Classification of TTV and related viruses (anelloviruses).

Ten years after the identification of the first partial sequences of Torque teno virus (TTV), more than 200 full-length related genomes have been characterized in humans and in several animal species. As suspected in the earlier stages of their description, a considerable genetic variability characterizes TTV and related viruses, the current members of the floating genus Anellovirous. Since information related to anelloviruses diversity is in constant evolution, the challenge in their taxonomic classification is to take into account all pertinent parameters, along with the taxonomic situation of other viruses having circular single-stranded DNA genomes. Past, present and future phylogenetic and taxonomic considerations are exposed.

[Anelloviruses (TTV and variants): state of the art 10years after their discovery]. / Les anellovirus (TTV et variants): données actuelles dix ans après leur découverte.

Ten years after their discovery, anelloviruses combine some characteristics making them particularly intriguing. In support of their extreme genetic diversity and high prevalence in various populations, their natural history is still poorly understood along with their implication in human health. These viruses have been identified in blood and blood-derived products, and are probably remarkable examples of co-existence and co-evolution in their various hosts. This article presents epidemiological and molecular characterizing this new viral family.

Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov.

Strain FF10(T) (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal. Here we used a polyphasic study including phenotypic and genomic analyses to describe the strain FF10(T). Results support strain FF10(T) being a Gram-positive coccus, facultative anaerobic bacterium, catalase-negative, non-motile and non-spore forming. The sequenced genome counts 2.46 Mb with one chromosome but no plasmid. It exhibits a G+C content of 40.4% and contains 2471 protein-coding and 45 RNA genes. On the basis of these data, we propose the creation of Streptococcus varani sp. nov.

4D-π-1A type ß-substituted ZnII-porphyrins: ideal green sensitizers for building-integrated photovoltaics.

Two novel green ß-substituted ZnII-porphyrins, G1 and G2, based on a 4D-π-1A type substitution pattern have been synthesized. Their enhanced push-pull character, by reduction of H-L energy gaps, promotes broadening and red-shifting of absorption bands. The effective synthetic pathway and the remarkable spectroscopic properties make G2 ideal for BIPV application.

Detection of gastrin mRNA in fresh human colonic carcinomas by reverse transcription-polymerase chain reaction.

To investigate the hypothesis that gastrin might be synthesized by tumour tissues in cancer of the colon, samples from six human colon tumours, one hepatic metastasis, four normal colonic mucosal samples and two antral and one fundic gastric mucosal samples from nine patients were analysed to determine whether gastrin mRNA was present. RNA was extracted from surgical specimens by ultracentrifugation on a CsCl cushion, purified using the guanidinium thiocyanate method, reverse-transcribed and amplified by polymerase chain reaction. Gastrin mRNA was detected in each colonic carcinoma sample (including the hepatic metastasis), while no such signal was observed in normal colon biopsies. Positive and negative controls (gastric antrum and fundus respectively) gave the expected results. In each of the positive samples, the chemiluminescent revelation of amplified products after Southern blotting corresponded to gastrin mRNA without the intron. These findings demonstrate the ability of primary and metastatic human colonic tumours to produce gastrin mRNA. Since malignant cell lines have been reported to produce gastrin peptide, and since gastrin receptors were present in some cases, our results support the idea that gastrin may be involved in an autocrine mechanism.

Detection of gastrin mRNA in paraffin-embedded samples of normal antral mucosae using polymerase chain reaction technique.

Gastrin, a peptide hormone produced by the G cells of the gastric antrum, plays a major role in the regulation of digestive mucosal growth. Although some light has been shed on the peptidic aspects of this hormone's mode of action and the co-regulatory activity in which it is involved along with the other gastrointestinal hormones, little is known at present about the modes of expression of its mRNA at the tissue level. A few attempts have been made so far to detect the transcript, mostly using molecular hybridization techniques. Here it was proposed to detect gastrin mRNA using a RT-PCR technique on a series of paraffin-embedded samples of normal human antrum processed with various fixatives commonly used in histology. The transcript was detectable in all the 7-microns sections of the samples treated with either formalin or Carnoy's solution, whereas Bouin's solution, which is also used as a fixative in histology, was found to have inhibitory effects on the method described here.

