Evolution in a chronic RNA virus infection: selection on HTLV-I tax protein differs between healthy carriers and patients with tropical spastic paraparesis

Analysis of Nucleotide Sequence of Tax, miRNA and LTR of Bovine Leukemia Virus in Cattle with Different Levels of Persistent Lymphocytosis in Russia

Bovine Leukemia Virus (BLV) is the etiological agent of enzootic bovine leucosis (EBL), a lymphoproliferative disease of the bovine species. In BLV-infected cells, the long terminal repeat (LTR), the viral Tax protein and viral miRNAs promote viral and cell proliferation as well as tumorigenesis. Although their respective roles are decisive in BLV biology, little is known about the genetic sequence variation of these parts of the BLV genome and their impact on disease outcome. Therefore, the objective of this study was to assess the relationship between disease progression and sequence variation of the BLV Tax, miRNA and LTR regions in infected animals displaying either low or high levels of persistent lymphocytosis (PL). A statistically significant association was observed between the A(+187)C polymorphism in the downstream activator sequence (DAS) region in LTR (p-value = 0.00737) and high lymphocytosis. Our study also showed that the mutation A(−4)G in the CAP site occurred in 70% of isolates with low PL and was not found in the high PL group. Conversely, the mutations G(−133)A/C in CRE2 (46.7%), C(+160)T in DAS (30%) and A(310)del in BLV-mir-B4-5p, A(357)G in BLV-mir-B4-3p, A(462)G in BLV-mir-B5-5p, and GA(497–498)AG in BLV-mir-B5-3p (26.5%) were often seen in isolates with high PL and did not occur in the low PL group. In conclusion, we found several significant polymorphisms among BLV genomic sequences in Russia that would explain a progression towards higher or lower lymphoproliferation. The data presented in this article enabled the classification between two different genotypes; however, clear association between genotypes and the PL development was not found.

Intrahost variations in the envelope receptor-binding domain (RBD) of HTLV-1 and STLV-1 primary isolates

Four primate (PTLV), human (HTLV) and simian (STLV) T-cell leukemia virus types, have been characterized thus far, with evidence of a simian zoonotic origin for HTLV-1, HTLV-2 and HTLV-3 in Africa. The PTLV envelope glycoprotein surface component (SUgp46) comprises a receptor-binding domain (RBD) that alternates hypervariable and highly conserved sequences. To further delineate highly conserved motifs in PTLV RBDs, we investigated the intrahost variability of HTLV-1 and STLV-1 by generating and sequencing libraries of DNA fragments amplified within the RBD of the SUgp46 env gene. Using new and highly cross-reactive env primer pairs, we observed the presence of Env quasispecies in HTLV-1 infected individuals and STLV-1 naturally infected macaques, irrespective of the clinical status. These intrahost variants helped us to define highly conserved residues and motifs in the RBD. The new highly sensitive env PCR described here appears suitable for the screening of all known variants of the different PTLV types and should, therefore, be useful for the analysis of seroindeterminate samples.

Cellular immune response to HTLV-1

There is strong evidence at the individual level and the population level that an efficient cytotoxic T lymphocyte (CTL) response to HTLV-1 limits the proviral load and the risk of associated inflammatory diseases such as HAM/TSP. This evidence comes from host population genetics, viral genetics, DNA expression microarrays and assays of lymphocyte function. However, until now there has been no satisfactory and rigorous means to define or to measure the efficiency of an antiviral CTL response. Recently, methods have been developed to quantify lymphocyte turnover rates in vivo and the efficiency of anti-HTLV-1 CTLs ex vivo. Data from these new techniques appear to substantiate the conclusion that variation between individual hosts in the rate at which a single CTL kills HTLV-1-infected lymphocytes is an important determinant, perhaps the decisive determinant, of the proviral load and the risk of HAM/TSP. With these experimental data, it is becoming possible to refine, parameterize and test mathematical models of the immune control of HTLV-1, which are a necessary part of an understanding of this complex dynamic system.

Observation of positive selection within hypervariable regions of a newly identified DNA virus (SEN virus)(1)

To elucidate the evolution of SEN virus (SEN-V), serial sequences of chronically SEN-V-infected patients were analyzed. In the hypervariable regions, non-synonymous substitutions significantly predominated. This could be attributed to positive selection in evading immune surveillance of the hosts and to establish a persistent infection. On the basis of the sequences in the two open reading frames of SEN-V DNA, the rate of synonymous substitutions was 7.32 x 10(-4) per site per year. Since this rate is close to RNA viruses and higher than other DNA viruses, the SEN-V might be replicated by machinery with poor or no proofreading function.

