Complete nucleotide sequence of an African human T-lymphotropic virus type II subtype b isolate (HTLV-II-Gab): molecular and phylogenetic analysis

Genetic diversity of STLV-2 and interspecies transmission of STLV-3 in wild-living bonobos

There are currently four known primate T-cell lymphotropic virus groups (PTLV1-4), each of which comprises closely related simian (STLV) and human (HTLV) viruses. For PTLV-1 and PTLV-3, simian and human viruses are interspersed, suggesting multiple cross-species transmission events; however, for PTLV-2 this is not so clear because HTLV-2 and STLV-2 strains from captive bonobos (Pan paniscus) form two distinct clades. To determine to what extent bonobos are naturally infected with STLV, we screened fecal samples (n = 633) from wild-living bonobos (n = 312) at six different sites in the Democratic Republic of Congo (DRC) for the presence of STLV nucleic acids. STLV infection was detected in 8 of 312 bonobos at four of six field sites, suggesting an overall prevalence of 2.6% (ranging from 0 to 8%). Six samples contained STLV-2, while the two others contained STLV-3, as determined by phylogenetic analysis of partial tax and Long Terminal Repeats (LTR) sequences. The new STLV-2 sequences were highly diverse, but grouped with previously identified STLV-2 strains as a sister clade to HTLV-2. In contrast, the new STLV-3 sequences did not cluster together, but were more closely related to STLVs from sympatric monkey species. These results show for the first time that fecal samples can be used to detect STLV infection in apes. These results also show that wild-living bonobos are endemically infected with STLV-2, but have acquired STLV-3 on at least two occasions most likely by cross-species transmission from monkey species on which they prey. Future studies of bonobos and other non-human primate species in Central Africa are needed to identify the simian precursor of HTLV-2 in humans.

HTLV-2B strains, similar to those found in several Amerindian tribes, are endemic in central African Bakola Pygmies

BACKGROUND

The presence and origin of endemic foci of human T-lymphotropic virus type 2 (HTLV2) infection in Africa remain a matter of debate.

METHODS

To better appreciate such determinants, we performed a survey of 1918 inhabitants from Cameroon forest areas, including 1051 Bakola Pygmies and 867 Bantus.

RESULTS

The overall HTLV-1/2 seroprevalence was 4% (49 cases of HTLV-1 and 27 cases of HTLV-2 infection). Both infections were mainly restricted to the Bakola Pygmies, with surprisingly no HTLV-2 infections in the Bantu population. Both HTLV-1 and HTLV-2 seroprevalences increased with age. There was evidence of ongoing HTLV-2 transmission in this population. Lymphoid T cell lines producing HTLV-2 were established. HTLV-2 long terminal repeat sequences (672 base pairs) obtained from 7 infected Bakola were highly similar to each other (<1% nucleotide divergence), as well as to Amerindian HTLV-2B strains. Analyses on a complete sequence (8954 base pairs) confirmed that it was a typical HTLV-2 subtype B strain. Along with molecular clock analysis, these data strongly suggest that HTLV-2 has been endemic in the Bakola Pygmy population for a long time.

CONCLUSIONS

This study demonstrates clearly an HTLV-2 endemicity with ongoing transmission in an African population. Furthermore, it give insights into central questions regarding the origins and evolution rate of HTLV-2 and the migrations of infected populations.

