Limited sequence divergence of HTLV-I of Indian HAM/TSP patients from a prototype Japanese isolate

Human T Lymphotropic Virus Type 1 (HTLV-1): Molecular Biology and Oncogenesis

Human T lymphotropic viruses (HTLVs) are complex deltaretroviruses that do not contain a proto-oncogene in their genome, yet are capable of transforming primary T lymphocytes both in vitro and in vivo. There are four known strains of HTLV including HTLV type 1 (HTLV-1), HTLV-2, HTLV-3 and HTLV-4. HTLV-1 is primarily associated with adult T cell leukemia (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HTLV-2 is rarely pathogenic and is sporadically associated with neurological disorders. There have been no diseases associated with HTLV-3 or HTLV-4 to date. Due to the difference in the disease manifestation between HTLV-1 and HTLV-2, a clear understanding of their individual pathobiologies and the role of various viral proteins in transformation should provide insights into better prognosis and prevention strategies. In this review, we aim to summarize the data accumulated so far in the transformation and pathogenesis of HTLV-1, focusing on the viral Tax and HBZ and citing appropriate comparisons to HTLV-2.

Phylogenetic heterogeneity of new HTLV type 1 isolates from southern India in subgroup A

Seven isolates of human T cell leukemia virus type 1 (HTLV-1) were taken in southern India and phylogenetically analyzed to gain new insights into the origin and dissemination of HTLV-1 in the subcontinent. The new Indian HTLV-1s were found to be members of subgroup A (Transcontinental subgroup) of the Cosmopolitan group. They formed three different clusters (South African/Caribbean, Middle Eastern, and East Asian clusters). These results demonstrate that Indian HTLV-1s are genetically heterogeneous and include the most divergent strain of subgroup A. On the basis of these results, we speculate that subgroup A HTLV- 1s may have been present for thousands of years in India.

Quantitative in situ PCR assay of HTLV-1 infected cells in peripheral blood lymphocytes of patients with ATL, HAM/TSP and asymptomatic carriers

We established an in situ PCR (IS-PCR) method that amplified the pX region of human T cell lymphotropic virus type 1 (HTLV-1) proviral DNA. The procedure was highly sensitive in accurately detecting the number of cells infected with HTLV-1. We estimated the number of HTLV-1 infected cells in peripheral blood lymphocytes (PBL) from patients with HAM/TSP, ATL and asymptomatic carriers. ATL patients (n = 5) had 8-93% IS-PCR positive cells for HTLV-1 and these percentages correlated with the clinical stages. Asymptomatic carriers (n = 3) had 0.8-3.8% (mean 1.1%, S.D. 1.7) positive cells. HAM/TSP patients (n = 10) had 3.1-8.5% (5.8% (5.8%, 2.7) positive cells. Patients with shorter duration of illness showed larger percentages compared with patients with longer duration. In one HAM/TSP patient, the number of IS-PCR positive cells decreased from 5.1% to 1.5% coincident with the times of lymphocytapheresis treatment. Our studies may suggest that an increased viral load initiates the pathogenic process of HAM/TSP and the estimation of HTLV-1 proviral load by IS-PCR method is useful to understand the clinical state of HAM/TSP.

HTLV-Is in Argentina are phylogenetically similar to those of other South American countries, but different from HTLV-Is in Africa

To understand the origin and past dissemination of human T-cell leukemia/lymphotropic virus type I (HTLV-I) in Latin America, we conducted a phylogenetic study of five new HTLV-I isolates from Argentina. We sequenced partial fragments of long terminal repeats (LTR) of the new HTLV-Is, and then the sequences were subjected to a phylogenetic analysis for comparison with other HTLV-Is of various geographical origins. Our results indicated that all the isolates were members of the Cosmopolitan group. Furthermore, most (four out of five isolates) of the new HTLV-Is belonged to the Transcontinental (A) subgroup, the most widespread subgroup of the four subgroups in the Cosmopolitan group. In this subgroup, they were closely related to HTLV-Is found in other South American countries including those of Amerindians, and were different from those found in Africa. In contrast, the remaining one HTLV-I (ARGMF) did not show any clear similarity to known HTLV-I isolates belonging to the Cosmopolitan group. The close similarity of South American HTLV-Is strongly suggests a common origin of the virus in this continent. Our results do not support the proposed idea of recent introduction of HTLV-I into South America as a consequence of the slave trade from Africa, where phylogenetically different HTLV-Is predominate.

