Remnants of an Ancient Deltaretrovirus in the Genomes of Horseshoe Bats (Rhinolophidae).

Endogenous retrovirus (ERV) sequences provide a rich source of information about the long-term interactions between retroviruses and their hosts. However, most ERVs are derived from a subset of retrovirus groups, while ERVs derived from certain other groups remain extremely rare. In particular, only a single ERV sequence has been identified that shows evidence of being related to an ancient Deltaretrovirus, despite the large number of vertebrate genome sequences now available. In this report, we identify a second example of an ERV sequence putatively derived from a past deltaretroviral infection, in the genomes of several species of horseshoe bats (Rhinolophidae). This sequence represents a fragment of viral genome derived from a single integration. The time of the integration was estimated to be 11-19 million years ago. This finding, together with the previously identified endogenous Deltaretrovirus in long-fingered bats (Miniopteridae), suggest a close association of bats with ancient deltaretroviruses.

Representation of Biomedical Expertise in Ontologies: a Case Study about Knowledge Acquisition on HTLV viruses and their clinical manifestations.

In this paper, we introduce a set of methodological steps for knowledge acquisition applied to the organization of biomedical information through ontologies. Those steps are tested in a real case involving Human T Cell Lymphotropic Virus (HTLV), which causes myriad infectious diseases. We hope to contribute to providing suitable knowledge representation of scientific domains.

Caracterização das variantes genotípicas do HTLV em um grupo de pacientes acompanhados em hospital universitário do Estado do Rio de Janeiro / Characterization of genotypic variants of HTLV in a group of patients followed at a university hospital in the state of Rio de Janeiro

O Vírus Linfotrópico de Células T Humanas (HTLV) foi o primeiro retrovírus identificado emhumanos e posteriormente associado à leucemia/linfoma de células T do adulto (LTA). Podemseencontrar quatro tipos: HTLV-1, HTLV-2, HTLV-3 e HTLV-4, sendo os dois primeiros demaior prevalência. Estima-se que cerca de 10 milhões de pessoas no mundo e 2,5 milhões noBrasil, estejam infectadas pelo HTLV. O HTLV-1 possui sete subtipos e o HTLV-2, quatro.Recentemente, foi identificado o subtipo HTLV-1b no estado do Rio de Janeiro, sendoanteriormente encontrado somente na África Central. A análise dos subtipos é importante emestudos sobre a origem geográfica e disseminação dos isolados virais. O presente estudo tevecomo principal objetivo caracterizar as variantes genotípicas do HTLV em um grupo depacientes acompanhados no Hospital Universitário Pedro Ernesto – UERJ. Objetivou tambémcaracterizar o grupo quanto aos possíveis fatores de risco para infecção pelo HTLV, descrevera ocorrência de doenças associadas com HTLV, caracterizar o grupo quanto aos subtipos deHTLV, descrevendo-os de acordo com a naturalidade dos pacientes e caracterizar os casos depacientes com sorologia de WB indeterminado utilizando técnicas de biologia molecular. Foramestudados pacientes com a infecção pelo HTLV, sintomática ou assintomática, com sorologiapositiva ou indeterminada. As amostras foram submetidas ao teste confirmatório pela PCR. Ainfecção foi confirmada em 31 dos 33 participantes do estudo. Dentre os positivos, 28 foramHTLV-1a e os demais HTLV-2b. O gênero mais frequente foi o feminino. Pacientes adultos,casados e pardos foram os mais frequentes dentro das variáveis de faixa etária, estado civil egrupo étnico, respectivamente. A maioria dos pacientes relatou não saber se manteve contatosexual com portador de HTLV, não fazer uso de drogas injetáveis ou já ter realizado transfusãode sangue...

