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Pereson MJ, Sanabria DJ, Torres C, Liotta DJ, Campos RH, Schurr TG, Di Lello FA, Badano I. Evolutionary analysis of JC polyomavirus in Misiones' population yields insight into the population dynamics of the early human dispersal in the Americas. Virology 2023; 585:100-108. [PMID: 37327595 DOI: 10.1016/j.virol.2023.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND JC polyomavirus (JCV) has an ethno-geographical distribution across human populations. OBJECTIVE Study the origins of the population of Misiones (Argentina) by using JCV as genetic marker. METHODS Viral detection and characterization was conducted by PCR amplification and evolutionary analysis of the intergenic region sequences. RESULTS 22 out of 121 samples were positive for JCV, including 5 viral lineages: MY (n = 8), Eu-a (n = 7), B1-c (n = 4), B1-b (n = 2) and Af2 (n = 1). MY sequences clustered within a branch of Native American origin that diverged from its Asian counterpart about 21,914 years ago (HPD 95% interval 15,383-30,177), followed by a sustained demographic expansion around 5000 years ago. CONCLUSIONS JCV in Misiones reflects the multiethnic origin of the current population, with an important Amerindian contribution. Analysis of the MY viral lineage shows a pattern consistent with the arrival of early human migrations to the Americas and a population expansion by the pre-Columbian native societies.
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Affiliation(s)
- Matias J Pereson
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Daiana J Sanabria
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina
| | - Carolina Torres
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Instituto Nacional de Medicina Tropical-ANLIS ''Dr. Malbrán'', Neuquén y Jujuy S/n, N3370, Puerto Iguazú, Misiones, Argentina
| | - Rodolfo H Campos
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania. Philadelphia, PA 19104-6398, USA
| | - Federico A Di Lello
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Inés Badano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina; Universidad Nacional de Misiones. Red de Laboratorios. Laboratorio de Antropología Biológica y Bioinformática Aplicada (LABBA). Misiones, Argentina.
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Begay RL, Garrison NA, Sage F, Bauer M, Knoki-Wilson U, Begay DH, Becenti-Pigman B, Claw KG. Weaving the Strands of Life ( Iiná Bitł'ool): History of Genetic Research Involving Navajo People. Hum Biol 2020; 91:189-208. [PMID: 32549035 PMCID: PMC7895446 DOI: 10.13110/humanbiology.91.3.04] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/18/2020] [Indexed: 12/15/2022]
Abstract
To date, some genetic studies offer medical benefits but lack a clear pathway to benefit for people from underrepresented backgrounds. Historically, Indigenous people, including the Diné (Navajo people), have raised concerns about the lack of benefits, misuse of DNA samples, lack of consultation, and ignoring of cultural and traditional ways of knowing. Shortly after the Navajo Nation Human Research Review Board was established in 1996, the Navajo Nation recognized growing concerns about genetic research, and in 2002 they established a moratorium on human genetic research studies. The moratorium effectively has protected their citizens from potential genetic research harms. Despite the placement of the moratorium, some genetic research studies have continued using blood and DNA samples from Navajo people. To understand the history of genetic research involving Navajo people, the authors conducted a literature review of genetic or genetics-related research publications that involved Navajo people, identifying 79 articles from the years 1926 to 2018. To their knowledge, no known literature review has comprehensively examined the history of genetic research in the Navajo community. This review divides the genetic research articles into the following general classifications: bacteria or virus genetics, blood and human leukocyte antigens, complex diseases, forensics, hereditary diseases, and population genetics and migration. The authors evaluated the methods reported in each article, described the number of Navajo individuals reported, recorded the academic and tribal approval statements, and noted whether the study considered Diné cultural values. Several studies focused on severe combined immunodeficiency disease, population history, neuropathy, albinism, and eye and skin disorders that affect Navajo people. The authors contextualize Diné ways of knowing related to genetics and health with Western scientific concepts to acknowledge the complex philosophy and belief system that guides Diné people and recognizes Indigenous science. They also encourage researchers to consider cultural perspectives and traditional knowledge that has the potential to create stronger conclusions and better-informed, ethical, and respectful science.