Molecular epidemiology of 58 new African human T-cell leukemia virus type 1 (HTLV-1) strains: identification of a new and distinct HTLV-1 molecular subtype in Central Africa and in Pygmies

To gain new insights on the origin, evolution, and modes of dissemination of human T-cell leukemia virus type I (HTLV-1), we performed a molecular analysis of 58 new African HTLV-1 strains (18 from West Africa, 36 from Central Africa, and 4 from South Africa) originating from 13 countries. Of particular interest were eight strains from Pygmies of remote areas of Cameroon and the Central African Republic (CAR), considered to be the oldest inhabitants of these regions. Eight long-term activated T-cell lines producing HTLV-1 gag and env antigens were established from peripheral blood mononuclear cell cultures of HTLV-1 seropositive individuals, including three from Pygmies. A fragment of the env gene encompassing most of the gp21 transmembrane region was sequenced for the 58 new strains, while the complete long terminal repeat (LTR) region was sequenced for 9 strains, including 4 from Pygmies. Comparative sequence analyses and phylogenetic studies performed on both the env and LTR regions by the neighbor-joining and DNA parsimony methods demonstrated that all 22 strains from West and South Africa belong to the widespread cosmopolitan subtype (also called HTLV-1 subtype A). Within or alongside the previously described Zairian cluster (HTLV-1 subtype B), we discovered a number of new HTLV-1 variants forming different subgroups corresponding mainly to the geographical origins of the infected persons, Cameroon, Gabon, and Zaire. Six of the eight Pygmy strains clustered together within this Central African subtype, suggesting a common origin. Furthermore, three new strains (two originating from Pygmies from Cameroon and the CAR, respectively, and one from a Gabonese individual) were particularly divergent and formed a distinct new phylogenetic cluster, characterized by specific mutations and occupying in most analyses a unique phylogenetic position between the large Central African genotype (HTLV-1 subtype B) and the Melanesian subtype (HTLV-1 subtype C). We have tentatively named this new HTLV-1 genotype HTLV-1 subtype D. While the HTLV-1 subtype D strains were not closely related to any known African strain of simian T-cell leukemia virus type 1 (STLV-1), other Pygmy strains and some of the new Cameroonian and Gabonese HTLV-1 strains were very similar (>98% nucleotide identity) to chimpanzee STLV-1 strains, reinforcing the hypothesis of interspecies transmission between humans and monkeys in Central Africa.

Molecular epidemiology of HTLV-I in the world

The geographic distribution of human T-cell lymphotropic/leukemia virus type I (HTLV-I) was initially believed to be limited to southwestern Japan, the Caribbean basin, and Africa. However, extensive searches in recent years have discovered its existence in other areas of the world as well as in isolated, ethnic populations such as South Amerindians, Australo-Melanesian aborigines, religiously segregated Jews, and Pygmies. Previous genetic analyses indicated that HTLV-I can be phylogenetically classified into three major lineages: Melanesian, Central African, and Cosmopolitan groups. Recently, more detailed characterization using long terminal repeat sequences (the most variable genomic region) has revealed that the Cosmopolitan group consists of four subtypes: (A) Transcontinental, (B) Japanese, (C) West African, and (D) North African. Most HTLV-I isolates of the same ethnic group from distant locations and those from different groups inhabiting the same area showed phylogenetic similarities. These observations indicate the present distribution of this virus should be interpreted from the anthropological backgrounds of the virus-possessing populations as well as spatial contact among them. Thus, the molecular epidemiology of HTLV-I and its simian counterpart, STLV-I, provides us with important clues for understanding not only the origin and dissemination of this retrovirus but past human movements over the globe.

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.

