High genetic diversity revealed by the study of TLMV infection in French hemodialysis patients

TT virus-like minivirus (TLMV) was recently discovered as a human circovirus. Little is known about its natural history and molecular epidemiology. A study of TLMV infection is described in a population of French hemodialysis patients. TLMV DNA was tested by seminested PCR system located in the noncoding region in 81 patients divided into seven groups according to the origin of their renal disease. Quantitation of TLMV DNA in serum was carried out. Sequences from 28 patients were compared with 40 sequences retrieved from databases and 53 TLMV sequences cloned from the serum of a single patient. The prevalence of TLMV DNA in hemodialysis patients was 95.1%. In this study, 24 samples (29.6%) presented viral loads of > 125 equivalents of plasmid (Ep)/ml, and only 6 (7.8%) had viral loads of > 125 x 10(2) Ep/ml. A significant correlation (P < 0.029) was found between viral loads of > 125 x 10(2) Ep/ml and the neoplastic origin of end-stage renal disease. Analysis of 53 sequences cloned from a single individual demonstrated high sequence variability, as shown by the genetic distance of 40.2%. This genetic distance is comparable to that between the most divergent sequences of TLMV reported to date (43.5%). These data suggest that TLMV viral load is possibly related to the level of immunocompetence of hemodialysis patients; the genetic diversity of TLMV is extremely high; and co-infection by different strains is possible.     

High detection rates of TTV-like mini virus sequences in sera from Brazilian blood donors

TT virus (TTV) is an unenveloped virus with a single-stranded, circular DNA genome of 3,818-3,853 nucleotides (nt) that infects humans and non-human primates. Recently, the existence of a novel human virus, TTV-like mini virus (TLMV), that shows a genetic organization similar to that of TTV, but with smaller virion particle and genome, was proposed [Takahashi et al. (2000) Archives of Virology 145:979-993]. To date, no information is available with respect to the prevalence and pathogenicity of TLMV. A sensitive PCR assay was developed by using two oligonucleotide primers (LS2 and LA2) designed from the conserved non-coding region of the TLMV genome. One hundred thirty-seven sera from volunteer Brazilian blood donors were tested and 99 (72%) were TLMV DNA positive. No significant differences were observed between the groups of TLMV positive and negative subjects in relation to sex ratio, seroprevalence of TTV DNA, prevalence of anti-hepatitis A virus antibodies, area of residence, occurrence of daily contact with animals, family income, education level, and level of alanine aminotransferase. The specificity of the PCR assay was demonstrated after cloning of amplification products and determination of the nucleotide sequences (200-228 nt) of clones derived from 23 individuals. When DNAs extracted from TLMV/TTV-coinfected sera were submitted to PCR with LS2 and LA2 primers, the amplification products were derived exclusively from the TLMV genome. A markedly wide range of sequence divergence, even higher than that existent among TTV strains, was noted among TLMV isolates, with a maximum evolutionary distance of 0.80.     

Exposure to multiple subgenotypes of hepatitis A virus during an outbreak using matched serum and saliva specimens

Matched serum and saliva samples were collected simultaneously from 124 subjects exposed during a hepatitis A virus (HAV) outbreak at a daycare center in Rio de Janeiro, Brazil. All samples were tested for IgM and total anti-HAV antibodies by enzyme immunoassay (EIA). HAV was detected by nested PCR in serum, saliva, and water samples employing primers for the VP1/2A region of the viral RNA; all positive products were then sequenced. The viral load of the matched samples was determined by real-time PCR using the TaqMan system. HAV-RNA was identified by nested PCR in 37.7% of the saliva samples, 29% of the serum samples, and one drinking water sample. The mean HAV viral load was similar in the serum and saliva specimens (10(3) copies/ml). HAV genotypes IA and IB were detected in both specimen types, and the water sample isolate was classified as genotype IB, indicating the existence of more than one source of infection at the daycare center. In six infected patients, a different HAV subgenotype was found in their serum than in their saliva, and this unusual pattern of mixed HAV infection was investigated further by molecular cloning followed by nucleotide sequencing. All clones derived from the saliva samples belonged to subgenotype IB and shared 96.5-100% identity. However, clones derived from their corresponding serum sample belonged to subgenotype IA and shared 90.5-100% identity. This study showed the important role that non-invasive saliva samples can play in the molecular epidemiological analysis of a hepatitis A outbreak.     