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Affiliation(s)
- Rene L Begay
- Centers for American Indian and Alaska Native Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, College of Letters and Science, University of California, Los Angeles, Los Angeles, California, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Navajo Nation Human Research Review Board, Window Rock, Arizona, USA
| | - Franklin Sage
- Diné Policy Institute, Navajo Nation, Tsaile, Arizona, USA
| | | | | | - David H Begay
- Navajo Nation Human Research Review Board, Window Rock, Arizona, USA
- Diné Hataałii Association, Navajo Nation, USA
| | | | - Katrina G Claw
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA,
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Evolution and molecular epidemiology of polyomaviruses. INFECTION GENETICS AND EVOLUTION 2019; 79:104150. [PMID: 31870972 DOI: 10.1016/j.meegid.2019.104150] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 02/08/2023]
Abstract
Polyomaviruses (PyVs) are small DNA viruses that infect several species, including mammals, birds and fishes. Their study gained momentum after the report of previously unidentified viral species in the past decade, and especially, since the description of the first polyomavirus clearly oncogenic for humans. The aim of this work was to review the most relevant aspects of the evolution and molecular epidemiology of polyomaviruses, allowing to reveal general evolutionary patterns and to identify some unaddressed issues and future challenges. The main points analysed included: 1) the species and genera assignation criteria; 2) the hypotheses, mechanisms and timescale of the ancient and recent evolutionary history of polyomaviruses; and 3) the molecular epidemiology of human viruses, with special attention to JC, BK and Merkel cell polyomaviruses.
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Sanabria DJ, Mojsiejczuk LN, Torres C, Meyer AG, Mbayed VA, Liotta DJ, Campos RH, Schurr TG, Badano I. Genetic diversity of the JC polyomavirus (JCPyV) and mitochondrial DNA ancestry in Misiones, Argentina. INFECTION GENETICS AND EVOLUTION 2019; 75:104011. [PMID: 31446138 DOI: 10.1016/j.meegid.2019.104011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/01/2019] [Accepted: 08/19/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND The use of human and viral genetic markers offers a novel way to study human migration in multiethnic populations of Latin America. OBJECTIVES Our goal was to characterize the genetic diversity and geographical origins of JC Polyomavirus (JCPyV) and the genetic ancestry of mitochondrial DNA (mtDNA) in inhabitants from 25 de Mayo, Misiones-Argentina, a small village of largely German ancestry located close to the border with Brazil. We also evaluated the extent of agreement between viral and mtDNA markers for the different ancestry components of this population. STUDY DESIGN 68 individuals were analyzed for JCPyV and mtDNA diversity. JCPyV detection and typing was conducted in urine samples by PCR amplification, sequencing and phylogenetic analysis of the VP1 gene. mtDNA ancestry was assessed through HVS1 sequencing, with the resulting haplotypes being classified into haplogroups of Amerindian, European and African origin. The distribution of JCPyV diversity and mtDNA ancestry in the population was statistically evaluated by Fisher exact test and the level of agreement of both markers at the individual level was evaluated by Cohen's kappa coefficient. RESULTS Our analysis showed that 57.4% of the samples were positive for JCPyV. Of these, the 47.6% were Asian-American Type 2, 33.3% European Type 1 and 19.1% African Type 3 in origin. The mtDNA ancestry of the study participants was 33.3% Amerindian and 66.7% European. There was a significant difference among the distribution of JCPyV diversity and mtDNA ancestry (p = 0.009) and at the individual level there was no correlation between the distribution of the both markers (κ = 0.154, p = 0.297). CONCLUSION The apparent incongruence between JCPyV diversity and mtDNA ancestry may reflect the original settlement process and more recent migration to 25 de Mayo, the latter involving viral spread through migrants from Brazil. Some potential limitations to our interpretations are also discussed.
