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The laboratory mouse is the premier animal model for studying human disease and thousands of mutants have been identified or produced, most recently through gene-specific mutagenesis approaches. High throughput strategies by the International Knockout Mouse Consortium (IKMC) are producing mutants for all protein coding genes. Generating a knock-out line involves huge monetary and time costs so capture of both the data describing each mutant alongside archiving of the line for distribution to future researchers is critical. The European Mouse Mutant Archive (EMMA) is a leading international network infrastructure for archiving and worldwide provision of mouse mutant strains. It operates in collaboration with the other members of the Federation of International Mouse Resources (FIMRe), EMMA being the European component. Additionally EMMA is one of four repositories involved in the IKMC, and therefore the current figure of 1700 archived lines will rise markedly. The EMMA database gathers and curates extensive data on each line and presents it through a user-friendly website. A BioMart interface allows advanced searching including integrated querying with other resources e.g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server. EMMA database access is publicly available at http://www.emmanet.org.

The use of phylogenetic trees to describe the evolution of biological processes was established in the 1950s (Hennig 1952) and remains a fundamental approach to understanding the evolution of individual genes through to complete genomes; for example, in the mouse (Mouse Genome Sequencing Consortium 2002), rat (Gibbs et al. 2004), chicken (International Chicken Genome Sequencing Consortium 2004), and monodelphis (Mikkelsen et al. 2007) genome papers, and numerous papers on individual sequences. Now routine, the determination of vertebrate genome sequences provides a rich data source to understand evolution, and using phylogenetic trees of the genes is one of the best ways to organize these data. However, the increased set of genomes makes the compute and engineering tasks to form all the gene trees progressively more complex and harder for individual groups to use. The Ensembl project provides an accurate and consistent protein-coding gene set for all vertebrate genomes (International Human Genome Sequencing Consortium 2001; Dehal et al. 2002; Mouse Genome Sequencing Consortium 2002; Gibbs et al. 2004; Xie et al. 2005; Mikkelsen et al. 2007; Rhesus Macaque Genome Sequencing and Analysis Consortium 2007). Previously (until April 2006), Ensembl provided a basic method for tracing orthologs via the Best Reciprocal BLAST method, similar to approaches used in other genome analyses, such as Drosophila melanogaster (Adams et al. 2000) or human (International Human Genome Sequencing Consortium 2001). In June 2006 (Hubbard et al. 2007), we replaced this system with a phylogenetically sound, gene tree-based approach, providing a complete set of phylogenetic trees spanning 91% of genes across vertebrates. In addition to the vertebrates we have included a few important non-vertebrate species (fly, worm, and yeast) to act both as out groups and provide links to these model organisms. In this paper we provide the motivation, implementation, and benchmarking of this method and document the display and access methods for these trees. There have been a number of methods proposed for routine generation of genomewide orthology descriptions, including Inparanoid (Remm et al. 2001), MSOAR (Fu et al. 2007), OrthoMCL (Li et al. 2003), HomoloGene (Wheeler et al. 2008), TreeFam (Li et al. 2006), PhyOP (Goodstadt and Ponting 2006), and PhiGs (Dehal and Boore 2006). The first four, Inparanoid, MSOAR, OrthoMCL, and HomoloGene, focus on providing clusters (or linked clusters) of genes, without an explicit tree topology. PhyOP (Goodstadt and Ponting 2006) uses a tree-based method, but between pairs of closely related species, resolving paralogs accurately by using neutral substitution (as measured by d S, the synonymous substitution rate). TreeFam provides an explicit gene tree across multiple species, using both d S, d N (nonsynonymous substitution rate), nucleotide and protein distance measures, and the standard species tree to balance duplications vs. deletions to inform the tree construction, using the program TreeBeST (http://treesoft.sourceforge.net/treebest.shtml; L. Heng, A.J. Vilella, E. Birney, and R. Durbin, in prep.). The PhiGs method (Dehal and Boore 2006) is a leading phylogenetic-based method that produced a comprehensive phylogenetic resource for the genomes at the time it was run, and the basic outline of its analysis, which was clustering of protein sequences, followed by phylogenetic trees, is similar to the method presented here. However, the PhiGs resource covered a smaller number of species (23 vs. 45) and has been difficult to keep up to date with the advances in gene sets and genomes. Another major difference between PhiG-based phylogenetic trees and the phylogenetic trees presented here is that the former was calculated using a single maximum likelihood method based on protein evolution. In contrast, the Ensembl gene trees are calculated using a new method, TreeBeST, which integrates multiple tree topologies, in particular both DNA level and protein level models and combines this with a species-tree aware penalization of topologies, which are inconsistent with known species relationships. We show in this paper that this method produces trees that are more consistent with synteny relationships and less anomalous topologies than single protein-based phylogenetic methods. There are also many single phylogenetic tree-building approaches, many of them based on maximum likelihood methods; one leading method is PhyML (Guindon and Gascuel 2003). It is unclear what is the best method to use, in particular in the context of genome-wide tree building with constraints on computational costs and the need to robustly handle many complex scenarios usually involving large families with heterogeneous phylogenetic depths. In this paper, we benchmark in vertebrates the tree programs TreeBeST and PhyML, and the resulting trees to basic best reciprocal hit (BRH) methods, and cluster frameworks, in particular Inparanoid and HomoloGene. We also benchmark to a recent PhyOP data set. The PhyOP pipeline has recently switched to use the same tree-building program (TreeBeST) that we use, but differs in its input clusters. Although we adopted this same tree-building method, we describe here considerable novel engineering in the deployment of these methods across all vertebrates. Similar to the PhiGs resource, we have used the dense coverage of genomes to provide topologically based timings (i.e., the standard use of outgroups vs. subsequent lineages to bracket a duplication), in order to label duplication events.