Low hepatitis B prevalence among pre-school children in Denmark: saliva anti-HBc screening in day care centres

Although Denmark has a low hepatitis B virus (HBV) prevalence, HBV transmission has been reported in Danish day-care centres. The aim of this study was to validate saliva anti-HBc testing as a method for HBV screening, the applicability of saliva sampling to pre-school children, and to determine the HBV prevalence in Danish day-care centres with a high proportion of immigrants. For validation, paired saliva and plasma samples were obtained from blood donors and injecting drug users. Employees and children in day-care centres with a high proportion of immigrant children were offered saliva screening followed by blood test if positive. The specificity and sensitivity of anti-HBc tests on saliva was 100% (102 blood donors and four injecting drug users) and 85.9% (61 of 71 anti-HBc-positive injecting drug users), respectively. In all samples from HBsAg (n = 7) or anti-HBc IgM-positives (n = 9), anti-HBc was detected in saliva. Adequate saliva samples were obtained from 93% (588/634) of children and 100% (166/166) of employees participating in the day-care centre survey. Among children 55% were of non-Scandinavian origin and only one (0.2%, 95% CI [0.0; 1.0]) was HBV positive. Among employees the corresponding values were 22% and 7 (4.2%). The positive predictive value of the saliva test was 25% (1/4) among children and 88% (7/8) among adults. In conclusion, saliva testing is feasible for HBV screening among children in low prevalence populations, but any anti-HBc reactivity should be confirmed by plasma analysis. The HBV prevalence in pre-school children in Denmark is low even among immigrants from endemic areas.     

TLMV5＇非编码区基因的克隆与序列分析

目的　调查TTV阴性的非甲～庚型肝炎患者中TTV～like mini virus(TLMV)感染情况,对TLMV5＇非编码区(5＇NCR)部分基因进行分子克隆与序列分析。方法　采用巢式PCR技术检测53例T T V阴性的非甲～庚肝炎患者血清TLMV DNA,对PCR产物进行克隆、测序和分析。结果　53例病例中TLMV DNA阳性37例(69.8％),对其中8株TLMV基因克隆测序,并与Takahashi报道的TLMV序列(GenBank Accession No ab 026930、ab026931)比较,其核苷酸序列同源性在64％～83％之间。结论　在T TV阴性的非甲～庚肝炎患者中存在TLMV感染。TLMV5＇NCR基因变异性较大。TLMV的致病性及其与非甲～庚肝炎的关系尚有待进一步研究。     

Relationship between oral anaerobic bacteria and otitis media with effusion

Objective: In this study hypothesing the translocation of oral bacteria from oropharynx into the middle ear cavity may be involved in the pathogenesis of otitis media with effusion (OME), we aimed to investigate the presence and similarity of Fusobacterium nucleatum and Treponema denticola in saliva, nasopharyngeal secretion and the middle ear effusion samples from the children with OME.Methods: Totally 20 children with OME undergoing myringotomy and ventilation tube placement were attended. Stimulated saliva samples were collected after otorhinolaryngological and oral examinations were done. The middle ear effusion and nasopharyngeal secretions were collected during the operations. The presence of F. nucleatum and T. denticola were detected using 16SrRNA-based PCR. The clonal similarities of the bacteria were detected in the samples which the same bacteria had been detected in each samples of the same child. After DNA sequencing, clonal similarity was determined by 16SrRNA gene clone library analysis. The sequences from each clone were compared with similar sequences of reference organisms by FASTA search.Results: T. denticola was detected only in four (20%) saliva and in one (5%) nasopharyngeal sample. F. nucleatum was detected in 11 (55%) saliva, eight (40%) nasopharyngeal and six (30%) middle ear effusion samples. Sequences from F.nucleatum clones derived from three different anatomic sites within patients were similar in 33% of OME patients, indicating their genetic relatedness.Conclusions: Bacteria involved in this process most likely originate from the oropharynx since they show a close genetic relatedness with their oropharyngeal counterparts.     