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Affiliation(s)
- Daiana J Sanabria
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Laura N Mojsiejczuk
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Carolina Torres
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandro G Meyer
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Viviana A Mbayed
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Rodolfo H Campos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
| | - Ines Badano
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
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Levican J, Levican A, Ampuero M, Gaggero A. JC polyomavirus circulation in one-year surveillance in wastewater in Santiago, Chile. INFECTION GENETICS AND EVOLUTION 2019; 71:151-158. [PMID: 30905776 DOI: 10.1016/j.meegid.2019.03.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/19/2019] [Accepted: 03/20/2019] [Indexed: 11/27/2022]
Abstract
Human polyomavirus JC (JCPyV) is a widely distributed viral agent and because it high resistance against environmental conditions it is frequently recovered from diverse sources of water and is considered a good marker for human pollution. Phylogenetic analysis of JCPyV isolated in different part of the world has revealed 7 genotypes, which have been associated with specific populations or ethnics groups. This feature has been used to trace pre-historic and historic human migration patterns across the world. Although there are many reports describing genotypes distribution around the world, data on JCPyV genotypes in the southernmost areas of South America are scarce. The goal of this study is to detect and characterize the JCPyV that circulates in Santiago, Chile using sewage samples from wastewater treatment plants (WWTP). Sewage samples were obtained monthly during 1 year from three WWTPs which together process about 80% of wastewater generated in the city of Santiago, Chile. Our results show that JCPyV profusely circulates in Santiago, Chile, because it was detected in 80.56% of the samples, reinforcing the use of JCPyV as a feasible marker to assess human environmental pollution. JCPyV was detected in high frequency in influents and effluents samples, with the largest WWTPs showing the highest percentage of detection and viral loads. In the phylogenetic analysis the Chilean sequences clustered mainly with genotype 2A (Asian genotype). This is similar to that previously reported from Buenos Aires, Argentina and divergent to data from Brazil, where the circulation of European subtypes 1 and 4 and African subtypes 3 and 6 has been described.
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Affiliation(s)
- Jorge Levican
- Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Arturo Levican
- Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Manuel Ampuero
- Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Aldo Gaggero
- Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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Torres C, Barrios ME, Cammarata RV, Cisterna DM, Estrada T, Martini Novas S, Cahn P, Blanco Fernández MD, Mbayed VA. 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. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 542:192-202. [PMID: 26519580 DOI: 10.1016/j.scitotenv.2015.10.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/01/2015] [Accepted: 10/08/2015] [Indexed: 06/05/2023]
Abstract
New human polyomaviruses have been recently described. The aim of this work was to detect and characterize human polyomaviruses circulating in Argentina by recovering viruses from environmental and sewage samples and evaluating their potential role as viral indicators of human waste contamination. Analysis was performed in a wider context including viruses from clinical samples from an immunocompromised population. River water and sewage samples were analyzed as a strategy to study the molecular epidemiology of viruses excreted by millions of people. Samples belonged to the Matanza-Riachuelo River (2005-2006: n=25 and 2012: n=20) and sewage from Buenos Aires city and suburbs (2011 and 2013: n=24). Viral detection was performed by PCR and the amplified viral genomes were characterized by phylogenetic analysis. Polyomaviruses were detected in 95.8% of sewage samples, identifying BKPyV (87.5%), JCPyV (83.3%), MCPyV (8.3%) and HPyV6 (8.3%). Besides, one sample collected in 2009 resulted positive for HPyV7. In 2005-2006, polyomaviruses were detected in 84.0% of river water samples, with the highest detection for MCPyV (52.0%), followed by BKPyV (44.0%), JCPyV (20.0%) and MWPyV (4.0%). In 2012, polyomaviruses were detected in 85.0% of river samples, finding JCPyV (85.0%), BKPyV (75.0%), MCPyV (25.0%) and HPyV6 (25.0%). Also, polyomaviruses, including JCPyV, BKPyV and MCPyV, were detected in 63.2% of urine samples from patients infected with HIV (n=19). Characterization indicated the coexistence of different genotypes and variants for each virus, particularly in sewage. MCPyV sequences (the only sequences from Argentina) formed a monophyletic group with the single sequence available for South America (French Guiana). The high level of detection and viral diversity found by environmental surveillance, which involved the characterization of viruses not previously described in South America, reinforces the usefulness of this approach to monitor viral contamination and describe the viral epidemiology in the general population.