Resume Objectifs Les auteurs rapportent une etude de la prevalence de l’infection par le retrovirus HTLV-1 dans l’ouest de la Guyane francaise afin de connaitre les facteurs de risque d’infection et de transmission materno-infantile. Materiel et methode La seroprevalence HTLV-1 est etudiee chez l’ensemble des parturientes ayant accouche a Saint-Laurent entre juillet 1991 et juin 1993 en rapportant les differents facteurs de risque associes. Une analyse retrospective est effectuee ensuite chez les enfants de 18 mois a 12 ans nes des femmes HTLV-1 seropositives en etudiant chez les enfants la duree de l’allaitement et chez les meres le titre des anticorps anti-HTLV1 ainsi que la charge pro-virale. Resultats La seroprevalence HTLV-1 de l’ensemble des accouchees est de 4,4 %. Ce taux est plus eleve (5,7 %) dans l’ethnie Noir-Marron chez laquelle il croit avec l’âge et est significativement plus eleve en cas de gestite > 6, de parite > 4, d’antecedents d’avortement, de cesarienne et d’un facteur rhesus negatif. Cependant, apres ajustement sur l’âge, seuls la gestite et le facteur rhesus persistent. A partir de 81 femmes HTLV-1 seropositives, 216 enfants ont pu etre preleves. Le taux d’infection (10,6 %) est significativement plus eleve chez les filles (13,8 %) que chez les garcons (5,6 %). Il n’a pas ete retrouve d’infection chez les enfants ayant beneficie d’un allaitement artificiel. Le taux de transmission materno-infantile augmente significativement avec le titre des anticorps anti-HTLV-1 et une charge pro-virale importante chez la mere. Conclusion L’infection par le retrovirus HTLV-1, qui peut etre responsable de pathologies graves a l’âge adulte (leucemie, neuromyelopathie) doit etre depistee pendant la grossesse chez les femmes issues des zones a risque (Caraibes, Afrique intertropicale). En effet, en cas de seropositivite HTLV-1, les meres devront etre informees des risques de transmission et les enfants devront beneficier d’un allaitement artificiel.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

Chromosome 14 is one of five acrocentric chromosomes in the human genome. These chromosomes are characterized by a heterochromatic short arm that contains essentially ribosomal RNA genes, and a euchromatic long arm in which most, if not all, of the protein-coding genes are located. The finished sequence of human chromosome 14 comprises 87,410,661 base pairs, representing 100% of its euchromatic portion, in a single continuous segment covering the entire long arm with no gaps. Two loci of crucial importance for the immune system, as well as more than 60 disease genes, have been localized so far on chromosome 14. We identified 1,050 genes and gene fragments, and 393 pseudogenes. On the basis of comparisons with other vertebrate genomes, we estimate that more than 96% of the chromosome 14 genes have been annotated. From an analysis of the CpG island occurrences, we estimate that 70% of these annotated genes are complete at their 5' end.

