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      Isolation and genome characterization of Lloviu virus from Italian Schreibers’s bats

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          Abstract

          Lloviu cuevavirus (LLOV) was the first identified member of Filoviridae family outside the Ebola and Marburgvirus genera. A massive die-off of Schreibers’s bats ( Miniopterus schreibersii) in the Iberian Peninsula in 2002 led to its initial discovery. Recent studies with recombinant and wild-type LLOV isolates confirmed the zoonotic nature of the virus in vitro. We examined bat samples from Italy for the presence of LLOV in an area outside of the currently known distribution range of the virus. We detected one positive sample from 2020, sequenced the complete coding region of the viral genome and established an infectious isolate of the virus. In addition, we performed the first comprehensive evolutionary analysis of the virus, using the Spanish, Hungarian and the Italian sequences. The most important achievement of this study is the establishment of an additional infectious LLOV isolate from a bat sample using the SuBK12-08 cells, demonstrating that this cell line is highly susceptible to LLOV infection and confirming the previous observation that these bats are effective hosts of the virus in nature. This result further strengthens the role of bats as the natural hosts for zoonotic filoviruses.

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          Minimap2: pairwise alignment for nucleotide sequences

          Heng Li (2018)
          Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.
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            MEGA11: Molecular Evolutionary Genetics Analysis Version 11

            The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor , and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net .
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              Twelve years of SAMtools and BCFtools

              Abstract Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.
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                Author and article information

                Contributors
                kemenesi.gabor@gmail.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                13 July 2023
                13 July 2023
                2023
                : 13
                : 11310
                Affiliations
                [1 ]GRID grid.9679.1, ISNI 0000 0001 0663 9479, National Laboratory of Virology, Szentágothai Research Centre, , University of Pécs, ; Pécs, Hungary
                [2 ]GRID grid.9679.1, ISNI 0000 0001 0663 9479, Faculty of Sciences, Institute of Biology, , University of Pécs, ; Pécs, Hungary
                [3 ]GRID grid.189504.1, ISNI 0000 0004 1936 7558, Department of Virology, Immunology and Microbiology, , Boston University Chobanian & Avedisian School of Medicine, ; Boston, MA USA
                [4 ]GRID grid.189504.1, ISNI 0000 0004 1936 7558, National Emerging Infectious Diseases Laboratories, , Boston University, ; Boston, MA USA
                [5 ]GRID grid.189504.1, ISNI 0000 0004 1936 7558, Center for Emerging Infectious Diseases Policy and Research, , Boston University, ; Boston, MA USA
                [6 ]GRID grid.6292.f, ISNI 0000 0004 1757 1758, ST.E.R.N.A., Forlì, Department of Biological, Geological and Environmental Sciences, , University of Bologna, ; Bologna, Italy
                [7 ]UOC Virologia, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Roma, Italy
                [8 ]GRID grid.413454.3, ISNI 0000 0001 1958 0162, Institute of Systematics and Evolution of Animals, , Polish Academy of Sciences, ; Kraków, Poland
                [9 ]GRID grid.419593.3, ISNI 0000 0004 1805 1826, OIE Collaborating Centre and National Reference Centre for Infectious Diseases at the Animal-Human Interface, , Istituto Zooprofilattico Sperimentale delle Venezie, ; Legnaro, Italy
                [10 ]GRID grid.419190.4, ISNI 0000 0001 2300 669X, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, ; Madrid, Spain
                Author information
                http://orcid.org/0000-0002-7201-9646
                http://orcid.org/0000-0001-8454-3472
                http://orcid.org/0000-0003-3116-4633
                http://orcid.org/0000-0002-4693-9406
                http://orcid.org/0000-0002-3503-8901
                http://orcid.org/0000-0002-1910-4024
                http://orcid.org/0000-0002-3913-0430
                http://orcid.org/0000-0003-3547-9376
                http://orcid.org/0000-0003-2835-492X
                http://orcid.org/0000-0001-9775-3065
                Article
                38364
                10.1038/s41598-023-38364-7
                10344946
                37443182
                015deab6-be2f-497a-abdb-468e01fb0e97
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 18 April 2023
                : 6 July 2023
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100011019, Nemzeti Kutatási Fejlesztési és Innovációs Hivatal;
                Award ID: FK137778
                Award ID: FK131465
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000780, European Commission;
                Award ID: RRF-2.3.1-21-2022-00010
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R21AI169646
                Award Recipient :
                Funded by: University of Pécs
                Categories
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                © Springer Nature Limited 2023

                Uncategorized
                virology,viral reservoirs,infectious diseases
                Uncategorized
                virology, viral reservoirs, infectious diseases

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