HIV-1 V3 domain variation in brain and spleen of children with AIDS: Tissue-specific evolution within host-determined quasispecies

DNA coding for the principal neutralization epitope of HIV-1 (the V3 domain of the envelope glycoprotein gp120) was amplified by polymerase chain reaction from postmortem brain and spleen tissue of three perinatally infected children who died of AIDS with progressive encephalopathy. Sequences obtained directly (without cloning) from this DNA were compared with sequences of 52 molecular clones made from this DNA. Cluster analysis showed that V3 domain sequences from two of the three children were similar to sequences from the American MN/SC isolates, while those from one child were more closely similar to the Caribbean RF isolate. Comparison of sequences obtained directly with consensus sequences derived from cloned DNA showed that V3 sequences are characteristic for an individual host. In one child, the V3 sequence determined directly from brain DNA was very distant from the consensus brain clone sequence and from the spleen sequences, suggesting a diverging quasispecies distribution. Site-directed hybridization demonstrated that brain-specific sequences present in 33% of brain-derived clones were absent from clones derived from spleen. The evidence suggests that brain- and spleen-specific variants evolve independently within each host-delimited quasispecies.     

Molecular epidemiology of TTV-like mini virus in Norway

Summary.  TT virus (TTV), the first human circovirus to be discovered, appears to be present in most people; less is known about the prevalence of the related TTV-like mini virus (TLMV). A sensitive nested PCR, specific for TLMV, detected the virus in 48% of 201 sera (Norwegian blood donors) previously found to have a 90% prevalence of TTV. More samples were either positive for both or negative for both viruses than what would have been expected from a random distribution (p = 0.08). Sequence analysis revealed considerable heterogeneity of Norwegian TLMV as compared to international sequences, suggesting that TLMV is efficiently dispersed in human populations. June 27, 2001 October 11, 2001     

Limited sequence variation in human T-lymphotropic virus type 1 isolates from North American and African patients

Nucleotide sequences were determined from the env genes of three HTLV-I clones derived from two North American patients and one African patient with adult T-cell leukemia/lymphoma (ATLL). In addition, sequences from the pX region, between env and the 3'LTR, were determined from one of these isolates. These data were compared to sequences derived from HTLV-I isolates of two Japanese ATLL patients, a Japanese patient with HTLV-I-associated myelopathy or tropical spastic paraparesis (HAM/TSP) and a Caribbean ATLL patient. Nucleotide sequence variation was found to be less than 6% in coding and noncoding regions. Predicted amino acid sequences varied between 0.6 and 1.8% in the envelope, 0-3.7% in rex, 0.8-2.5% in the tax gene product, and 3-14.0% in the pX-I open reading frame. Comparisons of the predicted amino acid sequences of the surface envelope protein (SU-gp46) suggest that the variation between isolates of different geographical origins is greater than that between isolates obtained from the same region of the world.     

TLMV5‘非编码区基因的克隆与序列分析

目的 调查ＴＴＶ阴性的非甲￣庚型肝炎患者中ＴＴＶ－ｌｉｋｅ ｍｉｎｉ ｖｉｒｕｓ（ＴＬＭＶ）感染情况,对ＴＬＭＶ５’非编码区（５’ＮＣＲ）部分基因进行分子克隆与序列分析。方法 采用巢式ＰＣＲ技术检测５３例ＴＴＶ阴性的非甲－庚肝炎患者血清ＴＬＭＶ ＤＮＡ,对ＰＣＲ产物进行克隆、测序和分析。结果 ５３例病例中ＴＬＭＶ ＤＮＡ阳性３７例（６９．８％）,对其中８株ＴＬＭＶ基因克隆测序,并与Ｔａｋａｈａｓｈ     

Humoral immune response against a 70-kilodalton heat shock protein of Entamoeba histolytica in a group of patients with invasive amoebiasis.

