High prevalence of TT virus (TTV) in naive chimpanzees and in hepatitis C virus-infected humans: frequent mixed infections and identification of new TTV genotypes in chimpanzees.

A recently discovered DNA virus, TT virus (TTV), is prevalent in humans. In the present study, the genetic heterogeneity of TTV was evaluated in hepatitis C virus (HCV)-infected patients and in chimpanzees. TTV DNA was detected by PCR in serum samples from all ten HCV-infected patients studied; at least five major TTV genotypes, all previously identified in humans, were recovered. Eight patients were infected with multiple variants of TTV. TTV DNA was detected by PCR in serum samples from 11 (65%) of 17 naive chimpanzees bred in captivity; a persistent infection was present in three of six animals. At least five chimpanzees were infected with more than one TTV variant. Detection of TTV DNA in chimpanzee faecal samples suggests the possibility of faecal-oral transmission. Phylogenetic analysis of ORF1 sequences amplified from chimpanzees identified three major genotypes which had not previously been recognized in humans.

High prevalence of TT virus (TTV) infection in patients on maintenance hemodialysis: frequent mixed infections with different genotypes and lack of evidence of associated liver disease.

Recently, a novel DNA virus, TT virus (TTV), was identified in patients with post-transfusion non-A-G hepatitis. We analyzed the prevalence and clinical implications of TTV infection in a cohort of 96 Spanish patients on long-term hemodialysis. TTV DNA was detected by nested PCR in 51 (53%) of 96 patients, a prevalence significantly higher than that found in healthy blood donors. Persistent liver test abnormalities were found in only 2 (7.7%) of 26 patients infected with TTV alone, compared with 12 (75%) of 16 patients infected with hepatitis C or hepatitis B virus, or both (P < 0.01). Mixed infections with multiple strains of TTV, including different major genotypes, were common in patients on hemodialysis. These patients had received a significantly greater number of blood units (22.7 +/- 20) compared with patients apparently infected with a single strain of TTV (8.9 +/- 11) (P = 0.01). Phylogenetic analyses of TTV from infected patients identified strains of genotypes 1, 2, 3, and 4. In summary, TTV infection was common in patients on hemodialysis but was not associated with liver disease

HIV type 1 subtypes in Malaysia, determined with serologic assays: 1992-1996.

We investigated the molecular epidemiology of HIV-1 subtypes in Malaysia among injecting drug users (IDUs) and sexual transmission risk groups, using serologic and genetic techniques. Frozen sera collected at a general hospital, a blood bank, several drug treatment centers, and an STD clinic in Kuala Lumpur, between 1992 and 1996, were investigated retrospectively. V3 peptide serotyping and monomeric gp120 capture serotyping were used to study 89 known HIV-1-infected subjects. The methods differentiate subtypes B, E, and C. V3 peptide and gp120 capture results were comparable. No subtype C-specific reactive sera were found; one specimen was dually reactive for subtypes C and B, using the V3 peptide ELISA; and four were durally reactive for subtypes E and C using this assay. Genotypic analysis of HIV-1 gag RNA in serum was done on a subset of subjects and confirmed serologic findings. HIV-1 subtypes differed significantly by risk category: of 53 IDUs, 29 (55%) were infected with subtype B and 19 (36%) were infected with subtype E, 3 (6%) were dually reactive, and 2 (4%) were not typable. Of 36 persons with heterosexual risks, 29 (81%) were infected with subtype E, 5 (14%) were infected with subtype B, and 2 (5%) were not typable. Persons with IDU risks were significantly more likely to be infected with subtype B than were those with sexual risks (OR 5.89; 95% CI, 1.94-18.54; p < 0.001). Subtypes B and E of HIV-1 appear to predominate in Malaysia; subtype B was more prevalent among IDUs; subtype E was more prevalent among all other groups. These results may have important HIV-1 vaccine implications.

Experimental infection of chimpanzees with hepatitis C virus of genotype 5a: genetic analysis of the virus and generation of a standardized challenge pool.

