Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8+ T Cells.

Virus-specific CD8 T cell response seems to play a significant role in the outcome of hepatitis delta virus (HDV) infection. However, the HDV-specific T cell epitope repertoire and mechanisms of CD8 T cell failure in HDV infection have been poorly characterized. We therefore aimed to characterize HDV-specific CD8 T cell epitopes and the impacts of viral mutations on immune escape. In this study, we predicted peptide epitopes binding the most frequent human leukocyte antigen (HLA) types and assessed their HLA binding capacities. These epitopes were characterized in HDV-infected patients by intracellular gamma interferon (IFN-γ) staining. Sequence analysis of large hepatitis delta antigen (L-HDAg) and HLA typing were performed in 104 patients. The impacts of substitutions within epitopes on the CD8 T cell response were evaluated experimentally and by in silico studies. We identified two HLA-B*27-restricted CD8 T cell epitopes within L-HDAg. These novel epitopes are located in a relatively conserved region of L-HDAg. However, we detected molecular footprints within the epitopes in HLA-B*27-positive patients with chronic HDV infections. The variant peptides were not cross-recognized in HLA-B*27-positive patients with resolved HDV infections, indicating that the substitutions represent viral escape mutations. Molecular modeling of HLA-B*27 complexes with the L-HDAg epitope and its potential viral escape mutations indicated that the structural and electrostatic properties of the bound peptides differ considerably at the T cell receptor interface, which provides a possible molecular explanation for the escape mechanism. This viral escape from the HLA-B*27-restricted CD8 T cell response correlates with a chronic outcome of hepatitis D infection. T cell failure resulting from immune escape may contribute to the high chronicity rate in HDV infection.IMPORTANCE Hepatitis delta virus (HDV) causes severe chronic hepatitis, which affects 20 million people worldwide. Only a small number of patients are able to clear the virus, possibly mediated by a virus-specific T cell response. Here, we performed a systematic screen to define CD8 epitopes and investigated the role of CD8 T cells in the outcome of hepatitis delta and how they fail to eliminate HDV. Overall the number of epitopes identified was very low compared to other hepatotropic viruses. We identified, two HLA-B*27-restricted epitopes in patients with resolved infections. In HLA-B*27-positive patients with chronic HDV infections, however, we detected escape mutations within these identified epitopes that could lead to viral evasion of immune responses. These findings support evidence showing that HLA-B*27 is important for virus-specific CD8 T cell responses, similar to other viral infections. These results have implications for the clinical prognosis of HDV infection and for vaccine development.

High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods.

Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.

Relevance of a full-length genomic RNA standard and a thermal-shock step for optimal hepatitis delta virus quantification.

Hepatitis D virus (HDV) is a defective RNA virus that requires the surface antigens of hepatitis B virus (HBV) (HBsAg) for viral assembly and replication. Several commercial and in-house techniques have been described for HDV RNA quantification, but the methodologies differ widely, making a comparison of the results between studies difficult. In this study, a full-length genomic RNA standard was developed and used for HDV quantification by two different real-time PCR approaches (fluorescence resonance energy transfer [FRET] and TaqMan probes). Three experiments were performed. First, the stability of the standard was determined by analyzing the effect of thawing and freezing. Second, because of the strong internal base pairing of the HDV genome, which leads to a rod-like structure, the effect of intense thermal shock (95°C for 10 min and immediate cooling to -80°C) was tested to confirm the importance of this treatment in the reverse transcription step. Lastly, to investigate the differences between the DNA and RNA standards, the two types were quantified in parallel with the following results: the full-length genomic RNA standard was stable and reliably mimicked the behavior of HDV-RNA-positive samples, thermal shock enhanced the sensitivity of HDV RNA quantification, and the DNA standard underquantified the HDV RNA standard. These findings indicate the importance of using complete full-length genomic RNA and a strong thermal-shock step for optimal HDV RNA quantification.

Removability of a small aperture intracorneal inlay for presbyopia correction.

