile ( Crocodylus porosus)

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          Abstract

          Saltwater crocodilepox virus (SwCRV), belonging to the genus Crocodylidpoxvirus, are large DNA viruses posing an economic risk to Australian saltwater crocodile ( Crocodylus porosus) farms by extending production times. Although poxvirus-like particles and sequences have been confirmed, their infection dynamics, inter-farm genetic variability and evolutionary relationships remain largely unknown. In this study, a poxvirus infection dynamics study was conducted on two C. porosus farms. One farm (Farm 2) showed twice the infection rate, and more concerningly, an increase in the number of early- to late-stage poxvirus lesions as crocodiles approached harvest size, reflecting the extended production periods observed on this farm. To determine if there was a genetic basis for this difference, 14 complete SwCRV genomes were isolated from lesions sourced from five Australian farms. They encompassed all the conserved genes when compared to the two previously reported SwCRV genomes and fell within three major clades. Farm 2′s SwCRV sequences were distributed across all three clades, highlighting the likely mode of inter-farm transmission. Twenty-four recombination events were detected, with one recombination event resulting in consistent fragmentation of the P4c gene in the majority of the Farm 2 SwCRV isolates. Further investigation into the evolution of poxvirus infection in farmed crocodiles may offer valuable insights in evolution of this viral family and afford the opportunity to obtain crucial information into natural viral selection processes in an in vivo setting.

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          Most cited references26

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          A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints.

          We have developed a modified BOOTSCAN algorithm that may be used to screen nucleotide sequence alignments for evidence of recombination without prior identification of nonrecombinant reference sequences. The algorithm is fast and includes a Bonferroni corrected statistical test of recombination to circumvent the multiple testing problems encountered when using the BOOTSCAN method to explore alignments for evidence of recombination. Using both simulated and real datasets we demonstrate that the modified algorithm is more powerful than other phylogenetic recombination detection methods and performs almost as well as one of the best substitution distribution recombination detection methods.
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            An exact nonparametric method for inferring mosaic structure in sequence triplets.

            Statistical tests for detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern or a signal that would be unlikely to appear under clonal reproduction. Dozens of such tests have been described, but many are hampered by long running times, confounding of selection and recombination, and/or inability to isolate the mosaic-producing event. We introduce a test that is exact, nonparametric, rapidly computable, free of the infinite-sites assumption, able to distinguish between recombination and variation in mutation/fixation rates, and able to identify the breakpoints and sequences involved in the mosaic-producing event. Our test considers three sequences at a time: two parent sequences that may have recombined, with one or two breakpoints, to form the third sequence (the child sequence). Excess similarity of the child sequence to a candidate recombinant of the parents is a sign of recombination; we take the maximum value of this excess similarity as our test statistic Delta(m,n,b). We present a method for rapidly calculating the distribution of Delta(m,n,b) and demonstrate that it has comparable power to and a much improved running time over previous methods, especially in detecting recombination in large data sets.
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              Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences

              Highlights • Recombination is very relevant in generating genetic variability in viral populations. • Viral recombination has important consequences for different areas of research. These include molecular biology, virology and evolutionary biology. It also impacts the daily practice of clinicians and public health officials. • Here we review three important aspects of viral recombination: (i) molecular mechanisms of model DNA- and RNA-viruses, (ii) methods for detection, characterization and quantification in viral populations, (iii) its impact on the evolutionary analysis of viral populations.
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                Author and article information

                Journal
                Viruses
                Viruses
                viruses
                Viruses
                MDPI
                1999-4915
                02 December 2019
                December 2019
                : 11
                : 12
                : 1116
                Affiliations
                [1 ]Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
                [2 ]Centre for Crocodile Research, Noonamah, NT 0837, Australia; sally@ 123456crocresearch.com.au (S.R.I.); research@ 123456crocresearch.com.au (J.L.M.)
                [3 ]School of Psychological and Clinical Sciences, Charles Darwin University, Darwin, NT 0909, Australia
                [4 ]Berrimah Veterinary Laboratory, Northern Territory Government, Darwin, 0801 Northern Territory, Australia; Rachel.DeAraujo@ 123456nt.gov.au (R.D.A.); Nikki.Elliott@ 123456nt.gov.au (N.E.); Lorna.Melville@ 123456nt.gov.au (L.M.)
                [5 ]Department of Agriculture Sciences, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia; T.Beddoe@ 123456latrobe.edu.au
                Author notes
                [* ]Correspondence: s.sarker@ 123456latrobe.edu.au (S.S.); k.helbig@ 123456latrobe.edu.au (K.J.H.); Tel.: +61-3-9479-2317 (S.S.); +61-3-9479-6650 (K.J.H.); Fax: +61-3-9479-1222 (S.S.); +61-3-9479-1222 (K.J.H.)
                Author information
                https://orcid.org/0000-0002-2685-8377
                https://orcid.org/0000-0002-8895-2414
                https://orcid.org/0000-0001-6306-2821
                Article
                viruses-11-01116
                10.3390/v11121116
                6950651
                31810339
                0477ad1e-5d14-4e84-b8f0-2812deb0db40
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 16 September 2019
                : 29 November 2019
                Categories
                Article

                Microbiology & Virology
                saltwater crocodilepox virus,infection dynamics,complete genome,evolution,genetic recombination

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