Tax & rex: overlapping genes of the Deltaretrovirus group

Bovine leukemia virus and human T-cell leukemia viruses I and II, members of the Deltaretrovirus group, have two regulatory genes, tax and rex, that are coded in overlapping reading frames. We found that sequence variations in the rex gene of each virus result in amino acid differences significantly more often than variations in the tax gene. For all three viruses the highest ratio of non-synonymous to synonymous changes was found in the rex gene. In the overlapping regions of tax and rex, the second codon position of Rex corresponds to the third codon position of Tax. Nucleotide C was present in all genes of the three viruses at the highest frequency and this bias was most pronounced in the rex gene. More specifically we found that the C bias and nucleotide variation is greatest at the second codon position of Rex and the third codon position of Tax in the area of tax/rex overlap. Changes in the second codon position of Rex always resulted in amino acid change whereas changes in the third codon position of Tax resulted in amino acid changes less than a third of the time. Analysis of the amino acid frequencies in both proteins shows that there is a disproportionately large percentage of the amino acids alanine, proline, serine and threonine (the four amino acids whose second codon position is C) in Rex. These findings led us to hypothesize that the Rex protein can withstand more amino acid changes than can the Tax protein suggesting that the Tax protein experiences higher evolutionary constraints and is the more conserved of the two proteins.

Complete nucleotide sequences of the genomes of two Brazilian specimens of human T lymphotropic virus type 2 (HTLV-2)

We report the complete nucleotide sequences of the genomes of two human T cell lymphotropic viruses type 2 (HTLV-2) isolated from a Kayapó Indian (K96 isolate) and from an inhabitant of an urban region in the south of Brazil (RP329 isolate). The general structure of the K96 and RP329 genomes did not differ from that of other HTLV-2 genomes described in the literature. The K96 genome consisted of 8955 bp and the RP329 genome consisted of 8964 bp. The general similarity between the nucleotide sequences of the K96 and RP329 genomes was 99.4%. Comparison between the nucleotide sequences of the K96 and RP329 genomes and the nucleotide sequences of isolates considered to be HTLV-2 prototypes of subtype 2a (Mo isolate), 2b (NRA isolate), and 2d (Efe2 isolate) showed a global similarity of 98.8, 95.6, and 93.3%, respectively, for the RP329 isolate, and of 99.1, 95.6, and 93.3%, respectively, for the K96 isolate. Phylogenetic analysis permitted the classification of the K96 and RP329 isolates as HTLV-2 subtype 2a. Detailed phylogenetic analyses of the LTR, env, and Tax regions showed that the Brazilian isolates tend to form a distinct phylogenetic subgroup within subtype 2a, previously called HTLV-2c, which differs from the subtype 2a isolates found in North America, Europe, and Africa. The K96 genome is the first HTLV-2 genome obtained from a Brazilian Indian that was completely sequenced, whereas the RP329 genome represents the first specimen derived from an inhabitant of a Brazilian urban region who was not coinfected with HIV-1.

Human T-lymphotropic virus type II RFLP subtypes a0 and b4/b5 are associated with different demographic and geographic characteristics in the United States

Human T-lymphotropic virus type II (HTLV-II) prevalence is very low among the general U.S. population, intermediate among American Indians, and high among injecting drug users and their sexual partners. However, the transmission dynamics underlying this distribution are not well described. We obtained blood specimens from 493 blood donors found to be seropositive for HTLV-II at blood centers in five U.S. cities. Nested polymerase chain reaction was used to amplify a 672-bp region of the HTLV-II long terminal repeat region, and restriction fragment length polymorphism (RFLP) analysis was performed to classify each virus into subtypes as defined by Switzer et al. (1995, J. Virol. 69, 621-632). Associations between RFLP subtype and other characteristics were analyzed using multivariable logistic regression. HTLV-II subtype a0 was independently associated with age over 30 years (odds ratio (OR) = 2.12, 95% confidence interval (CI) 1.13-3.99) and with Black race/ethnicity (OR = 2.00, 95% CI 1.10-3.65 versus Hispanic race/ethnicity). Conversely, HTLV-II RFLP subtypes b4 and b5 were significantly more common among American Indian (OR = 3.77, 95% CI 1.23-11.57) and Other race/ethnicity (OR = 4.22, 95% CI 1.25-14.27, both versus Black race/ethnicity) and at the Oklahoma City blood center (OR = 3.57, 95% CI 1.08-11.84 compared to Washington, DC/Baltimore). There may have been at least two transmission foci of HTLV-II in the United States: a modest HTLV-II subtype a0 epidemic of unknown source in the 1960s and 1970s spread predominantly among Black persons in several geographic areas and a smaller focus of HTLV-II subtypes b4/b5 among non-Black individuals in Oklahoma and perhaps in other areas not examined by this study.

