Genetic diversity and evolution of hepatitis C virus in the Latin American region

Variation in Hepatitis C Virus Subtype Distribution during 20 Years in Venezuela

OBJECTIVE

Hepatitis C virus (HCV) infection is a public health problem and a major cause of chronic hepatitis. This virus exhibits a great genetic variability, with 8 genotypes and numerous subtypes. The aim of this study was to evaluate the fluctuations of HCV subtypes during 2 decades in Venezuela.

METHODS

HCV genotypes were determined by direct sequencing of the 5'-noncoding region in 392 isolates circulating in patients attended during the years 2014-2015. HCV subtype assignment was confirmed in a subset of samples (n = 24) by partial sequencing of the NS5B region. The genotype distribution was compared with the one observed in a previous study of patients followed up during the years 1994-1996 and 2005-2006.

RESULTS

Some variation was observed in the HCV genotype distribution over these 20 years. HCV genotype 1b prevalence was reduced significantly from 1994-1995 to 2004-2005, as previously described, and then remained constant. During the last 10 years, a significant decrease of HCV subtype 2b (36/237 in 2005-2006 vs. 24/392 in 2014-2015, p < 0.001) was observed. Patients infected with HCV G2acj were significantly older than the ones infected with G1 (53 vs. 47 years, p = 0.004), and male sex was significantly more prevalent among G3a-infected patients compared to the other ones (71 vs. 47%, p = 0.047).

CONCLUSIONS

Fluctuations in HCV subtype distribution have been observed over 2 decades in Venezuela. Different major mode of transmission and susceptibility to the available HCV treatment during each period might be playing a role in the observed fluctuations in HCV subtype distribution.

The First Complete Genome Sequences of Hepatitis C Virus Subtype 2b from Latin America: Molecular Characterization and Phylogeographic Analysis

The hepatitis C virus (HCV) has remarkable genetic diversity and exists as eight genotypes (1 to 8) with distinct geographic distributions. No complete genome sequence of HCV subtype 2b (HCV-2b) is available from Latin American countries, and the factors underlying its emergence and spread within the continent remain unknown. The present study was conducted to determine the first full-length genomic sequences of HCV-2b isolates from Latin America and reconstruct the spatial and temporal diversification of this subtype in Brazil. Nearly complete HCV-2b genomes isolated from two Brazilian patients were obtained by direct sequencing of long PCR fragments and analyzed together with reference sequences using the Bayesian coalescent and phylogeographic framework approaches. The two HCV-2b genomes were 9318 nucleotides (nt) in length (nt 37-9354). Interestingly, the long RT-PCR technique was able to detect co-circulation of viral variants that contained an in-frame deletion of 2022 nt encompassing E1, E2, and p7 proteins. Spatiotemporal reconstruction analyses suggest that HCV-2b had a single introduction in Brazil during the early 1980s, displaying an epidemic history characterized by a low and virtually constant population size until the present time. These results coincide with epidemiological data in Brazil and may explain the low national prevalence of this subtype.

Comparison of direct sequencing of the NS5B region with the Versant HCV genotype 2.0 assay for genotyping of viral isolates in Mexico

Hepatitis C virus (HCV) infection affects an estimated 71 million people worldwide. HCV is classified into eight genotypes and >70 subtypes. Determination of HCV genotype is important for selection of type and duration of antiviral therapy, and genotype is also a predictor of treatment response. The most commonly used HCV genotyping method in clinical laboratories is a hybridization-based line probe assay (LiPA; Versant HCV Genotype 2.0). However, these methods have a lack of specificity in genotype identification and subtype assignment. Here, we compared the performance of Versant HCV Genotype 2.0 with the gold standard direct sequencing of the NS5B region, in 97 samples from Mexican patients. We found a genotypic concordance of 63.9% between these methods. While 68 samples (70%) were classified into HCV genotype 1 (GT1) by NS5B sequencing, it was not true for 17 samples (17.5%), which were not match HCV subtype by LiPA. Furthermore, nine of the 33 samples classified by NS5B sequencing as GT1a were not identified by LiPA. Use of direct sequencing could improve selection of the optimal therapy, avoid possible failures of therapy and avoid high costs resulting from incorrect genotyping tests in settings without broad access to pangenotypic regimens.