The role of cytotoxic T lymphocytes in human T-cell lymphotropic virus type 1 infection

The vast majority of individuals infected with human T-cell lymphotropic virus type 1 have a strong and persistently activated cytotoxic T lymphocyte response to the virus. Experimental work investigating the effects of human T-cell lymphotropic virus-specific cytotoxic T lymphocytes is conflicting. One significant body of work suggests that specific cytotoxic T lymphocytes are protective and help to reduce the risk of disease. However, another body of work implies that specific cytotoxic T lymphocytes play an important role in the development of disease. Here we use a theoretical model to explore the role of cytotoxic T lymphocytes in persistent infection. A way of reconciling the apparently contradictory data is proposed and experimentally testable predictions are made.

Frequency of the CCRdelta32 allele in Brazilians: a study in colorectal cancer and in HTLV-I infection

The identification of a 32-bp deletion in the cc-chemokine receptor-5 gene (CCR5delta32 allele) that renders homozygous individuals highly resistant to HIV infection has prompted worldwide investigations of the frequency of the CCR5delta32 allele in regional populations. It is important to ascertain if CCR5delta32 is a factor to be considered in the overall epidemiology of HIV in individual populations. With this in mind we determined the CCR5delta32 allele frequency in a large sample (907 individuals) of the southeastern Brazilian urban population, stratified as follows: 322 healthy unrelated individuals, 354 unselected colorectal cancer patients, and 229 blood donors. The three groups displayed essentially identical allelic frequencies of CCR5delta32 and pairwise comparisons did not show significant differences. Thus, our results can be pooled to provide a reliable estimate of the CCR5delta32 allele frequency in the southeastern Brazil of 0.053 ± 0.005. The blood donors comprised 50 HTLV-I serologically negative individuals, 115 non-symptomatic individuals HTLV-I positive by ELISA but with indeterminate Western blot results, 49 healthy blood donors HTLV-I positive both at ELISA and Western blot and 15 patients with clinical spinal cord disease (HAM). A suggestive trend was observed, with the CCR5delta32 frequencies decreasing progressively in these four categories. However, when we applied Fischer's exact test no significant differences emerged. We believe that further studies in larger cohorts should be performed to ascertain whether the CCR5delta32 allele influences the chance of becoming infected or developing clinical symptoms of HTLV-I infection.

Is human T-cell lymphotropic virus type I really silent?

The role of the cellular immune response to human T-cell lymphotropic virus type I (HTLV-I) is not fully understood. The low level of HTLV-I protein expression in peripheral blood lymphocytes has led to the widely held belief that HTLV-I is transcriptionally silent in vivo. However, most HTLV-I-infected individuals mount a strong and persistently activated cytotoxic T-lymphocyte (CTL) response to the virus; this observation implies that there is abundant chronic transcription of HTLV-I genes. Here we show that HTLV-I Tax protein expression rises quickly in freshly isolated peripheral blood lymphocytes, but that expressing cells are rapidly killed by CTLs. Mathematical analysis of these results indicates that the CTL response is extremely efficient and that the half-life of a Tax-expressing cell is less than a day. We propose that HTLV-I protein expression in circulating lymphocytes is undetectable by current techniques because of the efficiency of the CTL-mediated immune surveillance in vivo.

HTLV-1 infections

Human T lymphotropic virus type 1 (HTLV-1) causes disabling and fatal diseases, yet there is no vaccine, no satisfactory treatment, and no means of assessing the risk of disease or prognosis in infected people. Recent research on the molecular virology and immunology of HTLV-1 shows the importance of the host's immune response in reducing the risk of these diseases, and is beginning to explain why some HTLV-1 infected people develop serious illnesses whereas most remain healthy life long carriers of the virus. These findings might be applicable to other persistent virus infections such as human immunodeficiency virus, hepatitis B, and hepatitis C.

Up-regulation of human T lymphotropic virus type 1 (HTLV-1) tax/rex mRNA in infected lung tissues

