1
|
Population history in Okinawa based on JC virus and ALDH2 genotypes. Sci Rep 2020; 10:7331. [PMID: 32355181 PMCID: PMC7192937 DOI: 10.1038/s41598-020-64194-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/11/2020] [Indexed: 11/09/2022] Open
Abstract
AbstractIt is widely known that people in Okinawa originated from the Jomon people, and are generally tolerant to alcohol. However, some individuals in mainland Japan lack alcohol tolerance due to a mutation in the human mitochondrial aldehyde dehydrogenase 2 (ALDH2) gene. Furthermore, the JC virus (JCV) genotype MY, which is related to the Jomon people, has not been found in Okinawa. In this study, to analyze the origin of the Okinawan people, we investigated the relationship between the JCV genotype and ALDH2 genotype. We collected 108 JCV positive samples from Okinawa. Only CY genotype JCV, and not the MY genotype, was detected. Among JCV-positive samples, a variant of ALDH2 (Glu/Lys heterozygote) was detected in 31 samples (29%) and wild-type ALDH2 (Glu/Glu homozygote) was detected in 77 samples (71%). Another variant of ALDH2 (Lys/Lys homozygote) was not detected. Among carriers of CY genotype JCV, wild-type ALDH2 was much more frequent in people living in Okinawa than in mainland Japan (P < 0.05). Our results suggested that the original inhabitants of Okinawa were people who carried MY genotype JCV and wild-type ALDH2; and that after the extinction of these original inhabitants, people who carried CY genotype JCV and wild-type ALDH2 migrated to the area. Due to the founder effect, CY genotype JCV and wild-type ALDH2 became dominant. Over a long period, many people with the variant ALDH2 migrated to Okinawa; the variant allele increased in frequency, but other JCV genotypes were eliminated.
Collapse
|
2
|
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.
Collapse
|
3
|
Miyamori D, Ishikawa N, Idota N, Kakiuchi Y, McLean S, Kitamura T, Ikegaya H. Tracing Jomon and Yayoi ancestries in Japan using ALDH2 and JC virus genotype distributions. INVESTIGATIVE GENETICS 2016; 6:14. [PMID: 26719788 PMCID: PMC4696161 DOI: 10.1186/s13323-015-0031-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND According to the dual structure model, the modern Japanese ethnic population consists of a mixture of the Jomon people, who have existed in Japan since at least the New Stone Age, and the Yayoi people, who migrated to western Japan from China around the year 300 bc Some reports show that the Yayoi are linked to a mutation of the aldehyde dehydrogenase 2 gene (ALDH2). Recent viral studies indicate two major groups found in the Japanese population: a group with the CY genotype JC virus (JCV) and a group with the MY genotype JCV. It is unclear whether either genotype of the JC virus is related to the Jomon or Yayoi. In this study, we attempted to detect JCV genotypes and ALDH2 mutations from the DNA of 247 Japanese urine samples to clarify the relationship between the dual structure model and the JCV genotype through ALDH2 mutation analysis and JCV genotyping. FINDINGS The ALDH2 polymorphism among 66 JC virus-positive samples was analyzed, and it was found that the ALDH2 variant is significantly higher in the population with CY genotype JCV (51.5 %) than in the population with the MY genotype (24.2 %) (p < 0.05). CONCLUSION From these findings, it may be inferred that the ALDH2 mutation, which is related to the Yayoi, is related to CY genotype JCV. When the Yayoi migrated to the Japanese archipelago, they brought the ALDH2 mutation as well as the CY genotype JCV.
Collapse
Affiliation(s)
- Daisuke Miyamori
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566 Japan
| | - Noboru Ishikawa
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566 Japan
| | - Nozomi Idota
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566 Japan
| | - Yasuhiro Kakiuchi
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566 Japan
| | - Stuart McLean
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566 Japan
| | | | - Hiroshi Ikegaya
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566 Japan
| |
Collapse
|
4
|
Yogo Y, Sugimoto C, Zhong S, Homma Y. Evolution of the BK polyomavirus: epidemiological, anthropological and clinical implications. Rev Med Virol 2009; 19:185-99. [PMID: 19530118 DOI: 10.1002/rmv.613] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BK polyomavirus (BKV) is essentially ubiquitous in all human populations worldwide. Asymptomatic infection with this virus occurs during early childhood, leading to life-long persistence in the kidney. BKV has four subtypes that can be identified using serological and genotyping methods. The evolutionary aspects of BKV have remained poorly understood due to the limited availability of BKV genomes, since urinary excretion of BKV DNA is detected primarily in immunocompromised individuals. However, we have found that BKV DNA sequences can often be amplified from non-immunocompromised elderly individuals, using a highly sensitive polymerase chain reaction (PCR) with highly concentrated urinary DNA as the source of viral DNA. Using this approach, we have PCR-amplified and sequenced a large number of partial and complete BKV genomes from various human populations worldwide and conducted a series of evolutionary studies using these sequences. We have shown that subtypes I and IV evolved into four and six subgroups, respectively, with each having a close relationship with a particular human population. In addition, we have provided evidence supporting the hypothesis that BKV strains with the archetypal transcriptional control region (TCR) circulate in the human population. In this review, we describe these findings and discuss their epidemiological, anthropological and clinical implications.