Performance of molecular methods for identification of unusual subtypes of hepatitis C virus genotype 2

Introduction: Hepatitis C virus (HCV) displays high genetic variability, with seven genotypes and numerous subtypes. The determination of the viral type has been essential for the selection and timing of antiviral treatment. In Venezuela, HCV genotype 2 is relatively diverse, being particularly prevalent subtype 2j. Objective: To evaluate the performance of methodologies for genotyping HCV, particularly for identification of subtype 2j. Materials and methods: HCV genotype and subtype were determined by reverse hybridization technique (LiPA) and sequencing of the HCV 5’UTR and NS5B regions. Results: A total of 65 samples from HCV-infected patients were analyzed. PCR amplifications of the 5’UTR region exhibited the highest sensitivity (100% vs 91% for LiPA and 77% for NS5B). Genotype determination, taking as reference test NS5B, showed 100% concordance with the other methods, and 67% and 59% for subtypes with 5´NC and LiPA, respectively. NS5B sequencing allowed the identification of subtypes 2j and 2s, which were not detected by the other methods. A specific LiPA pattern was not observed for HCV subtype 2j. Conclusion: Although being the methodology with lowest sensitivity for amplification of HCV RNA, sequencing NS5B region remains a powerful tool for correct discrimination of the different HCV subtypes, which is of epidemiological relevance.

Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa

HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869-1902) before the introduction of HCV-2k in 1901 (1867-1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization.

Low Risk of Hepatitis B Virus Reactivation in HBsAg-negative/Anti-HBc-positive Carriers Receiving Rituximab for Rheumatoid Arthritis: A Retrospective Multicenter Italian Study

OBJECTIVE

Patients with resolved hepatitis B virus (HBV) infection, i.e., hepatitis B surface antigen (HBsAg)-negative/antihepatitis B core antigen (anti-HBc)-positive, undergoing rituximab (RTX)-based chemotherapy for hematological malignancies without anti-HBV prophylaxis are at risk of HBV reactivation, but the risk in such patients receiving RTX for rheumatological disorders is not clear. We evaluated this risk in HBsAg-negative/anti-HBc-positive patients with rheumatoid arthritis (RA) undergoing RTX without prophylaxis.

METHODS

Thirty-three HBsAg-negative/anti-HBc-positive outpatients with RA with undetectable HBV DNA by sensitive PCR assay [73% women, median age 60 years, 85% with HBsAg antibodies (anti-HBs), 37% with antihepatitis B envelope antigen] received a median of 3 cycles of RTX (range 1-8) over 34 months (range 0-80) combined with disease-modifying antirheumatic drugs (DMARD) without prophylaxis. All underwent clinical and laboratory monitoring during and after RTX administration, including serum HBsAg and HBV DNA measurements every 6 months or whenever clinically indicated.

RESULTS

None of the patients seroreverted to HBsAg during RTX treatment, but 6/28 (21%) showed a > 50% decrease in protective anti-HBs levels, including 2 who became anti-HBs-negative. One patient (3%) who became HBV DNA-positive (44 IU/ml) after 6 months of RTX treatment was effectively rescued with lamivudine before any hepatitis flare occurred. Among the 14 patients monitored for 18 months (range 0-70) after RTX discontinuation, no HBV reactivation was observed.

CONCLUSION

The administration of RTX + DMARD in patients with RA with resolved HBV infection leads to a negligible risk of HBV reactivation, thus suggesting that serum HBsAg and/or HBV DNA monitoring but not universal anti-HBV prophylaxis is justified.

Immunogenicity and safety of concomitant administration of a combined hepatitis A/B vaccine and a quadrivalent meningococcal conjugate vaccine in healthy adults

BACKGROUND

This phase 3b randomized, open-label study evaluated the immunogenicity and safety of coadministration of a hepatitis A and/or B vaccine with a quadrivalent oligosaccharide meningococcal CRM197 -conjugate vaccine (MenACWY-CRM), in the context of an accelerated hepatitis A and/or B immunization schedule.