In order to investigate the humoral immune response against Entamoeba histolytica a lambda ZapII cDNA library was constructed from trophozoites of the pathogenic E. histolytica strain SFL-3. The library was screened with serum IgG from a patient with invasive amoebiasis. Forty-nine immunopositive lambda clones were isolated and partial sequences from the inserts were obtained. By comparison of the sequences with the merged database MIPSX from the Martinsried Institute for Protein Sequences we were able to identify homologous proteins for 36 of the clones. Twenty-six of the clones encoded intracellular proteins, among these, the major part (16 clones) were highly homologous to the eukaryotic 70-kDa heat shock proteins (Hsps). The open reading frame of one complete clone encodes a protein of 656 amino acid residues of 71.5 kDa which has 69.8% sequence identity with the human Hsp70 protein. In a larger screening experiment only 3 out of 12 patients detected with their IgG the phage which expressed the 70-kDa heat shock protein(s).     

Hepatitis B surface antigen particles with all four subtypic determinants: point mutations of hepatitis B virus DNA inducing phenotypic changes or double infection with viruses of different subtypes.

Hepatitis B surface antigen (HBsAg) particles carry the common determinant, a, as well as d or y and w or r subtype determinants, and are classified into the four major subtypes, i.e., adw, adr, ayw and ayr. Rare sera contain HBsAg particles with all four subtype determinants (adywr). Target sequences (nucleotides 38-550) in the S gene of hepatitis B virus (HBV) DNA in two such sera were amplified by the polymerase chain reaction. Individual amplification products were cloned in an M13 phage vector. The HBV DNA clones obtained were subtyped by determining the second letters of codon 122 and 160 for lysine (AAA/AAG) or arginine (AGA/AGG), which specify the d or y and w or r determinants, respectively. From one serum (S-63), two adw, 10 adr and 58 ayr clones were obtained. When the two adw clones and two representatives each of the adr and ayr clones were compared against each other, for the sequence of 235 base pairs representing nucleotides 295-529 in the S gene, they differed only by 0.4-2.1% (average 1.2%). These results indicated multiple point mutations of a single HBV strain of subtype ayr and co-infection of hepatocytes with the original HBV strain and its mutant of subtype adw as the mechanism for the production of HBsAg/adywr particles. From the other serum (K-45), 1 adw, 73 adr and 4 ayw clones were obtained. The adw clone and two representative adr clones differed only by 0-1.7% in the S gene sequences, but they differed by 8.5% or greater from two representative ayw clones. HBsAg/adywr particles in this serum, therefore, could be explained by double infection of hepatocytes with two HBV strains of different subtypes (adr and ayw).     

Coinfection with multiple TT virus strains belonging to different genotypes is a common event in healthy Brazilian adults

Testing of the DNA of TT virus (TTV) was done with serum samples obtained from 191 persons working in a public hospital of the city of Rio de Janeiro, Brazil. TTV DNA was detected by PCR in the sera of 125 (65.4%) individuals. PCR products were cloned, and sequences with a length of 159 bases surrounding the TATA signal region were determined for 100 clones derived from 31 individuals. One clone from each of 23 subjects was sequenced, while 7 to 19 clones from eight individuals were sequenced. None of the sera contained a viral sequence identical to that of any other individual. Phylogenetic analysis revealed the existence of a divergent TTV genotype possessing a single-base deletion at position 140. Among the eight persons for whom various sequences were analyzed, six were coinfected with between two and seven TTV strains belonging to different genotypes. The results suggest that coinfection with multiple TTV strains belonging to different genotypes is a common event in healthy Brazilian adults.     

