Stefano Dettori

HCV genetic variability: from quasispecies evolution to genotype classification

HCV is a ssRNA virus belonging to the Flaviviruses and is found worldwide worldwide in humans. Following primary infection, persistent infection develops in more than 85% of cases, which in up to 30% of cases, may progress to liver disease, cirrhosis and hepatocellular carcinoma. The virus presents a high degree of genetic variability owing to the combination of a lack of proofreading by the RNA-dependent RNA polymerase and a high level of viral replication. This genetic variability allows the classification of genotypes, subtypes, isolates and quasispecies to which epidemiological and pathogenetic significance may be associated. The features and biological implications of HCV variability and of quasispecies dynamics in infection transmission, mechanisms of chronicity and resistance to antiviral therapy are discussed.

Molecular heterogeneity and new subtypes of HCV genotype 4

The subtype distribution of HCV genotype 4 was studied in two different African countries, Egypt and Tanzania. The HCV isolates were obtained from epidemiological studies involving, respectively, 135 hepatopatic patients and 1043 pregnant women and outpatients. Sequence comparison and phylogenetic analysis of the NS5b genome region (nt 8327-8499) were performed. Fourteen out of 18 isolates from Egypt, but only 3 out of 6 isolates from Tanzania clustered in the same branch of subtype 4a. Three new proposed subtypes have been identified. The first includes 1 isolate from Egypt (EGY15); the second, 2 isolates from Egypt (EGY193 and EGY44) and 2 isolates from Tanzania (D776, D61); and the third, 1 isolate from Egypt (EGY47) and 1 isolate from Tanzania (D70). These isolates cluster in branches different from any other, corresponding to a known subtype of genotype 4. In conclusion, remarkable genetic heterogeneity has been found among genotype 4 isolates simultaneously circulating in a restricted area. This was particularly observed in the study performed in Tanzania. Potential concern about the sensitivity of diagnostic assays and possible implications in the development of future vaccines have been stressed.

Molecular characterisation of HCV genotype 4 isolates circulating in Italy.

The characteristics of genotype 4 subtype variability of HCV isolates circulating in Italy were studied. The viral isolates were identified from 736 HCV‐RNA positive sera originated from seroepidemiological studies undertaken in 4 different regions of North, South Italy and Sardinia. 24 out of 28 genotype 4 isolates (86%) were classified by phylogenetic analysis of E1 genome region (915–1128) as belonging to subtype 4d (Neighbour Joining Method). Three isolates classified as subtype 4a were detected in haemophilic patients, possibly related to infections from blood products. One isolate classified as a new subtype derived from an Eritrean patient subjected to haemodialysis. Very high genome homogeneity (mean 4.3%) was shown by genetic comparisons (DNA dist programs Phylip Package) for all the 4d isolates relative to the studies performed in Veneto, Calabria and Sardinia and originated from subjects from the general population and outpatients (19 subtype 4d isolates out of 24). In the 3 studies different prevalence rates of HCV genotype 4 (3.1%, 1.3%, 14% respectively) were found. In contrast a considerable degree of heterogeneity, both intragroup and with the other groups (mean 8.2% and 8.7%, respectively) was observed among subtype 4d isolates identified in the patients of a haemodialysis centre in Apulia region. In conclusion the subtype 4d of genotype 4 was highly prevalent and endemic in Italy. An elevated level of viral heterogeneity was observed in one study carried out in a region of Southern Italy. This can be related to a longer period of past endemicity of this genotype and to a high level of exposure to reinfections in particular categories of patients such as haemodialysis patients. J. Med. Virol. 62:84–90, 2000.

Identification of low HBV-DNA levels by nucleic acid amplification test (NAT) in blood donors