METHODS

A total of 252 healthy adult subjects were randomized to three groups to receive hepatitis A/B only (HepA/B), hepatitis A/B coadministered with MenACWY-CRM (HepA/B+MenACWY-CRM), or MenACWY-CRM only (MenACWY-CRM). Hepatitis A and/or B vaccination was administered in the form of a single booster dose or a primary three-dose series, depending on the hepatitis A and/or B vaccination history of subjects. Antibody responses to hepatitis A/B vaccination were assessed 1 month following the last hepatitis A and/or B dose. Serum bactericidal activity with human complement (hSBA) against meningococcal serogroups A, C, W-135, and Y was assessed 1 month post-MenACWY-CRM vaccination. Safety was monitored throughout the study.

RESULTS

At 1 month following the final hepatitis A and/or B vaccination, concomitant administration of hepatitis A/B and MenACWY-CRM was non-inferior to administration of hepatitis A/B alone in terms of geometric mean concentrations of antibodies against the hepatitis A and B antigens. One month post-MenACWY-CRM vaccination, the percentages of subjects achieving hSBA titers ≥8 for serogroups A, C, W-135, and Y in the HepA/B+MenACWY-CRM group (76, 87, 99, and 94%, respectively) were comparable to those in the MenACWY-CRM group (67, 82, 96, and 88%, respectively). The percentages of subjects reporting adverse events (AEs) were similar across study groups and a majority of the reported AEs were mild to moderate in nature. There were no study vaccine-related serious AEs.

CONCLUSIONS

MenACWY-CRM can be administered concomitantly with a hepatitis A and/or B vaccine in the context of an accelerated hepatitis A and/or B immunization schedule without increasing safety concerns or compromising the immune responses to any of the vaccine antigens. [NCT01453348].

Sequence conservation of the region targeted by the Abbott RealTime HCV viral load assay

The Abbott RealTime (RT) HCV assay targets the 5' untranslated region (UTR) of the HCV genome. Here, we analyzed the sequence variability of the assay target regions from 1,092 specimens. Thermodynamic modeling of the percentage of primers/probes bound at the assay annealing temperature was performed to assess the potential effect of sequence variability. An analysis of this large data set revealed that the primer and probe binding sites of the RealTime HCV viral load assay are highly conserved and that naturally occurring sequence polymorphisms are not expected to discernibly impact assay performance.

Molecular epidemiology and putative origin of hepatitis C virus in random volunteers from Argentina

AIM: To study the subtype prevalence and the phylogenetic relatedness of hepatitis C virus (HCV) sequences obtained from the Argentine general population, a large cohort of individuals was analyzed.

METHODS: Healthy Argentinian volunteers (n = 6251) from 12 provinces representing all geographical regions of the country were studied. All parents or legal guardians of individuals younger than 18 years provided informed written consent for participation. The corresponding written permission from all municipal authorities was obtained from each city or town where subjects were to be included. HCV RNA reverse transcription-polymerase chain reaction products were sequenced and phylogenetically analyzed. The 5’ untranslated region (5’UTR) was used for RNA detection and initial genotype classification. The NS5B polymerase region, encompassing nt 8262-8610, was used for subtyping.

RESULTS: An unexpectedly low prevalence of HCV infection in the general population (0.32%) was observed. Our data contrasted with previous studies that reported rates ranging from 1.5% to 2.5%, mainly performed in selected populations of blood donors or vulnerable groups. The latter values are in keeping with the prevalence reported by the 2007 Argentinian HCV Consensus (approximately 2%). HCV subtypes were distributed as follows: 1a (25%), 1b (25%), 2c (25%), 3a (5%), and 2j (5%). Two isolates ascribed either to genotype 1 (5%) or to genotype 3 (5%) by 5’UTR phylogenetic analysis could not be subtyped. Subtype 1a sequences comprised a highly homogeneous population and clustered with United States sequences. Genotype 1b sequences represented a heterogeneous population, suggesting that this genotype might have been introduced from different sources. Most subtype 2c sequences clustered close to the 2c reported from Italy and Southern France.

CONCLUSION: HCV has a low prevalence of 0.32% in the studied general population of Argentina. The pattern of HCV introduction and transmission in Argentina appears to be a consequence of multiple events and different for each subtype.

