Genetic diversity of the JC polyomavirus (JCPyV) and mitochondrial DNA ancestry in Misiones, Argentina

Infection, Genetics and Evolution - Tập 75 - Trang 104011 - 2019
Daiana J. Sanabria1,2, Laura N. Mojsiejczuk2,3, Carolina Torres3, Alejandro G. Meyer1, Viviana A. Mbayed2,3, Domingo J. Liotta1, Rodolfo H. Campos3, Theodore G. Schurr4, Ines Badano1,2
1Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
2Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
3Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
4Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania. Philadelphia, PA 19104-6398, USA

Tài liệu tham khảo

Achilli, 2008, The phylogeny of the four pan-American mtDNA haplogroups: Implications for evolutionary and disease studies, PLoS ONE, 3, 10.1371/journal.pone.0001764 Agostini, 1997, Asian genotypes of JC virus in Native Americans and in a Pacific Island population: markers of viral evolution and human migration, Proc Natl Acad Sci U S A, 94, 14542, 10.1073/pnas.94.26.14542 Agostini, 2001, Genotypes of JC virus in East, Central and Southwest Europe, J Gen Virol, 82, 1221, 10.1099/0022-1317-82-5-1221 Assetta, 2017, The biology of JC polyomavirus, Biol Chem, 398, 839, 10.1515/hsz-2016-0345 Badano, 2018, Mitochondrial DNA ancestry, HPV infection and the risk of cervical cancer in a multiethnic population of northeastern Argentina, PLoS ONE, 13, 10.1371/journal.pone.0190966 Bartolomé, 2000 Bofill-Mas, 2001, Potential transmission of human polyomaviruses through the gastrointestinal tract after exposure to virions or viral DNA, J Virol, 75, 10290, 10.1128/JVI.75.21.10290-10299.2001 Boldorini, 2011, Serological evidence of vertical transmission of JC and BK polyomaviruses in humans, J Gen Virol, 92, 1044, 10.1099/vir.0.028571-0 Catelli, 2011, The impact of modern migrations on present-day multi-ethnic Argentina as recorded on the mitochondrial DNA genome, BMC Genet, 12, 77, 10.1186/1471-2156-12-77 Cayres-Vallinoto, 2012, Human JCV infections as a bio-anthropological marker of the formation of Brazilian Amazonian Populations, PLoS ONE, 7, 10.1371/journal.pone.0046523 Chang, 2002, High incidence of JC viruria in JC-seropositive older individuals, J Neurovirol, 8, 447, 10.1080/13550280260422758 Corach, 2010, Inferring continental ancestry of Argentineans from autosomal, Y-chromosomal and mitochondrial DNA, Ann Hum Genet, 74, 65, 10.1111/j.1469-1809.2009.00556.x Cui, 2004, Chinese strains (Type 7) of JC virus are afro-asiatic in origin but are phylogenetically distinct from the Mongolian and Indian strains (Type 2D) and the Korean and Japanese strains (Type 2A), J Mol Evol, 58, 568, 10.1007/s00239-003-2579-2 Darriba, 2012, jModelTest 2: More models, new heuristics and parallel computing, Nat Methods, 9, 772, 10.1038/nmeth.2109 Fernandez-Cobo, 2002, Strains of JC virus in Amerind-speakers of North America (Salish) and South America (Guaraní), Na-Dene-speakers of New Mexico (Navajo), and modern Japanese suggest links through an ancestral Asian population, Am J Phys Anthropol, 118, 154, 10.1002/ajpa.10085 Firth, 2010, Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses, Mol Biol Evol, 27, 2038, 10.1093/molbev/msq088 Gallero, 2009 Gallero, 2010, La territorialización de la germaneidad en los alemanes-brasileños de Misiones, Argentina, Iberoamericana, 39, 77 Gallero, 2009, 16, 245 Hall, 1999, BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT, Nucleic Acids Symp Ser, 41, 95 Hirsch, 2013, The human JC polyomavirus (JCPyV): Virological background and clinical implications, APMIS, 121, 685, 10.1111/apm.12128 Holmes, 2008, Evolutionary history and phylogeography of human viruses, Annu Rev Microbiol, 62, 307, 10.1146/annurev.micro.62.081307.162912 Ikegaya, 2005, Genetic diversity of JC virus in the Saami and the Finns: implications for their population history, Am J Phys Anthropol, 128, 185, 10.1002/ajpa.20189 Instituto Provincial de Estadísticas y Censos (IPEC), 2015 Kato, 1997, Lack of evidence for the transmission of JC polyomavirus between human populations, Arch Virol., 142, 875, 10.1007/s007050050125 Kemp, 2010, Human variation in the Americas: The integration of archeology and biological anthropology, 12 Kitamura, 1990, High incidence of urinary JC virus excretion in nonimmunosuppressed older patients, J Infect Dis, 161, 1128, 10.1093/infdis/161.6.1128 Kitamura, 1994, Transmission of the human polyomavirus JC virus occurs both within the family and outside the family, J Clin Microbiol., 32, 2359, 10.1128/jcm.32.10.2359-2363.1994 Kitchen, 2008, Utility of DNA viruses for studying human host history: case study of JC virus, Mol Phylogenet Evol, 46, 673, 10.1016/j.ympev.2007.09.005 