Evolution of hepatitis C virus variants following blood transfusion from one infected donor to several recipients: a long-term follow-up

Characterization of Hepatitis C Virus (HCV) Envelope Diversification from Acute to Chronic Infection within a Sexually Transmitted HCV Cluster by Using Single-Molecule, Real-Time Sequencing

In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d. In total, 50 samples were analyzed by using SMRT sequencing. By using 7 passes of circular consensus sequencing, the error rate was reduced to 0.37%, and the median number of sequences was 612 per sample. A further reduction of insertions was achieved by alignment against a sample-specific reference sequence. However, in vitro recombination during PCR amplification could not be excluded. Phylogenetic analysis supported close relationships among HCV sequences from the four male subjects and subsequent transmission from one subject to his female partner. Transmission was characterized by a strong genetic bottleneck. Viral genetic diversity was low during acute infection and increased upon progression to chronicity but subsequently fluctuated during chronic infection, caused by the alternate detection of distinct coexisting lineages. SMRT sequencing combines long reads with sufficient depth for many phylogenetic analyses and can therefore provide insights into within-host HCV evolutionary dynamics without the need for haplotype reconstruction using statistical algorithms.IMPORTANCE Next-generation sequencing has revolutionized the study of genetically variable RNA virus populations, but for phylogenetic and evolutionary analyses, longer sequences than those generated by most available platforms, while minimizing the intrinsic error rate, are desired. Here, we demonstrate for the first time that PacBio SMRT sequencing technology can be used to generate full-length HCV envelope sequences at the single-molecule level, providing a data set with large sequencing depth for the characterization of intrahost viral dynamics. The selection of consensus reads derived from at least 7 full circular consensus sequencing rounds significantly reduced the intrinsic high error rate of this method. We used this method to genetically characterize a unique transmission cluster of sexually transmitted HCV infections, providing insight into the distinct evolutionary pathways in each patient over time and identifying the transmission-associated genetic bottleneck as well as fluctuations in viral genetic diversity over time, accompanied by dynamic shifts in viral subpopulations.

Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source

BACKGROUND

Molecular phylogenetic analyses are used increasingly in the epidemiological investigation of outbreaks and transmission cases involving rapidly evolving RNA viruses. Here, we present the results of such an analysis that contributed to the conviction of an anesthetist as being responsible for the infection of 275 of his patients with hepatitis C virus.

RESULTS

We obtained sequences of the NS5B and E1-E2 regions in the viral genome for 322 patients suspected to have been infected by the doctor, and for 44 local, unrelated controls. The analysis of 4,184 cloned sequences of the E1-E2 region allowed us to exclude 47 patients from the outbreak. A subset of patients had known dates of infection. We used these data to calibrate a relaxed molecular clock and to determine a rough estimate of the time of infection for each patient. A similar analysis led to an estimate for the time of infection of the source. The date turned out to be 10 years before the detection of the outbreak. The number of patients infected was small at first, but it increased substantially in the months before the detection of the outbreak.

CONCLUSIONS

We have developed a procedure to integrate molecular phylogenetic reconstructions of rapidly evolving viral populations into a forensic setting adequate for molecular epidemiological analysis of outbreaks and transmission events. We applied this procedure to a large outbreak of hepatitis C virus caused by a single source and the results obtained played a key role in the trial that led to the conviction of the suspected source.

Increased risk of transmission of hepatitis C in open heart surgery compared with vascular and pulmonary surgery

BACKGROUND

We report a case of patient-to-surgeon transmission of hepatitis C virus (HCV), and the subsequent transmission of HCV to surgical patients.

METHODS

In 2007, a cardiac surgeon tested positive for hepatitis C. A complete look-back investigation was initiated that involved screening of all patients on the surgeon's operating lists between September 2004 and April 2007. Genotyping and phylogenetic analyses were performed where HCV RNA was detected.

RESULTS

Of the 499 patients invited to HCV testing, 431 responded, 13 of whom were found anti-HCV positive. One patient, who had surgery in August 2005, was found most likely to be the source of transmission to the surgeon. Of the 270 patients who had surgery after this incident, 10 became infected, giving an estimated rate of transmission of 3.7%. The HCV polymerase chain reaction positive samples were found to be the same genotype 1a strain by phylogenetic analyses. All the 10 subsequently infected patients had undergone open heart surgery, whereas none of the 103 noncardiac patients became infected, giving an estimated risk of transmission during open heart surgery of 6.0% (95% confidence interval [3.3% to 10.7%]).

CONCLUSIONS

The transmission rate from an HCV positive surgeon to patients in a cardiothoracic setting was higher than previously reported and significantly higher during open heart surgery compared with vascular and pulmonary surgery. These results indicate the need for unequivocal routines for testing and handling of HCV positive health care workers and patients.

The epidemiology of hepatitis C infection in the United States

BACKGROUND

The prevalence of hepatitis C virus (HCV) infection in the United States has remained constant from 1988 through 2002, although the peak age of infection has increased. While the number of new HCV cases is declining, the rates of HCV-associated morbidity and mortality are increasing. We reviewed the risk factors for HCV infection, the laboratory methods used to diagnose it, the dynamics of disease progression, and the natural history of HCV infection.