Hepatitis B surface antigen inhibits MICA and MICB expression via induction of cellular miRNAs in hepatocellular carcinoma cells

Hepatitis B surface antigen (HBsAg) seropositivity is an important risk factor for hepatocellular carcinoma (HCC), and HBsAg-transgenic mice have been reported to spontaneously develop HCC. The major histocompatibility complex class I-related molecules A and B (MICA and MICB) are NKG2D ligands that play important roles in tumor immune surveillance. In the present study, we found that HBsAg overexpression in HepG2 cells led to upregulation of 133 and downregulation of 9 microRNAs (miRNAs). Interestingly, several HBsAg-induced miRNAs repressed the expression of MICA and MICB via targeting their 3'-untranslated regions. In addition, the expression of MICA and MICB was significantly reduced upon HBsAg overexpression, which was partially restored by inhibiting the activities of HBsAg-induced miRNAs. Moreover, HBsAg-overexpressing HCC cells exhibited reduced sensitivity to natural killer cell-mediated cytolysis. Taken together, our data suggest that HBsAg supresses the expression of MICA and MICB via induction of cellular miRNAs, thereby preventing NKG2D-mediated elimination of HCC cells.

HCV genotype determination in monoinfected and HIV co-infected patients in Cuba

With the aim to characterize the HCV genotype distribution in Cuba, sera were collected from two subgroups: HCV-monoinfected and HCV/HIV co-infected patients. A combination of reverse transcription-PCR using genotype-specific primers, restriction fragment length polymorphism and sequencing was used to determine the genotype of 84 samples. Seventy-nine (94%) showed single infections (10 [12%] were genotype 1a and 69 [82%] genotype 1b) and 5 (6%) samples corresponded to mixed infections (2 [2%] with genotypes 1a/3a and 1 sample [1%] each with 1b/3a, 1b/4a and 1a/1b/3a). HCV/HIV co-infected subjects had a higher frequency of mixed infections (p=0.08), infection with genotype 3a (p=0.18) and for the first time genotype 4a was found. There was no association of any demographic characteristics with any specific genotype although HCV/HIV co-infected patients showed a tendency to have mixed genotypes in those older than 45 years of age (p=0.11). Phylogenetic analysis showed that HCV isolates clustered with subtypes 1b (n=15, maximal genetic distance 2.51%) and 1a (n=2, maximal genetic distance 0.35%). This report presents the prevalence of HCV genotypes in monoinfected and HIV co-infected patients, mixed HCV infections in HCV/HIV co-infected men who have sex with men with high-risk sexual practices and for the first time identifies that the uncommon genotype 4a can be present in a patient co-infected with HIV.

Antiviral activity of TMC435 monotherapy in patients infected with HCV genotypes 2-6: TMC435-C202, a phase IIa, open-label study

BACKGROUND & AIMS

TMC435 is an investigational, once-daily, oral NS3/4A protease inhibitor currently in phase III development for the treatment of hepatitis C virus (HCV) infection. Phase I and II studies in patients infected with HCV genotype 1 have demonstrated that TMC435 is generally well tolerated, has a pharmacokinetic profile that supports once daily dosing, and demonstrates potent antiviral activity. This phase IIa study (TMC435-C202; NCT00812331) was conducted to investigate the antiviral activity, safety, tolerability, and pharmacokinetics of TMC435 in treatment-naїve patients infected with HCV genotypes 2-6.

METHODS

The study consisted of 7 days of monotherapy with TMC435 (200mg once daily). Patients could begin treatment with pegylated interferon/ribavirin from day 8 with a follow-up period up to days 37-42.

RESULTS

Thirty-seven patients were enrolled in Germany, Belgium and Thailand. For the primary end point at day 8, the mean (± standard error) change in plasma HCV ribonucleic acid (log(10)IU/ml) from baseline was the greatest for genotypes 6 (-4.35 ± 0.29) and 4 (-3.52 ± 0.43), followed by genotypes 2 (-2.73 ± 0.71) and 5 (-2.19 ± 0.39). No antiviral activity was evident for genotype 3. Viral breakthrough occurred in six patients during the monotherapy phase and in six additional patients during PegIFN/RBV-only period. All adverse events were mild or moderate and there were no discontinuations during the TMC435 monotherapy period.