TT virus: a study of molecular epidemiology and transmission of genotypes 1, 2 and 3.

BACKGROUND: TT virus (TTV) is a recently discovered virus, which is not related to any other known virus infecting humans. OBJECTIVES: To investigate: (i) the world-wide distribution of the three major TTV genotypes; and (ii) the possible routes of viral transmission. STUDY DESIGN: (i) The phylogenetic distribution of 494 TTV isolates originating from 31 countries was analysed, using partial ORF1 sequences. (ii) Faeces samples (n=22) and saliva samples (n=72) from French individuals were tested for the presence of TTV DNA. (iii) Viral titres in paired serum and saliva samples were compared. RESULTS: (i) Genotypes 1, 2 and 3 were distributed world-wide, with a high proportion of type 1 in Asia (71%) and no type 3 identified in Africa to date. In the USA, 77% of isolates were grouped in four clusters only (genetic distances <10%). This was also the case of 76% of French isolates, 76% of Japanese isolates, and 89% of Hong Kong isolates. (ii) TTV DNA was detected in 18% of faeces samples and 68% of saliva samples tested. (iii) Viral titre in saliva samples was 100-1000 times higher than that of the corresponding serum. CONCLUSIONS: (i) The observed epidemiological distribution of TTV isolates is compatible with an ancient dissemination of viral ancestors belonging to the different genotypes and a slow genetic evolution in sedentary populations. (ii) Besides the possible transmission of TTV by the parental and oral-faecal routes, the high titre of TTV DNA observed in saliva raises the hypothesis of the viral transmission by saliva droplets. This route of transmission could explain the high degree of exposure to viral infection observed in the general population.

TT virus infection: prevalence of elevated viraemia and arguments for the immune control of viral load.

BACKGROUND: The most recent polymerase chain reaction (PCR) detection protocols for the TT virus (TTV) permit one to identify the presence of viral DNA in the serum of a majority of healthy individuals, in the absence of any particular risk factor. This is in contrast with previous epidemiological studies that reported a higher prevalence of TTV infection in populations such as haemodialysis patients (HD), haemophiliacs, intravenous drug users or diabetics. OBJECTIVES: To show that these discrepant results were due to the different sensitivity (number of viral copies detected) of the detection protocols used in initial and more recent epidemiological studies. STUDY DESIGN AND RESULTS: We designed a standardised primary PCR assay that detects only viraemia >5x10(3) to 5x10(4) copies/ml for genotypes 1, 2 and 3, and compared the results of this test with those of a nested PCR assay which is 100-fold more sensitive. Viraemia >5x10(3) to 5x10(4) copies/ml were statistically more frequent in HD patients (54.3%), diabetics (54.7%), and HIV-infected patients with CD4 cells <200/mm(3) (69%) than in blood donors (37%) or HIV-infected patients with CD4 cells >500/mm(3) (33%). CONCLUSIONS: These data suggest a possible relationship between the prevalence of elevated viral loads and the level of immunocompetence of the populations studied, and therefore that of an immune control of TTV viraemia. This corroborates previous findings showing that the stimulation of the immune system by an interferon treatment was able to clear TTV viraemia.

Comparison of systems performance for TT virus detection using PCR primer sets located in non-coding and coding regions of the viral genome.