The Human T-Cell Lymphotropic Virus (HTLV) was the first human retrovirusidentified and associated to leukemia/lymphoma, adult T-cells (ATL). Can be found four types:HTLV-1, HTLV-2, HTLV-3 and HTLV-4. The first two are the most prevalent. About 10 millionpeople around the world and 2.5 million in Brazil, are infected with HTLV. The HTLV-1 typeis subdivided into seven subtypes and HTLV-2 in four. Recently, HTLV-1b was identified in thestate of Rio de Janeiro. This subtype it was found only in Central Africa. The analysis ofsubtypes is important in studies of geographical origin and dissemination of viral isolates. Thepresent study aimed to characterize the genotypic variants of HTLV in a group of patientstreated at University Hospital Pedro Ernesto - UERJ. Aimed to characterize the group as to thepossible risk factors for HTLV infection, describing the occurrence of diseases associated withHTLV, characterized the group as to the HTLV subtypes; correlations between subtypes andlocal of infection; assess risk factors and confirm or exclude cases of patients with indeterminateor not typed serology. This study characterized the group as to the possible risk factors forHTLV infection, describing the occurrence of diseases associated with HTLV, characterized thegroup as the subtypes of HTLV, describing them according to the naturalness of patients andcharacterize the cases of patients with serology indeterminate WB using molecular biologytechniques. Patients were studied with HTLV, symptomatic or asymptomatic, with positive orindeterminate WB serology. The specimens were subjected to confirmatory testing by PCR.The infection was confirmed in 31 of 33 study participants. Among positives, 28 were HTLV-1a and other HTLV-2b. The most frequent was the female gender. Adult patients, married andbrowns were the most frequent within the variables of age, marital status and ethnic group,respectively...

Short communication: no evidence of HTLV-3 and HTLV-4 infection in New York State subjects at risk for retroviral infection.

The primate T-cell lymphoma viruses (PTLV) are divided into six distinct species. The biology and epidemiology of PTLV-1 and PTLV-2 are very well understood. However, that of PTLV-3, 4, 5, and 6 are not. Recently, in Cameroon, three and one humans were shown to be infected with HTLV-3 and HTLV-4, respectively. We undertook a study to ascertain whether any of these two retroviruses were present in the peripheral blood mononuclear cell DNA of New York State subjects deemed at risk for PTLV infection. Samples were analyzed by PTLV-3 and PTLV-4 specific PCR assays from the following human and simian subject types: African-American medical clinic patients; HTLV EIA+, WB indeterminate blood donors; intravenous drug users; patients with leukemia, lymphoma, myelopathy, polymyositis, or AIDS; and African chimpanzees. None of the 1200 subjects was positive for HTLV-3 or 4. The data indicate that, at the time of sample collection, no evidence exists for the dissemination of HTLV-3 or 4 to New York State. Continued epidemiological studies are warranted to explore the worldwide prevalence rates and dissemination patterns of HTLV-3 and 4 infections, and their possible disease associations.

Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4.

BACKGROUND: Human T-lymphotropic virus type 4 (HTLV-4) is a new deltaretrovirus recently identified in a primate hunter in Cameroon. Limited sequence analysis previously showed that HTLV-4 may be distinct from HTLV-1, HTLV-2, and HTLV-3, and their simian counterparts, STLV-1, STLV-2, and STLV-3, respectively. Analysis of full-length genomes can provide basic information on the evolutionary history and replication and pathogenic potential of new viruses. RESULTS: We report here the first complete HTLV-4 sequence obtained by PCR-based genome walking using uncultured peripheral blood lymphocyte DNA from an HTLV-4-infected person. The HTLV-4(1863LE) genome is 8791-bp long and is equidistant from HTLV-1, HTLV-2, and HTLV-3 sharing only 62-71% nucleotide identity. HTLV-4 has a prototypic genomic structure with all enzymatic, regulatory, and structural proteins preserved. Like STLV-2, STLV-3, and HTLV-3, HTLV-4 is missing a third 21-bp transcription element found in the long terminal repeats of HTLV-1 and HTLV-2 but instead contains unique c-Myb and pre B-cell leukemic transcription factor binding sites. Like HTLV-2, the PDZ motif important for cellular signal transduction and transformation in HTLV-1 and HTLV-3 is missing in the C-terminus of the HTLV-4 Tax protein. A basic leucine zipper (b-ZIP) region located in the antisense strand of HTLV-1 and believed to play a role in viral replication and oncogenesis, was also found in the complementary strand of HTLV-4. Detailed phylogenetic analysis shows that HTLV-4 is clearly a monophyletic viral group. Dating using a relaxed molecular clock inferred that the most recent common ancestor of HTLV-4 and HTLV-2/STLV-2 occurred 49,800 to 378,000 years ago making this the oldest known PTLV lineage. Interestingly, this period coincides with the emergence of Homo sapiens sapiens during the Middle Pleistocene suggesting that early humans may have been susceptible hosts for the ancestral HTLV-4. CONCLUSION: The inferred ancient origin of HTLV-4 coinciding with the appearance of Homo sapiens, the propensity of STLVs to cross-species into humans, the fact that HTLV-1 and -2 spread globally following migrations of ancient populations, all suggest that HTLV-4 may be prevalent. Expanded surveillance and clinical studies are needed to better define the epidemiology and public health importance of HTLV-4 infection.