Collapse
Affiliation(s)
- Yoshiaki Yogo
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | | | | | | |
Collapse
|
5
|
Zhong S, Jeong BH, Ikegaya H, Kim YS, Xu Y, Zhu M, Chao Y, Suzuki M, Kitamura T, Homma Y, Yogo Y. Comparison of the distribution patterns of BK polyomavirus lineages among China, Korea and Japan: implications for human migrations in northeast Asia. Microbiol Immunol 2009; 53:266-76. [PMID: 19457167 DOI: 10.1111/j.1348-0421.2009.00121.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BKV is widespread among humans, infecting children asymptomatically and then persisting in renal tissue. Based on the serological or phylogenetic method, BKV isolates worldwide are classified into four subtypes (I-IV), with subtypes I and IV further divided into several genetically-distinct subgroups. Since, similarly to JCV, a close relationship exists between BKV lineages and human populations, BKV should be useful as a marker to trace human migrations. To elucidate ancient human migrations in northeast Asia, urine samples were collected from immunocompetent elderly patients in Shanghai, China; Anyang, South Korea; and various locations in Japan. Partial and complete BKV genomes from these samples were amplified and sequenced using PCR, and the determined sequences were classified into subtypes and subgroups by phylogenetic and SNP analyses. In addition, based on an SNP analysis, the major subtype I subgroup (I/c) was classified into two subdivisions, I/c/Ch and I/c/KJ. The distribution patterns of BKV subgroups and subdivisions among the three regions were compared. Some aspects of the subgroup and subdivision distribution were more similar between Korea and Japan, but others were more similar between China and Korea or between China and Japan. Based on these findings, we inferred various northeast Asian migrations. Most of the JCV-based inferences of northeastern Asian migrations were consistent with those based on BKV, but the previously suggested migration route from the Asian continent to the Japanese archipelago seemed to need revision.
Collapse
Affiliation(s)
- Shan Zhong
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Yogo Y, Zhong S, Xu Y, Zhu M, Chao Y, Sugimoto C, Ikegaya H, Shibuya A, Kitamura T. Conserved archetypal configuration of the transcriptional control region during the course of BK polyomavirus evolution. J Gen Virol 2008; 89:1849-1856. [PMID: 18632955 DOI: 10.1099/vir.0.2008/000836-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BK polyomavirus (BKV) is widespread among humans, asymptomatically infecting children and then persisting in renal tissue. The transcriptional control region (TCR) of the BKV genome is variable among clinical isolates. Thus, archetypal TCRs with a common basic configuration generally occur in BKV isolates from the urine of immunocompromised patients, but rearranged TCRs that possibly arise from the archetypal configuration have also been detected in clinical specimens. To examine the hypothesis that archetypal strains represent wild-type strains circulating in the human population (the archetype hypothesis), we analysed 145 complete viral genomes amplified directly from the urine of non-immunocompromised individuals worldwide. These genomes included 82, three, two and 58 sequences classified as belonging to subtypes I, II, III and IV, respectively. Rearranged TCRs with long duplications or deletions were detected from two subtype I and two subtype IV genomes, but not from the other 141 genomes (thus, the TCRs of these genomes were judged to be archetypal). The variations in the archetypal TCRs were nucleotide substitutions and single-nucleotide deletions, most of which were unique to particular subtypes or subgroups. We confirmed that the four complete BKV genomes with rearranged TCRs did not form a unique lineage on a phylogenetic tree. Collectively, the findings demonstrate that the archetypal TCR configuration has been conserved during the evolution of BKV, providing support for the archetype hypothesis. Additionally, we suggest that 'archetype' should be used as a conceptual term that denotes a prototypical structure that can generate various rearranged TCRs during viral growth in vivo and in vitro.