Kunitake, 1995, Parent-to-child transmission is relatively common in the spread of the human polyomavirus JC virus, J Clin Microbiol, 33, 1448, 10.1128/jcm.33.6.1448-1451.1995 Landis, 1977, An application of hierarchical kappa-type statistics in the assessment of majority agreement among multiple observers, Biometrics, 33, 363, 10.2307/2529786 Larkin, 2007, Clustal W and Clustal X version 2.0, Bioinformatics, 23, 2947, 10.1093/bioinformatics/btm404 Lee, 2017, Mitochondrial nucleoid: shield and switch of the mitochondrial genome, Oxid Med Cell Longev, 2017, 10.1155/2017/8060949 Miranda, 2003, Genetic diversity of JC virus in the modern Filipino population: implications for the peopling of the Philippines, Am J Phys Anthropol, 120, 125, 10.1002/ajpa.10155 Pakendorf, 2005, Mitochondrial DNA and human evolution, Annu Rev Genomics Hum Genet., 6, 165, 10.1146/annurev.genom.6.080604.162249 Rambaut A. FigTree v. 1.4.0 Rambaut Rigby, 2000, Statistical methods in epidemiology. v. Towards an understanding of the kappa coefficient, Disabil Rehabil, 22, 339, 10.1080/096382800296575 Ronquist, 2012, MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, Syst Biol, 61, 539, 10.1093/sysbio/sys029 Salzano, 2014, Interethnic admixture and the evolution of Latin American populations, Genet Mol Biol, 37, 151, 10.1590/S1415-47572014000200003 Schaan, 2017, Ribeiro-Dos-Santos Â. mtDNA structure: the women who formed the Brazilian Northeast, BMC Evol Biol., 17, 185, 10.1186/s12862-017-1027-7 Schurr, 2004, Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: evolutionary and demographic evidence, Am J Hum Biol, 16, 420, 10.1002/ajhb.20041 Schurr, 1990, Amerindian mitochondrial DNAs have rare Asian mutations at high frequencies, suggesting they derived from four primary maternal lineages, Am J Hum Genet, 46, 613 Shackelton, 2006, JC virus evolution and its association with human populations, J Virol, 80, 9928, 10.1128/JVI.00441-06 Sharp, 2011, Evaluating the evidence for virus/host co-evolution, Curr Opin Virol, 1, 436, 10.1016/j.coviro.2011.10.018 Stoner, 2000, JC virus as a marker of human migration to the Americas, Microbes Infect, 2, 1905, 10.1016/S1286-4579(00)01339-3 Sugimoto, 2002, JC virus strains indigenous to northeastern Siberians and Canadian Inuits are unique but evolutionally related to those distributed throughout Europe and Mediterranean areas, J Mol Evol, 55, 322, 10.1007/s00239-001-2329-2 Suzuki, 2002, Asian genotypes of JC virus in Japanese-Americans suggest familial transmission, J Virol, 76, 10074, 10.1128/JVI.76.19.10074-10078.2002 Takasaka, 2004, Subtypes of BK virus prevalent in Japan and variation in their transcriptional control region, J Gen Virol, 85, 2821, 10.1099/vir.0.80363-0 Takasaka, 2006, Phylogenetic analysis of major African genotype (Af2) of JC virus: Implications for origin and dispersals of modern Africans, Am J Phys Anthropol, 129, 465, 10.1002/ajpa.20208 Torres, 2016, High diversity of human polyomaviruses in environmental and clinical samples in Argentina: Detection of JC, BK, Merkel-cell, Malawi, and human 6 and 7 polyomaviruses, Sci Total Environ, 542, 192, 10.1016/j.scitotenv.2015.10.047 Torroni, 1993, Asian affinities and continental radiation of the four founding Native American mtDNAs, Am J Hum Genet, 53, 563 Torroni, 1996, Classification of European mtDNAs from an analysis of three European populations, Genetics, 144, 1835, 10.1093/genetics/144.4.1835 Torroni, 2006, Harvesting the fruit of the human mtDNA tree, Trends Genet, 22, 339, 10.1016/j.tig.2006.04.001 van Oven, 2009, Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation, Hum Mutat, 30, E386, 10.1002/humu.20921 Weissensteiner, 2016, HaploGrep 2: Mitochondrial haplogroup classification in the era of high-throughput sequencing, Nucleic Acids Res, 44, W58, 10.1093/nar/gkw233 White, 2011, Pathogenesis of Progressive Multifocal Leukoencephalopathy - Revisited, J Infect Dis, 203, 578, 10.1093/infdis/jiq097 Yanagihara, 2002, JC virus genotypes in the western Pacific suggest Asian mainland relationships and virus association with early population movements, Hum Biol, 74, 473, 10.1353/hub.2002.0037 Yogo, 2004, JC virus genotyping offers a new paradigm in the study of human populations, Rev Med Virol, 14, 179, 10.1002/rmv.428 Zheng, 2004, Unambiguous identification of JC polyomavirus strains transmitted from parents to children, Arch Virol, 149, 261, 10.1007/s00705-003-0214-6 Zheng, 2005, Characterization of the VP1 loop mutations widespread among JC polyomavirus isolates associated with progressive multifocal leukoencephalopathy, Biochem Biophys Res Commun, 333, 996, 10.1016/j.bbrc.2005.06.012