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Affiliation(s)
- Carolina Torres
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, Ciudad Autónoma de Buenos Aires (C1113AAD), Argentina; CONICET, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires (C1033AAJ), Argentina.
| | - Melina Elizabeth Barrios
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, Ciudad Autónoma de Buenos Aires (C1113AAD), Argentina
| | - Robertina Viviana Cammarata
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, Ciudad Autónoma de Buenos Aires (C1113AAD), Argentina; CONICET, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires (C1033AAJ), Argentina
| | - Daniel Marcelo Cisterna
- Servicio de Neurovirosis, INEI-ANLIS "Dr. Carlos G. Malbrán", Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires (C1282AFF), Argentina
| | - Tatiana Estrada
- División Infectología, Hospital General de Agudos "Juan A. Fernández", Cerviño 3356, Ciudad Autónoma de Buenos Aires (C1425AGP), Argentina
| | - Sergio Martini Novas
- División Infectología, Hospital General de Agudos "Juan A. Fernández", Cerviño 3356, Ciudad Autónoma de Buenos Aires (C1425AGP), Argentina
| | - Pedro Cahn
- División Infectología, Hospital General de Agudos "Juan A. Fernández", Cerviño 3356, Ciudad Autónoma de Buenos Aires (C1425AGP), Argentina
| | - María Dolores Blanco Fernández
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, Ciudad Autónoma de Buenos Aires (C1113AAD), Argentina; CONICET, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires (C1033AAJ), Argentina
| | - Viviana Andrea Mbayed
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, Ciudad Autónoma de Buenos Aires (C1113AAD), Argentina; CONICET, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires (C1033AAJ), Argentina
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Karalic D, Lazarevic I, Knezevic A, Cupic M, Jevtovic D, Jovanovic T. Distribution of JC virus genotypes among serbian patients infected with HIV and in healthy donors. J Med Virol 2013; 86:411-8. [DOI: 10.1002/jmv.23796] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Danijela Karalic
- University of Belgrade, Faculty of Medicine, Institute of Microbiology and Immunology; Belgrade Serbia
| | - Ivana Lazarevic
- University of Belgrade, Faculty of Medicine, Institute of Microbiology and Immunology; Belgrade Serbia
| | - Aleksandra Knezevic
- University of Belgrade, Faculty of Medicine, Institute of Microbiology and Immunology; Belgrade Serbia
| | - Maja Cupic
- University of Belgrade, Faculty of Medicine, Institute of Microbiology and Immunology; Belgrade Serbia
| | - Djordje Jevtovic
- University of Belgrade, Faculty of Medicine, Clinics of Infectious and Tropical Diseases, Clinical Center of Serbia; Belgrade Serbia
| | - Tanja Jovanovic
- University of Belgrade, Faculty of Medicine, Institute of Microbiology and Immunology; Belgrade Serbia
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Erickson RP. Autosomal recessive diseases among the Athabaskans of the southwestern United States: recent advances and implications for the future. Am J Med Genet A 2010; 149A:2602-11. [PMID: 19842189 DOI: 10.1002/ajmg.a.33052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Genetic and linguistic data suggest that the Na-Dene, of which the Athabaskans are the largest group, are part of a later immigration into the Americas than the first Amerind immigration. Whether a second and third immigration can be separated seems unlikely but continued cross-Bering Strait exchanges may have masked what was a greater separation in the past. The movement of tribes into Siberia appears to have involved a genetic bottleneck leading to at least one disease allele shared by Eskimo/Aleuts and Navajos and a second possibly shared by the Navajo and a Siberian population, but not the same Siberian population that share deep linguistic affinities with the Navajo. A second bottleneck appears to have occurred with the migration of Athabaskans from Northwest North America to the Southwestern United States along the Rocky Mountains. This bottleneck is reflected in several rare recessive diseases shared by the Navajo and Apache. Finally, the Navajo were captured and imprisoned under conditions which led to severe population loss. This, and the "hiding away" of a small number of Navajos in what is now the Western portion of the reservation, led to a Navajo-specific bottleneck(s) resulting in an increased frequency of several rare recessive diseases among the Navajo. Prejudice against human genetic research is high among the Southwestern Athabaskans but attempts to bridge the gap are now occurring. The involvement of Navajo scientists in this process is especially encouraging.
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Affiliation(s)
- Robert P Erickson
- Department of Pediatrics, University of Arizona, Tucson, Arizona 85701, USA.