New strain of human T lymphotropic virus (HTLV) type 3 in a Pygmy from Cameroon with peculiar HTLV serologic results.

A search for human T lymphotropic virus (HTLV) types 1 and 2 and related viruses was performed by serological and molecular means on samples obtained from 421 adult villagers from the southern Cameroon forest areas. One individual (a 56-year-old Baka Pygmy hunter) was found to be HTLV-3 infected; however, there was a low proviral load in blood cells. Complete sequence analysis of this virus (HTLV-3Lobak18) indicated a close relationship to human HTLV-3Pyl43 and simian STLV-3CTO604 strains. Plasma samples from Lobak18, the HTLV-3 infected individual, exhibited a peculiar "HTLV-2-like" pattern on Western blot analysis and were serologically untypeable by line immunoassay. These results were different from those for the 2 previously reported HTLV-3 strains, raising questions about serological confirmation of infection with such retroviruses.

The human HTLV-3 and HTLV-4 retroviruses: new members of the HTLV family.

Human T cell leukemia/lymphoma virus Type 1 and 2 (HTLV-1 and HTLV-2), together with their simian counterparts (STLV-1, STLV-2), belong to the Primate T lymphotropic viruses group (PTLV). HTLV-1 infects 15 to 20million people worldwide, while STLV-1 is endemic in a number of simian or ape species living in Africa or Asia. The high percentage of homologies between HTLV-1 and STLV-1 strains, led to the demonstration that most HTLV-1 subtypes arose from interspecies transmission between monkeys and humans. STLV-3 viruses belong to the third PTLV type and are equally divergent from HTLV-1 than from HTLV-2. They are endemic in several monkey species that live in West, Central, and East Africa. In 2005, we and others reported the discovery of the human homolog (HTLV-3) of STLV-3 in two asymptomatic inhabitants from South Cameroon whose sera exhibited HTLV indeterminate serologies. More recently, we reported a third case of HTLV-3 infection in Cameroon suggesting that this virus is not rare in the human population living in Central Africa. Together with STLV-3, these three human viral strains belong therefore to the PTLV-3 type. A fourth HTLV type (HTLV-4) was also discovered in the same geographical area. Current studies are aimed at determining the prevalence, distribution and modes of transmission of these viruses as well as their possible association with human diseases. Furthermore, molecular characterization of their viral transactivator Tax is ongoing in order to look for possible oncogenic properties.

Discovery of a new human T-cell lymphotropic virus (HTLV-3) in Central Africa.

