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Relatives of rubella virus in diverse mammals

  • 1.

    Lambert, N., Strebel, P., Orenstein, W., Icenogle, J. & Poland, G. A. Rubella. Lancet 385, 2297–2307 (2015).

    PubMed  PubMed Central  Article  Google Scholar 

  • 2.

    Zhou, Y., Ushijima, H. & Frey, T. K. Genomic analysis of diverse rubella virus genotypes. J. Gen. Virol. 88, 932–941 (2007).

    CAS  PubMed  Article  Google Scholar 

  • 3.

    Chen, J.-P., Strauss, J. H., Strauss, E. G. & Frey, T. K. Characterization of the rubella virus nonstructural protease domain and its cleavage site. J. Virol. 70, 4707–4713 (1996).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 4.

    Perelygina, L. et al. Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies. PLoS Pathog. 15, e1008080 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 5.

    DuBois, R. M. et al. Functional and evolutionary insight from the crystal structure of rubella virus protein E1. Nature 493, 552–556 (2013).

    CAS  PubMed  Article  ADS  Google Scholar 

  • 6.

    McCarthy, M., Lovett, A., Kerman, R. H., Overstreet, A. & Wolinsky, J. S. Immunodominant T-cell epitopes of rubella virus structural proteins defined by synthetic peptides. J. Virol. 67, 673–681 (1993).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 7.

    Maton, W. G. Some account of a rash liable to be mistaken for scarlatina. Med. Trans. R. Coll. Physicians 5, 149–165 (1815).

    Google Scholar 

  • 8.

    Cooper, L. Z. The history and medical consequences of rubella. Rev. Infect. Dis. 7, S2–S10 (1985).

    PubMed  Article  Google Scholar 

  • 9.

    Gregg, N. M. Congenital cataract following German measles in the mother. Aust. N. Z. J. Ophthalmol. 3, 35–46 (1941).

    Google Scholar 

  • 10.

    Parkman, P. D., Buescher, E. L. & Artenstein, M. S. Recovery of rubella virus from army recruits. Proc. Soc. Exp. Biol. Med. 111, 225–230 (1962).

    CAS  PubMed  Article  Google Scholar 

  • 11.

    Weller, T. H. & Neva, F. A. Propagation in tissue culture of cytopathic agents from patients with rubella-like illness. Proc. Soc. Exp. Biol. Med. 111, 215–225 (1962).

    Article  Google Scholar 

  • 12.

    Swan, C., Tostevin, A. L. & Black, G. H. Final observations on congenital defects in infants following infectious diseases during pregnancy, with special reference to rubella. Med. J. Aust. 2, 889–908 (1946).

    CAS  PubMed  Article  Google Scholar 

  • 13.

    Edmunds, W. J., Gay, N. J., Kretzschmar, M., Pebody, R. G. & Wachmann, H. The pre-vaccination epidemiology of measles, mumps and rubella in Europe: implications for modelling studies. Epidemiol. Infect. 125, 635–650 (2000).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 14.

    Gonzales, J. A. et al. Association of ocular inflammation and rubella virus persistence. JAMA Ophthalmol. 137, 435–438 (2019).

    PubMed  Article  Google Scholar 

  • 15.

    Grant, G. B., Reef, S. E., Patel, M., Knapp, J. K. & Dabbagh, A. Progress in rubella and congenital rubella syndrome control and elimination — worldwide, 2000–2016. MMWR Morb. Mortal. Wkly. Rep. 66, 1256–1260 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  • 16.

    Namuwulya, P. et al. Phylogenetic analysis of rubella viruses identified in Uganda, 2003–2012. J. Med. Virol. 86, 2107–2113 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

  • 17.

    Kretsinger, K., Strebel, P., Kezaala, R. & Goodson, J. L. Transitioning lessons learned and assets of the global polio eradication initiative to global and regional measles and rubella elimination. J. Infect. Dis. 216, S308–S315 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  • 18.

    Wolfe, N. D., Dunavan, C. P. & Diamond, J. Origins of major human infectious diseases. Nature 447, 279–283 (2007).

    CAS  PubMed  PubMed Central  Article  ADS  Google Scholar 

  • 19.

    Fahr, J. in Mammals of Africa. Vol. IV: Hedgehogs, Shrews and Bats (eds Happold, M. & Happold, D. C. D.) 380–383 (Bloomsbury, 2013).

  • 20.

