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      Prevalence of feline immunodeficiency virus and feline leukaemia virus in domestic cats in Hungary

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          Abstract

          Objectives

          Feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) are retroviruses affecting cats worldwide. The objectives of the study were to estimate the prevalence of these retroviruses in domestic cats in Hungary and to characterise the phylogenetic relationships of FIV strains.

          Methods

          A total of 335 anticoagulated whole-blood samples obtained from both a healthy and ill cat population were examined for the presence of FIV and FeLV with two methods: ELISA and PCR. Statistical analysis was carried out to analyse the data obtained. Sequencing and phylogenetic analysis of partial polymerase ( pol) gene sequences was performed to describe circulating FIV subtypes.

          Results

          Statistical analysis showed 11.8% and 9.9% true prevalence of FeLV and FIV, respectively, with ELISA. The apparent prevalence calculated from the PCR results were 17.3% for FeLV and 13.1% for FIV. Phylogenetic analysis of partial pol gene sequences obtained from 22 FIV strains showed that all observed Hungarian strains belonged to FIV subtype B. The strains were grouped into several monophyletic subgroups reflecting the geographic locations of the origin of the samples. The overall mean genetic similarity between the analysed strains was 98.2%.

          Conclusions and relevance

          We report the first thorough overview of the prevalence of FeLV and FIV in Hungary, which is relatively high, and give insight into the genetic diversity of Hungarian strains of FIV.

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          Most cited references52

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          MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

          We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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            A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

            Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
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              Recent developments in the MAFFT multiple sequence alignment program.

              The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater challenges in both scalability and accuracy than those of 5 years ago. As increasing amounts of sequence data are being generated by large-scale sequencing projects, scalability is now critical in many situations. The requirement of accuracy has also entered a new stage since the discovery of functional noncoding RNAs (ncRNAs); the secondary structure should be considered for constructing a high-quality alignment of distantly related ncRNAs. To deal with these problems, in 2007, we updated MAFFT to Version 6 with two new techniques: the PartTree algorithm and the Four-way consistency objective function. The former improved the scalability of progressive alignment and the latter improved the accuracy of ncRNA alignment. We review these and other techniques that MAFFT uses and suggest possible future directions of MSA software as a basis of comparative analyses. MAFFT is available at http://align.bmr.kyushu-u.ac.jp/mafft/software/.
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                Author and article information

                Journal
                JFMS Open Rep
                JFMS Open Rep
                JOR
                spjor
                JFMS Open Reports
                SAGE Publications (Sage UK: London, England )
                2055-1169
                10 December 2019
                Jul-Dec 2019
                : 5
                : 2
                : 2055116919892094
                Affiliations
                [1 ]Department of Pathology, University of Veterinary Medicine, Budapest, Pest, Hungary
                [2 ]Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Pest, Hungary
                [3 ]Institute of Virology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Sachsen, Germany
                [4 ]VetCore Facility for Research, University of Veterinary Medicine, Vienna, Austria
                Author notes
                [*]Anna Szilasi DVM, Department of Pathology, University of Veterinary Medicine, István u. 2., Budapest, Pest 1078, Hungary Email: szilasi.anna@ 123456univet.hu
                Author information
                https://orcid.org/0000-0002-1634-6730
                https://orcid.org/0000-0001-7485-3661
                Article
                10.1177_2055116919892094
                10.1177/2055116919892094
                6904780
                31839979
                4bc6f88e-9278-4632-aa4d-d5cd5d88eeee
                © The Author(s) 2019

                This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License ( http://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages ( https://us.sagepub.com/en-us/nam/open-access-at-sage).

                History
                Funding
                Funded by: Emberi Eroforrások Minisztériuma, FundRef https://doi.org/10.13039/501100005881;
                Award ID: 17896-4/2018/FEKUTSTRAT
                Categories
                Short Communication
                Custom metadata
                July-December 2019
                ts1

                immunodeficiency virus,leukaemia virus,prevalence,phylogeny,hungary

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