HLA-A*0201 transgenic, H-2D(b)/mouse beta2-microglobulin double-knockout mice were used to compare and optimize the immunogenic potential of 17HIV 1-derived,HLA-A0201-restricted epitopic peptides. A tyrosine substitution in position 1 of the epitopic peptides, which increases both their affinity for and their HLA-A0201 molecule stabilizing capacity, was introduced in a significant proportion, having verified that such modifications enhance their immunogenicity in respect of their natural antigenicity. Based on these results, a 13-polyepitope construct was inserted in the pre-S2 segment of the hepatitis B middle glycoprotein and used for DNA immunization. Long-lasting CTL responses against most of the inserted epitopes could be elicited simultaneously in a single animal with cross-recognition in several cases of their most common natural variants.

The aim of this study was to investigate the distribution of human T-cell leukemia virus type 1 (HTLV-1) in various organs of serially sacrificed squirrel monkeys (Saimiri sciureus) in order to localize the reservoir of the virus and to evaluate the relationship between viral expression and the humoral or cellular immune response during infection. Six squirrel monkeys infected with HTLV-1 were sacrificed 6, 12, and 35 days and 3, 6, and 26 months after inoculation, and 20 organs and tissues were collected from each animal. PCR and reverse transcription-PCR (RT-PCR) were performed with gag and tax primers. Proviral DNA was detected by PCR in peripheral blood mononuclear cells (PBMCs) of monkeys sacrificed 6 days after inoculation and in PBMCs, spleens, and lymph nodes of monkeys sacrificed 12 and 35 days and 3, 6, and 26 months after inoculation. Furthermore, tax/rex mRNA was detected by RT-PCR in the PBMCs of two monkeys 8 to 12 days after inoculation and in the spleens and lymph nodes of the monkey sacrificed on day 12. In this animal, scattered HTLV-1 tax/rex mRNA-positive lymphocytes were detected by in situ hybridization in frozen sections of the spleen, around the germinal centers and close to the arterial capillaries. Anti-HTLV-1 cell-mediated immunity was evaluated at various times after inoculation. Anti-p40 Tax and anti-Env cytolytic T-cell responses were detected 2 months after infection and remained detectable thereafter. When Tax peptides were used, this response appeared to be directed against various Tax epitopes. Our results indicate that squirrel monkeys represent a promising animal model for studying the early events of HTLV-1 infection and for evaluating candidate vaccines against HTLV-1. Human T-cell leukemia/lymphoma virus type 1 (HTLV-1), the causative agent of adult T-cell leukemia (36) and tropical spastic paraparesis/HTLV-1-associated myelopathy (TSP/ HAM) (10), has also been associated with pediatric infectious dermatitis (22), uveitis (24), and some cases of arthropathy (13) and polymyositis (25). Owing to the inherent difficulty of obtaining human specimens in early HTLV-1 infection, a relevant animal model is essential for better understanding of the seeding of HTLV-1 in various organs. We showed recently that the squirrel monkey Saimiri sciureus, a South American nonhuman primate which is free of simian T-cell leukemia virus, is susceptible to experimental infection with syngeneic or allogeneic HTLV-1-immortalized cells (19). As in humans, such experimental inoculation leads to chronic infection, HTLV-1 provirus being detectable in peripheral blood mononuclear cells (PBMCs) by PCR up to 36 months after inoculation. Chronically infected monkeys, like HTLV-1-infected humans, develop high titers of antibodies against the structural proteins of the virus (19). In infections with human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV), the lymph nodes are reservoirs that contain a large viral load during the asymptomatic stage (8, 29). A significant percentage of latently infected lymphocytes are found in the lymph nodes and constitute a target for later viral reactivation (7). Indeed, during clinical latency in HIV or SIV infection, productively infected cells are detected at higher frequency in lymph nodes than in peripheral blood, indicating the progressive involvement of the lymphoid organs in HIV infection (2, 21, 27). These findings show that HIV is widely disseminated in lymphoid tissue relatively early in infection. In contrast, little is known about the role of the lymphoid tissues in the early phases of HTLV-1 infection. The aim of the present study was to investigate the early events in HTLV-1 infection and specifically the distribution of the HTLV-1 provirus in various organs of serially sacrificed squirrel monkeys, to localize the reservoir of the latent virus, and to evaluate the humoral and cellular immune responses to infection.

