Evidence for two phylogenetic clusters within hepatitis C virus (HCV) genotype 2 inferred from analysis of complete coding sequences of 15 HCV strains.

The aim of this study was to gain further insight into the evolution and classification of hepatitis C virus (HCV) by assessing the subtype distribution of 273 genotype 2 strains isolated from French blood donors from 1990 to 2010 and by determining complete coding sequences in subtype 2 strains. These classified into 7 of the established subtypes and into 15 additional lineages not yet assigned to a known subtype. Phylogenetic tree construction showed two well-supported clusters. Cluster 1 included most subtype 2 strains while cluster 2 included subtype 2l and one unassigned subtype 2. Full genome sequencing was performed on 15 genotype 2 strains belonging to both clusters, that is, one subtype 2b, two subtype 2c, three subtype 2i, two subtype 2j, one subtype 2k, two subtype 2l, and four unassigned strains. Genomes included a 9042- to 9108-nucleic acid open reading frame coding for a polyprotein comprising 3014-3036 amino acids. Mean nucleotide distances between subtypes belonging to the first cluster was 20.2 ± 1.4% while the mean distance between the two clusters was 25.9 ± 0.3%. Analysis indicated that the bifurcation between subtype 2l and other subtype 2 strains occurred early in the evolutionary process. Subtype 2l retained a genomic feature characteristic of non-genotype 2, that is, absence of the 60-nucleotide insertion in the NS5A region. This finding suggests that appearance and fixation of this insertion occurred late in the evolutionary history of HCV type 2 and that its absence is an ancestral feature of HCV.

Molecular epidemiology of KI and WU polyomaviruses in healthy blood donors, south-eastern France.

The epidemiology of human polyomaviruses KI (KIPyV) and WU (WUPyV) in healthy populations is described poorly in the literature. The frequency of KIPyV and WUPyV viraemia was evaluated in a cohort of blood donors from south-eastern France. Plasma samples (n=640) were investigated for the presence of KIPyV/WUPyV DNA using a conserved real-time PCR detection system (VP2 gene). Three plasma samples (3/640; ∼0.5%) exhibited a positive fluorescence signal, with a low viral load (<500 copies/ml plasma); no additional amplicons were identifiable by agarose gel analysis. Sequencing highlighted the KIPyV origin of the three amplified sequences and the occurrence of point mutations. The sustained detection of KIPyV DNA in two serial samples (9 months) was in favor of a possible persistence of the virus in blood of healthy individuals. Further studies will be needed in order to explore both the prevalence and potential clinical impact of KIPyV/WUPyV on infected hosts.

Toscana virus inhibits the interferon beta response in cell cultures.

Toscana virus (TOSV) is an emerging pathogen in the Mediterranean basin where it causes summertime outbreaks of aseptic meningitis and meningoencephalitis. Many aspects of TOSV biology remain unknown including the possible implication of an amplifying mammalian host besides its vector. The three experiments described here were designed to assess the relationship between TOSV and type-I interferon (IFN) response. The main findings were as follows. First, TOSV growth in Vero cells is sensitive to an antiviral state induced by low-dose addition of exogenous IFN beta (IFN-ß) (10IU/ml). Second, no IFN-ß mRNA or IFN-ß was detectable after infection of HeLa and 293T cells by TOSV. Finally, TOSV inhibits IFN-ß production induced by Sendaï virus, a well known inducer of IFN-ß production. In addition to showing that TOSV can inhibit the IFN-ß response, these findings suggest that anti-IFN capability is maintained by regular contact with that of a mammalian host.

Evolution of Anelloviridae strains distribution in serial blood and biopsy samples from a renal transplant patient.

A few studies investigated the natural history of viruses belonging to the family Anelloviridae in transplant patient. The case of a 64-year-old kidney transplant recipient is described. Molecular analysis of serial blood samples collected before and after transplant was performed during a period of 510 days. Two kidney biopsies were also analyzed. All blood samples tested positive for Anelloviridae DNA, with the identification of sequences belonging to the three taxonomic genera identified in humans. Sequences distribution during the follow-up was multimodal. A sequence nearly identical to one present in the blood before transplant was further characterized in one biopsy sample.

Parvovirus 4 in French in-patients: a study of hemodialysis and lung transplant cohorts.