Human T-cell Leukemia virus type 1 (HTLV-1) and type 2 (HTLV-2) are pathogenic retroviruses that infect humans and cause severe hematological and neurological diseases. Both viruses have simian counterparts (STLV-1 and STLV-2). STLV-3 belongs to a third group of lymphotropic viruses which infect numerous African monkeys species. Among 240 Cameroonian plasma tested for the presence of HTLV-1 and/or HTLV-2 antibodies, 48 scored positive by immunofluorescence. Among those, 27 had indeterminate western-blot pattern. PCR amplification of pol and tax regions, using HTLV-1, -2 and STLV-3 highly conserved primers, demonstrated the presence of a new human retrovirus in one DNA sample. tax (180 bp) and pol (318 bp) phylogenetic analyses demonstrated the strong relationships between the novel human strain (Pyl43) and STLV-3 isolates from Cameroon. The virus, that we tentatively named HTLV-3, originated from a 62 years old Bakola Pygmy living in a remote settlement in the rain forest of Southern Cameroon. The plasma was reactive on MT2 cells but was negative on C19 cells. The HTLV 2.4 western-blot exhibited a strong reactivity to p19 and a faint one to MTA-1. On the INNO-LIA strip, it reacted faintly with the generic p19 (I/II), but strongly to the generic gp46 (I/II) and to the specific HTLV-2 gp46. The molecular relationships between Pyl43 and STLV-3 are thus not paralleled by the serological results, as most of the STLV-3 infected monkeys have an "HTLV-2 like" WB pattern. In the context of the multiple interspecies transmissions which occurred in the past, and led to the present-day distribution of the PTLV-1, it is thus very tempting to speculate that this newly discovered human retrovirus HTLV-3 might be widespread, at least in the African continent.

[New human retroviruses: HTLV-3 and HTLV-4]. / Les nouveaux rétrovirus humains HTLV-3 et HTLV-4.

Human T cell leukemia/lymphoma virus Type 1 and 2 (HTLV-1 and HTLV-2), together with their simian counterparts (STLV-1, STLV-2 and STLV-3), belong to the Primate T lymphotropic viruses group (PTLV). HTLV-1 infects 15 to 20 million people worldwide, while STLV-1 is endemic in a number of simian species living in the Old World. Due to the high percentage of homologies between HTLV-1 and STLV-1 strains, it has now been widely accepted that most HTLV-1 subtypes arose from interspecies transmission between monkeys and humans. On the opposite, there is no close human homolog of the two STLV-2 strains that have been discovered in African bonobos chimpanzees. These results suggest that the interspecies transmission that lead to the present day HTLV-2 must have occurred in a distant past. STLV-3 viruses are very divergent, both from HTLV-1 and from HTLV-2. They are endemic in several monkey species that live in west, central and east Africa. Recently, two laboratories independently reported the discovery of the human homolog (HTLV-3) of STLV-3 in two inhabitants from south Cameroon whose sera exhibited HTLV indeterminate serologies. Together with STLV-3, these two viruses belong therefore to the PTLV-3 group. In addition, a fourth HTLV type (HTLV-4) was also discovered in the same geographical area. Current studies are aimed at determining the molecular characterization of these viruses. In particular, the possible oncogenic properties of their viral transactivator Tax is being investigated, as well as their modes of transmission and their possible association with human diseases.

The human T-cell lymphoma/leukemia viruses.

The primate T-cell lymphoma/leukemia viruses belong to an oncogenic genus of complex retroviruses. Members of this genus have been shown to be pathogenic in man. The human T-cell lymphoma/leukemia virus (HTLV) type I has been linked in the etiology of T-cell malignancies and "autoimmune-like" neurologic and rheumatic disorders; a related virus, HTLV-II, is becoming increasingly associated with similar disorders. Cell transformation is thought to be caused predominantly by the effects of the viral regulatory protein, Tax. An additional induced host cell molecule, adult T-cell lymphoma-derived factor, may contribute to cell immortalization. Like the DNA tumor viruses, HTLV activates transcription of cellular proto-oncogenes and inhibits cellular mechanisms of tumor suppression, cell cycle arrest, and apoptosis. However, individuals who are able to mount a strong cell-mediated immune response and limit viral entry into uninfected cells do not develop associated malignancies. Unfortunately, HTLV-induced malignancies are difficult to treat with conventional chemotherapy, and disease progression is often rapid with a median survival of less than 2 years. There are, however, some novel approaches that have yet to be fully tested that may have greater efficacy in the treatment of HTLV-induced diseases. In the future, better screening and detection methods, along with new vaccines and therapies, may contribute to the increased prevention and control of HTLV infection and its associated diseases.

Likelihood analysis of phylogenetic networks using directed graphical models.

