Evidence of intratypic recombination in natural populations of hepatitis C virus

Colina, Rodney; Casañe, Didier; Vásquez, Silvia; García-Aguirre, Laura; Chunga, Ausberto; Romero, Héctor; Khan, Baldip; Cristina, Juan

doi:10.1099/vir.0.19472-0

Cited by 114 publications

(92 citation statements)

References 52 publications

(43 reference statements)

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“…Only one of the intragenotype recombinants described involved genotype 4 [140] , four involved different subtypes of genotype 1 and the remaining four involved different subtypes of genotype 6. Examples of recombinants (1a/1b) have been identified in Peru as well as in Uruguay [111,141] and (1a/1c) in Japan and in India [142,143] . Interestingly, although the recombinants reported in Modified from ref.…”

Section: Recombinationmentioning

confidence: 99%

Hepatitis C virus genetic variability and evolution

Echeverría

Moratorio

Cristina

et al. 2015

WJH

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Hepatitis C virus (HCV) has infected over 170 million people worldwide and creates a huge disease burden due to chronic, progressive liver disease. HCV is a singlestranded, positive sense, RNA virus, member of the Flaviviridae family. The high error rate of RNA-dependent RNA polymerase and the pressure exerted by the host immune system, has driven the evolution of HCV into 7 different genotypes and more than 67 subtypes. HCV evolves by means of different mechanisms of genetic variation. On the one hand, its high mutation rates generate the production of a large number of different but closely related viral variants during infection, usually referred to as a quasispecies. The great quasispecies variability of HCV has also therapeutic implications since the continuous generation and selection of resistant or fitter variants within the quasispecies spectrum might allow viruses to escape control by antiviral drugs. On the other hand HCV exploits recombination to ensure its survival. This enormous viral diversity together with some host factors has made it difficult to control viral dispersal. Current treatment options involve pegylated interferon-α and ribavirin as dual therapy or in combination with a direct-acting antiviral drug, depending on the country. Despite all the efforts put into antiviral therapy studies, eradication of the virus or the development of a preventive vaccine has been unsuccessful so far. This review focuses on current available data reported to date on the genetic mechanisms driving the molecular evolution of HCV populations and its relation with the antiviral therapies designed to control HCV infection. Hepatitis C virus genetic variability and evolution no preventive vaccine, and though antiviral therapy has been improved in the past few years, not all patients eradicate the virus as a result of it. The main reason lies in the intrinsic genetic variability that characterises RNA viruses, such as HCV, whose RNA polymerase lacks proof-reading activity, leading to a high mutation rate and the generation of a wide range of genome variants better known as a quasispecies. Therefore this review summarises current data on HCV quasispecies dynamics, antiviral therapy and recombination events.Echeverría N, Moratorio G, Cristina J, Moreno P. Hepatitis C virus genetic variability and evolution. World J Hepatol 2015; 7(6): 831845 Available from:

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Section: Recombinationmentioning

confidence: 99%

Hepatitis C virus genetic variability and evolution

Echeverría

Moratorio

Cristina

et al. 2015

WJH

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“…Recombination crossover point was NS5B in the intra-genotype recombination case found in Peru, not in the genome coding the first non-structural protein. [Colina et al, 2004 The genotype of HCV influences on the outcome of interferon treatment [Zein, 2000] and the interferon sensitivity has been attributed to the sequence variability of NS5A and E2. [Gale et al, 1998;Gale et al, 1997;Pavio et al, 2002;Polyak et al, 2001;Taylor et al, 2005;Taylor et al, 1999] The recombination events at NS2 in St Petersburg [Kalinina et al, 2002] Bootstrap values (>70%) are given on blanches as percentages from 1,000…”

Section: Identification Of the Recombination Crossover Pointmentioning

confidence: 99%

“…In fact, the natural inter-and intra-genotypic recombinants of HCV (RF1_2k/1b and RF2_1a/1b) were recently found and the crossover points were clearly indicated in NS2 and NS5B regions, respectively. [Colina et al, 2004;Kalinina et al, 2002] The HCV recombination has been reported only in these cases to date. [Simmonds et al, 2005] Several studies reported that the positive rate for anti-HCV was 2.2% among blood donors (Metro Davao, 1990) [Arguillas et al, 1991], and 4.6% among inmates (Metro Manila) [Katayama et al, 1996] in the Philippines.…”