BACKGROUND: the heterogeneity of the TT virus (TTV) DNA prevalence values reported from comparable human cohorts suggests that diagnostic PCR protocols still require to be optimized. OBJECTIVES: to design TTV PCR primer sets with low genotype restriction and to compare their performances with commonly used amplification systems. STUDY DESIGN: we compared full length TTV genomic sequences and identified conserved nucleotide patterns in the 5' and 3' non-coding regions of the viral genome. This permitted to design two new primer sets usable for the PCR amplification of the most divergent human isolates of TTV described to date. The performances of these amplification systems were compared with those of three other PCR systems earlier used for prevalence studies. RESULTS: the primer systems P5Bx and P3Bx exhibited higher PCR scores than the other systems tested; 14 to 34% improvement values were obtained, and divergent positive results of earlier described PCR systems were confirmed systematically by our new detection assays. CONCLUSIONS: an optimized detection of TT virus DNA is a pre-requisite for the accurate epidemiological survey of viral infection and for the realization of phylogenetic studies. Such PCR systems with low genotype restriction will be helpful in the future for a better knowledge of natural history of TT virus infection.

Strategies for the sequence determination of viral dsRNA genomes.

The genetic study of viruses having dsRNA genomes is hampered by the technical difficulty of complete sequence determination of dsRNA. Optimised methods are described here for sequencing dsRNAs, which meet three different situations: (1) genomes that can be obtained in fairly high amounts (>20 ng per separated segment); (2) genomes with limited amounts of RNA that can be detected by electrophoretic gel separation and staining; (3) genomes that cannot be detected by electrophoretic gel separation and staining. These methods include improved Single Primer Amplification Technique protocols, an adaptation of the SMART methodology, and a new method permitting the selective enzymatic removal of dsRNA segments. Strategies permitting adaptation of these protocols to the full-length determination of dsRNA viral genomes are described. Each of the protocols is described for sequence determination of a chosen dsRNA virus.

Evaluation of four PCR systems amplifying different genomic regions for molecular diagnosis of GB virus C infections.

Diagnosis of GB virus C (GBV-C) infection is based on RT-PCR methodology that detects genomic viral RNA. Four sets of primers located in different genomic regions were compared. These primers were used to amplify a reference panel of sera used by the French blood banks, including five positive sera, five negative sera and 10-fold serial dilutions of one positive serum. Three sets of primers located in the 5'UTR, NS3 and NS5a genomic regions gave comparable results with undiluted sera. When diluted sera were tested, the most sensitive protocol was that using a set of primers and a probe selected within the 5'UTR, together with a colorimetric detection based on DNA enzyme immunoassay.

Screening for HBV, HCV and HIV genomes in blood donations: shortcomings of pooling revealed by a multicentre study simulating real-time testing.

This study was undertaken in order to determine whether screening of viremic blood donations by testing of pooled donor samples could constitute a technically feasible transfusional safety measure. A pilot study of real-time simulation, on a day-to-day basis, of screening of three viral genomes (hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV)) was conducted by five French Blood Centers on plasma samples collected from blood donors and studied within undiluted samples and within sample pools of various sizes. This study was carried out within time conditions compatible with the release of platelets. For the detection of HCV and HIV genomes, the five laboratories achieved a sensitivity that decreased with the size of the sample pool. Four were successful in detecting all undiluted samples. In the 1/10 diluted samples, four failed to detect one HIV or HCV sample. In the 1/100 diluted samples, all laboratories failed to detect one or more HIV or HCV samples. For HBV genome, no participating laboratories detected all of the samples of the panel, even undiluted samples, and the sample pooling considerably affected sensitivity. The improvement and standardization of assays needs to be attained, and training of laboratories appears to be a step crucial for routine screening of viral genomes in blood donations.

Lessons from a multicentre study of the detectability of viral genomes based on a two-round quality control of GB virus C (GBV-C)/hepatitis G virus (HGV) polymerase chain reaction assay.