Tax mutation associated with tropical spastic paraparesis/human T-cell leukemia virus type I-associated myelopathy

Tumaco, Colombia, is an area with elevated rates of tropical spastic paraparesis/human T-cell leukemia virus type I (HTLV-I)-associated myelopathy (TSP/HAM). We have identified a mutation in nucleotide 7959 of the tax gene of 14 Tumaco HTLV-I isolates (14 positive of 14 tested) that was present in 5 of 14 (35%) TSP/HAM patients from Japan and in 8 of 11 (72%) TSP/HAM patients from other geographic locations. In contrast, this mutation was found in only 2 of 21 (9.5%) HTLV-I-infected subjects outside of Tumaco who did not have TSP/HAM. tax clones with nucleotide mutations including one at nucleotide 7959 showed a greater ability to transactivate the HTLV-I U3 promoter. However, this effect was not observed when two clones that differed only in nucleotide 7959 were compared. These results suggest that HTLV-I-infected individuals carrying isolates with this tax mutation are at higher risk for developing TSP/HAM.

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.

Prevalence of HTLV-I/II antibodies in HIV seropositive and HIV seronegative STD patients in Vellore region in southern India

This retrospective study was designed to determine the relationship between human T-lymphotropic virus (HTLV) type-I/II infection and human immunodeficiency virus (HIV) infection among sexually promiscuous persons in southern India. Stored sera collected between 1986 and 1993 from 822 male and 488 female patients attending clinics for sexually transmitted diseases (STD), for the purpose of HIV serosurveillance, were used. They comprised 376 HIV-positive sera and 934 HIV-negative sera. They were screened for HTLV-I/II antibody by a particle agglutination test and repeatedly reactive sera were confirmed by an immunofluorescence test and a western blot test. Five (2.4%) of 212 HIV-seropositive men were confirmed positive for HTLV-I/II antibody, while none of the 610 HIV-seronegative men were positive; the difference in prevalence between HIV-seropositive and seronegative men was statistically significant (p < 0.001). Nine (5.5%) of 164 HIV-seropositive women and 3 (0.9%) of 324 HIV-seronegative women were positive for HLTV-I/II antibody (p < 0.005). All HIV-seropositives taken together, had a significantly higher prevalence of HTLV-I/II (3.7%; 14/376) compared with HIV seronegatives (0.3%; 3/934; p < 0.001). Thus, in southern India, HTLV infection, like HIV infection, is sexually transmitted, though less effectively.

Molecular epidemiology of HTLV type I in Japan: evidence for two distinct ancestral lineages with a particular geographical distribution

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.

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.

Phylogenetic subtypes of human T-lymphotropic virus type I and their relations to the anthropological background

Isolates of human T-lymphotropic virus type I (HTLV-I) were phylogenetically analyzed from native inhabitants in India and South America (Colombia and Chile) and from Ainu (regarded as pure Japanese descendants from the preagricultural "Jomon" period). Their genomes were partially sequenced together with isolates from Gabon in central Africa and from Ghana in West Africa. The phylogenetic tree was constructed from the sequence data obtained and those of previously reported HTLV-I isolates and simian T-lymphotropic virus type I (STLV-I) isolates. The heterogeneity of HTLV-I was recently recognized, and one major type, generally called the "cosmopolitan" type, contained Japanese, Caribbean, and West African isolates. The phylogenetic tree constructed in the present study has shown that this cosmopolitan type can be further grouped into three lineages (subtypes A, B, and C). Subtype A consists of some Caribbean, two South American, and some Japanese isolates, including that from the Ainu, in addition to an Indian isolate, and subtype B consists of other Japanese isolates in addition to another Indian isolate, suggesting that there might be at least two ancestral lineages of the Japanese HTLV-I. Subtype A implies a close connection of the Caribbean and South American natives with the Japanese and thereby a possible migration of the lineage to the American continent via Beringia in the Paleolithic era. Subtype C consists of the West African and other Caribbean isolates, indicating that not all but part of the Caribbean strains directly originated from West Africa probably during the period of slave trade. The tree also has shown that the HTLV-I isolate from Gabon in central Africa forms a cluster with STLV-I from a chimpanzee, suggesting a possible interspecies transmission between man and the chimpanzee in the past. No specific clustering was observed in the tree in relation to manifestations of the disease such as adult T-cell leukemia and HTLV-I-related neurological disorders. Thus, the topology of the phylogenetic tree reflects the movement of people carrying the virus in the past.