Collapse
Affiliation(s)
- Yoshiaki Yogo
- Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Shan Zhong
- Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yawei Xu
- Department of Cardiovascular Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yan Chang Road, Shanghai 200072, PR China
| | - Mengyun Zhu
- Department of Cardiovascular Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yan Chang Road, Shanghai 200072, PR China
| | - Yuegen Chao
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yan Chang Road, Shanghai 200072, PR China
| | - Chie Sugimoto
- Tsukuba Primate Research Center, National Institute of Biomedical Innovation, 1 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hiroshi Ikegaya
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ayako Shibuya
- Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Tadaichi Kitamura
- Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| |
Collapse
|
7
|
IKEGAYA HIROSHI, SHAN ZHONG, SHIMIZU HANA, SEKIYAMA MAKIKO, SOEMANTRI AUGUSTINUS, ISHIDA TAKAFUMI, NAKAZAWA MINATO, OHTSUKA RYUTARO, TAKASAKA TOMOKAZU, SHIBUYA AYAKO, KITAMURA TADAICHI, YOGO YOSHIAKI. The Pacific lineage (2E) of JC polyomavirus is prevalent in Sumba Island, Eastern Indonesia. ANTHROPOL SCI 2008. [DOI: 10.1537/ase.070529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- HIROSHI IKEGAYA
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo
| | - ZHONG SHAN
- Department of Urology, Faculty of Medicine, The University of Tokyo
| | - HANA SHIMIZU
- Department of Human Ecology, School of International Health, Graduate School of Medicine, The University of Tokyo
| | - MAKIKO SEKIYAMA
- Transdisciplinary Initiative for Global Sustainability (TIGS), Integrated Research System for Sustainability Science (IR3S), The University of Tokyo
| | | | - TAKAFUMI ISHIDA
- Unit of Human Biology and Genetics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - MINATO NAKAZAWA
- Gunma University Graduate School of Medicine, Department of Socio-Environmental Medicine, Public Health Division
| | | | | | - AYAKO SHIBUYA
- Department of Urology, Faculty of Medicine, The University of Tokyo
| | | | - YOSHIAKI YOGO
- Department of Urology, Faculty of Medicine, The University of Tokyo
| |
Collapse
|
8
|
Zheng HY, Nishimoto Y, Chen Q, Hasegawa M, Zhong S, Ikegaya H, Ohno N, Sugimoto C, Takasaka T, Kitamura T, Yogo Y. Relationships between BK virus lineages and human populations. Microbes Infect 2007; 9:204-13. [PMID: 17208484 DOI: 10.1016/j.micinf.2006.11.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 11/15/2006] [Accepted: 11/15/2006] [Indexed: 11/16/2022]
Abstract
BK polyomavirus (BKV) is ubiquitous in human populations, infecting children asymptomatically and then persisting in the kidney, in which it can cause nephropathy in renal transplant patients. BKV isolates are classified into four subtypes (I-IV) using serological or genotyping methods, and subtype I is further divided into four subgroups, Ia, Ib-1, Ib-2, and Ic, based on DNA sequence variations. To clarify whether there is an association between BK virus lineages and human populations, we examined BKV-positive urine samples collected from immunocompetent individuals at various locations in Europe, Africa, and Asia. Partial BKV DNA sequences (n=299) in these samples were determined and subjected to phylogenetic and single nucleotide polymorphism analysis to classify BKV isolates around the world. The validity of the classification was confirmed by analyses based on complete BKV DNA sequences. Subtype I was the major subtype throughout the studied regions, and subtype IV was prevalent only in Asia and Europe. Subtype-I subgroups showed close relationships to major geographical areas. It has recently been shown that JC virus (a human polyomavirus closely related to BKV) co-evolved with human populations, and the present study thus suggests that host-linked evolution is the general mode of polyomavirus evolution. Additionally, our results indicate certain unique aspects of the relationship between BKV and humans.