    Jetz, W., McPherson, J. M. & Guralnick, R. P. Integrating biodiversity distribution knowledge: toward a global map of life. Trends Ecol. Evol. 27, 151–159 (2012).

    Article  Google Scholar 

  • 21.

    O’Shea, T. J., Bogan, M. A. & Ellison, L. E. Monitoring Trends in Bat Populations of the United States and Territories: Status of the Science and Recommendations for the Future. Information and Technology Report USGS/BRD/ITR–2003–0003 (US Department of the Interior, US Geological Survey Washington, 2003).

  • 22.

    Landau, I. & Chabaud, A.-G. Description de Plasmodium cyclopsi n. sp. parasite du Microchirotère Hipposideros cyclops à Makokou (Gabon). Ann. Parasitol. Hum. Comp. 53, 247–253 (1978).

    CAS  PubMed  Article  Google Scholar 

  • 23.

    Schaer, J. et al. High diversity of West African bat malaria parasites and a tight link with rodent Plasmodium taxa. Proc. Natl Acad. Sci. USA 110, 17415–17419 (2013).

    CAS  PubMed  Article  ADS  Google Scholar 

  • 24.

    Michaux, J. R., Libois, R. & Filippucci, M.-G. So close and so different: comparative phylogeography of two small mammal species, the yellow-necked fieldmouse (Apodemus flavicollis) and the woodmouse (Apodemus sylvaticus) in the Western Palearctic region. Heredity 94, 52–63 (2005).

    CAS  PubMed  Article  Google Scholar 

  • 25.

    Labuda, M. et al. Tick-borne encephalitis virus transmission between ticks cofeeding on specific immune natural rodent hosts. Virology 235, 138–143 (1997).

    CAS  PubMed  Article  Google Scholar 

  • 26.

    Klempa, B. et al. Complex evolution and epidemiology of Dobrava–Belgrade hantavirus: definition of genotypes and their characteristics. Arch. Virol. 158, 521–529 (2013).

    CAS  PubMed  Article  Google Scholar 

  • 27.

    Sibold, C. et al. Dobrava hantavirus causes hemorrhagic fever with renal syndrome in central Europe and is carried by two different Apodemus mice species. J. Med. Virol. 63, 158–167 (2001).

    CAS  PubMed  Article  Google Scholar 

  • 28.

    Oktem, I. M. et al. Dobrava–Belgrade virus in Apodemus flavicollis and A. uralensis mice, Turkey. Emerg. Infect. Dis. 20, 121–125 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

  • 29.

    Doty, J. B. et al. Isolation and characterization of Akhmeta virus from wild-caught rodents (Apodemus spp.) in Georgia. J. Virol. 93, e00966-19 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 30.

    Prpić, J. et al. First evidence of hepatitis E virus infection in a small mammal (yellow-necked mouse) from Croatia. PLoS ONE 14, e0225583 (2019).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 31.

    Hofmann, J., Renz, M., Meyer, S., von Haeseler, A. & Liebert, U. G. Phylogenetic analysis of rubella virus including new genotype I isolates. Virus Res. 96, 123–128 (2003).

    CAS  PubMed  Article  Google Scholar 

  • 32.

    Abernathy, E. et al. Analysis of whole genome sequences of 16 strains of rubella virus from the United States, 1961–2009. Virol. J. 10, 32 (2013).

    PubMed  PubMed Central  Article  Google Scholar 

  • 33.

    Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protocols 10, 845–858 (2015).

    CAS  PubMed  Article  Google Scholar 

  • 34.

    Wolinsky, J. S. et al. An antibody- and synthetic peptide-defined rubella virus E1 glycoprotein neutralization domain. J. Virol. 67, 961–968 (1993).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 35.

    Guy, C., Thiagavel, J., Mideo, N. & Ratcliffe, J. M. Phylogeny matters: revisiting ‘a comparison of bats and rodents as reservoirs of zoonotic viruses’. R. Soc. Open Sci. 6, 181182 (2019).

    PubMed  PubMed Central  Article  ADS  Google Scholar 

  • 36.

    Luis, A. D. et al. A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special? Proc. R. Soc. Lond. B 280, 20122753 (2013).

    Google Scholar 

  • 37.

    Olival, K. J. et al. Host and viral traits predict zoonotic spillover from mammals. Nature 546, 646–650 (2017).

    CAS  PubMed  PubMed Central  Article  ADS  Google Scholar 

  • 38.

    Frey, T. K. Neurological aspects of rubella virus infection. Intervirology 40, 167–175 (1997).

    CAS  PubMed  Article  Google Scholar 

  • 39.