OBJECTIVE To evaluate the presence of HBV-DNA in 22,765 consecutive blood donors, who donated blood in the period from January 2006 to August 2007 at a transfusion centre in Lazio, a region in central Italy with low HBV endemicity. METHODS Each donation was individually tested using immunoenzymatic assays and nucleic acid amplification technologies (NAT). Samples that were reactive to generic NAT, Procleix Ultrio Assay were tested for HBV-DNA, HCV-RNA and HIV1-RNA by Discriminatory Procleix Ultrio NAT Assay. In samples that were reactive to generic NAT and negative for HBsAg, HCV-RNA and HIV1-RNA, HBV-DNA was further tested using Cobas TaqMan and an in-house nested PCR following an ultracentrifugation step. Sequence analysis confirmed HBV-DNA positivity. RESULTS Generic NAT identified 31 (0.13%) reactive sera. HBV-DNA discriminatory NAT identified 15 positive sera; HBsAg was positive in 12 sera. Of the 5 generic NAT-reactive/discriminatory NAT-negative/HBsAg-negative sera and of the 3 HBsAg-negative/HBV-DNA discriminatory NAT-positive sera, 7 were positive to Cobas TaqMan or the in-house PCR after ultracentrifugation. The overall HBV-DNA positivity was 0.083% [19 of 22,765 donors: 12 HBsAg-positive (HBV-DNA range 10(2)-10(4) IU/mL), 7 HBsAg-negative/anti-HBc positive (HBV-DNA< 6 IU/mL)]. CONCLUSIONS For blood transfusion safety, the significance of the finding of very low HBV-DNA levels should be further investigated. Our data indicate that in areas with a low HBV endemicity, single NAT assays may not always identify blood donations with very low HBV-DNA levels.

Genotyping HCV isolates from Italy by type-specific PCR assay in the core region

A revision of the polymerase chain reaction (PCR) core procedure was performed for genotyping hepatitis C virus (HCV) in 139 patients from Italy. This procedure, developed prior to the identification of new genotypes, may be inadequate in several geographical areas. We proposed a new typing mixture in which primers for types 2c and 4, that are reported to be circulating in Italy, were added and a primer for type 2b was substituted. Using the modified procedure, 139 HCV-positive patients were analysed. The HCV genotype was identified in 96.4% of the cases. We observed double infections and unclassified genotypes in 5 (3.6%) and 5 (3.6%) patients, respectively. The classification of isolates into genotypes and subtypes 2b, 2c and 4 was confirmed by sequence analysis. Furthermore, the efficiency and accuracy of the modified core procedure were evaluated by parallel testing of 107 out of 139 samples using the line probe assay, and demonstrated a 98.9% degree of concordance. The results demonstrated the specificity of the selected primers for type 2c, 2b and 4 and confirmed the circulation of types 2c and 4 in Italy. In conclusion, the proposed modified PCR procedure is the only primer-specific PCR genotyping method available for identification of the 2c and 4 genotypes reported to be circulated in Italy and other European countries.

Diagnosis of HEV infection by serological and real-time PCR assays: a study on acute non-A-C hepatitis collected from 2004 to 2010 in Italy.

BackgroundThe impact of hepatitis E in developed countries, like Italy, still requires a clear definition. In the present study, we evaluated HEV infection in patients with acute non-A-C hepatitis by an approach comparing data from Real-time PCR and serological assays.MethodsIn a first analysis, sera from 52 patients hospitalized with a diagnosis of acute viral non-A-C hepatitis in Italy were tested by in-house Real-Time PCR assay for identification of Hepatitis E Virus (HEV) RNA and by anti-HEV IgM and IgG assays. In a subsequent analysis, selected samples were evaluated by additional IgM tests to confirm diagnosis.ResultsAmong the 52 samples, 21 showed positive results for all three markers (IgM, IgG and HEV RNA). One patient showed HEV RNA as single marker. Uncertain results were found in 8 samples while the remaining 22 were negative for all markers. Further analysis of the 8 undefined samples by additional IgM tests confirmed HEV infection in 1 patient. Overall, acute HEV infections were reliably identified in 23 (44.2%) out of 52 patients.ConclusionsIn the present paper, we performed a study evaluating HEV infection in 52 sporadic non-A-C acute hepatitis cases. All samples were collected from 2004 to 2010 in Italy. By a diagnostic strategy based on genomic and serological assays we identified HEV infections in 23 out of 52 patients (44.2%), a percentage higher than previous estimates. Thus, the actual impact of HEV infections in Italy needs to be further evaluated on a national scale by a diagnostic strategy based on multiple and last generation assays.

Molecular evolution of HCV genotype 2c persistent infection following mother-to-infant transmission.

Summary. The molecular evolution of HCV 2c in a case of vertical transmission was studied by comparing the virus quasispecies in the sera from the mother and from the child in a two-year follow-up. The positivity of HCV-RNA since the delivery accounted for an in-utero infection. The Core-E1 genome region (nt 928-1225) was amplified by polymerase chain reaction (PCR) from serum samples collected at delivery and at 3, 9, 18 and 24 months after birth. The RIBA pattern was characterised by isolated anti-c22 positivity in the serum from mother and in sera from the child during the first 9 months. Additional presence of anti-c33 was observed afterwards. Genetic relatedness among isolates and with a mother minor variant serum (Mo1.13) was found (mean variability ranged between 0.79% and 1.20%). From phylogenetic analysis this variant was identified as the origin of one of the two main lineages that included all isolates from child sera at 9, 18 and 24 months. The variability analysis has shown that high viral heterogeneity is present in the child serum collected at birth (3.16%). In this phase the dn/ds index (1.26%) indicates the presence of strong selective pressures. The development of child specific immune response at 9th month was concurrent with the disappearance of two mutants at positions 11 and 104 of E1.This rare case of inutero mother-to-infant transmission can be considered as a model to elucidate the HCV quasispecies diversification during the first stage of infection.

