Nucleotide sequence analysis of an HTLV-I isolate from a Chilean patient with HAM/TSP

Phenotypic and genotypic comparisons of human T-cell leukemia virus type 1 reverse transcriptases from infected T-cell lines and patient samples

It is well established that cell-free infection with human T-cell leukemia virus type 1 (HTLV-1) is less efficient than that with other retroviruses, though the specific infectivities of only a limited number of HTLV-1 isolates have been quantified. Earlier work indicated that a post-entry step in the infectious cycle accounted for the poor cell-free infectivity of HTLV-1. To determine whether variations in the pol gene sequence correlated with virus infectivity, we sequenced and phenotypically tested pol genes from a variety of HTLV-1 isolates derived from primary sources, transformed cell lines, and molecular clones. The pol genes and deduced amino acid sequences from 23 proviruses were sequenced and compared with 14 previously published sequences, revealing a limited number of amino acid variations among isolates. The variations appeared to be randomly dispersed among primary isolates and proviruses from cell lines and molecular clones. In addition, there was no correlation between reverse transcriptase sequence and the disease phenotype of the original source of the virus isolate. HTLV-1 pol gene fragments encoding reverse transcriptase were amplified from a variety of isolates and were subcloned into HTLV-1 vectors for both single-cycle infection and spreading-infection assays. Vectors carrying pol genes that matched the consensus sequence had the highest titers, and those with the largest number of variations from the consensus had the lowest titers. The molecular clone from CS-1 cells had four amino acid differences from the consensus sequence and yielded infectious titers that were approximately eight times lower than those of vectors encoding a consensus reverse transcriptase.

HTLV-I infection associated with disease in aboriginal Indians from British Columbia: a serological and PCR analysis

BACKGROUND

Recent epidemiology studies have demonstrated the presence of HTLV-I and its close relative, HTLV-II in several aboriginal populations in North, Central and South America but not in Canadian Indian populations. HTLV-II appears to be more prevalent than HTLV-I in aboriginal populations of the Americas. Recently several clinical cases of HTLV-I associated myelopathy/tropical spastic paraparesis (HAM/TSP) and a case of adult T-cell leukemia (ATL) have been identified in British Columbian Indians. This data suggests that a new endemic area of HTLV-I infection may be present within British Columbian Indian population. However, it has recently been shown that HTLV-II may also be associated with a neurological disease similar to HAM/TSP.

OBJECTIVES

The purpose of the work reported here was to demonstrate whether HTLV-I, HTLV-II or both were responsible for the diseases seen in the British Columbian Indians.

STUDY DESIGN

In this study serological and gene amplification techniques were used to determine whether HTLV-I or HTLV-II was present in four families and three unrelated individuals all from different bands of aboriginal Native Indians in British Columbia. In each family, one member had an HTLV-associated disease, three cases of HAM/TSP and one case of ATL. Of the three individual aboriginal natives unrelated to the four families, two had HAM/TSP while the third was asymptomatic for HTLV-associated diseases.

RESULTS

This study demonstrated the presence of HTLV-I in the aboriginal Indians with disease and in some of their family members. HTLV-II was not detected in any of the British Columbian Indians tested in this study.

CONCLUSIONS

These British Columbian Indians represent the first Canadian aboriginal Indians with HTLV-I infection and associated diseases. Furthermore, the British Columbian Indian population may represent a previously unrecognized endemic population of HTLV-I infection.

Sequence and phylogenetic analysis of human T cell lymphotropic virus type 1 from Tumaco, Colombia

Human T cell lymphotropic virus type 1 (HTLV-1) is a retrovirus that causes leukemia and the neurological disorder HTLV-1 associated myelopathy or tropical spastic paraparesis (HAM/TSP). Infection with this virus - although it is distributed worldwide - is limited to certain endemic areas of the world. Despite its specific distribution and slow mutation rate, molecular epidemiology on this virus has been useful to follow the movements of human populations and routes of virus spread to different continents. In the present study, we analyzed the genetic variability of a region of the env gene of isolates obtained from individuals of African origin that live on the Pacific coast of Colombia. Sequencing and comparison of the fragment with the same fragment from different HTLV-1 isolates showed a variability ranging from 0.8% to 1.2%. Phylogenetic studies permit us to include these isolates in the transcontinental subgroup A in which samples isolated from Brazil and Chile are also found. Further analyses will be necessary to determine if these isolates were recently introduced into the American continent or if they rather correspond to isolates introduced during the Paleolithic period.

