Next-Generation Sequencing of 5' Untranslated Region of Hepatitis C Virus in Search of Minor Viral Variant in a Patient Who Revealed New Genotype While on Antiviral Treatment

Next-generation sequencing analysis of new genotypes appearing during antiviral treatment of chronic hepatitis C reveals that these are selected from pre-existing minor strains

Coinfection with more than one hepatitis C virus (HCV) genotype is common, but its dynamics, particularly during antiviral treatment, remain largely unknown. We employed next-generation sequencing (NGS) to analyse sequential serum and peripheral blood mononuclear cell (PBMC) samples in seven patients with transient presence or permanent genotype change during antiviral treatment with interferon and ribavirin. Specimens were collected right before the therapy initiation and at 2, 4, 6, 8, 12, 20, 24, 36, 44 and 48 weeks during treatment and 6 months after treatment ceased. A mixture of two different genotypes was detected in the pretreatment samples from five patients and the minor genotype constituted 0.02 to 38 %. A transient or permanent change of the predominant genotype was observed in six patients. In three cases genotype 3 was replaced as the predominant genotype by genotype 4, in two cases genotype 3 was replaced by genotype 1, and in one subject genotype 1 was replaced by genotype 4. The PBMC- and serum-derived sequences were frequently discordant with respect to genotype and/or genotype proportions. In conclusion, pre-existing minor HCV genotypes can be selected rapidly during antiviral treatment and become transiently or permanently predominant. In coinfections involving genotype 3, genotype 3 was eliminated first from both the serum and PBMC compartments. The PBMC- and serum-derived HCV sequences were frequently discordant with respect to genotype and/or genotype proportions, suggesting that they constitute separate compartments with their own dynamics.

Virological and Immunological Outcomes of Coinfections

Coinfections involving viruses are being recognized to influence the disease pattern that occurs relative to that with single infection. Classically, we usually think of a clinical syndrome as the consequence of infection by a single virus that is isolated from clinical specimens. However, this biased laboratory approach omits detection of additional agents that could be contributing to the clinical outcome, including novel agents not usually considered pathogens. The presence of an additional agent may also interfere with the targeted isolation of a known virus. Viral interference, a phenomenon where one virus competitively suppresses replication of other coinfecting viruses, is the most common outcome of viral coinfections. In addition, coinfections can modulate virus virulence and cell death, thereby altering disease severity and epidemiology. Immunity to primary virus infection can also modulate immune responses to subsequent secondary infections. In this review, various virological mechanisms that determine viral persistence/exclusion during coinfections are discussed, and insights into the isolation/detection of multiple viruses are provided. We also discuss features of heterologous infections that impact the pattern of immune responsiveness that develops.

Next-Generation Sequencing of Hepatitis C Virus (HCV) Mixed-Genotype Infections in Anti-HCV-Negative Blood Donors

The infection with more than one hepatitis C virus (HCV) genotype especially in subjects with a high risk of multiple HCV exposures has been demonstrated. The role of HCV mixed-genotype infection in viral persistence and treatment effect is not fully understood. The prevalence of such infection varies greatly depending on the technique used for genotype determination and studied population. Next-generation sequencing (NGS) which is suitable for extensive analysis of complex viral populations is a method of choice for studying mixed infections. The aim of the present study was to determine the prevalence of mixed-genotype HCV infections in the Polish seronegative, HCV-RNA-positive blood donors (n = 76). Two-step PCR was used for amplification of 5'-UTR of HCV. Using pyrosequencing altogether, 381,063 reads were obtained. The raw reads were trimmed and subjected to similarity analysis against the entire unfiltered NCBI nt database. Results obtained from NGS were compared with the standard genotyping. One (1.3%) mixed-genotype [3a, 2989 reads (94.8%); 1b, 164 reads (5.2%)] infection was found in a sample diagnosed as genotype 3a only by routine testing. Two samples were identified with different genotypes, compared to routine testing. In conclusion, NGS is a sensitive method for HCV genotyping. The prevalence of mixed-genotype HCV infections in blood donors is low.