Human T cell leukemia virus type I (HTLV-I) is a persistent virus that causes adult T cell leukemia and tropical spastic paraparesis/HTLV-I–associated myelopathy. Studies on rabbits have shown that viral proteins encoded by the open reading frames pX-I and pX-II are required for the establishment of the persistent infection. To examine the in vivo production of these proteins in humans, we have investigated whether cytotoxic T lymphocytes isolated from HTLV-I–infected individuals recognized pX-I and pX-II peptides. CD8+ T lymphocytes to pX-I and pX-II peptides were detected in HTLV-I–infected individuals, whatever their clinical status, and even in the absence of any antigenic restimulation. These findings indicate that the HTLV-I pX-I and pX-II proteins are chronically synthesized in vivo, and are targets of the natural immune response to the virus.

Homozygous HLA-A2.1 transgenic H-2Kb°Db° double knockout (KO) mice were created. Their potential to develop HLA-A2.1-restricted cytolytic responses was compared with that of their classical transgenic counterparts, which still express H-2Kb, Db molecules. On cell surfaces, both strains express similar amounts of chimeric (α1α2 domains of human, α3 cytoplasmic domains of mouse) HLA-A2.1 molecules in noncovalent association with mouse β2-microglobulin. Compared with mice that are totally deprived of histocompatibility class Ia molecules (H-2Kb°Db° double KO), the expression of HLA-A2.1 in transgenic/double KO mice resulted in sizeable increase in the periphery of CD8+ T cells with a normally diversified TCR repertoire. A biased education in favor of HLA-A2.1, ascribable to the absence of H-2 class Ia molecules, was evidenced in these transgenic/double KO mice by their improved capacity to mount HLA-restricted cytolytic responses, regardless of whether they were virally infected or injected with synthetic epitopic peptide. HLA class I transgenic, H-2 class Ia KO mice should represent useful animal models for the preclinical evaluation of vaccine formulations aiming at the induction of HLA class I-restricted CTL responses.

An epidemiological study was performed in French Guiana (population 115,000) to determine the prevalence and incidence of adult T-cell leukemia/lymphoma (ATL) associated with human T-cell leukemia/lymphoma virus type I (HTLV-I). From January 1990 to December 1993, all suspected cases of ATL were enrolled in this study, and their clinical, epidemiological and immunovirological features were analyzed. Out of the 19 suspected cases, 18 were considered as ATL associated with HTLV-I (8 acute forms, 8 lymphoma types and 2 smoldering cases). Before this study, only 2 ATL cases had been reported in French Guiana over a 10-year period. This demonstrates that the number of ATL cases is greatly underestimated in most tropical HTLV-I endemic areas unless a specific disease search is performed. The mean age of the patients was 41 years. While HTLV-I antibodies were present in all cases, molecular studies demonstrated a clonal integration of HTLV-I in the tumoral cells in 7 cases out of the 9 tested. Fifteen patients died within a year of diagnosis. The crude incidence rate of ATL in French Guiana is around 3.5/100,000/year, a situation similar to that found in the Caribbean and in HTLV-I-endemic regions of Japan. However it reaches around 30/100,000/year (highest incidence ever described) in a small remote ethnic group of African origin (around 6200 inhabitants). Possible causes of ATL clustering in this ethnic group are presented. © 1995 Wiley-Liss, Inc.

