scholarly journals Time and Mode of Epidemic HCV-2 Subtypes Spreading in Europe: Phylodynamics in Italy and Albania

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 327
Author(s):  
Erika Ebranati ◽  
Alessandro Mancon ◽  
Martina Airoldi ◽  
Silvia Renica ◽  
Renata Shkjezi ◽  
...  
Keyword(s):  
Hepatitis C ◽  
African Origin ◽  
Effective Number ◽  
Phylogeographic Analysis ◽  
Exponential Increase ◽  
Genotype 2 ◽  
History Of ◽  
Prevalent Subtype ◽  
Hcv Genotype 2 ◽  
Phylodynamic Analysis

Hepatitis C virus (HCV) genotype 2 causes about 10% of global infections and has the most variable circulation profile in Europe. The history of “endemic” HCV-2 subtypes has been satisfactorily reconstructed, instead there is little information about the recent spread of the “epidemic” subtypes, including HCV-2c. To investigate the origin and dispersion pathways of HCV-2c, 245 newly characterized Italian and Albanian HCV-2 NS5B sequences were aligned with 247 publicly available sequences and included in phylogeographic and phylodynamic analyses using the Bayesian framework. Our findings show that HCV-2c was the most prevalent subtype in Italy and Albania. The phylogeographic analysis suggested an African origin of HCV-2c before it reached Italy about in the 1940s. Phylodynamic analysis revealed an exponential increase in the effective number of infections and Re in Italy between the 1940s and 1960s, and in Albania between the 1990s and the early 2000s. It seems very likely that HCV-2c reached Italy from Africa at the time of the second Italian colonization but did not reach Albania until the period of dramatic migration to Italy in the 1990s. This study contributes to reconstructing the history of the spread of epidemic HCV-2 subtypes to Europe.

scholarly journals Time And Mode Of Epidemic Hcv-2 Subtypes Dispersal In Europe: Phylodynamics Of Hcv-2c In Italy And Albania

2021 ◽  
Author(s):  
Erika Ebranati ◽  
Alessandro Mancon ◽  
Martina Airoldi ◽  
Silvia Renica ◽  
Renata Shkjezi ◽  
...  
Keyword(s):  
Bayesian Approach ◽  
Temporal Scale ◽  
Effective Number ◽  
Guinea Bissau ◽  
Exponential Increase ◽  
Replication Number ◽  
Prevalent Subtype ◽  
Spatio Temporal ◽  
Phylodynamic Analysis ◽  
The Bayesian Approach

Newly characterising 245 Italian and Albanian HCV-2 NS5B sequences collected between 2001 and 2016 was used to reconstruct the origin and dispersion pathways of HCV-2c. The tree of a subset of these sequences aligned with 247 publicly available sequences was reconstructed in spatio-temporal scale using the Bayesian approach, and the effective replication number (Re) was estimated using the birth-death model. Our findings show that HCV-2c was the most prevalent subtype in Italy and Albania, and that GT2 originated in Guinea Bissau in the XVI century and spread to Europe in the XX century. The HCV-2c subtype had two internal nodes respectively dating back to the 1930s and 1950s having as most probable locations Ghana and Italy, respectively. Phylodynamic analysis revealed an exponential increase in the effective number of infections and Re in both Italy between the 1950s and 1980s, and Albania between the 1990s and the early 2000s. It seems very likely that HCV-2c reached Italy from Africa at the time of the second Italian colonisation (1936-1941), but did not reach Albania until the period of dramatic migration to Italy in the 1990s.

scholarly journals Genetic History of Hepatitis C Virus in Venezuela: High Diversity and Long Time of Evolution of HCV Genotype 2

PLoS ONE ◽  
2010 ◽  
Vol 5 (12) ◽  
pp. e14315 ◽  
Author(s):  
Maria Z. Sulbarán ◽  
Federico A. Di Lello ◽  
Yoneira Sulbarán ◽  
Clarisa Cosson ◽  
Carmen L. Loureiro ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Hcv Genotype ◽  
Genetic History ◽  
Genotype 2 ◽  
Long Time ◽  
History Of ◽  
Hcv Genotype 2 ◽  
High Diversity

scholarly journals Full-length sequences of 11 hepatitis C virus genotype 2 isolates representing five subtypes and six unclassified lineages with unique geographical distributions and genetic variation patterns