The aim of this study was to determine whether multicentre quality controls for the detectability of viral genomes could contribute to the improvement of diagnostic performance in the participating laboratories. The study was carried out during two successive rounds, during which 18 laboratories specialized in nucleic acid testing analyzed, through a polymerase chain reaction (PCR) assay, a common panel of GB virus C (GBV-C)/hepatitis G virus (HGV) RNA-positive and -negative samples. During the first round, the laboratories used either an 'in-house' PCR procedure or a partly standardized commercial test. After decoding the results of the first round, the procedures of the participating laboratories were compared in order to establish a consensus procedure deduced from those of the laboratories which provided the best results. During the second round, each participating laboratory could use the resulting consensus procedure, or its own procedure, or both. The results of this quality control study indicated that, whatever method used, even specialized and trained laboratories may give false-negative or false-positive results. The commercial assay did not guarantee a systematic high quality level of results. The striking heterogeneity of results observed among laboratories using the same commercial assay confirm that molecular biology methods need skilled technicians. The results of this quality control study suggest that full standardization of viral genome detection, including all steps of the procedure, is necessary and that the laboratories performing PCR should participate in repeated quality control studies, whatever technique is being used.

The human gastrin/cholecystokinin receptors: type B and type C expression in colonic tumors and cell lines.

The CCK-type B receptors are recognized by gastrin, which is known to be possibly involved in the development of gastro-intestinal cancers; alternate splicing of exon 4 of the human CCK-B receptor gene gives 2 different mRNA isoforms, the exact significance of which still remains to be elucidated. The recently described CCK-type C receptors recognize gastrin but do not discriminate between mature and immature forms of the hormone. A series of healthy and tumoral colon samples, the associated hepatic metastases and four colonic cell lines were examined for gene expression of the 2 isoforms of the CCK-B receptor and the CCK-C receptor using reverse transcription-polymerase chain reaction. Gastrin mRNA expression was also investigated. The short isoform of the CCK-B was detected in 80% of the normal colon tissues, 76.5% of the colon tumors, 100% of the metastasis samples and 75% of the colonic cell lines; whereas the long isoform, which is presumably more strongly activated by gastrin, was expressed in 50% of the normal colon samples, 23% of the colon tumors, 43% of the hepatic metastases and 1 cell line (Sk-Co15). However, although CCK-C transcript was detected in 100% of the tumors tested and gastrin mRNA in 86.5%, only 16.5% also expressed the long isoform of the CCK-B receptor. The gastrin/CCK-B receptor might therefore be involved in an hypothetic autocrine proliferative loop only in some colonic tumors, and the receptor mainly involved in this loop may well be the CCK-C receptor, since its mRNA is expressed as often as gastrin mRNA in tumors and cell lines.

Is hepatitis C virus-RNA detection by nested polymerase chain reaction clinically relevant in hemodialysis patients?

We have prospectively studied in hemodialysis (HD) patients the evolution of hepatitis C virus (HCV) viremia and the putative relationships between the viremia and the biological markers of liver disease. For each of 22 HD patients having detectable antibodies to HCV (anti-HCV+), we looked four times for serum HCV-RNA by nested PCR (N-PCR), in April and November 1992, November 1993 and May 1994. We checked the transaminases (Trans) and the gamma glutamyl transpeptidase (gamma(GT)) levels on the same day as blood tests for the N-PCR. Abnormal Trans or gamma(GT)++ values were considered if they exceeded the upper limit of the normal level for our laboratory. Fifteen patients (68%) were intermittently N-PCR positive (N-PCR+): 3 patients were N-PCR+ at three determinations, 7 were N-PCR+ at two determinations and 5 only one time. Two patients (9%) were always N-PCR+ and five (23%) always negative. No correlation between an abnormal value of either Trans or gamma(GT) and viremia was evidenced at successive determinations. In conclusion, the majority (68%) of the anti-HCV+ patients had intermittent HCV N-PCR+. Among the anti-HCV+ patients, 77% were viremic. Since HCV viremia is often transitory and since there is no correlation between N-PCR positivity and the increase in Trans or gamma(GT) activities, HCV-RNA detection by N-PCR is probably not clinically relevant in anti-HCV+ HD patients.