PURPOSE: To evaluate the safety of the corneal inlay removal procedure and the reversibility of visual acuities, corneal topography, and corneal biomicroscopy changes in a series of cases. METHODS: Ten cases implanted with one of three versions of the AcuFocus Kamra Inlay (ACI 7000, 7000T, and 7000PDT; AcuFocus, Inc., Irvine, CA) were followed for a minimum of 6 months after corneal inlay removal. RESULTS: The reason for removal was related to subjective dissatisfaction with visual symptoms (8 of 10 patients) such as night glare, photophobia, starburst, blurry vision, and halos. One case of removal was related to inadvertent thin flap and the final case was related to insufficient near vision. Mean uncorrected distance visual acuity (UDVA) and uncorrected near visual acuity (UNVA) was 0 ± 0.1 logMAR (Snellen 20/20) and 0.5 ± 0.2 logMAR (Snellen 20/40), respectively, preoperatively and 0.1 ± 0.1 logMAR (Snellen 20/25) and 0.5 ± 0.1 logMAR (Snellen 20/63), respectively, 6 months after corneal inlay removal. Mean corrected distance visual acuity (CDVA) and corrected near visual acuity (CNVA) was 0 ± 0.1 logMAR (Snellen 20/20) and 0 ± 0.1 logMAR (Snellen 20/20), respectively, preoperatively and 0 ± 0.1 logMAR (Snellen 20/20) and 0.1 ± 0.1 logMAR (Snellen 20/25), respectively, 6 months after corneal inlay removal. Mean root mean square (RMS) higher-order aberration (HOA) was 0.50 ± 0.12 (range: 0.30 to 0.70) preoperatively and 0.69 ± 0.14 (range: 0.48 to 0.95) 6 months after corneal inlay removal (P < .8). Weak positive correlation was found between Δt Implant-Removal (Δt I-R), RMS spherical, coma, and HOA at 6 months (Δt I-R vs RMS spherical was r = 0.2, r(2) = 0.5, P < .7; Δt I-R vs RMS coma was r = 0.8, r(2) = 0.6, P < .3; and Δt I-R vs HOA r = 0.8; r(2) = 0.6, P < .9). CONCLUSION: This study suggests that after removal of the corneal inlay, corneal topography and corneal aberrometry are not permanently affected. In more than 60% of patients, CNVA, CDVA, UNVA, and UDVA were similar to the preoperative value.

Ultra-deep pyrosequencing analysis of the hepatitis B virus preCore region and main catalytic motif of the viral polymerase in the same viral genome.

Hepatitis B virus (HBV) pregenomic RNA contains a hairpin structure (ε) located in the preCore region, essential for viral replication. ε stability is enhanced by the presence of preCore variants and ε is recognized by the HBV polymerase (Pol). Mutations in the retrotranscriptase domain (YMDD) of Pol are associated with treatment resistance. The aim of this study was to analyze the preCore region and YMDD motif by ultra-deep pyrosequencing (UDPS). To evaluate the UDPS error rate, an internal control sequence was inserted in the amplicon. A newly developed technique enabled simultaneous analysis of the preCore region and Pol in the same viral genome, as well as the conserved sequence of the internal control. Nucleotide errors in HindIII yielded a UDPS error rate <0.05%. UDPS study confirmed the possibility of simultaneous detection of preCore and YMDD mutations, and demonstrated the complexity of the HBV quasispecies and cooperation between viruses. Thermodynamic stability of the ε signal was found to be the main constraint for selecting main preCore mutations. Analysis of ε-signal variability suggested the essential nature of the ε structural motif and that certain nucleotides may be involved in ε signal functions.

Prevalence of Respiratory Infections during the 2018-2020 Period in the Paediatric Population of Primary Care Centres in Central Catalonia.

Following the COVID-19 pandemic, policies such as social distancing, hand washing, and the use of masks were implemented, which could play an important role in the reduction of infectious diseases. An observational, descriptive, cross-sectional study was conducted to observe the prevalence of respiratory infections in children under 15 years of age during the 2018-2020 period in Primary Care centres in Central Catalonia. In 2020, there was a 44.3% decrease in total consultations for respiratory infections compared to 2019. All respiratory infections exhibited a significant decrease except flu-like syndrome; children between the ages of 6 and 12 had the highest prevalence of flu-like syndrome (87.6%), and the SARS-CoV-2-19 infection was most frequent (4%) among those between the ages of 12 and 15. Compared to urban centres, rural centres presented a higher prevalence of all infections except flu-like syndrome and SARS-CoV-2. In conclusion, the COVID-19 pandemic caused a significant decrease in the number of consultations for respiratory infections in the paediatric population, except for flu-like syndrome, which increased in cases in January, February, and March 2020. No differences were found between sexes, although differences were found in the distribution of the different age groups.