Collapse
Affiliation(s)
- Huai-Ying Zheng
- Department of Urology, Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8655, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
ZHENG HUAIYING, TAKASAKA TOMOKAZU, OHNO NORIKAZU, SUGIMOTO CHIE, KITAMURA TADAICHI, YOGO YOSHIAKI. Human dispersals based on a global phylogenetic analysis of JC virus isolates of genotype B1-b. ANTHROPOL SCI 2007. [DOI: 10.1537/ase.061017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- HUAI-YING ZHENG
- Department of Urology, Faculty of Medicine, The University of Tokyo
| | | | - NORIKAZU OHNO
- Department of First Anatomy, School of Dentistry, Aichi-Gakuin University
| | - CHIE SUGIMOTO
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo
- Tsukuba Primate Research Center, National Institute of Biomedical Innovation
| | | | - YOSHIAKI YOGO
- Department of Urology, Faculty of Medicine, The University of Tokyo
| |
Collapse
|
10
|
Chen Q, Zheng HY, Zhong S, Ikegaya H, He HX, Wei W, He YY, Kobayashi N, Honjo T, Takasaka T, Takahashi S, Kitamura T, Yogo Y. Subtype IV of the BK polyomavirus is prevalent in East Asia. Arch Virol 2006; 151:2419-29. [PMID: 16830069 DOI: 10.1007/s00705-006-0814-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
BK polyomavirus (BKV) is ubiquitous in human populations, infecting children asymptomatically and then persisting in the kidney. Using either serological or genotyping methods, BKV isolates have been classified into four subtypes (I-IV), with subtype I mainly detected in all countries studied so far. To elucidate the subtype of BKV prevalent in East Asia, we examined BKV-positive urine samples collected from immunocompetent elderly patients in Mongolia, Northeast China, Northwest China, Southeast China, Southwest China, Vietnam and Japan. The 287-bp typing region of the viral genome in each of these samples was PCR-amplified and sequenced, and a phylogenetic tree was constructed. According to the tree, BKV isolates in East Asia were unambiguously classified into subtype I or IV (subtypes II and III were not detected). In Japan, subtype I was mainly detected and subtype IV was rare, whereas in the other regions subtype IV was detected frequently, at rates ranging from 24 to 100%. Thus, East Asia (excluding Japan) is a region in which subtype-IV BKV is prevalent, a finding that requires the view of the geographic distribution of BKV subtypes to be revised. Furthermore, we present evidence that the immunological states of urine donors do not affect the pattern of BKV subtypes.
Collapse
Affiliation(s)
- Q Chen
- Department of Urology, Faculty of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- Thierry Wirth
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University Konstanz, 78457 Konstanz, Germany.
| | | | | |
Collapse
|
12
|
TAKASAKA TOMOKAZU, OHTA NOBUTAKA, ZHENG HUAIYING, IKEGAYA HIROSHI, SAKURADA KOICHI, KITAMURA TADAICHI, YOGO YOSHIAKI. JC polyomavirus lineages common among Kiribati Islanders: implications for human dispersal in the Pacific. ANTHROPOL SCI 2006. [DOI: 10.1537/ase.050719] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
| | | | - HUAI-YING ZHENG
- Department of Urology, Faculty of Medicine, The University of Tokyo
- Japanese Foundation for AIDS Prevention
| | | | | | | | - YOSHIAKI YOGO
- Department of Urology, Faculty of Medicine, The University of Tokyo
| |
Collapse
|
13
|
SARUWATARI LEI, ZHENG HUAIYING, IKEGAYA HIROSHI, TAKASAKA TOMOKAZU, GUO JING, KITAMURA TADAICHI, YOGO YOSHIAKI, OHNO NORIKAZU. Dispersal of southeastern Asians based on a global phylogenetic analysis of JC polyomavirus isolates of genotype SC. ANTHROPOL SCI 2006. [DOI: 10.1537/ase.050629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- LEI SARUWATARI
- Department of Anatomy, School of Dentistry, Aichi-Gakuin University
| | - HUAI-YING ZHENG
- Department of Urology, Faculty of Medicine, The University of Tokyo
- Japanese Foundation for AIDS Prevention
| | | | | | - JING GUO
- Department of Biochemistry, University of Alberta
| | | | - YOSHIAKI YOGO
- Department of Urology, Faculty of Medicine, The University of Tokyo
| | - NORIKAZU OHNO
- Department of Anatomy, School of Dentistry, Aichi-Gakuin University
| |
Collapse
|
14
|
Zheng HY, Ikegaya H, Takasaka T, Matsushima-Ohno T, Sakurai M, Kanazawa I, Kishida S, Nagashima K, Kitamura T, Yogo Y. Characterization of the VP1 loop mutations widespread among JC polyomavirus isolates associated with progressive multifocal leukoencephalopathy. Biochem Biophys Res Commun 2005; 333:996-1002. [PMID: 15964545 DOI: 10.1016/j.bbrc.2005.06.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Accepted: 06/06/2005] [Indexed: 11/20/2022]
Abstract
Recently, we found that JC polyomavirus (JCPyV) associated with progressive multifocal leukoencephalopathy (PML) frequently undergoes amino acid substitutions (designated VP1 loop mutations) in the outer loops of the major capsid protein, VP1. To further characterize the mutations, we analyzed the VP1 region of the JCPyV genome in brain-tissue or cerebrospinal fluid samples from 20 PML patients. VP1 loop mutations occurred far more frequently than silent mutations. Polymorphic residues were essentially restricted to three positions (55, 60, and 66) within the BC loop, one (123) within the DE loop, and three (265, 267, and 269) within the HI loop. The mutations at most polymorphic residues showed a trend toward a change to specific amino acids. Finally, we presented evidence that the VP1 loop mutations were associated with the progression of PML. These findings should form the basis for elucidating the biological significance of the VP1 loop mutations.