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Knowles WA. Discovery and epidemiology of the human polyomaviruses BK virus (BKV) and JC virus (JCV). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 577:19-45. [PMID: 16626025 DOI: 10.1007/0-387-32957-9_2] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Although discovered over thirty years ago, many aspects of the epidemiology of BKV and JCV in the general population, such as the source of infectious virus and the mode of transmission, are still unknown. Primary infection with both BKV and JCV is usually asymptomatic, and so age seroprevalence studies have been used to indicate infection. BKV commonly infects young children in all parts of the world, with the exception of a few very isolated communities, adult seroprevalence rates of 65-90% being reached by the age of ten years. In contrast, the pattern of JCV infection appears to vary between populations; in some anti-JCV antibody is acquired early as for BKV, but in others anti-JCV antibody prevalence continues to rise throughout life. This indicates that the two viruses are probably transmitted independently and by different routes. Whilst BKV DNA is found infrequently in the urine of healthy adults, JCV viruria occurs universally, increasing with age, with adult prevalence rates often between 20% and 60%. Four antigenic subtypes have been described for BKV and eight genotypes are currently recognized for JCV. The latter have been used to trace population movements and to reconstruct the population history in various communities.
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10
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Sampei MA, Canó EN, Fagundes U, Lima EEDS, Rodrigues D, Sigulem DM, Baruzzi RG. Avaliação antropométrica de adolescentes Kamayurá, povo indígena do Alto Xingu, Brasil Central (2000-2001). CAD SAUDE PUBLICA 2007; 23:1443-53. [PMID: 17546335 DOI: 10.1590/s0102-311x2007000600019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Accepted: 01/03/2007] [Indexed: 11/22/2022] Open
Abstract
Apesar da proximidade dos grupos indígenas do Alto Xingu com a sociedade, os estudos têm mostrado adequação do peso para estatura e déficit de estatura para idade das crianças desses povos. Em relação aos adolescentes, pouco se conhece sobre suas condições nutricionais. O presente estudo teve como objetivo avaliar o estado nutricional de adolescentes Kamayurá, valendo-se de variáveis antropométricas. As medidas de peso, estatura, pregas cutâneas e circunferências corporais foram coletadas de 65 adolescentes, sendo 31 indivíduos masculinos e 34 femininos. As médias de estatura em relação à idade foram menores do que aquelas encontradas na Pesquisa Nacional sobre Saúde e Nutrição e na população de referência do National Center for Health Statistics. Houve taxa elevada de sobrepeso no sexo masculino (38,7%) e no feminino (23,5%); a obesidade foi encontrada em uma adolescente (2,9%). Nenhum adolescente com sobrepeso apresentou ambas as pregas tricipital e subescapular acima do percentil 90. Não houve casos de déficit nutricional em adolescentes de ambos os sexos. Apesar da alta prevalência de sobrepeso, o estado nutricional dos adolescentes em estudo é adequado, dada a baixa adiposidade.
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Affiliation(s)
- Miriam A Sampei
- Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Marselhesa 630, São Paulo, SP 04020-060, Brazil.
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Abstract
Mitochondrial DNA and microsatellite sequences are powerful genetic markers for inferring the genealogy and the population genetic structure of animals but they have only limited resolution for organisms that display low genetic variability due to recent strong bottlenecks. An alternative source of data for deciphering migrations and origins in genetically uniform hosts can be provided by some of their microbes, if their evolutionary history correlates closely with that of the host. In this review, we first discuss how a variety of viruses, and the bacterium Helicobacter pylori, can be used as genetic tracers for one of the most intensively studied species, Homo sapiens. Then, we review statistical problems and limitations that affect the calculation of particular population genetic parameters for these microbes, such as mutation rates, with particular emphasis on the effects of recombination, selection and mode of transmission. Finally, we extend the discussion to other host-parasite systems and advocate the adoption of an integrative approach to both sampling and analysis.
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Affiliation(s)
- Thierry Wirth
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University Konstanz, 78457 Konstanz, Germany.