[New agents for the treatment of hepatitis C]. / Nuevos agentes para el tratamiento de la hepatitis C.

The current treatment of Chronic Hepatitis C (CHC) is based on the combination of peginterferon alpha 2a or 2b and ribavirin. This treatment achieves Sustained Virological Response (SVR) rates in more than 50% of the patients. The SVR rates are higher in genotype 2 and 3 patients than in genotype 1, which account for more than 50%. For this reason, the development of new drugs is needed. The knowledge of Hepatitis C Virus (HCV) replication cycle and the characterisation of the viral enzymes allow targets to be defined with the ability to inhibit HCV enzymes. The present overview analyses the first two NS3/NS4 protease inhibitors approved for the treatment of CHC, boceprevir and telaprevir. Both increase rates of SVR in naïve and in previously treated patients with the advantage that in some cases therapy can be shortened. However, these drugs have new side effects such as a rash and an increase in the rate of anaemia.

Prevalence of SARS-CoV-2 antibodies and risk factors in the pandemic epicentre of Catalonia.

To define the seroprevalence of antibodies against SARS-CoV-2 in the municipality of Vilanova del Camí (in the region of Conca d'Ódena, Barcelona, Spain) and to know the risk factors associated with positive seroprevalence. Cross-sectional descriptive study. The population of Vilanova del Camí had the opportunity to voluntarily attend two screenings (October and December 2020) for antibodies against the nucleocapsid protein of SARS-CoV-2 using a Rapid Diagnostic Test (RDT) (Salocor (Salofa Oy). Participants in the screening signed an informed consent form. From the 3,610 attendees at the screening, 2,170 patients were randomly selected. The relationship between antibody test results and other demographic (sex, age, morbidity index) and clinical (diagnoses, smoking and drugs) variables was analysed. The prevalence of antibodies against SARS-CoV-2 was 9.6% (95% CI of 8.4% to 10.9%) and was similar for men and women but increased with age. Among complex chronic patients, 14.3% had antibodies against SARS-CoV-2, and among patients with advanced chronic disease, 25% had antibodies against SARS-CoV-2. Age, AMG (Adjusted Morbidity Groups) index, COVID-19 diagnosis and contact with a COVID-19 case were risk factors for positive seroprevalence. A higher seroprevalence was detected in the October screening (12.16%) than in the December screening (8.38%). In the December screening, obesity was a risk factor for positive seroprevalence. This study demonstrates the high seroprevalence of antibodies against SARS-CoV-2 in the pandemic epicentre of Catalonia.

Hepatitis B Virus Variants with Multiple Insertions and/or Deletions in the X Open Reading Frame 3' End: Common Members of Viral Quasispecies in Chronic Hepatitis B Patients.

Deletions in the 3' end region of the hepatitis B virus (HBV) X open reading frame (HBX) may affect the core promoter (Cp) and have been frequently associated with hepatocellular carcinoma (HCC). The aim of this study was to investigate the presence of variants with deletions and/or insertions (Indels) in this region in the quasispecies of 50 chronic hepatitis B (CHB) patients without HCC. We identified 103 different Indels in 47 (94%) patients, in a median of 3.4% of their reads (IQR, 1.3-8.4%), and 25% (IQR, 13.1-40.7%) of unique sequences identified in each quasispecies (haplotypes). Of those Indels, 101 (98.1%) caused 44 different altered stop codons, the most commonly observed were at positions 128, 129, 135, and 362 (putative position). Moreover, 39 (37.9%) Indels altered the TATA-like box (TA) sequences of Cp; the most commonly observed caused TA2 + TA3 fusion, creating a new putative canonical TATA box. Four (8%) patients developed negative clinical outcomes after a median follow-up of 9.4 (8.7-12) years. In conclusion, we observed variants with Indels in the HBX 3' end in the vast majority of our CHB patients, some of them encoding alternative versions of HBx with potential functional roles, and/or alterations in the regulation of transcription.

Quantitative longitudinal evaluations of hepatitis delta virus RNA and hepatitis B virus DNA shows a dynamic, complex replicative profile in chronic hepatitis B and D.