CONCLUSIONS

The results of this phase IIa proof-of-concept trial provide evidence that TMC435 has a spectrum of activity against multiple HCV genotypes, except for genotype 3. In this study, TMC435 was generally safe and well tolerated.

Etiology and Viral Genotype in Patients with End-Stage Liver Diseases admitted to a Hepatology Unit in Colombia

Hepatitis B virus (HBV) and hepatitis C virus (HCV) infections are the principal risk factor associated to end-stage liver diseases in the world. A study was carried out on end-stage liver disease cases admitted to an important hepatology unit in Medellin, the second largest city in Colombia. From 131 patients recruited in this prospective study, 71% of cases were diagnosed as cirrhosis, 12.2% as HCC, and 16.8% as cirrhosis and HCC. Regarding the risk factors of these patients, alcohol consumption was the most frequent (37.4%), followed by viral etiology (17.6%). Blood and/or hepatic tissue samples from patients with serological markers for HCV or HBV infection were characterized; on the basis of the phylogenetic analysis of HCV 5' UTR and HBV S gene, isolates belonged to HCV/1 and HBV/F3, respectively. These results confirm the presence of strains associated with poor clinical outcome, in patients with liver disease in Colombia; additionally, HBV basal core promoter double mutant was identified in HCC cases. Here we show the first study of cirrhosis and/or HCC in Colombian and HBV and HCV molecular characterization of these patients. Viral aetiology was not the main risk factor in this cohort but alcohol consumption.

Trends and projections of hepatitis C virus epidemiology in Latin America

BACKGROUND AND AIM

The purpose of the present investigation is to provide an analysis of previous works on the epidemiology of the hepatitis C virus (HCV) infection from six countries throughout Latin America, to forecast the future HCV prevalence trends in Argentina, Brazil, Mexico and Puerto Rico, and to outline deficiencies in available data, highlighting the need for further research.

METHODS

Data references were identified through indexed journals and non-indexed sources. Overall, 1080 articles were reviewed and 150 were selected based on their relevance to this work. When multiple data sources were available for a key assumption, a systematic process using multi-objective decision analysis (MODA) was used to select the most appropriate sources. When data were missing, analogues were used. Data from other countries with similar risk factors and/or population compositions were used as a proxy to help predict the future trends in prevalence.

RESULTS

The review indicates that the dominant genotype is type 1. HCV prevalence in the analysed countries ranges from 1 to 2.3%. The Latin American countries have been very proactive in screening their blood supplies, thus minimizing the risk of transmission through transfusion. This suggests that other risk factors are set to play a major role in continued new infections. The number of diagnosed and treated patients is low, thereby increasing the burden of complications such as liver cirrhosis or hepatocellular carcinoma. The HCV prevalence, according to our modelling is steady or increasing and the number of infected individuals will increase.

CONCLUSIONS

The results herein reported should provide a foundation for informed planning efforts to tackle hepatitis.

Antibodies to the envelope glycoprotein of human T cell leukemia virus type 1 robustly activate cell-mediated cytotoxic responses and directly neutralize viral infectivity at multiple steps of the entry process

Infection of human cells by human T cell leukemia virus type 1 (HTLV-1) is mediated by the viral envelope glycoproteins. The gp46 surface glycoprotein binds to cell surface receptors, including heparan sulfate proteoglycans, neuropilin 1, and glucose transporter 1, allowing the transmembrane glycoprotein to initiate fusion of the viral and cellular membranes. The envelope glycoproteins are recognized by neutralizing Abs and CTL following a protective immune response, and therefore, represent attractive components for a HTLV-1 vaccine. To begin to explore the immunological properties of potential envelope-based subunit vaccine candidates, we have used a soluble recombinant surface glycoprotein (gp46, SU) fused to the Fc region of human IgG (sRgp46-Fc) as an immunogen to vaccinate mice. The recombinant SU protein is highly immunogenic and induces high titer Ab responses, facilitating selection of hybridomas that secrete mAbs targeting SU. Many of these mAbs recognize envelope displayed on the surface of HTLV-1-infected cells and virions and several of the mAbs robustly antagonize envelope-mediated membrane fusion and neutralize pseudovirus infectivity. The most potently neutralizing mAbs recognize the N-terminal receptor-binding domain of SU, though there is considerable variation in neutralizing proficiency of the receptor-binding domain-targeted mAbs. By contrast, Abs targeting the C-terminal domain of SU tend to lack robust neutralizing activity. Importantly, we find that both neutralizing and poorly neutralizing Abs strongly stimulate neutrophil-mediated cytotoxic responses to HTLV-1-infected cells. Our data demonstrate that recombinant forms of SU possess immunological features that are of significant utility to subunit vaccine design.