Sequence of the env gene of some KwaZulu-Natal, South African strains of HTLV type I

Phylogenetic analysis of HTLV-I suggests three main subtypes, namely, cosmopolitan, Central African, and Australo-Melanesian. HTLV-I is endemic in KwaZulu-Natal, South Africa. However, sequence data on the local strains are limited to the LTR region. The env gene of the local strain was amplified and sequenced from the peripheral blood of five seropositive individuals. Four had HTLV-I-associated myelopathy and one had infective eczema. The sequence analysis of the env gene showed a greater then 99% homology of the local strains. They were closely related to the North American strains (99.3%), followed by the Japanese strains (98.3-98.9%). Phylogenetic studies linked the local strains to the cosmopolitan subtype. This study provides new sequence data on the env gene of the local HTLV-I strain.

An apparent case of human T-cell lymphotropic virus type II (HTLV-II)-associated neurological disease: a clinical, molecular, and phylogenetic characterisation

Several studies have reported an association between HTLV-II and a neurological condition which has come to be called HTLV-II-associated myelopathy and is similar, in some cases, to HTLV-I-associated myelopathy. To further explore the establishment of an etiological link between this virus and neurological disease, we determined the HTLV status of three individuals, one of which presented with symptoms of progressive ataxia. Since the patient with neurological disease and her husband were HTLV-II positive, we had the potential to study one of few cases of an HTLV-II-associated neurological disorder, and the first case in Canada. However, although the individual with the neurological disease was HTLV-II positive, we discovered that her brother, who displays the same clinical symptoms, was not positive for either HTLV-II or HTLV-I. Thus, disease association with HTLV-II became unsupportable. We present here, nevertheless, the first sequence and phylogenetic analysis of an HTLV-II isolate in Canada. This study suggests that cases of HTLV-II and neurological disease must be carefully investigated before any etiological conclusions can be made.

Cloning and expression of a human T-lymphotropic virus type 1 protein with reverse transcriptase activity

Unlike most other characterized retroviruses, there is little published information on the biochemical properties of human T-lymphotropic virus type 1 (HTLV-1) reverse transcriptase (RT). Specifically, no reports of a cloned functional RT enzyme have been published. Since the RT enzyme is an essential component of the virus, our objective was to clone, express, and purify a functional RT enzyme from HTLV-1. Our approach was to clone and express a protein of approximately 60 to 65 kDa that we hypothesized would correspond to the RT region encoded by the pol reading frame. The predicted region encoding the RT enzyme comprised nucleotides 2617 to 4312 of the HTLV-1 MT-2 isolate. A putative RT gene was obtained by PCR and was ligated into various prokaryotic expression vectors. A novel cloning approach allowed us to generate a stable clone in the prokaryotic expression vector pGEX-4T-1 and produce a recombinant protein of approximately 60 to 65 kDa. The partially purified protein displays RT activity in both amplification RT (AMP-RT) assays and traditional RT assays. This is the first report of a cloned protein from HTLV-1 which displays RT activity and is the first step in the characterization of HTLV-1 RT.

Molecular detection and isolation of human T-cell lymphotropic virus type I (HTLV-I) from patients with HAM/TSP in São Paulo, Brazil

BACKGROUND

Infection with HTLV-I is etiologically linked with HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP). However some patients with chronic progressive paraparesis resembling HAM/TSP have been shown to be infected with HTLV-II.

OBJECTIVE

To clarify the role of each of these human retroviruses in the etiology of HAM/TSP in São Paulo, Brazil.

STUDY DESIGN

A detailed serological and molecular analysis of HTLV-I/II infection was performed in a cohort of 19 patients with HAM/TSP attending a neurological clinic.

RESULTS

Plasma samples analyzed for anti-HTLV-I/II antibodies using a Western blot assay, comprising HTLV-I (rgp46I)- and HTLV-II (rgp46II)-specific recombinant env epitopes, demonstrated reactivity to rgp46I and hence were typed as seropositive for HTLV-I. Presence of HTLV genomic sequences in peripheral blood mononuclear cells (PBMC) was sought after by PCR using consensus primers SK 110 and SK 111 for the pol region of HTLV proviral DNA followed by hybridization with type-specific probes--SK 112 (HTLV-I) and SK 188 (HTLV-II). Southern blots from all individuals hybridized with SK 112 but not with SK 188, further confirming HTLV-I infection. Cocultivation of PBMC from eight of these patients with activated lymphocytes from normal individuals resulted in active viral production, detected as presence of soluble p24gag antigen in culture supernatants. Investigation of risk factors for HTLV-I infection in these individuals revealed that five out of 19 patients studied (26.3%) had received blood transfusions previous to disease onset.