Non-toxigenic pattern II and III Bacteroides fragilis strains: coexistence in the same host

Diarrhoeic stool samples from 334 0-5-year-old children were analysed with respect to the incidence of Bacteroides fragilis as well as other enteropathogens. B. fragilis was recovered in 9.3% (31/334) of the samples, and 79 strains were examined for the presence of the bft gene or the BfPAI flanking region using polymerase chain reaction assays. No enterotoxigenic B. fragilis strains were detected. In 29% (9/31) of the samples the coexistence of both II and III non-toxigenic B. fragilis (NTBF) patterns could be seen. In 51.6% (16/31) of the samples there existed a pattern II NTBF only, and in 19.4% (6/31) only pattern III could be detected. Strains from the same patient representing different patterns were submitted to pulsed-field gel electrophoresis assays. Fingerprints obtained by this technique showed that there was strong heterogeneity among strains from different individuals. However, different patterns from the same individual shared 100% similarity.     

Molecular cloning of hepatitis C virus genome from a single Japanese carrier: sequence variation within the same individual and among infected individuals.

A hepatitis C virus (HCV) genome was isolated and sequenced from a single Japanese patient with chronic non-A, non-B hepatitis. The genome (HCV-JT), which was constructed with 23 cDNA clones, consisted of 9436 nucleotides with a long open reading frame which could encode a sequence of 3010 amino acid residues. To study the sequence variation of the HCV genome in an individual, we analyzed another sequence of the HCV genome (HCV-JT') constructed with different cDNA clones derived from the same patient. The nucleotide variation between HCV-JT and -JT' was less than 1%, and was distributed throughout the genome except in the 5' non-coding region, where no variation was observed. The diversity was higher (1.6%) in the putative envelope protein region than in other regions. The nucleotide and deduced amino acid sequences of HCV-JT showed homologies of about 91 and 95%, respectively, with those of other Japanese HCV isolates. The nucleotide diversity was high in the gp 70 region (corresponding to the NS 1 region of flaviviruses) and low in the 5' non-coding and p22 (putative core protein) regions. A similar pattern of distribution of nucleotide changes was observed on comparison of HCV-JT with an American isolate HCV-US, where the homologies in nucleotide and amino acid sequences were about 79 and 85%, respectively. Base transversions contributed about 50% of the total base exchanges between the Japanese and American HCV sequences, but only 20% or less of those among Japanese HCV or among American HCV sequences. Thus, the Japanese and American HCVs are genetically distinguishable, supporting our earlier prediction that these two HCVs could be classified as different subtypes.     

Differences in the antigens recognized by cytolytic T cells on two successive metastases of a melanoma patient are consistent with immune selection

We have studied the patterns of antigens recognized by autologous cytolytic T lymphocytes (CTL) on two melanoma cell lines derived from metastases that were removed from patient LB33 at several years distance. Cell line LB33-MEL. A was obtained after surgery in 1988. A large number of CTL clones directed against LB33-MEL. A was obtained with blood lymphocytes collected from the patient in 1990. In vitro selection of melanoma cells that were resistant to these CTL clones indicated that at least five different antigens were recognized on LB33-MEL. A by autologous CTL. Four of these antigens were found to be presented by HLA-A28, B13, B44 and Cw6, respectively. The patient remained disease-free until 1993 when a metastasis was detected and was used to obtain cell line LB33-MEL. B. This cell line proved resistant to lysis by all the CTL clones directed against the LB33-MEL. A cells and showed no expression of HLA class I molecules except for HLA-A24. Using LB33-MEL. B cells to stimulate blood lymphocytes collected from the patient in 1994 we derived CTL clones that lysed these cells. All these CTL clones recognized a new antigen presented by HLA-A24. These results suggest that in patient LB33 the melanoma cells may have lost the expression of several HLA molecules under the selective pressure of an anti-tumor CTL response.     