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Ikegaya H, Zheng HY, Saukko PJ, Varesmaa-Korhonen L, Hovi T, Vesikari T, Suganami H, Takasaka T, Sugimoto C, Ohasi Y, Kitamura T, Yogo Y. Genetic diversity of JC virus in the Saami and the Finns: implications for their population history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005; 128:185-93. [PMID: 15778974 DOI: 10.1002/ajpa.20189] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The JC virus (JCV) genotyping method was used to gain insights into the population history of the Saami and the Finns, both speaking Finno-Ugric languages and living in close geographic proximity. Urine samples from Saami and Finns, collected in northern and southern Finland, respectively, were used to amplify a 610-bp JCV-DNA region containing abundant type-specific mutations. Based on restriction site polymorphisms in the amplified fragments, we classified JCV isolates into one of the three superclusters of JCV, type A, B, or C. All 15 Saami isolates analyzed and 41 of 43 Finnish isolates analyzed were classified as type A, the European type, and two samples from Finns were classified as type B, the African/Asian type. We then amplified and sequenced a 583-bp JCV-DNA region from the type A isolates of Saami and Finns. According to type-determining nucleotides within the region, we classified type A isolates into EU-a1, -a2, or -b. Most type A isolates from Saami were classified as EU-a1, while type A isolates from Finns were distributed among EU-a1, EU-a2, and EU-b. This trend in the JCV-genotype distribution was statistically significant. On a phylogenetic tree based on complete sequences, most of the type A isolates from Saami were clustered in a single clade within EU-a1, while those from Finns were distributed throughout EU-a1, EU-a2, and EU-b. These findings are discussed in the context of the population history of the Saami and the Finns. This study provides new complete JCV DNA sequences derived from populations of anthropological interest.
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Affiliation(s)
- Hiroshi Ikegaya
- Department of Forensic Medicine, University of Turku, Turku, Finland 20520.
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Pavesi A. Utility of JC polyomavirus in tracing the pattern of human migrations dating to prehistoric times. J Gen Virol 2005; 86:1315-1326. [PMID: 15831942 DOI: 10.1099/vir.0.80650-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
JC virus (JCV) is a double-stranded DNA polyomavirus co-evolving with humans since the time of their origin in Africa. JCV seems to provide new insights into the history of human populations, as it suggests an expansion of humans from Africa via two distinct migrations, each carrying a different lineage of the virus. A possible alternative to this interpretation could be that the divergence between the two lineages is due to selective pressures favouring adaptation of JCV to different climates, thus making any inference about human history debatable. In the present study, the evolution of JCV was investigated by applying correspondence analysis to a set of 273 fully sequenced strains. The first and more important axis of ordination led to the detection of 61 nt positions as the main determinants of the divergence between the two virus lineages. One lineage includes strains of types 1 and 4, the other strains of types 2, 3, 7 and 8. The distinctiveness of the Caucasian lineage (types 1 and 4), largely diffused in the northern areas of the world, was almost entirely ascribed to synonymous substitutions. The findings provided by the subsequent axes of ordination supported the view of an evolutionary history of JCV characterized by genetic drift and migration, rather than by natural selection. Correspondence analysis was also applied to a set of 156 human mitochondrial genome sequences. A detailed comparison between the substitution patterns in JCV and mitochondria brought to light some relevant advantages of the use of the virus in tracing human migrations.
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Affiliation(s)
- Angelo Pavesi
- Department of Genetics Anthropology & Evolution, University of Parma, Parco Area delle Scienze 11/A, I-43100 Parma, Italy
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Bolnick DAW, Shook BAS, Campbell L, Goddard I. Problematic use of Greenberg's linguistic classification of the Americas in studies of Native American genetic variation. Am J Hum Genet 2004; 75:519-22. [PMID: 15284953 PMCID: PMC1182033 DOI: 10.1086/423452] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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15
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Zheng HY, Zhao P, Suganami H, Ohasi Y, Ikegaya H, Kim JC, Sugimoto C, Takasaka T, Kitamura T, Yogo Y. Regional distribution of two related Northeast Asian genotypes of JC virus, CY-a and -b: implications for the dispersal of Northeast Asians. Microbes Infect 2004; 6:596-603. [PMID: 15158194 DOI: 10.1016/j.micinf.2004.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2003] [Accepted: 02/20/2004] [Indexed: 11/24/2022]
Abstract
JC virus (JCV) is a useful marker to trace human dispersal. Two genotypes of JCV (MY and CY) are mainly distributed in Northeast Asia. The population history of people carrying MY has been studied in some detail but that of people carrying CY remains poorly understood. To gain insights into the population history of Northeast Asians carrying CY we analyzed the genetic variation in CY isolates. We constructed a neighbor-joining phylogenetic tree from 28 complete CY DNA sequences: on the resultant tree the CY DNA sequences diverged into two clades, designated CY-a and -b, each clustered with a high bootstrap probability. The split into CY-a and -b was estimated to have occurred about 10 000 years ago, based on K(s) values (synonymous substitutions per synonymous site) and the suggested rate of synonymous nucleotide substitutions. Comparison of the 28 complete CY sequences revealed six nucleotide mismatches between CY-a and -b, one of which showed a restriction fragment length polymorphism (RFLP). We then PCR-amplified a region of the genome containing this polymorphic site from many CY isolates in various Northeast Asian populations and classified the isolates into CY-a or -b according to the RFLP analysis. CY-a was more abundant than CY-b in various Chinese and Japanese populations but CY-b was more abundant than CY-a in South Koreans. On the basis of the present findings we inferred the population history in East Asians carrying CY.