METHODS

Medline searches were performed using the key word HCV, together with incidence, risk factors, demographics, diagnostic methods, disease progression, natural history, normal alanine aminotransferase (ALT), fibrosis, and hepatocellular carcinoma (HCC).

RESULTS

Three characteristics-abnormal serum ALT, history of injection drug use, and blood transfusion before 1992-identified 85% of HCV-positive individuals 20-59 years old. About 75%-85% of acutely infected individuals progress to chronic infection, with up to 20% developing liver cirrhosis over 20-25 years, putting them at increased risk for end-stage liver disease and/or HCC. HCV-associated cirrhosis is the leading cause of liver transplantation in the United States. Rates of infection are higher in non-Hispanic blacks than in non-Hispanic whites and Mexican Americans and higher in men than in women. In the United States, over 70% of HCV-infected individuals are infected with genotype 1.

CONCLUSIONS

HCV infection is more prevalent than human immunodeficiency virus or hepatitis B virus infection and is particularly common among certain demographic groups. Individual rates of fibrosis progression vary, but identification of host and viral characteristics associated with disease progression may reveal the mechanisms of HCV-associated hepatic fibrosis/cirrhosis.

High genetic variability and evidence for plant-to-plant transfer of Banana mild mosaic virus

A total of 154 partial nucleotide sequences within the Banana mild mosaic virus (BanMMV) ORF1, which encodes the viral RNA-dependent RNA polymerase (RdRp), was obtained from 68 distinct infected banana accessions originating from various locations worldwide. The 310 nt sequences displayed a high level of variability with a mean pairwise nucleotide sequence divergence level of 20.4 %. This situation resulted essentially from a high rate of synonymous mutations. A similar analysis was performed for a limited selection of 10 banana accessions (30 sequences) on the region comprising approximately the last 310 nt of the BanMMV genome. This region corresponds to the 3' end of ORF5, which encodes the coat protein (234 nt), and to the 3' non-coding region. This analysis confirmed the high level of diversity observed in the RdRp dataset, characterized by a high level of synonymous mutations. Analysis of intra-host diversity indicated the existence of two distinct situations, with some plants containing only closely related sequence variants, whereas others contained widely divergent isolates. Analyses indicated that BanMMV genetic diversity is not structured by the geographical origin of the infected Musa accessions or by their genotype. This situation may be, in part, explained by the exchange of banana germplasm between different parts of the world and also by plant-to-plant transfer of virus isolates, the evidence for which is, for the first time, provided by this study.

Strategically examining the full-genome of dengue virus type 3 in clinical isolates reveals its mutation spectra

BACKGROUND

Previous studies presented the quasispecies spectrum of the envelope region of dengue virus type 3 (DENV-3) from either clinical specimens or field-caught mosquitoes. However, the extent of sequence variation among full genomic sequences of DENV within infected individuals remains largely unknown.

RESULTS

Instead of arbitrarily choosing one genomic region in this study, the full genomic consensus sequences of six DENV-3 isolates were used to locate four genomic regions that had a higher potential of sequence heterogeneity at capsid-premembrane (C-prM), envelope (E), nonstructural protein 3 (NS3), and NS5. The extent of sequence heterogeneity revealed by clonal sequencing was genomic region-dependent, whereas the NS3 and NS5 had lower sequence heterogeneity than C-prM and E. Interestingly, the Phylogenetic Analysis by Maximum Likelihood program (PAML) analysis supported that the domain III of E region, the most heterogeneous region analyzed, was under the influence of positive selection.

CONCLUSION

This study confirmed previous reports that the most heterogeneous region of the dengue viral genome resided at the envelope region, of which the domain III was under positive selection pressure. Further studies will need to address the influence of these mutations on the overall fitness in different hosts (i.e., mosquito and human) during dengue viral transmission.

Diverse hepatitis C virus glycoproteins mediate viral infection in a CD81-dependent manner

We recently reported that retroviral pseudotypes bearing the hepatitis C virus (HCV) strain H and Con1 glycoproteins, genotype 1a and 1b, respectively, require CD81 as a coreceptor for virus-cell entry and infection. Soluble truncated E2 cloned from a number of diverse HCV genotypes fail to interact with CD81, suggesting that viruses of diverse origin may utilize different receptors and display altered cell tropism. We have used the pseudotyping system to study the tropism of viruses bearing diverse HCV glycoproteins. Viruses bearing these glycoproteins showed a 150-fold range in infectivity for hepatoma cells and failed to infect lymphoid cells. The level of glycoprotein incorporation into particles varied considerably between strains, generally reflecting the E2 expression level within transfected cells. However, differences in glycoprotein incorporation were not associated with virus infectivity, suggesting that infectivity is not limited by the absolute level of glycoprotein. All HCV pseudotypes failed to infect HepG2 cells and yet infected the same cells after transduction to express human CD81, confirming the critical role of CD81 in HCV infection. Interestingly, these HCV pseudotypes differed in their ability to infect HepG2 cells expressing a panel of CD81 variants, suggesting subtle differences in the interaction of CD81 residues with diverse viral glycoproteins. Our current model of HCV infection suggests that CD81, together with additional unknown liver specific receptor(s), mediate the virus-cell entry process.