BACKGROUND & AIMS: This study presents a real-time reverse-transcription PCR (rt-RT-PCR) assay for hepatitis delta virus (HDV) RNA quantification, designed to clarify the interplay between HDV and hepatitis B virus (HBV) in chronic infection. METHODS: Serum HDV-RNA and HBV-DNA were analysed by rt-RT-PCR in a cross-sectional study of 37 untreated chronic HDV patients, 25 of whom were also longitudinally studied. RESULTS: In the cross-sectional study, both viruses were active in 15 (40.5%) patients and inactive in 4 (10.8%); HDV alone was active in 12 (32.4%) and HBV in 6 (16.2%). The longitudinal study showed seven replication profiles, with considerable fluctuating activity of one or both viruses, including alternating predominance. In 20% of cases, longitudinal HBV/HDV viral loads differed from cross-sectional results, indicating a risk of misinterpreting HBV/HDV interactions when assessing a single determination. Fluctuating HBV replication only increased in the presence of fluctuating HDV activity. HBsAg levels, stable in HBV single infection, fluctuated in HDV chronic infection. The results of both the cross-sectional and longitudinal study call into question the major suppressor effect of HDV over HBV, revealing an important role of HBV. CONCLUSIONS: Longitudinal evaluation of viremia shows a complex interaction between HBV and HDV and is essential to understand the pathophysiology of chronic HDV infection.

Successful use of entecavir for a severe case of reactivation of hepatitis B virus following polychemotherapy containing rituximab.

BACKGROUNDS/AIMS: Hepatitis B virus (HBV) reactivation following treatment with rituximab has been reported in patients with either HBsAg-positive, or HBsAg-negative and anti-HBc positive infection. Patients with severe reactivation often have a fatal outcome despite treatment with lamivudine. The use of entecavir has not been reported in patients with severe HBV reactivation. METHODS: We present a case of a HBsAg-negative patient diagnosed with chronic lymphocytic leukemia who received a chemotherapeutic regimen that included rituximab, who subsequently presented with severe HBV reactivation with ascites, jaundice and coagulopathy and was treated with entecavir. A review of the literature and underlying HBV associated mutations are discussed. RESULTS: Entecavir produced a rapid and sustained suppression of HBV that was associated with rapid clinical improvement without any side effects. CONCLUSION: Entecavir is an efficacious and safe treatment for severe HBV reactivation.

Use of the novel INNO-LiPA line probe assay for detection of hepatitis B virus variants that confer resistance to entecavir therapy.

A line probe assay (INNO-LiPA DR, version 3) for the detection of hepatitis B virus mutations that confer resistance to entecavir therapy was evaluated. The INNO-LiPA DR assay is a highly sensitive assay that is easily applicable for the detection and monitoring of entecavir resistance-conferring mutations and is more sensitive than sequencing for the detection of mixed sequences.

Formulating stable hexosome dispersions with a technical grade diglycerol-based surfactant.

We report on the phase behavior of a technical grade and commercially available diglycerol monoisostearate, C41V, and its use for the preparation of nanostructured liquid crystal dispersions (hexosomes). C41V in water forms a reverse hexagonal liquid crystal at room temperature and in a wide range of concentrations (0.5-95 wt%); this hexagonal liquid crystal is stable up to 70 °C. A simple and effective method has been developed to disperse hexosomes with an encapsulated active molecule (Ketoprofen) that consists of (1) producing a nano-emulsion stabilized by an amphiphilic block copolymer (Pluronic F127) and containing ethyl acetate and C41V by using ultrasounds and (2) evaporating the solvent to produce hexosomes. The size of the hexosomes and ultrasound dispersion time is markedly reduced by using ethyl acetate as an auxiliary solvent with an optimal initial ratio of C41V:ethyl acetate of 50:50. Dynamic light scattering shows that the size of the hexosomes decreases as the concentration of stabilizer F127 or encapsulated Ketoprofen is increased. The lattice parameter in the hexagonal structure is calculated from small angle scattering data to be ca. 5.3  nm and is only slightly dependent on the amount of F127 and/or encapsulated Ketoprofen. Cryo electron microscopy reveals that the samples contain hexosomes and these coexist with spherical, likely F127 micelles. Lastly, hexosomes show a pH responsive release of Ketoprofen which could be useful for target delivery in the gastrointestinal tract.

Adefovir for chronic hepatitis B treatment: identification of virological markers linked to therapy response.