Six major genotypes (genotypes 1-6) of hepatitis C virus (HCV) have been identified. These genetic variants are being transmitted to chimpanzees, the only recognized animal model for the study of HCV. Genotype 5a (strain SA13), a variant found primarily in South Africa, has been transmitted to chimpanzees for the first time. Experimental infection of 2 chimpanzees was characterized by early appearance of viremia and peak virus titers of 10(5)-10(6) genome equivalents/mL. The HCV infection was resolved by week 15 after inoculation in 1 chimpanzee and persisted in the other. Both chimpanzees became anti-HCV-positive by week 14 after inoculation. Both chimpanzees developed viral hepatitis. The infectivity titer of a genotype 5a challenge pool prepared from the first passage of HCV in a chimpanzee was approximately 10(4) infectious doses/mL. Finally, sequence analysis of strain SA13 confirmed that genotype 5a is genetically distinct from other genotypes of HCV.

The molecular epidemiology of HIV-1 among male sex workers in northern Thailand.

Male commercial sex workers (CSWs) in northern Thailand are at high risk for HIV-1 infection and may be exposed to multiple subtypes of HIV-1 through sexual contact with men and women from Thailand, other Asian nations, and the West. We studied 103 male Thai nationals working in gay bars and clubs in Chiang Mai city who participated in the 1994 sentinel surveillance of the Thai Ministry of Public Health using HIV serologic testing, DNA polymerase chain reaction methods, molecular cloning, differential colony hybridization, nucleotide sequencing, and a third hypervariable region (V3) peptide enzyme-linked immunoabsorbent assay to differentiate subjects infected with HIV-1 subtypes B, E, both, or neither. The majority (58%) reported heterosexual orientation, and 35 (34%) were married. Seventeen (16.5%) were HIV infected: 16 (94%) of 17 had HIV-1 subtype E; 1 had HIV-1 subtype B. Two subjects had dually reactive results by molecular techniques but colony hybridization sequencing revealed only HIV-1 subtype E. HIV-1 subtype E appears to be the predominant clade among male CSWs in northern Thailand. This may have important implications for the global kinetics of the HIV epidemic.

PIP: Male prostitutes in northern Thailand are at high risk for HIV-1 infection and may be exposed to multiple subtypes of HIV-1 through sexual contact with men and women from Thailand and elsewhere. Blood samples of 103 male Thai nationals working in gay bars and clubs in Chiang Mai collected during the Thai Ministry of Public Health's 1994 sentinel surveillance were studied to determine the prevalences of HIV-1 subtypes B and E in the population. The men reported having an average of 2.5 male clients per week and had been in the business from 1 month to 7 years, with a median duration of 4 months. HIV serologic testing, DNA polymerase chain reaction methods, molecular cloning, differential colony hybridization, nucleotide sequencing, and a third hypervariable region (V3) peptide enzyme-linked immunoabsorbent assay were used to differentiate subjects infected with HIV-1 subtypes B, E, both, or neither. 58% of the men reported a heterosexual orientation outside of work and 34% were married. 72.1% reported inconsistent or no condom use with sex partners. 17 (16.5%) were infected with HIV. Of those infected, 16 (94%) had HIV-1 subtype E and 1 had subtype B.

Evolution and probable transmission of intersubtype recombinant human immunodeficiency virus type 1 in a Zambian couple.

The extraordinary genetic diversity of human immunodeficiency virus type 1 (HIV-1) results from the introduction of mutations by an error-prone reverse transcriptase and from recombination of the two RNA genomes packaged in the virion during the synthesis of proviral DNA. The occurrence of multiple, genetically distant HIV-1 subtypes and their geographic intermixing set up conditions for dramatic, rather than gradual, changes in genotype whenever genomes from different subtypes are copackaged in virions. Here we describe, for the first time, the sequential generation of multiple different, but related, intersubtype HIV-1 recombinants within an infected individual. Full-length gag and env genes were recovered directly from peripheral blood mononuclear cells or from primary virus cultures, using serial blood samples from a Zambian woman and a sample from her spouse. DNA sequencing and phylogenetic analysis established that two different A/C recombinant forms of HIV-1 predominated at two time points in the woman. A related but distinct recombinant HIV-1 was recovered from her spouse. Intersubtype recombination apparently played a central role in the evolution of HIV-1 in this couple and may contribute substantially to the rapid emergence of HIV-1 variants whenever mixed-subtype HIV-1 infections occur.

Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand.