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Affiliation(s)
- Huai-Ying Zheng
- Department of Urology, Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Tokyo 113-8655, Japan.
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16
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Pavesi A. Detecting Traces of Prehistoric Human Migrations by Geographic Synthetic Maps of Polyomavirus JC. J Mol Evol 2004; 58:304-13. [PMID: 15045485 DOI: 10.1007/s00239-003-2552-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2003] [Accepted: 09/19/2003] [Indexed: 10/26/2022]
Abstract
The polyomavirus JC (JCV) is a double-stranded DNA virus that is ubiquitous in human populations and is excreted in urine by a large percentage of individuals (20-70%). The strong genetic stability, combined with a mechanism of transmission mainly within the family, makes JCV a good marker of human migrations. In this study, the coevolution of JCV with its human host is investigated by using over a thousand nucleotide sequences deposited in the EMBL database; they correspond to the IG region, which is the genomic region with the highest rate of variation. The pattern of genetic diversity in JCV is evaluated by the principal coordinates analysis and the construction of synthetic maps. The first principal coordinate supports the existence of two distinct virus lineages, both arising from the ancestral African type. The first synthetic map suggests a two-migration model of the human dispersal out of Africa, thus implying a more complex picture than that known from human genes. The second principal coordinate points out the distinctiveness of strains coming from Asian/Amerind populations. The picture yielded by the second synthetic map appears to be more consistent with that known from human genes. In fact, it provides evidence of a deep split of the Asian lineage of JCV into two main branches: one diffusing in Japan and Americas, the other in Southeast Asia. The view that JCV, with its peculiar feature of a dual early emergence from Africa, can provide new information about the evolutionary history of our ancestors is discussed.
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Affiliation(s)
- Angelo Pavesi
- Department of Genetics Anthropology Evolution, University of Parma, Parco Area delle Scienze 11/A, 1-43100 Parma, Italy.
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TAKASAKA TOMOKAZU, MIRANDA JASMINJIJI, SUGIMOTO CHIE, PARAGUISON RUBIGILDA, ZHENG HUAIYING, KITAMURA TADAICHI, YOGO YOSHIAKI. Genotypes of JC virus in Southeast Asia and the western Pacific: implications for human migrations from Asia to the Pacific. ANTHROPOL SCI 2004. [DOI: 10.1537/ase.00086] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- TOMOKAZU TAKASAKA
- Laboratory of Viral Infection, Department of Microbiology and Immunology, the Institute of Medical Science, The University of Tokyo
| | - JASMIN JIJI MIRANDA
- National Institute of Molecular Biology and Biotechnology, University of the Philippines
| | - CHIE SUGIMOTO
- Laboratory of Viral Infection, Department of Microbiology and Immunology, the Institute of Medical Science, The University of Tokyo
| | - RUBIGILDA PARAGUISON
- National Institute of Molecular Biology and Biotechnology, University of the Philippines
| | - HUAI-YING ZHENG
- Laboratory of Viral Infection, Department of Microbiology and Immunology, the Institute of Medical Science, The University of Tokyo
| | | | - YOSHIAKI YOGO
- Laboratory of Viral Infection, Department of Microbiology and Immunology, the Institute of Medical Science, The University of Tokyo
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Abstract
Polyomavirus hominis 1, better known as BK virus (BKV), infects up to 90% of the general population. However, significant clinical manifestations are rare and limited to individuals with impaired immune functions. BKV has been associated with diverse entities such as haemorrhagic cystitis, ureteric stenosis, vasculopathy, pneumonitis, encephalitis, retinitis, and even multi-organ failure. In addition, BKV has been implicated in autoimmune disease and possibly cancer. Due to high prevalence and frequent reactivation, the role of BKV in some of these pathologies has been difficult to define. Development of BKV diseases is likely to require complementing determinants in the host, the target organ, and possibly the virus, that are subject to modulators such as immunosuppression. These complex aspects are highlighted in polyomavirus-associated nephropathy (PAN), an emerging disease in renal allograft recipients that may jeopardise the progress in renal transplantation accomplished in the past 10 years. Intervention is difficult due to the lack of specific antivirals and relies mostly on improving immune control. Diagnostic strategies using urine cytology and BKV load measurements in plasma have led to earlier diagnosis of PAN, which increased the success rate of intervention. Case series suggest that cidofovir might be effective, especially when combined with reduced immunosuppression.