HTLV-1 has been implicated in certain pulmonary diseases. We previously demonstrated that expression of HTLV-1 tax/rex mRNA, encoding the transcriptional transactivator Tax, was closely associated with infiltration of activated T lymphocytes into lung tissue. To explore mechanisms of tax/rex expression in the lung, tax/rex mRNA expression and proviral DNA load were compared between peripheral blood mononuclear cells (PBMC) and bronchoalveolar lavage cells (BALC) from four patients with HTLV-1-associated myelopathy (HAM/TSP) and 13 carriers with various pulmonary symptoms. Semiquantitative detection of tax/rex mRNA strongly suggested that the lung was a preferential site for its expression. Proviral DNA loads in non-HAM/TSP carriers were variable but correlated well between PBMC and BALC in each individual, and revealed no relationship with tax/rex mRNA expression. In contrast, both cell groups from four HAM/TSP patients expressed detectable tax/rex mRNA accompanied by high proviral DNA load. The ratio of tax/rex mRNA expression to proviral DNA load was higher in BALC than in PBMC in three of four carriers and in three of four HAM/TSP patients, suggesting up-regulation of tax/rex mRNA in infected lung tissue. To analyse differences in distribution of HTLV-1 quasispecies between the two tissues, phylogenetic analysis was performed for sequence sets of the proviral tax open reading frame (ORF: 1059 bp) derived from PBMC and BALC of two infected individuals. Sequences derived from the two tissues distributed similarly to branches of phylogenetic trees, and there was no evidence of selective distribution of certain quasispecies in the lung. Our results suggest the presence of tissue-specific conditions that activate viral expression in infected cells in the lung. Constitutive exposure of this tissue to foreign antigens leading to up-regulation of basal viral promoter activity is likely to be one such mechanism.

The dynamics of HTLV-I and the CTL response

Dominik Wodarz and colleagues describe a mathematical model for the in vivo dynamics of human T-cell leukaemia virus type 1 (HTLV-I) infection and the virus-specific cytotoxic T lymphocyte response. They show that a high rate of viral replication is consistent with the relative sequence invariance of HTLV-I and might be necessary to maintain a persistent infection.

Genetic control and dynamics of the cellular immune response to the human T-cell leukaemia virus, HTLV-I

About 1% of people infected with the human T-cell leukaemia virus, type 1 (HTLV-I) develop a disabling chronic inflammatory disease of the central nervous system known as HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Patients with HAM/TSP have a vigorous immune response to HTLV-I, and it has been widely suggested that this immune response, particularly the HTLV-I-specific cytotoxic T-lymphocyte (CTL) response, causes the tissue damage that is seen in HAM/TSP. In this paper we summarize recent evidence that a strong CTL response to HTLV-I does in fact protect against HAM/TSP by reducing the proviral load of HTLV-I. We conclude that HTLV-I is persistently replicating at a high level, despite the relative constancy of its genome sequence. These results imply that antiretroviral drugs could reduce the risk of HAM/TSP by reducing the viral load, and that an effective anti-HTLV-I vaccine should elicit a strong CTL response to the virus. The dynamic nature of the infection also has implications for the epidemiology and the evolution of HTLV-I.

The origin and evolution of human T-cell lymphotropic virus types I and II

Studies on human T-cell lymphotropic virus types I (HTLV-I) and II (HTLV-II) are briefly reviewed from the viewpoint of molecular evolution, with special reference to the evolutionary rate and evolutionary relationships among these viruses. In particular, it appears that, in contrast to the low level of variability of HTLV-I among different isolates, individual isolates form quasispecies structures. Elucidating the mechanisms connecting these two phenomena will be one of the future problems in the study of the molecular evolution of HTLV-I and HTLV-II.

Functional conservation of HTLV-1 rex balances the immune pressure for sequence variation in the rex gene

Naturally occurring mutations in Human T-cell Leukemia Virus Type 1 (HTLV-1) Tax protein lead to loss of recognition by cytotoxic T-lymphocytes. Most of these mutations also abolish or severely impair the transactivation function of Tax. Ninety percent of the rex gene, which encodes the viral regulator of mRNA splicing (Rex), overlaps with the tax gene. In this paper, we report that four previously described point mutations in tax that abolished CTL recognition and activity did not alter either the dimerisation function or the ability to export viral mRNA of the corresponding Rex proteins. Rex proteins containing two other amino acid changes were likewise functional. However, five Rex deletion mutants, predominantly but not exclusively found in HAM/TSP patients, had all lost these functions. We conclude that, although the Tax protein is subject to strong CTL-mediated selection, there are stronger functional constraints on amino acid variation in Rex. This may limit the variation in the tax/rex nucleotide sequence which results in immune evasion.

Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts

Clonal diversifications of HIV virus were monitored by periodic samplings on each of the six patients with regard to 183- to 335-bp segments of the env gene, which invariably included the functionally critical V3 region. Subsequently, six individual phylogenetic trees of viral variants were constructed. It was found that at one time or another during the course of disease progression, viral variants were inexplicably released from a strong negative selection against nonsynonymous base substitutions, possibly indicating positive selection. This resulted in concentrated amino acid substitutions at five specific sites within the V3 region. It was noted that these sites were often involved as antigenic determinants that provoked the host immune response and that these sites were also involved in the determination of viral phenotypes as to their cell tropism, syncytium formation capability, and replication rates.