Isolation, cloning, and complete nucleotide sequence of a phenotypically distinct Brazilian isolate of human T-lymphotropic virus type II (HTLV-II)

Analysis of human T-lymphotropic virus type II (HTLV-II) isolates from North America and Europe have demonstrated the existence of two molecular subtypes of the virus, HTLV-IIa and HTLV-IIb. Recently, studies on HTLV-II infections in Brazil have revealed isolates that are related phylogenetically to the HTLV-IIa subtype but have a HTLV-IIb phenotype with respect to the transactivating protein, tax. To more clearly define this relationship, HTLV-II was isolated from peripheral blood of an IVDA from Sao Paulo, Brazil (SP-WV), and the complete provirus was cloned and sequenced. Comparison of HTLV-II(SP-WV) nucleotide sequences to other available complete HTLV-II proviral sequences revealed that HTLV-II(SP-WV) is most closely related to HTLV-II(Mo), the prototypic HTLV-IIa subtype sequence. Phylogenetic analysis of LTR, env, and tax regions unequivocally demonstrated that HTLV-II(SP-WV) and all other Brazilian sequences examined are members of the IIa subtype. The predicted amino acid sequences of the major coding regions of HTLV-II(SP-WV) are also most closely related to HTLV-II(Mo), with the important exception of tax. The tax protein encoded by HTLV-II(SP-WV) is 96-99% identical to the tax of IIb isolates and is similar in that it has an additional 25 amino acids at the carboxy-terminus compared to the HTLV-II(Mo) tax with which it shares 91% identity. Analysis of tax stop codon usage of a number of HTLV-IIa isolates from North American, Europe, and Brazil demonstrated that isolates from the last region appear to be unique in their extended tax phenotype. It could be demonstrated that the extended tax proteins in the HTLV-IIb and Brazilian isolates had equivalent ability to transactivate the viral LTR, and studies with deletion mutants indicated that the extended C-terminus is not essential for transactivation. In contrast, the HTLV-IIa tax was found to have a greatly diminished ability to transactivate the viral LTR, which appeared to be a consequence of reduced expression of the protein. The studies show that although the Brazilian strains do not represent an entirely new subtype based on nucleotide sequence analysis they are a phenotypically unique molecular variant within the HTLV-IIa subtype.

Genomic Evolution, Patterns of Global Dissemination, and Interspecies Transmission of Human and Simian T-cell Leukemia/Lymphotropic Viruses

Using both env and long terminal repeat (LTR) sequences, with maximal representation of genetic diversity within primate strains, we revise and expand the unique evolutionary history of human and simian T-cell leukemia/lymphotropic viruses (HTLV/STLV). Based on the robust application of three different phylogenetic algorithms of minimum evolution–neighbor joining, maximum parsimony, and maximum likelihood, we address overall levels of genetic diversity, specific rates of mutation within and between different regions of the viral genome, relatedness among viral strains from geographically diverse regions, and estimation of the pattern of divergence of the virus into extant lineages. Despite broad genomic similarities, type I and type II viruses do not share concordant evolutionary histories. HTLV-I/STLV-I are united through distinct phylogeographic patterns, infection of 20 primate species, multiple episodes of interspecies transmission, and exhibition of a range in levels of genetic divergence. In contrast, type II viruses are isolated from only two species (Homo sapiens and Pan paniscus) and are paradoxically endemic to both Amerindian tribes of the New World and human Pygmy villagers in Africa. Furthermore, HTLV-II is spreading rapidly through new host populations of intravenous drug users. Despite such clearly disparate host populations, the resultant HTLV-II/STLV-II phylogeny exhibits little phylogeographic concordance and indicates low levels of transcontinental genetic differentiation. Together, these patterns generate a model of HTLV/STLV emergence marked by an ancient ancestry, differential rates of divergence, and continued global expansion.