Genetic history of hepatitis C virus in Venezuela: high diversity and long time of evolution of HCV genotype 2

BACKGROUND

The subtype diversity of the hepatitis C virus (HCV) genotypes is unknown in Venezuela.

METHODOLOGY/PRINCIPAL FINDINGS

Partial sequencing of the NS5B region was performed in 310 isolates circulating in patients from 1995 to 2007. In the samples collected between 2005 and 2007, HCV genotype 1 (G1) was the most common genotype (63%), composed as expected of mainly G1a and G1b. G2 was the second most common genotype (33%), being G2a almost absent and G2j the most frequent subtype. Sequence analysis of the core region confirmed the subtype assignment performed within the NS5b region in 63 isolates. The complete genome sequence of G2j was obtained. G2j has been described in France, Canada and Burkina Fasso, but it was not found in Martinique, where several subtypes of G2 circulate in the general population. Bayesian coalescence analysis indicated a most recent common ancestor (MRCA) of G2j around 1785, before the introduction of G1b (1869) and G1a (1922). While HCV G1a and G1b experienced a growth reduction since 1990, coincident with the time when blood testing was implemented in Venezuela, HCV G2j did not seem to reach growth equilibrium during this period.

CONCLUSIONS/SIGNIFICANCE

Assuming the introduction of G2j from Africa during the slave trade, the high frequency of G2j found in Venezuela could suggest: 1- the introduction of African ethnic groups different from the ones introduced to Martinique or 2- the occurrence of a founder effect. This study represents an in-depth analysis of the subtype diversity of HCV in Venezuela, which is still unexplored in the Americas and deserves further studies.

Molecular epidemiology of hepatitis C virus genotypes in west Mexico

The identification of hepatitis C virus (HCV) genotypes and subtypes may be helpful to identify the source of an HCV outbreak among a specific group of individuals within a given country or the pattern of spread throughout nations worldwide. Mexico is a transit country for people who migrate north towards the United States from Central and South America, however, to date, no Mexican HCV sequences have been reported. The present study was conducted to identify the HCV genotypes and subtypes prevalent in Mexico by DNA sequencing and phylogenetic analysis in the NS5B region of the HCV genome. Serum samples from a total of 75 anti-HCV positive patients were included in this study. Out of the 75 samples, 48 cases (64%) were amplifiable in the 5' UTR and 46 (61%) in NS5B region. HCV genotype 1a determined in 54.3% (25/46) was predominant in this cohort, followed by 1b 21.8% (10/46), 2b 13% (6/46), 3a 6.5% (3/46), and 2a 4.4% (2/46). Phylogenetic analysis showed that HCV sequences of genotype 1 (1a and 1b) were clustering more closely to the United States isolates published previously. These results may suggest that both Mexico and the United States share an epidemiological network of HCV genotype 1 while other genotypes represent sporadic infections that are specific to Mexico.

Diversity of hepatitis B and C viruses in Chile

Although there is a low prevalence rate (around 1% of the population) of infection with hepatitis B virus (HBV) and hepatitis C virus (HCV) in Chile, little is known about the diversity and molecular characteristics of the circulating viruses. In the present study, 40 HBV and 57 HCV samples from Santiago City, Chile, were examined. The phylogenetic analysis of HBV samples showed the autochthonous genotype F as the most represented genotype in the study (67.5%), while genotypes A, B, C, and D were less frequent (7.5%, 5%, 7.5%, and 12.5%, respectively). The frequency of circulation of HBV genotypes observed is in accordance with the genetic background of the Chilean population. Most of the HCV samples tested belonged to subtype 1b (82%). The coalescent analysis conducted for both the NS5A and NS5B regions of the HCV strains showed similar population growth rates, with a most recent common ancestor estimated to date between 1893 and 1901. This result may indicate that genotype 1b strains circulating in Chile have epidemiological features similar to those described for HCV genotype 1b in Brazil and the United States. However, the most recent common ancestor for Chile is older than that reported recently for genotype 1b in Argentina.

