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      Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia

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          Abstract

          Background

          As the largest group of mammalian species, which are also widely distributed all over the world, rodents are the natural reservoirs for many diverse zoonotic viruses. A comprehensive understanding of the core virome of diverse rodents should therefore assist in efforts to reduce the risk of future emergence or re-emergence of rodent-borne zoonotic pathogens.

          Results

          This study aimed to describe the viral range that could be detected in the lungs of rodents from Mainland Southeast Asia. Lung samples were collected from 3284 rodents and insectivores of the orders Rodentia, Scandentia, and Eulipotyphla in eighteen provinces of Thailand, Lao PDR, and Cambodia throughout 2006–2018. Meta-transcriptomic analysis was used to outline the unique spectral characteristics of the mammalian viruses within these lungs and the ecological and genetic imprints of the novel viruses. Many mammalian- or arthropod-related viruses from distinct evolutionary lineages were reported for the first time in these species, and viruses related to known pathogens were characterized for their genomic and evolutionary characteristics, host species, and locations.

          Conclusions

          These results expand our understanding of the core viromes of rodents and insectivores from Mainland Southeast Asia and suggest that a high diversity of viruses remains to be found in rodent species of this area. These findings, combined with our previous virome data from China, increase our knowledge of the viral community in wildlife and arthropod vectors in emerging disease hotspots of East and Southeast Asia.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s40168-020-00965-z.

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          Most cited references91

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          A new coronavirus associated with human respiratory disease in China

          Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health 1–3 . Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing 4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China 5 . This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.
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            MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

            We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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              Interactive Tree Of Life (iTOL) v4: recent updates and new developments

              Abstract The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.
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                Author and article information

                Contributors
                wuzq2009@ipbcams.ac.cn
                zdsys@vip.sina.com
                Journal
                Microbiome
                Microbiome
                Microbiome
                BioMed Central (London )
                2049-2618
                21 January 2021
                21 January 2021
                2021
                : 9
                Affiliations
                [1 ]GRID grid.506261.6, ISNI 0000 0001 0706 7839, NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, , Chinese Academy of Medical Sciences & Peking Union Medical College, ; Beijing, PR China
                [2 ]GRID grid.506261.6, ISNI 0000 0001 0706 7839, Key Laboratory of Respiratory Disease Pathogenomics, , Chinese Academy of Medical Sciences & Peking Union Medical College, ; Beijing, PR China
                [3 ]GRID grid.420826.a, ISNI 0000 0004 0409 4702, EcoHealth Alliance, ; New York, NY USA
                [4 ]Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Vietnam
                [5 ]GRID grid.269823.4, ISNI 0000 0001 2164 6888, Wildlife Conservation Society, Health Program, ; Bronx, NY USA
                [6 ]GRID grid.9723.f, ISNI 0000 0001 0944 049X, Faculty of Veterinary Technology, , Kasetsart University, ; Bangkok, Thailand
                [7 ]GRID grid.10223.32, ISNI 0000 0004 1937 0490, Faculty of Tropical Medicine, , Mahidol University, ; Bangkok, Thailand
                [8 ]GlaxoSmithKline Vaccines, Singapore City, Singapore
                [9 ]GRID grid.418537.c, Virology Unit, , Institut Pasteur in Cambodia, ; Phnom Penh, Cambodia
                [10 ]GRID grid.464500.3, ISNI 0000 0004 1758 1139, Yunnan Institute of Parasitic Diseases, ; Pu’er, PR China
                [11 ]GRID grid.17063.33, ISNI 0000 0001 2157 2938, Department of Laboratory Medicine and Pathobiology, , University of Toronto, ; Toronto, Canada
                Article
                965
                10.1186/s40168-020-00965-z
                7818139
                0253c1da-49c5-456d-b1d0-fa24cdc019d8
                © The Author(s) 2021

                Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 81772228
                Award Recipient :
                Funded by: Mega-projects of Science Research for the thirteenth Five-Year Plan (CN)
                Award ID: 2018ZX10101001
                Award Recipient :
                Funded by: CAMS Innovation Fund for Medical Sciences
                Award ID: 2016-I2M-1-014 and 2017-I2M-B&R-12
                Award Recipient :
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                © The Author(s) 2021

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