Dynamic study of HBsAg and HBeAg in saliva samples from patients with hepatitis B infection: diagnostic and epidemiological significance

Analysis of 505 cases history of patients among men with viral hepatitis demonstrates that HBV infected patients represent 68.9% of the total and that a non-parenteral rate of transmission is the most likely means of hepatitis B infection. Saliva and serum testing for the presence of specific HBV markers (HBsAg, HBeAg and HBV DNA) at different phases of the infection process were carried out to review the diagnostic and epidemiological value of saliva samples from patients with acute viral hepatitis B. The frequency of HBsAg detection by Enzyme Immune Assay (EIA) in saliva of patients in acute period was found to correlate with the frequency of its detection in serum. In early convalescence the frequency of detection of that antigen in serum (59.5% of patients) was significantly higher than in saliva (23.8%) (P < 0.001).The frequencies of HBeAg detection by EIA in saliva samples was significantly higher than that in serum samples in both acute phase (84.3% and 28.1% of patients, respectively) and in early convalescence (56.2% and 3.1% of patients, respectively). The study of frequencies of detection of these antigens in the dynamics of the disease up to the total recovery of patients (observations were carried out for the period of 60 days and longer) showed that in most patients there was a faster disappearance HBsAg from saliva than from serum. By the end of second month this antigen was detected in saliva of only 8.3% of patients whereas in serum in the same period HBsAg was detected in 33.3% of patients. HBeAg became undetectable in blood whereas HBs-antigenemia was still pronounced, and a month after the beginning of the disease it was not found in serum specimens. In saliva, HBeAg was detected in 95.8% of patients observed directly after admission. A month after the beginning of the disease it was detected in saliva of 66.7% of patients and, by the end of observation period, in 12.5% of patients recovered from viral hepatitis. HBV DNA revealed by PCR in saliva and serum of HBV-infected patients was detected in acute period not only in serum (84.6% of cases) but also in saliva (46.2% of cases). The data illustrate the diagnostic value of saliva and point to the possible role of saliva as a source of HBV infection.     

Analysis of the full-length genome of hepatitis B virus in the serum and cerebrospinal fluid of a patient with acute hepatitis B and transverse myelitis

Although many extrahepatic manifestations have been described in patients with acute or chronic hepatitis B, there are few reports about neurological disorders. We describe a 55-year-old man who contracted acute hepatitis B virus (HBV) infection and transverse myelitis. His neurological findings were gradually reduced along with the recovery from hepatitis. The cerebrospinal fluid (CSF) was revealed to be positive for HBsAg and HBV DNA. Full-length sequences of HBV in his serum and CSF were determined, and it was revealed that these two isolates had mutations at nucleotide (nt) 1762/1764 in the core promoter region and nt 1896 in the precore region. They were identical to each other except for two ambiguous codes at nt 2020 and 2631 in the CSF isolate. After cloning of the amplicons, substitutions at nt 2020 and 2631 were found in 6 (38%) of the 16 CSF clones. One clone of the 6 CSF clones had an additional substitution at nt 2119. These substitutions were not found in 16 serum clones. The presence of HBV clones unique to CSF suggests that HBV was a possible causative agent of the myelitis.     

Oropharyngeal candidiasis in HIV(+) patients may influence the selection of HIV-1 protease variants

Approximately 500 HIV-1 protease gene (pro) sequences were obtained from oral tissues (gingival cuff, buccal mucosa, tongue, palate) as well as saliva and peripheral blood mononuclear cells (PBMC) of 80 HIV-1 positive patients by nested amplification and manual sequencing of PCR products. By visual inspection each patient in this study exhibited a unique sequence profile. HIV-1 pro sequences obtained from patients with oropharyngeal candidiasis (OPC(+) patients) had significantly higher numbers of mutations than sequences from OPC(-) patients, but OPC(+) patients were no more likely to accumulate protease inhibitor resistance mutations than OPC(-) patients. Although the sequences for each patient were predominantly consistent between PBMC and oral tissues, approximately 10% of the patients demonstrated tissue specificity, and patients that demonstrated tissue specificity tended to be OPC(+). Furthermore, HIV-1 pro sequences derived from OPC lesions demonstrated unique mutations in approximately 30% of the patients who provided paired OPC(+/-) samples of the same tissue type. These data provide evidence for minimal compartmentalization of HIV-1 in oral tissues, yet some patients demonstrate minor variation between the HIV-1 pro sequences obtained from an OPC lesion and those obtained from a non-lesion site of similar tissue.