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.

Epidemiology of hepatitis virus B and C

Hepatitis B and C virus infections constitute a significant health problem in Latin America. Approximately 400,000 new cases of hepatitis B per year and 10 million people infected with hepatitis C are estimated to occur. HBV and HCV genotype distribution may reflect the different patterns of migration to the Americas: Genotype F and H of HBV correspond to the Amerindian genotype. Overall, Genotype 1 is the most prevalent HCV genotype in the Caribbean and in South and Central America. Hepatitis B and C epidemiology needs to be considered in the context of dissimilar social and economic aspects among the countries of the region. Behaviors, cultural and ethical aspects, as well as environmental and organizational processes affect directly the way these diseases are approached in their diagnosis, treatment and prevention.

Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region

Background

Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Previous and recent studies have suggested a diversification of type 1 HCV in the South American region. The degree of genetic variation among HCV strains circulating in Bolivia and Colombia is currently unknown. In order to get insight into these matters, we performed a phylogenetic analysis of HCV 5' non-coding region (5'NCR) sequences from strains isolated in Bolivia, Colombia and Uruguay, as well as available comparable sequences of HCV strains isolated in South America.

Methods

Phylogenetic tree analysis was performed using the neighbor-joining method under a matrix of genetic distances established under the Kimura-two parameter model. Signature pattern analysis, which identifies particular sites in nucleic acid alignments of variable sequences that are distinctly representative relative to a background set, was performed using the method of Korber & Myers, as implemented in the VESPA program. Prediction of RNA secondary structures was done by the method of Zuker & Turner, as implemented in the mfold program.

Results

Phylogenetic tree analysis of HCV strains isolated in the South American region revealed the presence of a distinct genetic lineage inside genotype 1. Signature pattern analysis revealed that the presence of this lineage is consistent with the presence of a sequence signature in the 5'NCR of HCV strains isolated in South America. Comparisons of these results with the ones found for Europe or North America revealed that this sequence signature is characteristic of the South American region.

Conclusion

Phylogentic analysis revealed the presence of a sequence signature in the 5'NCR of type 1 HCV strains isolated in South America. This signature is frequent enough in type 1 HCV populations circulating South America to be detected in a phylogenetic tree analysis as a distinct type 1 sub-population. The coexistence of distinct type 1 HCV subpopulations is consistent with quasispecies dynamics, and suggests that multiple coexisting subpopulations may allow the virus to adapt to its human host populations.

Systematic evaluation of allele-specific real-time PCR for the detection of minor HIV-1 variants with pol and env resistance mutations

Allele-specific PCR (ASPCR) is a highly sensitive, and reproducible method for the study of minor HIV-1 variants harboring resistance mutations and is significantly less labor-intensive and time-consuming than other techniques used for similar purposes. Furthermore, ASPCR has multiple applications in HIV research: it provides earlier and more sensitive detection of evolving resistance mutations, a more accurate assessment of transmitted drug-resistant mutants and a better evaluation of resistance selection after post-exposure or mother-to-child-transmission prophylaxis programs. This article outlines the principles of ASPCR and illustrates technical challenges in the design and application of ASPCR protocols by describing ASPCR assays developed for detecting resistance mutations in the protease (PR)- and reverse transcriptase (RT)-coding regions of pol and env. The assays achieved sensitivities of <1% for the D30N mutation in HIV-1 PR, M184V and I mutations in RT, and V38A in gp41. This method can be easily adapted to the quantitative detection of other mutations in HIV-1 or other viruses by introducing minor modifications to the methods described. In addition, ASPCR can be used to assess the dynamics of mutant populations in the viral quasispecies in response to changing selection pressures, allowing inferences on viral fitness in vivo through mathematical modeling.