The epidemiology and the clinical implication of human parvovirus 4 (PARV4) in human populations is still under evaluation. The distribution of PARV4 DNA was determined in cohorts of French hemodialysis and lung transplant patients. Plasma samples (n=289) were tested for PARV4 by real-time PCR assay (ORF2), and amplification products selected at random were sequenced. Analysis of available serological and biological markers was also undertaken. Fifty-seven samples out of 185 (30.8%) were positive for PARV4 DNA in the cohort of hemodialysis patients. A higher prevalence of the virus was identified in patients with markers of HBV infection. PARV4 was also identified in 14 out of 104 samples (13.5%) from lung transplant recipients, with no clear-cut association with available clinical markers. Point mutations located on the zone of real-time detection were identified for some amplification products. This study describes the detection of PARV4 in the blood of hemodialysis and lung transplanted patients with significant difference in prevalence in these two cohorts. Further studies will be needed in order to understand better both the potential implication in host health and the natural history of this virus.

Identification of viral DNA (Anelloviridae) in a 200-year-old dental pulp sample (Napoleon's Great Army, Kaliningrad, 1812).

Ancient human remains are potential sources of biological information including traces of past infections, since previous studies have demonstrated the effective detection of several bacterial agents or host-integrated viruses in old biological remnants like tissues or teeth. Studies of skeletal dental pulp samples are of particular interest since this location is potentially exposed to bloodborne agents during life through its vascularization, and could be considered as well preserved from environment after death of the host. DNA viruses belonging to the family Anelloviridae are highly present in human populations where they harbor an extreme genetic diversity but a yet undefined implication in hosts' health. We hypothesized that anelloviruses would be detected in ancient remains and that they may also serve as tracer viruses for the study of other viral agents. We analyzed 200-year-old dental pulp samples from remains of soldiers of Napoleon's Great Army during the Russian Retreat. Successful detection of Anelloviridae DNA by PCR was obtained for 1/21 ancient samples tested. The sequence identified showed 23% nucleotide divergence with the closest group of modern isolates (genus Gammatorquevirus), and was confirmed as phylogenetically distinct from those identified in saliva samples from the two investigators in charge of the study (genera Alphatorquevirus and Betatorquevirus). PCR directed toward the human beta globin gene was also performed. Negative controls were negative. Our results demonstrate that an ubiquitary, non-integrated, DNA virus is detectable from ancient biological material, with potential developments in terms of evolution studies or subsequent molecular investigations involving further viral agents.

Prevalence of IgG antibodies against West Nile virus in blood donors during the 2003 outbreak in Tunisia.

This study aimed to evaluate the prevalence of anti-West Nile virus (WNV) IgG among two populations of Tunisian blood donors living in areas where human outbreaks of WNV have occurred. Cohorts A (Monastir) and B (Mahdia) included 742 and 102 blood donors respectively. Sera were tested by IgG ELISA test and results were confirmed by PRNT test. WNV neutralizing antibodies were detected in 32 (4.3%) and in 14 (13.7%) sera in cohorts A and B respectively. The prevalence of anti-WNV IgG was significantly higher in cohort B than in cohort A (P<0.001) and was significantly lower in females than in males (P<0.001).

Analysis of hepatitis C virus strains circulating in Republic of the Congo.

The aim of this study was to assess the seroprevalence, viremia, genotype distribution, and demographic history of hepatitis C virus (HCV) in the Republic of the Congo. Testing was carried out on sera samples collected in 2005 from 807 Bantus belonging to the Kongo, Teke, and Ngala subgroups and 80 Pygmies. Positive HCV serology was found in 50 (5.6%) individuals including 31 (60%) who were viremic. Seroprevalence increased with age with a cutoff at 50 years: 2.8% <50 versus 12% >50. Twenty-one strains belonged to four described subtypes, that is, 4c in eight cases, 4h in two, 4k in three, and 4r in eight. Ten strains could not be assigned to any known subtype and may represent six new variants, that is, subtype 4 in five cases and subtype 2 in one. Evolutionary analysis of subtype 4c and 4r sequences indicated a period of enhanced transmission in the mid-twentieth century probably due to iatrogenic causes. This study underlines the high genetic diversity of strains in the Republic of the Congo with nine subtypes 4 and one subtype 2.

Sensitivity of two hepatitis B virus, hepatitis C virus (HCV), and human immunodeficiency virus (HIV) nucleic acid test systems relative to hepatitis B surface antigen, anti-HCV, anti-HIV, and p24/anti-HIV combination assays in seroconversion panels.