A method for computing the likelihood of a set of sequences assuming a phylogenetic network as an evolutionary hypothesis is presented. The approach applies directed graphical models to sequence evolution on networks and is a natural generalization of earlier work by Felsenstein on evolutionary trees, including it as a special case. The likelihood computation involves several steps. First, the phylogenetic network is rooted to form a directed acyclic graph (DAG). Then, applying standard models for nucleotide/amino acid substitution, the DAG is converted into a Bayesian network from which the joint probability distribution involving all nodes of the network can be directly read. The joint probability is explicitly dependent on branch lengths and on recombination parameters (prior probability of a parent sequence). The likelihood of the data assuming no knowledge of hidden nodes is obtained by marginalization, i.e., by summing over all combinations of unknown states. As the number of terms increases exponentially with the number of hidden nodes, a Markov chain Monte Carlo procedure (Gibbs sampling) is used to accurately approximate the likelihood by summing over the most important states only. Investigating a human T-cell lymphotropic virus (HTLV) data set and optimizing both branch lengths and recombination parameters, we find that the likelihood of a corresponding phylogenetic network outperforms a set of competing evolutionary trees. In general, except for the case of a tree, the likelihood of a network will be dependent on the choice of the root, even if a reversible model of substitution is applied. Thus, the method also provides a way in which to root a phylogenetic network by choosing a node that produces a most likely network.

Assessment of a new immunoassay for serological confirmation and discrimination of human T-cell lymphotropic virus infections.

The present study evaluated a new confirmatory assay for antibodies to human T-cell lymphotropic virus type 1 and 2 (HTLV-1 and HTLV-2) proteins performed with serum samples from various commercial sources. The new test is a line immunoassay (LIA) with a nylon membrane sensitized with the most relevant antigens of HTLVs: the envelope gp46 and gp21 as well as the gag p24 and p19 antigens, represented by either recombinant proteins or synthetic peptides. A total of 176 serum or plasma samples were tested, of which 66 were HTLV-1 positive, 72 were HTLV-2 positive, and 38 were HTLV negative; of the 38 HTLV-negative samples 23 were indeterminate by Western blotting (WB). Serially diluted samples (n = 33) from HTLV-1- and HTLV-2-infected patients were also analyzed to determine the sensitivity of the new assay. The new confirmatory assay (INNO-LIA HTLV) performed markedly better than WB assays for those samples reactive by screening. Accurate confirmation of the presence of HTLV-1 and HTLV-2 antibodies and accurate discrimination of HTLV-1 and HTLV-2 antibodies were obtained for all the HTLV-seropositive samples. Due to its enhanced specificity and sensitivity, the new assay not only improves the ability to confirm and discriminate HTLV infections but also eliminates the vast majority of WB-indeterminate and false-positive specimens.

Serological and nucleic acid analyses for HIV and HTLV infection on archival human plasma samples from Zaire.

In order to better understand the genomic diversity and molecular phylogeny of the human retroviruses, the plasmas from 250 Zairean patients collected in 1969 were tested for antibodies to human T-cell lymphoma and human immunodeficiency viruses (HTLV or HIV) using ELISA and confirmatory Western blots and for viral nucleic acids by reverse transcriptase-directed PCR (RT-PCR). Interestingly, none of the patients was confirmed positive for HIV, even though this region is now endemic for HIV-1. However, 74 (30%) and 3 (1%) of the samples were positive for antibodies to HTLV-I and II, respectively. Forty-four of 74 (59%) Western blot-positive Zairean samples were RT-PCR positive for HTLV-I, while 1 of 3 (33%) of HTLV-II-seropositive samples was RT-PCR positive. On the contrary, none of the Western blot-negative or indeterminate samples were RT-PCR positive for either HTLV-I or HTLV-II. We have cloned and sequenced 140 bp of the pol gene flanked by SK110/SK111 from 8 HTLV-I- and 1 HTLV-II-positive archival samples from Zaire. The HTLV-I isolates from Zaire cluster together as a phylogenetic group, diverging from the prototype Japanese HTLV-I (ATK) by a range of 1.4 to 3.6%. Their close homology to some African STLV-I isolates suggests relatively recent interspecies transmission. The Zairean HTLV-II isolate is closely grouped with the HTLV-II substrain of isolates found in Paleo-Amerindians of the New World, making it unlikely that it represents an endemic African strain.

