For 10 other samples for genotype 1, 8 for genotype 2 and 5 for genotype 4, classification was based on NS5B only, while for 15 samples genotype 1 , 5 genotype 2 and 11 genotype 4 , genotyping was based on core region only Table 4.
No phylogenetic relationship was found between the two sequences nor with previously described recombinant strains indicating the presence of two distinct viruses in both patients Fig.
Due to the large number of sequences obtained in this study, only sequences of the two putative recombinant viruses were shown in the phylogenetic trees. Phylogenetic trees of the sequences derived from the core and NS5B regions of the putative recombinant viruses described in this work.
The neighbour-joining tree is based on the core a and NS5B b sequences. The sequences of putative recombinant viruses described here are shown in bold. Previously reported recombinants in Cameroon are underlined [ 18 ]. The reliability of the tree topologies was estimated by bootstrap analysis with pseudoreplicate data sets and for clarity, all bootstrap less than 70 have been omitted.
Regarding the classification of HCV at the subtype level, subtype 4f was the more prevalent Among the sequences obtained in the core regions, subtype 1e was identified in 49 For In the NS5B regions, more subtypes were identified and 80 NS5B was not able to assign subtype for samples Therefore, HCV genotyping is essential for the therapeutic management of HCV infection and a variety of technologies have been developed for HCV genotypes determination.
In this study, amplification rates were high and similar for core and NS5B regions Other studies have reported different results with a higher amplification rate for the core region compared to NS5B [ 15 ]. Difficulty with NS5B region could sometimes be due to inadequate primer design, choice of highly polymorphic annealing sequences as well as low viral load [ 13 ]. In China, Cai et al. This situation could be explained by different HCV genetic diversity in both countries where genotypes 1, 3 and 6 are present in China, while genotypes 1, 2 and 4 are found in Cameroon.
HCV has a high genetic variability and our result is consistent with the genetic diversity of the virus in Cameroon where genotypes 1, 2 and 4 are found [ 3 , 4 ]. The great genetic diversity of HCV virus in Cameroon provides a good environment for the co-circulation of multiples genotypes and subtypes which could lead to dual infections and the emergence recombinants.
We found discordant genotypes with respect to core genotype 4 and NS5B genotype 1 in two samples 0. However, data presented here is insufficient to establish the two sequences as recombinants because only Sanger sequencing on nested RT-PCR fragments has been performed.
However, characterization of near full length genomes will be more informative and also will help to confirm the mosaic pattern of these two viruses by Simplot analysis. Two other cases involving the same genotypes were previously reported in Cameroon [ 15 ]. This could probably be explained by the fact that genotypes 1 and 4 are prevalent in Cameroon compared to genotype 2 [ 1 , 24 ]. Recombination is a common phenomenon that occurs during replication of RNA viruses and this impact diagnosis, treatment and follow-up of infected patients [ 21 ].
Although, this phenomenon is rare in HCV virus, we should pay more attention on it because it is relevant for clinical management of the infection regarding prognosis, natural history, and treatment recommendations as well as viral response [ 21 , 22 ]. Therefore, at least two regions should be used for HCV genotyping to identify recombinant viruses or multiple infections and help to improve the therapeutic management of infected patients.
This could be due to the fact that the NS5B gene has the highest phylogenetic signal compared to all the other HCV genes [ 3 ]. Therefore NS5B region is more suitable in epidemiological studies compared to core region [ 3 ].
Murphy et al. No intersubtype recombinant was identified, however, for some few samples, the subtypes was determined in one region and not classified in the other region. Our study has some limitations because no information on the treatment was available for all participants.
The high proportion of not classified samples at subtype level for both core and NS5B regions could be due to the lack of reference sequences of some subtypes in the phylogenetic analysis.
Data presented here is insufficient to establish the two sequences as recombinants. In this study, we found high amplification rates of HCV in both core and NS5B regions, and a good concordance was obtained at genotype level using both regions except for two samples where putative 1—4 recombinant strains were detected. However, even though recombination is rare in HCV infection, further studies are necessary to investigate clinical impacts of HCV recombinants. Global epidemiology of hepatitis C virus infection: an up-date of the distribution and circulation of hepatitis C virus genotypes.