Genetic variability and molecular epidemiology of human and simian T cell leukemia/lymphoma virus type I

In the past few years, numerous investigators have demonstrated that human T cell leukemia/lymphoma virus type I (HTLV-I) possesses a great genetic stability, and recent data indicate that viral amplification via clonal expansion of infected cells, rather than by reverse transcription, could explain this remarkable genetic stability. In parallel, the molecular epidemiology of HTLV-I proviruses showed that the few nucleotide changes observed between isolates were specific for the geographical origin of the patients but not for the type of the associated pathologies (adult T cell leukemia/lymphoma, tropical spastic paraparesis/HTLV-I-associated myelopathy). Thus, based on sequence and/or restriction fragment length polymorphism analysis of more than 250 HTLV-I isolates originating from the main viral endemic areas, three major molecular geographical subtypes (or genotypes) emerged, strongly supported by phylogenetic analysis (high bootstrap values). Each of these genotypes (Cosmopolitan, Central African, and Melanesian) appeared to arise from ancient interspecies transmission between monkeys infected with simian T cell leukemia/lymphoma virus type I and humans. Furthermore, careful sequences analyses indicate that, within (or alongside) these three main genotypes, there are molecular subgroups defined clearly by several specific mutations but not always supported by phylogenetic analyses. Thus in Japan, there is evidence for two ancestral HTLV-I lineages: the classical Cosmopolitan genotype, representing approximately 25% of the HTLV-I present in Japan and clustering in the southern islands; and a related subgroup that we called the Japanese group. Similarly, within the Central African cluster, there are molecular subgroups defined by specific substitutions in either the env or the long terminal repeat. Furthermore, recent data from our laboratory indicate the presence of a new molecular phylogenetic group (fourth genotype) found among inhabitants of Central Africa, particularly in Pygmies. While geographical subtypes vary from 2 to 8% between themselves, HTLV-I quasi-species present within an individual appear to be much lower, with a variability of < 0.5%.

Human T-lymphotropic virus type 1 in coastal natives of British Columbia: phylogenetic affinities and possible origins

Human T-lymphotropic virus type 1 (HTLV-1) infection has been discovered recently in people of Amerindian descent living in coastal areas of British Columbia, Canada. DNA sequencing combined with phylogenetic analysis and restriction fragment length polymorphism (RFLP) typing of HTLV-1 strains recovered from these British Columbia Indians (BCI) was conducted. Sequence-based phylogenetic trees distributed the BCI isolates among the Japanese subcluster (subcluster B) and the geographically widely distributed subcluster (subcluster A) of the large HTLV-1 cosmopolitan cluster. Long terminal repeat (LTR) RFLP typing revealed three distinct, equally frequent LTR cleavage patterns, two of which were of previously recognized Japanese and widely dispersed cosmopolitan types. A third, new cleavage pattern was detected which may have arisen by recombination between two other HTLV-1 genotypes. Our results suggest multiple origins for HTLV-1 in BCI, which are equally consistent with (i) a cluster of recent sporadic infections, (ii) ancient endemic vertical transmission through Amerindian lineages, or (iii) both.

Molecular characterization of human T-lymphotropic virus, type 1 (HTLV-1) found in Kuwait: close similarity with HTLV-1 isolates originating from Mashhad, Iran

Human T-lymphotropic virus, type 1 (HTLV-1) infection was detected in two unrelated Kuwaiti patients with tropical spastic paraparesis (HAM/TSP) and in the asymptomatic mother of one of them. The family roots of these patients were traced to the Najaf region of Iraq. The DNA sequence of three PCR-amplified fragments (env, 512 bp; pol, 140 bp; LTR, 704 bp) was determined for each of Kuwaiti HTLV-1 isolates (KUW-1,2,3). All three Kuwaiti HTLV-1 were identical in env and pol fragments and virtually identical in LTR. Two rare substitutions were found in the env and pol fragments. They were shared only with two isolates from Reunion Island (substitution in env), and two isolates from India and the Caribbean (substitution in pol). The sequences of env and pol fragments of the Middle Eastern HTLV-1 isolates were not available. However, the comparison of Kuwaiti isolates with representative Middle Eastern HTLV-1 was possible for the LTR fragment. The phylogenetic analysis of LTR sequences of KUW and 34 other HTLV-1 isolates has shown that Kuwaiti HTLV-1 belongs to a cosmopolitan "a" subtype of HTLV-1 and tends to cluster together with HTLV-1 originating from the Mashhad region of Iran. These results suggest that common origin of Mashhadi and Kuwaiti (Najafi) HTLV-1 and the possibility of another pocket of HTLV-1 infection in the Middle East, located in the Najaf region of Iraq.

