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      Whole-genome sequencing and phylogenetic analysis of rabies viruses from Jordan

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          Abstract

          Human fatalities caused by rabies are rarely reported in Jordan; however, domestic animals are more likely to fall victim to rabies compared to wild animals, at least this is the case in Jordan due to the presence of canine rabies. In this study, twelve brain samples from domestic and wild animals suspected of being infected with rabies virus from different regions of Jordan were collected during 2019. Seven of them tested positive using the fluorescent antibody test and real-time SYBR RT-PCR assay. Five specimens were from stray dogs and two from foxes. The whole genome sequences were obtained from the positive samples. Sequence analysis showed that one dog virus from Al Quwaysimah city located in Amman governorate, was closely related to an Israeli strain belonging to a Cosmopolitan ME1a clade. The genomes of the remaining six viruses (four from dogs and two from foxes) collected from different areas of Jordan were genetically-related to each other and clustered together with sequences from Iran and Turkey; all belong to Cosmopolitan ME2 clade. These sequences were analyzed with six other Jordanian rabies virus nucleoprotein (N) gene sequences available in the public database, five of them belong to ME1a clade and one belongs to ME1b clade. Rabies virus whole genome data is scarce across the Middle East. This study provides a better understanding of the molecular epidemiology of rabies virus in the region.

          Author summary

          In this study, we performed whole genome sequencing (WGS) for rabies virus (RABV) isolates from seven samples, five of which were of stray dogs, and the other two were from foxes. Specimens were collected from animals across Jordan, including Balqa, Amman, Irbid, Tafilah, and Madaba governorates. Six out of the seven isolates were belonging to the Cosmopolitan ME2 clade, which related to the Iranian and Turkish sequences. This is not the case previously, where the majority of the Jordanian isolates belong to Cosmopolitan ME1a clade and closely related to the sequences from Israel. This shift might be due to the applied regulations across borders between Jordan and Israel. Besides the growth in travel and trade movement between Jordan and Turkey, where the latter is a border country with Iran. These collected data, where such studies are not common in the Middle East countries, will enhance our understanding of the RABV evolution and epidemiology in the region for rapid and effective response for rabies virus outbreaks.

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          Most cited references31

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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              Fast and accurate long-read alignment with Burrows–Wheeler transform

              Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: Writing – review & editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: Software
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Negl Trop Dis
                PLoS Negl Trop Dis
                plos
                plosntds
                PLoS Neglected Tropical Diseases
                Public Library of Science (San Francisco, CA USA )
                1935-2727
                1935-2735
                20 May 2021
                May 2021
                : 15
                : 5
                : e0009431
                Affiliations
                [1 ] Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, Jordan
                [2 ] Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
                University of Glasgow, UNITED KINGDOM
                Author notes

                The authors have declared that no competing interests exist

                Author information
                https://orcid.org/0000-0003-0064-0190
                https://orcid.org/0000-0001-9638-8270
                https://orcid.org/0000-0001-9215-088X
                https://orcid.org/0000-0002-3243-6154
                https://orcid.org/0000-0002-6022-348X
                Article
                PNTD-D-20-02158
                10.1371/journal.pntd.0009431
                8171950
                34014930
                bb249d50-36a7-4172-9919-29e0f3cfe563
                © 2021 AL-Eitan et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 11 December 2020
                : 30 April 2021
                Page count
                Figures: 3, Tables: 1, Pages: 11
                Funding
                Funded by: Department for Environment, Food & Rural Affairs
                Award ID: SE0431/SE0433
                Funded by: The European Union's Horizon 2020 research and innovation programme
                Award ID: 871029 EVA-GLOBAL
                This work was financially supported by the UK Department for Environment, Food and Rural Affairs (Defra), Scottish and Welsh Government under grant agreement No. SE0431/SE0433. This study was also supported by the European Union's Horizon 2020 research and innovation programme under grant agreement No. 871029 EVA-GLOBAL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Lyssavirus
                Rabies Virus
                Biology and Life Sciences
                Microbiology
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                Microbial Pathogens
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                Custom metadata
                vor-update-to-uncorrected-proof
                2021-06-02
                All genomic sequences files are available from the European Nucleotide Archive (ENA) database (accession no. PRJEB41551).

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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