Evaluation of rapid tests for diagnosis of acute hepatitis E

BACKGROUND Hepatitis E virus diagnosis still presents difficulties due to discordant results among diagnostic tests. OBJECTIVES The aim of this study was to evaluate the performance of two rapid tests for detection of anti-HEV IgM antibodies. STUDY DESIGN The rapid tests were compared with three commercial anti-HEV ELISA assays and one Real-Time PCR assay on 59 sera from patients with acute viral non-AC hepatitis. RESULTS The presence of anti-HEV IgM antibodies was evaluated by two rapid tests (Wantai and Assure) on 25 HEV RNA positive samples. Anti-HEV IgM antibodies were detected in 24/25 and 23/25 samples respectively. The sensitivity and specificity of Wantai and Assure Rapid tests were evaluated using the 25 HEV RNA positive samples and 50 HEV RNA negative samples (including sera from acute-phase HAV and HBV infections and blood donors). Overall, the sensitivity of Wantai Rapid and Assure Rapid tests was 96.1% and 92.6% respectively; the specificity of the 2 tests was 100%. CONCLUSION Our data suggest the potential use of anti-HEV IgM rapid assays as a first line test in primary health care settings, particularly useful for patients with chronic liver disease or pregnant women who urgently need an antiviral treatment.

GB Virus C/Hepatitis G Virus Exposure in Italian Pediatric and Young Adult Thalassemic Patients

AbstractBackground: The aim was to estimate the prevalence and the persistence of GB virus C/hepatitis G virus (GBV-C/HGV) exposure markers in a group at high risk for transfusion-transmitted agents. Patients and Methods: Serum samples from 37 thalassemic patients were screened for GBV-C/HGV RNA by reverse transcription PCR (RT-PCR) and for antibodies to the envelope protein E2 of GBV-C/HGV (anti-E2). Results and Discussion: GBV-C/HGV RNA and anti-E2 were detected in 13 (35%) and 12 (32%) sera, repsectively. Contemporary presence of both markers was found in one patient. GBV-C/HGV exposure was found in 24 patients (64.8%). Mean levels of liver enzymes were similar in both exposed and unexposed GBV-C/HGV groups. 33 out of 35 patients showed no change in GBV-C/HGV RNA and anti-E2 status in sera taken 6 months apart. The rate of persistent infection was 92.3% and the anti-E2 seroconversion rate was 23% for sera taken at least 6 months apart. The temporal overlap between anti-E2 seroconversion and loss of detectable GBV-C/HGV RNA may last more than 6 months.

Nucleic acid testing (NAT) for HCV RNA in Italian transfusion centres: An external quality assessment

BACKGROUND We conducted an external quality assessment of the results obtained in Italian transfusion centre laboratories employing nucleic acid testing (NAT) for detection of HCV RNA in donated blood. STUDY DESIGN Of 110 transfusions centres in Italy, 101 voluntarily participated. Each laboratory received seven separate shipments of samples for HCV RNA testing by NAT. Each shipment contained 8 plasma samples for a total of 23 negative and 33 positive samples with viral loads ranging from 25 to 1000 IU/mL. RESULTS Of the 2080 HCV RNA-negative samples, 14 (0.7%) were reported as positive. The highest percent of false-negative results (6.9%) was found on samples from the first shipment with viral loads from 75 to 100 IU/mL. In subsequent shipments, the highest false-negative percentage ranged from 0.6% for samples with viral loads of 170-1000 IU/mL to 3.4% for samples with viral loads of 35-50 IU/mL. A false-negative rate of 4.9% occurred in samples in the sixth shipment with the lowest viral load (25IU/mL). Five (4.9%) centres were identified as having laboratories with low-performance. There were no significant differences among genotypes 1b, 2c and 3a with respect to percent of false-negative results reported. CONCLUSIONS Overall, the accuracy of NAT observed in this study of Italian transfusion centre laboratories was excellent for all HCV genotypes tested, even for samples with low HCV RNA titres.