Human immunodeficiency virus type 1 isolates of envelope genotype E are contributing substantially to the global pandemic. These strains appear to be mosaics, with the gag gene from clade A and the envelope from clade E; the parental clade E strain has not been found. Here we report the first full genomic sequence of one such mosaic virus, isolate CM240 from Thailand. Multiple breakpoints between the two parental genotypes have been found in a CM240 virus. The entire gag-pol region and most, if not all, of the accessory genes vif, vpr, tat, rev, and vpu appear to derive from clade A. The genotype switches to E shortly after the signal peptide of the envelope and back to clade A near the middle of gp41; thus, the portion of the envelope that lies on the cytoplasmic side of the membrane appears to be principally derived not from clade E, as previously thought, but from clade A. Another small segment not belonging to any recognized clade and presumably also contributed by the parental E strain has been found in the long terminal repeat. It may be significant that the implied virion structure resembles a pseudotype virus with the matrix and core from one clade and the outer envelope from another. In the long terminal repeat, differences were observed between CM240 and other clades in the number of NF-kappa B binding sites, the sequence of the TATA box, and the putative secondary structure of the transactivation response region stem-loop. The mosaic structure of a CM240 virion is suggestive of phenotypic differences which might have contributed to the emergence of this variant.

PIP: A new variant of human immunodeficiency virus (HIV)-1 with a mosaic genomic structure was identified in Thailand in 1992. This variant, termed genotype E, was characterized by an envelope gene sequence equidistant from genotypes A through D. The gag gene, encoding the matrix and core virus proteins, grouped with genotype A rather than forming a new clade. More than 500,000 Thais are estimated to be infected with the envelope clade E virus and its type 1 isolates, previously assumed to be rare outliers, are contributing substantially to the global acquired immunodeficiency syndrome pandemic. Reported here is the first complete genomic analysis of one such mosaic virus, isolate CM240 from Thailand. The entire gag-pol region and most of the accessory genes vif, vpr, tat, rev, and vpu appear to derive from clade A. The genotype switches to E shortly after the signal peptide of the envelope and back to clade A near the middle of gp41. Thus, the portion of the envelope that lies on the cytoplasmic side of the membrane appears to be derived from clade A. Another small segment presumably contributed by the parental E strain has been found in the long terminal repeat. The multiple crossover points detected in CM240 may reflect a common mechanism of frequent strand switching by reverse transcriptase. Full genomic analyses of other mosaic HIV-1 genomes are recommended to determine whether the breakpoints found in CM240 are recurrent and to identify the functional implications of the virion alterations.

Sequences and phylogenetic analysis of the nef gene from Thai subjects harboring subtype E HIV-1.

PIP: It has been demonstrated that nef-defective SIV can cause attenuated disease in rhesus monkeys and that animals immunized with a similar construct can be protected when challenged with wild-type, pathogenic SIV. This finding has sparked interest in the nef gene of HIV-1. It remains unclear, however, whether nef serves an analogous role in human HIV-1 infection; Deacon et al. have reported an association of deletions in the nef gene with an attenuated disease course in humans, although other work does not support a strict correlation between the structure or function of nef and rates of disease progression. The nef gene product has been shown to influence the infectivity and pathogenicity of HIV-1. nef may also have a role in the immune response to HIV-1. The current database of nef sequences is derived almost exclusively from subtype B viruses. The authors therefore sought to develop a database of nef sequences from subjects infected with HIV-1 subtype E. Whole-blood samples were collected from 103 male commercial sex workers in Chiang Mai, Thailand. 17 tested positive for infection with HIV-1, 16 of whom were infected with subtype E by gp120 characterization. Intersubject variation in subtype E nef genes at the nucleotide level ranged from 2.1-7.8%. Thai subtype E nef sequences are more tightly clustered than subtype B nef sequences, analogous to what is seen in env. The authors note that their subtype E nef sequences do not share the genotypic polymorphism in the area of residues 10-30 noted with subtype B nef. These data confirm the need to develop a set of subtype E-specific reagents.^ieng

Dual infection with human immunodeficiency virus type 1 of distinct envelope subtypes in humans.

Multiple genetic subtypes of human immunodeficiency virus type 1 (HIV-1) have been identified among internationally collected isolates. The HIV-1 epidemic in Thailand is largely due to B and E subtypes of virus. Dual infection with distinct HIV-1 subtypes would suggest that antiviral immunity evoked by one subtype can be incompletely protective against a second. Polymerase chain reaction typing and serologic typing were used to screen a panel of specimens from HIV-1-infected subjects in Thailand. Two persons simultaneously harbored HIV-1 of env subtypes B and E, and this was confirmed by colony hybridization with subtype-specific probes and nucleotide sequence analysis of a 630-bp fragment of gp120 from multiple molecular clones. In addition, both subtypes were identified in cocultured peripheral blood mononuclear cells from 1 individual. These data provide the first evidence of dual HIV-1 infection in humans and reinforce the need for polyvalent vaccines.