Human T-cell lymphotropic virus type I in Iranian-born Mashhadi Jews: genetic and phylogenetic evidence for common source of infection

High prevalence of human T-cell lymphotropic virus type I (HTLV-I) infection and disease has been identified among Iranian-born Mashhadi Jews, an ethnically segregated, highly inbred population. To determine the origin and genetic diversity of HTLV-I in this group, 1,039 bp spanning selected regions of the HTLV-I gag, pol, env and pX genes were enzymatically amplified and sequenced directly from DNA of five Mashhadi Jews (three with spastic myelopathy and two asymptomatic carriers). Alignment and comparison of these sequences with cosmopolitan and Australo-Melanesian topotypes of HTLV-I indicated that the HTLV-I strains from Mashhadi Jews, which were > or = 99.9% identical among themselves, exhibited considerable sequence similarity (> or = 99%) to HTLV-I strains from southern India, suggesting a common source of infection. Phylogenetic analysis, using the maximum parsimony method, was consistent with a single-source introduction of HTLV-I into the Mashhadi Jewish community.

Nucleotide sequence analysis of a full-length human T-cell leukemia virus type I from adult T-cell leukemia cells: a prematurely terminated PX open reading frame II

Human T-cell leukemia virus type 1 (HTLV-1) is etiologically associated with adult T-cell leukemia/lymphoma (ATL). The prototypic HTLV-1, ATK, is the only full-length provirus cloned from uncultured leukemic cells and completely sequenced prior to this study. We have determined the complete nucleotide sequence of another full-length HTLV-1 provirus cloned directly from leukemic cells. A premature termination codon was found in the second open reading frame (orf II) of the pX region. Our finding indicates that open reading frame II of the HTLV-1 pX region is not required for outgrowth of ATL leukemic clones in vivo.

Genetic and phylogenetic analyses of human T-cell lymphotropic virus type I variants from Melanesians with and without spastic myelopathy

Molecular variants of human T-cell lymphotropic virus type I (HTLV-I) have been isolated recently from lifelong residents of remote Melanesian populations, including a Solomon Islander with tropical spastic paraparesis/HTLV-I-associated myelopathy (TSP/HAM) or HTLV-I myeloneuropathy. To clarify the genetic heterogeneity and molecular epidemiology of disease-associated strains of HTLV-I, we enzymatically amplified, then directly sequenced representative regions of the gag, pol, env, and pX genes of HTLV-I strains from Melanesians with and without TSP/HAM, and aligned and compared these sequences with those of HTLV-I strains from patients with TSP/HAM or adult T-cell leukemia/lymphoma and from asymptomatic carriers from widely separated and culturally disparate populations. Overall, the HTLV-I variant from the Solomon Islander with TSP/HAM, like HTLV-I strains from asymptomatically infected Melanesians, diverged by approx 7% from cosmopolitan HTLV-I strain. No disease-specific viral sequences were found. Gene phylogenies, as determined by the unweighted pair-group method of assortment and by the maximum parsimony method, indicated that the Melanesian and cosmopolitan strains of HTLV-I have evolved along separate geographically dependent lineages, one comprised of HTLV-I strains from Papua New Guinea and the Solomon Islands, and the other composed of virus strains from Japan, India, the Caribbean, Polynesia, the Americas, and Africa. The total absence of nonhuman primates in Papua New Guinea and the Solomon Islands precludes any possibility that the Melanesian HTLV-I strains have evolved recently from the simian homolog of HTLV-I.

Human T cell leukemia virus type I infection and chronic myelopathy

The central nervous system (CNS) pathology of HTLV-I associated myelopathy or tropical spastic paraparesis (HAM/TSP) is reviewed, based mainly on 12 autopsy cases of Japanese HAM/TSP with a serological confirmation of HTLV-I infection. The essential histopathological feature of HAM/TSP is a chronic progressive inflammatory process heralded by parenchymal infiltration of memory CD4 cells. The inflammation involves both the grey and white matter of the spinal cord, and progresses for more than three years after the onset of neurological symptoms, resulting in preferential degeneration of the white matter. In cases with a history of more than nine years, however, the spinal cord lesions appears degenerative rather than inflammatory. Both the inflammation and the white matter degeneration are most conspicuous in the lower thoracic cord. The lateral funiculus is always and most severely affected. Although the parenchymal tissue degeneration is not confined to any particular long tracts, symmetrical degeneration of the lateral pyramidal tract is evident in all cases. The involvement of the posterior and anterior funiculi is variable and neurons are relatively well preserved. Since evidence for HTLV-I infection in the CNS is limited to detection of proviral DNA by the polymerase chain reaction (PCR) and isolation of the virus from CSF cells, autoimmune nature of the disease is suspected, but is supported by ample evidence for derangements of the host immune system compatible with those of autoimmune diseases. Recent studies on induction of white matter degeneration in the rat with a topographical similarity to human HAM/TSP is also briefly reviewed. However, in the rat disease, inflammatory cell infiltrations are inconspicuous.