BackgroundThe Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomic alignments and the protein homology predictions. The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future.ResultsWe present eHive, a new fault tolerant distributed processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block-branch diagrams. In the eHive system a MySQL database serves as the central blackboard and the autonomous agent, a Perl script, queries the system and runs jobs as required. The system allows us to define dataflow and branching rules to suit all our production pipelines. We describe the implementation of three pipelines: (1) pairwise whole genome alignments, (2) multiple whole genome alignments and (3) gene trees with protein homology inference. Finally, we show the efficiency of the system in real case scenarios.ConclusionseHive allows us to produce computationally demanding results in a reliable and efficient way with minimal supervision and high throughput. Further documentation is available at:http://www.ensembl.org/info/docs/eHive/.

Udgivelsesdato: 2008-Jan TreeFam (http://www.treefam.org) was developed to provide curated phylogenetic trees for all animal gene families, as well as orthologue and paralogue assignments. Release 4.0 of TreeFam contains curated trees for 1314 families and automatically generated trees for another 14,351 families. We have expanded TreeFam to include 25 fully sequenced animal genomes, as well as four genomes from plant and fungal outgroup species. We have also introduced more accurate approaches for automatically grouping genes into families, for building phylogenetic trees, and for inferring orthologues and paralogues. The user interface for viewing phylogenetic trees and family information has been improved. Furthermore, a new perl API lets users easily extract data from the TreeFam mysql database.

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view about chromatin structure has emerged, including its interrelationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded novel mechanistic and evolutionary insights about the functional landscape of the human genome. Together, these studies are defining a path forward to pursue a more-comprehensive characterisation of human genome function.

A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.

Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of individual genomes, and of the synteny and orthology relationships between them. It is also a framework for integration of any biological data that can be mapped onto features derived from the genomic sequence. Ensembl is available as an interactive Web site, a set of flat files, and as a complete, portable open source software system for handling genomes. All data are provided without restriction, and code is freely available. Ensembl's aims are to continue to “widen” this biological integration to include other model organisms relevant to understanding human biology as they become available; to “deepen” this integration to provide an ever more seamless linkage between equivalent components in different species; and to provide further classification of functional elements in the genome that have been previously elusive.

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

The increasing number of complete and nearly complete metazoan genome sequences provides a significant amount of material for large-scale comparative genomic analysis. Finding new effective methods to analyse such enormous datasets has been the object of intense research. Three main areas in comparative genomics have recently shown important developments: whole-genome alignment, gene prediction and regulatory-region prediction. Each of these areas improves the methods of deciphering long genomic sequences and uncovering what lies hidden in them.

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

A quantitative study of the T cell receptor repertoire was performed ex vivo on CD4 and CD8 T cell subsets of human T cell leukemia virus type I (HTLV-I)‐infected asymptomatic carriers and patients with HTLV-I‐associated myelopathy/tropical spastic paraparesis (HAM/ TSP). Indexes of oligoclonality that compiled all repertoire modifications were calculated for peripheral blood mononuclear cells and for CD4 and CD8 T cell subsets. Both patients with HAM/TSP and asymptomatic carriers had greater T lymphocyte expansions than did uninfected donors, which was independent of age and at least twice higher in the CD8 than in the CD4 cell compartment. Some expanded CD8 T cells corresponded to cytotoxic T lymphocytes directed against various epitopes of the immunodominant Tax protein. Patients with HAM/TSP had significantly higher CD8 cell expansions than did asymptomatic carriers. These results highlight the prognostic value of measuring CD8 T cell expansions during follow-up of HTLV-I infection. Human T cell leukemia virus type I (HTLV-I) is a persistent virus that infects 10‐20 million people worldwide. Although HTLV-I infection is asymptomatic in a majority of infected persons, in 1%‐5% of infected persons it is associated with the de

We investigated the serological, epidemiological and molecular aspects of human T-cell lymphotropic virus type I and II (HTLV-I/II) infection in the Amerindian populations of French Guiana by testing 847 sera. No HTLV-II antibodies were detected, but five individuals (0·59%) were seropositive for HTLV-I. Analysis of the nucleotide sequences of 522 bp of the env gene and the compete LTR showed that all of the strains from French Guiana belonged to the cosmopolitan subtype A. The similarities were greater between Amerindian and Creole strains than between Amerindian and Noir-Marron strains or than between Creole and Noir-Marron strains. Phylogenetic analysis showed two clusters: one of strains from Amerindians and Creoles, which belong to the transcontinental subgroup, and the other of strains from Noirs-Marrons, belonging to the West African subgroup. Our results suggest that the Amerindian HTLV-I strains are of African origin.