World J Gastroenterol. Article Google Scholar. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Distribution and heterogeneity of hepatitis C genotypes in hepatitis patients in Cameroon. J Med Virol. Hepatitis C virus infection among pregnant women in Yaounde, Cameroon: prevalence, viremia, and genotypes. Direct-acting antivirals: the endgame for hepatitis C?
Curr Opin Virol. J Med Chem. Bioorg Med Chem Lett. Chen, Y. World J. Giannini, C. Prevalence of mixed infection by different hepatitis C virus genotypes in patients with hepatitis C virus-related chronic liver disease. Tuveri, R. Hepatitis C virus genotypes in French haemophiliacs: Kinetics and reappraisal of mixed infections.
CO;2-T Al Balwi, M. Saudi J. Kidney Dis. PubMed Google Scholar. Parodi, C. Hu, Y. Comparison and application of a novel genotyping method, semiautomated primer-specific and mispair extension analysis, and four other genotyping assays for detection of hepatitis C virus mixed-genotype infections. Nieto-Aponte, L. Assessment of a novel automatic real-time PCR assay on the Cobas analyzer as a screening platform for HCV Genotyping in clinical practice: comparison with massive sequencing.
Mallory, M. Sohn, Y. Yang, R. Performance comparison of the versant HCV genotype 2. Liu, C. Rodriguez, C. A novel standardized deep sequencing-based assay for hepatitis C virus genotype determination.
Farag, M. Molecular assay and genotyping of hepatitis C virus among infected egyptian and saudi arabian patients. S Article Google Scholar. Navarro, D. Prescott, L. Sequence analysis of hepatitis C virus variants producing discrepant results with two different genotyping assays. CO;2-E McNaughton, A. Prevalence of mixed genotype hepatitis C virus infections in the UK as determined by genotype-specific PCR and deep sequencing.
Barzon, L. Applications of next-generation sequencing technologies to diagnostic virology. Nakatani, S. Quer, J. High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods. Hnatyszyn, H. Chronic hepatitis C and genotyping: the clinical significance of determining HCV genotypes. Pawlotsky, J. HCV guidance: recommendations for testing, managing, and treating hepatitis C, www.
Bagaglio, S. Pham, S. Frequent multiple hepatitis C virus infections among injection drug users in a prison setting. Smith, J. Dynamic coinfection with multiple viral subtypes in acute hepatitis C. Cunningham, E. Mixed HCV infection and reinfection in people who inject drugs-impact on therapy. Janiak, M. Gaspareto, K. Arch Virol. Zakalashvili, M. Liver Int. Del Campo, J. Hepatitis C virus deep sequencing for sub-genotype identification in mixed infections: A real-life experience.
Louis, Missouri. He did additional postgraduate training at the National Institutes of Health in allergy and immunology. Hirsch also served as the chief of hepatology at the Washington, D. Hirsch has held faculty appointments at the medical schools of both Georgetown and George Washington Universities.
Hirsch has extensive clinical practice serving patients with the hepatitis C virus. He also has years of experience in pharmaceutical research. He has served on advisory boards for industry, national medical societies, and regulatory bodies. Hepatitis C treatments are costly, but can lead to undetectable viral loads — at which point a person is considered cured.
Learn how to manage your…. Rick Nash was diagnosed with hepatitis C when he was 12 years old. Find out what he wishes he knew when he was diagnosed and how he eventually reached….
Certain medications and supplements can cause more harm to your liver than good. They can also interfere with your hepatitis C treatments. Learn which…. When you live with hepatitis C, it's important to take extra care of yourself and your liver to prevent complications. Find out how your diet…. Health Conditions Discover Plan Connect. Medically reviewed by Alana Biggers, M.
Hirsch, MD — Updated on August 31, What are hepatitis C genotypes? Hepatitis C has different genotypes. What does this mean? What is the current research into genotypes and treatments for each type? Does genotype predict response to DAA therapy like it did for interferon therapy?
Genotype usually determines the type of treatment a person receives. Are there other factors that affect treatment? About the doctor. Read this next. Medically reviewed by Jill Seladi-Schulman, Ph. Medically reviewed by Cameron White, M.
0コメント