    Bharadwaj, S. D. et al. Acute encephalitis with atypical presentation of rubella in family cluster, India. Emerg. Infect. Dis. 24, 1923–1925 (2018).

    PubMed  PubMed Central  Article  Google Scholar 

  • 40.

    Grant, G. B. et al. Accelerating measles and rubella elimination through research and innovation — findings from the Measles & Rubella Initiative research prioritization process, 2016. Vaccine 37, 5754–5761 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  • 41.

    Struhsaker, T. T. Ecology of an African Rain Forest: Logging in Kibale and the Conflict between Conservation and Exploitation (Univ. Press Florida, 1997).

  • 42.

    Plumptre, A. J. et al. The biodiversity of the Albertine Rift. Biol. Conserv. 134, 178–194 (2007).

    Article  Google Scholar 

  • 43.

    Ulrich, R. G. et al. Network “rodent-borne pathogens” in Germany: longitudinal studies on the geographical distribution and prevalence of hantavirus infections. Parasitol. Res. 103, S121–S129 (2008).

    PubMed  Article  Google Scholar 

  • 44.

    Schlegel, M. et al. Molecular identification of small mammal species using novel cytochrome b gene-derived degenerated primers. Biochem. Genet. 50, 440–447 (2012).

    CAS  PubMed  Article  Google Scholar 

  • 45.

    Foley, N. M. et al. How and why overcome the impediments to resolution: lessons from rhinolophid and hipposiderid bats. Mol. Biol. Evol. 32, 313–333 (2015).

    CAS  PubMed  Article  Google Scholar 

  • 46.

    Zhao, G. et al. VirusSeeker, a computational pipeline for virus discovery and virome composition analysis. Virology 503, 21–30 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 47.

    Bushnell, B. BBMap: a fast, accurate, splice-aware aligner. Version 37.78 https://sourceforge.net/projects/bbmap/ (2014).

  • 48.

    Andrews, S. FastQC. A quality control tool for high throughput sequence data. Version 0.11.5 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).

  • 49.

    Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 50.

    Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).

    CAS  PubMed  Article  Google Scholar 

  • 51.

    Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    CAS  Article  Google Scholar 

  • 52.

    Huson, D. H. et al. MEGAN community edition — interactive exploration and analysis of large-scale microbiome sequencing data. PLOS Comput. Biol. 12, e1004957 (2016).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 53.

    Wylezich, C., Papa, A., Beer, M. & Höper, D. A versatile sample processing workflow for metagenomic pathogen detection. Sci. Rep. 8, 13108 (2018).

    PubMed  PubMed Central  Article  ADS  CAS  Google Scholar 

  • 54.

    Scheuch, M., Höper, D. & Beer, M. RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets. BMC Bioinformatics 16, 69 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 55.

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 56.

    Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).

    MathSciNet  CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 57.

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 58.

    Hobman, T. C. & Gillam, S. In vitro and in vivo expression of rubella virus glycoprotein E2: the signal peptide is contained in the C-terminal region of capsid protein. Virology 173, 241–250 (1989).

    CAS  PubMed  Article  Google Scholar 

  • 59.

    Gasteiger, E. et al. in The Proteomics Protocols Handbook (ed Walker, J. M.) 571–607 (Humana Press, 2005).

  • 60.

    Forth, L. F. & Höper, D. Highly efficient library preparation for ion torrent sequencing using Y-adapters. Biotechniques 67, 229–237 (2019).

    CAS  PubMed  Article  Google Scholar 

  • 61.

    Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

    CAS  PubMed  Article  Google Scholar 

  • 62.

    Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).

    CAS  PubMed  Article  Google Scholar 

  • 63.

    Mitchell, A. L. et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47, D351–D360 (2019).

    CAS  PubMed  Article  Google Scholar 

  • 64.

    Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 65.

    Rose, A. S. & Hildebrand, P. W. NGL Viewer: a web application for molecular visualization. Nucleic Acids Res. 43, W576–W579 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 66.

    Benkert, P., Biasini, M. & Schwede, T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27, 343–350 (2011).

    CAS  PubMed  Article  Google Scholar 

  • 67.

    Korber, B. in Computational Analysis of HIV Molecular Sequences Ch. 4 (eds Rodrigo, A. G. & Learn, G. H.) 55–72 (Kluwer Academic Publishers, 2000).

  • 68.

    Leskovec, J. SNAP 2.1. http://snap.stanford.edu/snap-2.1/download.html (2013).


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