Section: Introductionmentioning

confidence: 99%

A natural inter-genotypic (2b/1b) recombinant of hepatitis C virus in the Philippines

Kageyama

Agdamag

Alesna³

et al. 2006

J. Med. Virol.

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The prevalence study and the characterization of hepatitis C virus (HCV) have been carried out in the Philippines and the sequence determination of 5'-untranslated region (5'-UTR)-Core and NS5B regions of HCV was performed in this study. An HCV strain (SE-03-07-1689) collected in Metro Manila, Philippines, belonged to discordant subtypes, 2b and 1b in 5'-UTR-Core and NS5B regions, respectively. The 9.3kb-sequence of this strain including the entire open reading frame were compared with those of the reference strains retrieved from the HCV sequences database (GenBank/EMBL/DDBJ) and indicated a recombination event.The computation of the sequence similarity mapped a crossover point within NS3region. This is the second report on the inter-genotype recombinant of HCV and the third one when an intra-genotype recombinant is included. This recombinant strain, SE-03-07-1689, is tentatively designated as RF3_2b/1b according to the suggestions used for other two HCV recombinants.

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“…An instance of such inter-genotypic recombination was observed between genotype 2k and 1b in St. Petersburg by Kalinina et al [9]. Colina et al [6] reported intra-typic recombination between genotype 1a and 1b. The potential for the emergence of novel genetic variants is high due to the increasing subtype diversity in various sub populations.…”

mentioning

confidence: 93%

Diversity of Hepatitis C virus in Southern India Based on 5′UTR Sequence

2012

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Hepatitis C virus (HCV) exhibits genotypespecific variations in geographical distribution as a consequence of drug and immune induced evolution. Present study was aimed at discerning the distribution and prevalence of the various genotypes and subtypes of HCV in southern India. The HCV positive patient's serum was collected from different hospitals and blood banks from the states of Kerala, Tamil Nadu, Andhra Pradesh and Karnataka. Among 114 HCV positive samples, we could find only 44 isolates that are found both positive in ELISA and RT-PCR. From these samples 5 0 untranslated region (5 0 UTR) were amplified, sequenced and sub typed. Analysis of 5 0 UTR region of the 44 isolates shows that, genotypes 1, 3, 4 and 6 are present with genotype 3 being the most frequent. The present study shows that HCV genotype 3 subtype B was the most prevalent, forming 47.7 % among the population in southern India. The present study urges for discovering novel therapeutic agents that should be specific to genotype 3 subtype B, for the management of HCV in southern India.Hepatitis C virus (HCV, genus: Hepacivirus, family: Flaviviridae) exists as six major genotypes and more than 60 defined subtypes. The genomic sequences of different HCV genotypes vary by 30-35 % between genotypes and by 20-25 % between subtypes [19]. Such genetic heterogeneity accounts for several of the differences observed in the prognosis of the disease, as well as in the differences seen in response to prophylactic treatment procedures. For example, in individuals infected with HCV genotype 1, complete and permanent clearance of the infection has been observed in only 10-20 % of those on monotherapy with interferon and 40-50 % in those on combination therapy with interferon and ribavirin. The disease tends to be chronic in the rest, ultimately ending in hepatocellular carcinoma. However, in the case of type 2 and 3, 50 % on mono-therapy and 70-80 % on combination therapy show sustained clearance of the virus [15,26

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Evidence of intratypic recombination in natural populations of hepatitis C virus

Cited by 114 publications

References 52 publications

Hepatitis C virus genetic variability and evolution

Hepatitis C virus genetic variability and evolution

A natural inter-genotypic (2b/1b) recombinant of hepatitis C virus in the Philippines

Diversity of Hepatitis C virus in Southern India Based on 5′UTR Sequence

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