BACKGROUND: Accurate determination of the infectious window period (IWP) that remains with individual-donation (ID) or minipool (MP) NAT compared to those with serology assays is essential for residual risk estimations. STUDY DESIGN AND METHODS: The relative sensitivity of the Procleix Tigris system (Gen-Probe/Chiron) used in ID-NAT format and cobas s 201 (Roche Molecular Systems) applied in 1:6 diluted samples to mimic six-minipool (MP6) nucleic acid test (NAT) was assessed by quadruplicate testing of five seroconversion panels per marker. A mathematical analysis based on the log-linear increase of viremia in the ramp-up phase, as established with bDNA 3.0 assays enabled estimation of the IWP for human immunodeficiency virus (HIV) and hepatitis B virus (HBV) assays. RESULTS: The mean IWPs were Tigris HIV RNA 5.5 days, s 201 (1:6) HIV RNA 7.4 days, GenScreen Plus p24/anti-HIV 17.8 days, PRISM anti-HIV 19.0 days, Tigris HBV DNA 20.6 days, s 201 (1:6) HBV DNA 22.6 days, Bio-Rad hepatitis B surface antigen (HBsAg) 37.8 days, and PRISM HBsAg 35.5 days. At estimated 50 percent NAT seroconversion rates, s 201 (1:6) and Tigris showed mean window-period reduction times (WPRTs) of 30.5 to 35.5 days to hepatitis C virus antibody (anti-HCV) assays, 10.4 to 13.5 days to anti-HIV, or combination p24/anti-HIV assays and 12.8 to 17.2 days to HBsAg assays. CONCLUSIONS: Tigris ID-NAT detected HIV RNA 2 days earlier than s 201 MP6-NAT, but the difference in sensitivity between the two NAT systems was not significant in HBV seroconversion panels. Insufficient seroconversion samples were available for reliable modeling of WPRT in early HCV infection, but 1.4 to 2.0 days could be predicted by translating analytical sensitivity data. Both multiplex NAT systems demonstrate significant WPRTs compared to (combined) antigen and antibody assays.

Comparison of the analytical and operational performance of two viral nucleic acid test blood screening systems: Procleix Tigris and cobas s 201.

BACKGROUND: The operational and analytical performance of two automated triplex hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) nucleic acid test (NAT) systems were compared in four screening laboratories of the French Blood Service. STUDY DESIGN AND METHODS: Two laboratories evaluated the Procleix Tigris system (Chiron/Gen-Probe) in individual donation (ID) format and two sites used the cobas s 201 system (Roche Molecular Systems) on minipools (MPs) of six donations. The analytical sensitivity, the specificity, and operational performance were compared. RESULTS: The ID to MP-NAT relative sensitivity factors in standard dilution panels of different genotypes varied between 8.7 and 21.9 for HCV RNA, 6.7 and 14.8 for HIV RNA, and 0.71 and 11.6 for HBV DNA. Tigris was 800-fold more sensitive than cobas s 201 (1:6) for a HIV group O sample, but did not detect the HIV-2 sample picked up by cobas s 201 with equal sensitivity as the HIV-1 group M samples. The specificity of both NAT systems after initial screening of 10,520 donations with Tigris and 1444 test pools on s 201 was 99.9 percent for both systems, but reached 100 percent after the repeat and pool resolution test algorithms. A higher throughput of the pool test protocol on cobas s 201 became apparent when the daily workload was more than 400 donations. CONCLUSIONS: Tigris ID-NAT format was significantly more sensitive than cobas s 201 MP-NAT in detecting HCV RNA and HIV RNA dilution panels, but despite the 1:6 dilution factor in s 201 the difference in sensitivity was not significant for some of the HBV genotype panels. Both NAT systems demonstrated acceptable operational performance, but for routine use further improvement in system reliability is desirable.

Molecular characterization of genotype 2 and 4 hepatitis C virus isolates in French blood donors.

The subtype distribution of 142 genotype 2 and 97 genotype 4 hepatitis C virus (HCV) isolates from the sera of 1,319 volunteer blood donors in France was determined by gene sequencing and by phylogenetic analysis of the NS5B region and E1 envelope. Findings underlined a wide range of subtypes in both genotypes, that is, 20 in HCV-2 and 11 in HCV-4. Eighteen of these 31 subtypes had not been defined previously. Some subtypes, that is, 2a, 2b, 2c, 2i, 2k, 4a, and 4d, showed numerous strains while subtypes in donors from West Africa or Central Africa showed an endemic profile with only a few strains. A Bayesian coalescence approach was used to estimate the demographic history of each HCV subtype. The estimated mean dates of the most recent common ancestors (MRCA) were 1,889 (confidence interval (CI), 1,842-1,930) for HCV-2a, 1,886 (CI, 1,843-1,921) for HCV-2b, 1,791 (CI, 1,699-1,848) for HCV-2c, 1,846 (CI, 1,803-1,878) for HCV-2i, 1,911 (CI, 1,879-1,937) for HCV-4a, and 1,957 (CI, 1,943-1,967) for HCV-4d. The period of spread for subtype 2b, 2c, and 2i was between 1900 and 1960 whereas rapid exponential spread for subtype 2a, 4a, and 4d occurred in the 1960s. The inferred histories of population growth indicated that transmission rates differed according to HCV subtype. These results may help to predict the future burden of HCV in France.