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Affiliation(s)
- Hans H Hirsch
- Division of Infectious Diseases, Department of Internal Medicine, University Hospitals Basel, and Transplantation Virology Laboratory, Institute of Medical Microbiology, University of Basel, Switzerland.
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Jeong BH, Lee KH, Choi EK, Kim K, Kim YS. Genotyping of the JC virus in urine samples of healthy Korean individuals. J Med Virol 2003; 72:281-9. [PMID: 14695671 DOI: 10.1002/jmv.10568] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A human polyomavirus, JC virus (JCV) is ubiquitous in humans and infects children asymptomatically. It persists in renal tissue and is excreted progeny in urine. DNAs from urine samples of 100 healthy Korean individuals were screened for the presence of JCV by polymerase chain reaction (PCR). Twenty of the samples were positive for JCV. JCV DNA was found in one individual (4%) in the 1-19-year group, two individuals (9%) in the 20-39-year group, ten individuals (38%) in the 40-59-year group, seven individuals (28%) in the over 60-year group. The prevalence of JC viral DNA was the highest in the 40-59-year-old Korean population. To investigate genotypes of JCV in Korea, the genotypes were determined by DNA sequence analysis of the regulatory region (333 bp) and the VT-intergenic region (656 bp) of DNA from the 20 JCV isolates. We have identified three distinctive JCV strains in the regulatory region and ten distinctive JCV strains in the VT-intergenic region of DNA from the 20 isolates. Based on restriction fragment length polymorphism (RFLP) analysis and phylogenetic analysis of the VT-intergenic region of JCV, two distinct subtypes, CY and type 2A (MY), were found to be prevalent in this Korean population. CY and type 2A of JCV were identified in 13 individuals (65%) and four individuals (20%), respectively. Interestingly, type 1, which was distributed mostly in Europe, was found in 3 (15%) isolates from healthy Korean individuals.
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Affiliation(s)
- Byung-Hoon Jeong
- Ilsong Institute of Life Science, The Hallym Academy of Sciences, Hallym University, Gwanyang-dong, Dongan-gu, Anyang, Kyonggi-do, Korea
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YOGO YOSHIAKI, ZHENG HUAIYING, HASEGAWA MASAMI, SUGIMOTO CHIE, TANAKA SHINTATU, HONJO TAKEO, KOBAYASHI NOBUYOSHI, OHTA NOBUTAKA, KITAMURA TADAICHI. Phylogenetic Analysis of JC Virus DNAs Detected in Ainus: An Attempt to Elucidate the Origin and Diversity of the Ainu. ACTA ACUST UNITED AC 2003. [DOI: 10.1537/asj.111.19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- YOSHIAKI YOGO
- Laboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
| | - HUAI-YING ZHENG
- Laboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Department of Urology, Faculty of Medicine, The University of Tokyo
| | - MASAMI HASEGAWA
- Department of Prediction and Control, The Institute of Statistical Mathematics
| | - CHIE SUGIMOTO
- Laboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
| | | | | | - NOBUYOSHI KOBAYASHI
- Laboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
| | - NOBUTAKA OHTA
- Department of Urology, Faculty of Medicine, The University of Tokyo
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