Genetic diversity of the envelope glycoprotein from human immunodeficiency virus type 1 isolates of African origin.

The genetic diversity of the envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) isolates was studied. HIV-1 isolates were obtained from eight countries in Africa: Djibouti, Gabon, Kenya, Senegal, Somalia, Uganda, Zaire, and Zambia. The DNA sequences encoding the complete HIV-1 envelope protein were PCR amplified and sequenced. Phylogenetic relationships among the 21 sequences from this study and the 32 previously published full-length env HIV-1 sequences were determined. Twenty of the newly sequenced African isolates could be assigned to envelope subtypes A, C, D, and G. One isolate, collected in Zambia, did not belong to any of the eight previously described subtypes and may represent a prototype sequence of its envelope subtype. The phylogenetic classification of these isolates was strongly supported by bootstrapping and the congruence of trees generated by either distance methods or maximum parsimony analysis. The data presented in this study confirm the existence of several genetic subtypes within the global HIV epidemic and broaden the genetic variability previously observed for envelope subtypes. The geographic spread of different subtypes was shown to be substantial, and the notion of cocirculation of subtypes was reinforced.

Two antigenically distinct subtypes of human immunodeficiency virus type 1: viral genotype predicts neutralization serotype.

At least five distinct genetic subtypes (genotypes) of human immunodeficiency virus type 1 (HIV-1) have been identified by DNA sequencing. Current vaccine candidates are based on virus strains from North America and Europe that represent only one subtype. The extent to which distinct genotypes of HIV-1 correspond to antigenically distinguishable serotypes is largely unknown and may be critically important to vaccine design. Cross-neuralization studies were done with viruses and plasma from two different genotypes. Based on neutralization susceptibility, 10 primary HIV-1 isolates from Thailand and the United States were classified into one of two antigenic subtypes that correlated with viral genotype. The existence of serotypes of HIV-1 suggests that a broadly effective vaccine may have to include strains from multiple subtypes. Neutralization of these primary HIV-1 isolates differed substantially from results with laboratory strains. Future neutralization studies using primary isolates and multiple genotypes may be important for assessment of HIV-1 antigenic diversity.

Genetic variants of HIV-1 in Thailand.

Serosurveys conducted prior to 1988 indicated a very low level of HIV-1 infection in Thailand, even among high-risk groups. The Ministry of Health has reported a dramatic increase in HIV-1 infection during the last three years. The geographic and demographic distribution of the epidemic is broad, involving multiple provinces and risk groups. Foci of higher incidence and prevalence have been noted in the urban center of Bangkok and in the northern provinces of Chiang Mai and Chiang Rai. Here we report the results of genetic characterization of 16 HIV-1 isolates from Thailand using a combination of polymerase chain reaction (PCR) typing and DNA sequencing. The complete sequence of gp160 (env) of five isolates, partial env sequence of six additional isolates, and the gag gene of two isolates were determined. Two highly distinct HIV-1 variants were found. One variant resembled those prevalent in North America and Europe; five of the isolates were of this type. The remaining eleven isolates were very similar to one another and represented a variant unlike any previously described. Phylogenetic tree analysis of complete env and gag genes placed the two variants on widely separated branches. Protein sequence comparisons indicate both general and specific features that distinguish the Northern Thailand variant both from the Bangkok variant and from virtually all previously sequenced HIV-1 isolates. A simple PCR test for distinguishing the two variants has been developed for use in epidemiologic surveys.

Genetic analysis of HIV-1 isolates from Zambia and an expanded phylogenetic tree for HIV-1.

Geographic variation in the HIV-1 virus is extensive but incompletely documented. We herein report the first genetic characterization of HIV-1 isolates from Zambia. The genomic region encoding the GAG polyprotein has been compared among 22 Zambian isolates and 14 North American isolates using a combination of polymerase chain reaction (PCR) and DNA sequencing methods. The Zambian isolates were similar to one another but distinct from other HIV-1 isolates. They exhibited a characteristic PCR "fingerprint" wherein certain primer combinations were unable to amplify because of mispairing. The sequence of the complete gag gene of three isolates from Zambia has been determined, and phylogenetic tree analysis placed them in a branch distinct from other African isolates and North American isolates. The PCR procedure used here may be widely applicable for genetic characterization of HIV-1.