A primate T-lymphotropic virus, PTLV-L, different from human T-lymphotropic viruses types I and II, in a wild-caught baboon (Papio hamadryas).

Searching for clues to the evolution of the primate T-lymphotropic viruses (PTLVs), which include the human and the simian T-lymphotropic viruses (HTLV and STLV), we have identified another PTLV, which differs sufficiently from the known PTLV-I and PTLV-II types to be designated here PTLV-L. The virus was isolated from a wild-born baboon (Papio hamadryas) from Eritrea. In a cDNA library a 1802-bp-long fragment was identified that extends from the env region, including the complete transmembrane protein gene, to part of the tax/rex gene. Homologies at the nucleotide sequence level of PTLV-L, prototype simian T-lymphotropic virus-PH969, with HTLV-I and -II, respectively, were 62% and 64% overall, 65% and 70% in the env region, and 80% and 80% in the partial tax/rex sequence. In the 5' part of the pX region a significant homology was seen only with HTLV-II (52%). Phylogenetic analysis based on the gene encoding the transmembrane protein indicates that PTLV-L represents a PTLV type with a long independent evolution, longer than any strain within the PTLV-I or PTLV-II groups. The finding of another PTLV type in African baboons is further evidence of the wide variety of PTLV found on this continent. Whether PTLV-L resembles PTLV-I and PTLV-II in the extension of its host range to other primates, including humans, remains to be seen.

Infection with the human immunodeficiency virus type 2.

PURPOSE: To review the clinical, epidemiologic, and biological features of infection with the human immunodeficiency virus type 2 (HIV-2). DATA IDENTIFICATION: Studies published since 1981 identified from MEDLINE searches, articles accumulated by the author, bibliographies of identified articles, and discussions with other investigators. STUDY SELECTION: Information for review was taken from the author's own studies, data from other investigators that have been submitted for publication, and from 131 of the more than 200 articles examined. DATA EXTRACTION: Pertinent studies were selected and the data synthesized into a review format. RESULTS OF DATA SYNTHESIS: Infection with HIV-2 is prevalent in West Africa and is increasingly being identified elsewhere. The human immunodeficiency virus type 2 is spread through sexual contact and via contaminated blood but, unlike HIV-1, perinatal transmission is limited. Human immunodeficiency virus type 2 is genetically much more closely related to the simian immunodeficiency virus (SIV) than to HIV-1; biological and demographic data suggest that HIV-2 may have originally been transmitted from monkeys to man. Although HIV-2 causes the acquired immunodeficiency syndrome (AIDS), the asymptomatic incubation period after infection with HIV-2 appears to be substantially longer than that following HIV-1 infection. Consistent with these clinical observations, genetic regulation of HIV-2 differs from that of HIV-1. Therapeutic studies of patients infected with HIV-2 are lacking. CONCLUSIONS: The human immunodeficiency virus type 2 is prevalent in West Africa and is now recognized on several other continents, including North America. Its epidemiology, biology, and clinical course differ from HIV-1. Therapeutic studies are needed.

[Classification of retroviruses]. / Classification des rétrovirus.

The retroviridae comprise a large number of viruses. In both nature and laboratories these viruses are associated with numerous diseases, including rapid or long latency malignancies, neurological disorders and immunodeficiency. The replication cycle is characterized by integration of the viral DNA into the host's genome after the reverse transcriptase copied the viral RNA into DNA. The discovery of human retroviruses had a late start. It was not until 1980 that the first oncovirus, the human T-leukaemia virus 1 (HTLV-1), was identified. The human immunodeficiency viruses (HIV-1 and HIV-2), belonging to the lentivirus subfamily, cause AIDS. Several simian virus, called simian immunodeficiency viruses (SIV) and related to HIV-1 and/or HIV-2 have been identified in monkeys and chimpanzees.