BACKGROUND: HBV variants rtA181V/T, rtN236T and rtl233V, which confer resistance to adefovir dipivoxil (ADV), are not detected in many non-responding patients. Virological characteristics useful for predicting response have not been clearly elucidated. We determined pretreatment virological markers to predict non-response and possible emergence of new variants during therapy. METHODS: This longitudinal study included 41 patients with chronic hepatitis B virus (HBV) infection receiving ADV monotherapy or ADV plus lamivudine (3TC). A fragment of HBV polymerase including catalytic domains was analysed for ADV-resistant variants. RESULTS: Complete virological response (CVR; HBV DNA < 2.5 log10 copies/ml) was observed in 15 (36.6%) patients and partial virological response (PVR; HBV DNA < 4 log, copies/ml) in 23 (56.1%) patients. On multivariate analyses, hepatitis B e antigen (HBeAg) status was independently associated with CVR (hazard ratio [HR] = 0.27, P = 0.002) and PVR (HR = 0.21, P < 0.001) and viral genotype with CVR (HR = 0.13, P = 0.01). Predictive values for HBeAg were 88% for PVR in HBeAg-negative and 79% for non-CVR in HBeAg-positive patients. Predictive values for viral genotype were 93% for non-CVR and 72% for non-PVR for genotype A. On sequencing, variant rt217R (associated with subgenotype A2) was predictive of non-CVR (100%) and non-PVR (72.7%); the rtS219A variant emerged during therapy in three non-PVR patients. Both positions are located in a region likely to be related to the substrate union site, as predicted by our structural model of the HBV polymerase. CONCLUSIONS: Virological pretreatment characteristics (HBeAg, viral genotype and rtL217R polymorphism) are potentially associated with ADV response. HBV polymerase structural modelling has provided a hypothesis to explain the molecular mechanism for ADV resistance associated with rtR217.

Mitochondrial plasmids of sugar beet amplified via rolling circle method detected during curtovirus screening.

Crops of sugar beet have been considerably impaired by infection with Beet curly top virus (BCTV) during the past decades. Quick and reliable diagnostic techniques are therefore desirable to detect this circular single-stranded DNA-containing geminivirus. Techniques combining either tissue printing or blot hybridization, or rolling circle amplification (RCA) and restriction fragment length polymorphism (RFLP) were compared. Although they easily detected BCTV with certainty, both exhibited apparent false positive results which have been scrutinized in closer detail. Uninfected control plants revealed unspecific signals due to probe attachment on tissue blots, and dominant fragment patterns upon RCA/RFLP which did not hybridize with BCTV-specific probes. Cloning and sequencing of these DNA fragments showed that they were amplified from mitochondrial plasmids. Examination of their genome structure revealed no relationship with geminiviruses or their satellites.

Quantitative characterization of hepatitis delta virus genome edition by next-generation sequencing.

AIM: To determine the capacity of next-generation sequencing (NGS) for quantifying edited and unedited HDV populations, and to confirm if edition is a general phenomenon taking place along the entire HDV region analyzed, as we previously reported (Homs M et al. PLoS One 2016, 11, e0158557). METHODS: Four serum samples from 4 patients with chronic HDV/HBV infection were included in the study. The region selected for analysis covered 360 nucleotides (nt), positions 910-1270 of the HDV genome, which included the HDAg ORF editing site (nt 1014 within codon 196). Quantification of edited and unedited genomes was performed by molecular cloning and Sanger sequencing and by NGS. To evaluate the reliability of the NGS values obtained, we combined a clone with an edited codon and one with an unedited codon in known percentages in a series of artificial mixtures, which were then analyzed by NGS. In addition, we determined the nt changes occurring over the complete amplified region after excluding the editing codon (196) to evaluate edition along it. RESULTS: In total, 11,208 quality-filtered sequences were obtained in the 4 samples. The 95% confidence intervals for the proportions of unedited populations by molecular cloning and NGS were overlapping, and those of cloning were wider, indicating that they are comparable and that NGS is more precise than cloning. Unedited genomes predominated over edited ones in all 4 samples analyzed by NGS and in 3 of the 4 samples analyzed by molecular cloning. In total, 83,276 quality-filtered sequences were obtained from the artificial mixtures. Percentages of the two viral populations detected by NGS in these mixtures were comparable to the expected percentages. Evaluation of edition along the HDV coding region showed that transitions were more frequent than transversions, accounting for 63.09% and 36.91%, respectively. Interestingly, among the 4 possible transition-type changes, G:A and A:G accounted for 73.86% of the total. CONCLUSION: Next-generation sequencing proved useful to quantify edited and unedited HDV genomes, and provided relevant information on the HDV quasispecies.

