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      Phylogenetic analysis linked fatal neurologic disease in leopards ( Panthera pardus) to Asia-5 lineage of canine distemper virus in Nepal

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          Highlights

          • Canine distemper virus (CDV) poses a serious threat to leopards in Nepal, with recent raising concern of transmission in wildlife – domestic interface.

          • CDV strains in leopards belong to the Asia-5 lineage, prevalent among dogs and wild carnivores in Nepal and neighboring India.

          • Leopard in Kathmandu might have acquired CDV through dog predation, further research in wildlife in the region is required to draw definitive conclusions.

          • Urgent measures, including vaccination for leopards and effective control of dog population, are recommended to minimize impact of CDV and safeguard leopard population.

          Abstract

          Canine distemper virus (CDV) is responsible for a highly contagious and often fatal neurological disease that affects various carnivores, including domestic dogs. In Nepal, recent reports of CDV exposure and illness in leopards ( Panthera pardus) have raised concerns about the transmission of the virus among domestic dogs and wild carnivores. To investigate the genetic lineage and spread of CDV, our study utilized archived post-mortem samples from four leopards that exhibited clinical signs suggestive of canine distemper infection. These leopards were rescued in the Palpa, Dolakha, Kathmandu, and Parbat districts. Our phylogenetic analysis revealed that the CDV strains circulating among the leopards belong to the Asia-5 lineage, which is also prevalent among dogs and wild carnivores in Nepal and neighboring India. The genetic relatedness between the leopard CDV sequences and those from both dogs and other carnivores within the Asia-5 lineage suggests that leopards in Nepal may have acquired the virus from multiple sources, potentially facilitated by their generalist dietary habits preying on dogs and even mesocarnivores. Furthermore, we inspected specific amino acid substitution in the hemagglutinin gene of leopard CDV, which also suggests possible transmission from both domestic dogs and non-canid hosts, although further research is needed to draw definitive conclusions. Given the vulnerable state of the leopard population in Nepal, already threatened by poaching and retaliatory killing, the emergence of CDV as a potential novel threat is deeply concerning. Comprehensive surveillance studies are essential to understand the dynamics of CDV spillover and to develop informed interventions. Urgent measures, including vaccination programs and effective control of the dog population, are needed to mitigate the impact of this disease and safeguard the future of Nepal's leopards and other wild carnivores.

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          MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

          Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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            jModelTest 2: more models, new heuristics and parallel computing.

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              MUSCLE: a multiple sequence alignment method with reduced time and space complexity

              Background In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles. Results We compare the speed and accuracy of MUSCLE with CLUSTALW, Progressive POA and the MAFFT script FFTNS1, the fastest previously published program known to the author. Accuracy is measured using four benchmarks: BAliBASE, PREFAB, SABmark and SMART. We test three variants that offer highest accuracy (MUSCLE with default settings), highest speed (MUSCLE-fast), and a carefully chosen compromise between the two (MUSCLE-prog). We find MUSCLE-fast to be the fastest algorithm on all test sets, achieving average alignment accuracy similar to CLUSTALW in times that are typically two to three orders of magnitude less. MUSCLE-fast is able to align 1,000 sequences of average length 282 in 21 seconds on a current desktop computer. Conclusions MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs. MUSCLE is freely available at .
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                Author and article information

                Contributors
                Journal
                Virus Res
                Virus Res
                Virus Research
                Elsevier
                0168-1702
                1872-7492
                25 September 2024
                December 2024
                25 September 2024
                : 350
                : 199463
                Affiliations
                [a ]National Trust for Nature Conservation, Khumaltar, Lalitpur, Nepal
                [b ]Center for Molecular Dynamics Nepal, Thapathali, Kathmandu, Nepal
                [c ]Chitwan National Park Office, Kasara, Chitwan, Nepal
                [d ]Annapurna Conservation Area Office, Pokhara, Kaski, Nepal
                [e ]Kathmandu University, Dhulikhel, Kavre, Nepal
                [f ]Directorate of Livestock and Fisheries Development, Koshi Province, Biratnagar, Morang, Nepal
                [g ]Nepal Agricultural Research Council, Khumaltar, Lalitpur, Nepal
                Author notes
                [* ]Corresponding author. naturalamir@ 123456gmail.com
                [1]

                Equal contributions.

                Article
                S0168-1702(24)00156-4 199463
                10.1016/j.virusres.2024.199463
                11460512
                39313099
                b1018869-1435-4840-a37a-d010d9f3dd2f
                © 2024 The Author(s)

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 20 June 2024
                : 4 September 2024
                : 10 September 2024
                Categories
                Article

                Microbiology & Virology
                canine distemper virus,leopards,panthera pardus,dogs,spillover,phylogenetic
                Microbiology & Virology
                canine distemper virus, leopards, panthera pardus, dogs, spillover, phylogenetic

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