Immunohistochemical detection of C-100 hepatitis C virus antigen in formaldehyde-fixed paraffin-embedded liver tissue. Correlation with serum, tissue and in situ RT-PCR results.

We localized HCV C-100 protein in liver biopsies of 15 patients with chronic hepatitis C using immunohistochemistry. The results were compared to serum, tissue extract analysis of HCV RNA and in situ RT-PCR described in a previous study. HCV was detected in 80% of the sera tested, in 40% of the tissue extracts and in 80% and 60% of the tissue sections tested by immunohistochemistry and in situ RT-PCR respectively. Compared to the serum positive cases, 83% and 67% of the cases were respectively positive with immunohistochemistry and in situ RT-PCR and 41% were positive with tissue extract detection. Compared to the tissue extract positive cases, 25% and 50% of the cases were respectively positive with immunohistochemistry and in situ RT-PCR. Finally, 75% of the cases positive by immunohistochemistry were also positive by in situ RT-PCR. These results underline the complementarity of the different methods for the precise diagnosis of hepatitis C.

Analysis of ELISA hepatitis C virus-positive blood donors population by polymerase chain reaction and recombinant immunoblot assay (RIBA). Comparison of second and third generation RIBA.

A new RIBA-3 (Chiron-Ortho Diagnostic System) was performed for discriminating uninterpretable results of RIBA-2. Recognition of antibodies to hepatitis C virus by RIBA-2 and RIBA-3 was compared among 95 ELISA-2 (second generation ELISA) positive blood donors and correlated with alanine-aminotransferase (ALAT) levels and viremia, using polymerase chain reaction (PCR). These studies led to three important conclusions. First, all ELISA-2-positive, RIBA-2-positive and ALAT-positive samples were found viremic compared with 73% of ELISA-2-positive, RIBA-2-positive and ALAT-negative samples. Then, the comparison of the different RIBAs allowed to conclude that RIBA-3 was more sensitive but less specific than RIBA-2. RIBA-3 was interesting to discriminate undetermined RIBA-2, owing to an improved specificity of C100-3 antigen. In fact, most of the C100-3 positive, RIBA-2 undetermined samples became RIBA-3 negative whereas C22-3 positive, RIBA-2 undetermined samples became RIBA-3 positive or undetermined. Finally, a significant correlation was found between the presence of antibodies against C33-c antigen and viremia.

The rediscovery of smallpox.

Smallpox is an infectious disease that is unique to humans, caused by a poxvirus. It is one of the most lethal of diseases; the virus variant Variola major has a mortality rate of 30%. People surviving this disease have life-long consequences, but also assured immunity. Historically, smallpox was recognized early in human populations. This led to prevention attempts--variolation, quarantine, and the isolation of infected subjects--until Jenner's discovery of the first steps of vaccination in the 18th century. After vaccination campaigns throughout the 19th and 20th centuries, the WHO declared the eradication of smallpox in 1980. With the development of microscopy techniques, the structural characterization of the virus began in the early 20th century. In 1990, the genomes of different smallpox viruses were determined; viruses could be classified in order to investigate their origin, diffusion, and evolution. To study the evolution and possible re-emergence of this viral pathogen, however, researchers can only use viral genomes collected during the 20th century. Cases of smallpox in ancient periods are sometimes well documented, so palaeomicrobiology and, more precisely, the study of ancient smallpox viral strains could be an exceptional opportunity. The analysis of poxvirus fragmented genomes could give new insights into the genetic evolution of the poxvirus. Recently, small fragments of the poxvirus genome were detected. With the genetic information obtained, a new phylogeny of smallpox virus was described. The interest in conducting studies on ancient strains is discussed, in order to explore the natural history of this disease.

Identification of a third member of the Anellovirus genus ("small anellovirus") in French blood donors.

We demonstrate for the first time that a putative third member of the genus Anellovirus (TTV/TTMV) is present in the blood of healthy persons (20% prevalence), and also in their PBMNC and saliva samples.