Both interferon alpha and lambda can reduce all intrahepatic HDV infection markers in HBV/HDV infected humanized mice.

Co-infection with hepatitis B (HBV) and D virus (HDV) is associated with the most severe course of liver disease. Interferon represents the only treatment currently approved. However, knowledge about the impact of interferons on HDV in human hepatocytes is scant. Aim was to assess the effect of pegylated interferon alpha (peg-IFNα) and lambda (peg-IFNλ), compared to the HBV-polymerase inhibitor entecavir (ETV) on all HDV infection markers using human liver chimeric mice and novel HDV strand-specific qRT-PCR and RNA in situ hybridization assays, which enable intrahepatic detection of HDV RNA species. Peg-IFNα and peg-IFNλ reduced HDV viremia (1.4 log and 1.2 log, respectively) and serum HBsAg levels (0.9-log and 0.4-log, respectively). Intrahepatic quantification of genomic and antigenomic HDV RNAs revealed a median ratio of 22:1 in untreated mice, resembling levels determined in HBV/HDV infected patients. Both IFNs greatly reduced intrahepatic levels of genomic and antigenomic HDV RNA, increasing the amounts of HDAg- and antigenomic RNA-negative hepatocytes. ETV-mediated suppression of HBV replication (2.1-log) did not significantly affect HBsAg levels, HDV productivity and/or release. In humanized mice lacking adaptive immunity, IFNs but not ETV suppressed HDV. Viremia decrease reflected the intrahepatic reduction of all HDV markers, including the antigenomic template, suggesting that intracellular HDV clearance is achievable.

Deep sequencing in the management of hepatitis virus infections.

The hepatitis viruses represent a major public health problem worldwide. Procedures for characterization of the genomic composition of their populations, accurate diagnosis, identification of multiple infections, and information on inhibitor-escape mutants for treatment decisions are needed. Deep sequencing methodologies are extremely useful for these viruses since they replicate as complex and dynamic quasispecies swarms whose complexity and mutant composition are biologically relevant traits. Population complexity is a major challenge for disease prevention and control, but also an opportunity to distinguish among related but phenotypically distinct variants that might anticipate disease progression and treatment outcome. Detailed characterization of mutant spectra should permit choosing better treatment options, given the increasing number of new antiviral inhibitors available. In the present review we briefly summarize our experience on the use of deep sequencing for the management of hepatitis virus infections, particularly for hepatitis B and C viruses, and outline some possible new applications of deep sequencing for these important human pathogens.

Evidence of an Exponential Decay Pattern of the Hepatitis Delta Virus Evolution Rate and Fluctuations in Quasispecies Complexity in Long-Term Studies of Chronic Delta Infection.

Chronic HDV infection can cause a severe form of viral hepatitis for which there is no specific treatment. Characterization of the hepatitis B or C viral quasispecies has provided insight into treatment failure and disease recurrence following liver transplantation, has proven useful to understand hepatitis B e antigen seroconversion, and has helped to predict whether hepatitis C infection will resolve or become chronic. It is likely that characterization of the hepatitis delta virus (HDV) quasispecies will ultimately have similar value for the management of this infection. This study sought to determine the RNA evolution rates in serum of chronic hepatitis delta (CHD) treatment-naïve patients, using next-generation sequencing methods. The region selected for study encompassed nucleotide positions 910 to 1270 of the genome and included the amber/W codon. Amber/W is a substrate of the editing process by the ADAR1 host enzyme and is essential for encoding the 2 delta antigens (HDAg). The amber codon encodes the small (unedited) HDAg form and the W codon the large (edited) HDAg form. The evolution rate was analyzed taking into account the time elapsed between samples, the percentage of unedited and edited genomes, and the complexity of the viral population. The longitudinal studies included 29 sequential samples from CHD patients followed up for a mean of 11.5 years. In total, 121,116 sequences were analyzed. The HDV evolution rate ranged from 9.5x10-3 to 1.2x10-3 substitutions/site/year and showed a negative correlation with the time elapsed between samples (p<0.05). An accumulation of transition-type changes was found to be responsible for higher evolution rates. The percentages of unedited and edited genomes and the quasispecies complexity showed no relationships with the evolution rate, but the fluctuations in the percentages of genomes and in complexity suggest continuous adaptation of HDV to the host conditions.