Collapse
Affiliation(s)
- Huai-Ying Zheng
- Department of Urology, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Zheng HY, Takasaka T, Noda K, Kanazawa A, Mori H, Kabuki T, Joh K, Oh-Ishi T, Ikegaya H, Nagashima K, Hall WW, Kitamura T, Yogo Y. New sequence polymorphisms in the outer loops of the JC polyomavirus major capsid protein (VP1) possibly associated with progressive multifocal leukoencephalopathy. J Gen Virol 2005; 86:2035-2045. [PMID: 15958683 DOI: 10.1099/vir.0.80863-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
JC polyomavirus(JCPyV) causes progressive multifocal leukoencephalopathy (PML) in patients with decreased immune competence. To elucidate genetic changes in JCPyV associated with the pathogenesis of PML, multiple complete JCPyV DNA clones originating from the brains of three PML cases were established and sequenced. Although unique rearranged control regions occurred in all clones, a low level of nucleotide variation was also found in the coding region. In each case, a parental coding sequence was identified, from which variant coding sequences with nucleotide substitutions would have been generated. A comparison between the parental and variant coding sequences demonstrated that all 12 detected nucleotide substitutions gave rise to amino acid changes. Interestingly, seven of these changes were located in the surface loops of the major capsid protein (VP1). Finally, 16 reported VP1 sequences of PML-type JCPyV (i.e. derived from the brain or cerebrospinal fluid of PML patients) were compared with their genotypic prototypes, generated as consensus sequences of representative archetypal isolates belonging to the same genotypes; 13 VP1 proteins had amino acid changes in the surface loops. In contrast, VP1 proteins from isolates from the urine of immunocompetent and immunosuppressed patients rarely underwent mutations in the VP1 loops. The present findings suggest that PML-type JCPyV frequently undergoes amino acid substitutions in the VP1 loops. These polymorphisms should serve as a new marker for the identification of JCPyV isolates associated with PML. The biological significance of these mutations, however, remains unclear.
Collapse
Affiliation(s)
- Huai-Ying Zheng
- Japanese Foundation for AIDS Prevention, Tokyo 105-0001, Japan
- Department of Urology, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Tomokazu Takasaka
- Department of Urology, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Kazuyuki Noda
- Department of Neurology, Juntendo University School of Medicine, Tokyo 113-0033, Japan
| | - Akira Kanazawa
- Department of Neurology, Juntendo University School of Medicine, Tokyo 113-0033, Japan
| | - Hideo Mori
- Department of Neurology, Juntendo University School of Medicine, Tokyo 113-0033, Japan
| | - Tomoyuki Kabuki
- Division of Infectious Diseases, Immunology and Allergy, Saitama Children's Medical Center, Iwatsuki 339-8551, Japan
| | - Kohsuke Joh
- Division of Infectious Diseases, Immunology and Allergy, Saitama Children's Medical Center, Iwatsuki 339-8551, Japan
| | - Tsutomu Oh-Ishi
- Division of Infectious Diseases, Immunology and Allergy, Saitama Children's Medical Center, Iwatsuki 339-8551, Japan
| | - Hiroshi Ikegaya
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kazuo Nagashima
- Laboratory of Molecular and Cellular Pathology, Hokkaido University Graduate School of Medicine, Kita-ku, Sapporo 060-8638, CREST, Japan
| | - William W Hall
- Department of Medical Microbiology, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Tadaichi Kitamura
- Department of Urology, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yoshiaki Yogo
- Department of Urology, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- Angelo Pavesi
- Department of Genetics Anthropology & Evolution, University of Parma, Parco Area delle Scienze 11/A, I-43100 Parma, Italy
| |
Collapse
|