The aim of this study was to compare rates of human T-cell lymphotropic virus type I (HTLV-I) seroprevalence in pregnant women belonging to different ethnic groups in French Guiana and to determine the risk factors associated with HTLV-I seropositivity. All 1,873 deliveries between 1 July 1991 and 30 June 1993 in the only gynecologic and obstetric unit at Saint Laurent du Maroni were enrolled. Serologic status could be established for 1,727 women, with 75 (4.3%) being HTLV-I seropositive. The HTLV-I seroprevalence rate differed significantly between ethnic groups: 5.7% for Noir-Marron (70/1,302), 6.3% for Haitian (3/50), and 0% for Creole (126), Amerindians (166), and Hmong (64). In Noir-Marron pregnant women, HTLV-I seropositivity was associated with a maternal age of > 35 years [odds ratio (OR), 3.3; 95% confidence interval (CI), 1.4-7.6], prior miscarriage (OR, 1.7; CI, 1-2.8), prior cesarean section (OR, 2.1; CI, 1.1-4.0), a parity > 4 (OR, 4.0; CI, 1.8-8.8), a gravidity > 6 (OR, 4.2; CI, 2.0-7.2), and a negative Rhesus factor (OR, 2.2; CI, 1.1-4.5). Two separate stepwise logistic regressions were done because gravidity and parity were highly correlated. HTLV-I seropositivity remained associated with a gravidity > 6 (OR, 3.9; CI, 2.1-7.4) and a negative Rhesus factor (OR, 2.6; CI, 1.2-5.3) for the first model and with a parity > 4 (OR, 4.1; CI, 1.9-9.0) and a negative Rhesus factor (OR, 2.5; CI, 1.2-5.1) for the second model.(ABSTRACT TRUNCATED AT 250 WORDS)

Japan is one of the highest endemic areas of the world for human T cell leukemia-lymphoma virus type I (HTLV-I). To gain new insight as to the origin of this virus in Japan and especially in the southern islands of the archipelago, we investigated the long terminal repeat (LTR) of 67 newly isolated HTLV-I proviral DNAs from peripheral blood mononuclear cells of HTLV-I-infected individuals for their restriction fragment length polymorphism (RFLP). The specimens were from Japanese living in different geographical areas (Hokkaido, Honshu, Kyushu, or the Ryukyu Islands) of Japan (59 cases) or Americans of Japanese ancestry living in Hawaii (8 cases). The analysis of the results, together with data for the 19 previously published LTR sequences, demonstrated the existence of 2 subtypes of HTLV-I in Japan. The first, which we propose to name Japanese subtype (previously named subtype III), is more frequent (67 of 86: 78%) than the second, the cosmopolitan subtype (previously named subtype II) (19 of 86: 22%). In parallel, a fragment of 413 base pairs of the U3/R region (nucleotide 22 to 434) was cloned and sequenced from 10 of the new Japanese samples. The alignment of these sequences and their comparison and phylogenetic analysis with previously published LTR HTLV-I sequences, demonstrated clearly the existence of the two distinct molecular subtypes of HTLV-I in Japan, diverging in this LTR region by about 1.6%. Furthermore, the study of the geographical distribution of the 2 subtypes among the 80 samples from patients whose place of residence in Japan was known showed an uneven distribution. While the Japanese subtype was present in all parts of Japan, the cosmopolitan subtype seemed to cluster in the southern islands of the archipelago (i.e., Kyushu and the Ryukyu Islands) as well as in immigrants from those areas who had lived in Hawaii for decades. These new molecular data raise questions and suggest hypotheses, discussed here, concerning the origin and means of dissemination of these human retrovirus subtypes in Japan.