2012 ◽  
Vol 93 (6) ◽  
pp. 1173-1184 ◽  
Author(s):  
Chunhua Li ◽  
Hong Cao ◽  
Ling Lu ◽  
Donald Murphy
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Complete Genome ◽  
Pcr Amplification ◽  
Full Length ◽  
African Origin ◽  
Genome Sequences ◽  
Virus Genotype ◽  
Variation Patterns ◽  
Genotype 2

In this study, we characterized full-length hepatitis C virus (HCV) genome sequences for 11 genotype 2 isolates. They were isolated from the sera of 11 patients residing in Canada, of whom four had an African origin. Full-length genomes, each with 18–25 overlapping fragments, were obtained by PCR amplification. Five isolates represent the first complete genomes of subtypes 2d, 2e, 2j, 2m and 2r, while the other six correspond to variants that do not group within any assigned subtypes. These sequences had lengths of 9508–9825 nt and each contained a single ORF encoding 3012–3106 aa. Predicted amino acids were carefully inspected and unique variation patterns were recognized, especially for a 2e isolate, QC64. Phylogenetic analysis of complete genome sequences provides evidence that there are a total of 16 subtypes, of which 11 have been described here. Co-analysis with 68 partial NS5B sequences also differentiated 18 assigned subtypes, 2a–2r, and eight additional lineages within genotype 2, which is consistent with the analysis of complete genome sequences. The data from this study will now allow 10 assigned subtypes and six additional lineages of HCV genotype 2 to have their full-length genomes defined. Further analysis with 2021 genotype 2 sequences available in the HCV database indicated that the geographical distribution of these subtypes is consistent with an African origin, with particular subtypes having spread to Asia and the Americas.

scholarly journals Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa

PLoS ONE ◽  
2016 ◽  
Vol 11 (4) ◽  
pp. e0153761 ◽  
Author(s):  
Mouna Rajhi ◽  
Kais Ghedira ◽  
Anissa Chouikha ◽  
Ahlem Djebbi ◽  
Imed Cheikh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
North Africa ◽  
Virus Genotype ◽  
Genotype 2 ◽  
History Of

scholarly journals Epidemic history of hepatitis C virus infection in two remote communities in Nigeria, West Africa

2012 ◽  
Vol 93 (7) ◽  
pp. 1410-1421 ◽  
Author(s):  
Joseph C. Forbi ◽  
Michael A. Purdy ◽  
David S. Campo ◽  
Gilberto Vaughan ◽  
Zoya E. Dimitrova ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
20Th Century ◽  
Hypervariable Region ◽  
Hcv Infection ◽  
Genotype 1 ◽  
Remote Communities ◽  
African Countries ◽  
Genotype 2 ◽  
History Of

We investigated the molecular epidemiology and population dynamics of HCV infection among indigenes of two semi-isolated communities in North-Central Nigeria. Despite remoteness and isolation, ~15 % of the population had serological or molecular markers of hepatitis C virus (HCV) infection. Phylogenetic analysis of the NS5b sequences obtained from 60 HCV-infected residents showed that HCV variants belonged to genotype 1 (n = 51; 85 %) and genotype 2 (n = 9; 15 %). All sequences were unique and intermixed in the phylogenetic tree with HCV sequences from people infected from other West African countries. The high-throughput 454 pyrosequencing of the HCV hypervariable region 1 and an empirical threshold error correction algorithm were used to evaluate intra-host heterogeneity of HCV strains of genotype 1 (n = 43) and genotype 2 (n = 6) from residents of the communities. Analysis revealed a rare detectable intermixing of HCV intra-host variants among residents. Identification of genetically close HCV variants among all known groups of relatives suggests a common intra-familial HCV transmission in the communities. Applying Bayesian coalescent analysis to the NS5b sequences, the most recent common ancestors for genotype 1 and 2 variants were estimated to have existed 675 and 286 years ago, respectively. Bayesian skyline plots suggest that HCV lineages of both genotypes identified in the Nigerian communities experienced epidemic growth for 200–300 years until the mid-20th century. The data suggest a massive introduction of numerous HCV variants to the communities during the 20th century in the background of a dynamic evolutionary history of the hepatitis C epidemic in Nigeria over the past three centuries.

scholarly journals Performance of Three Common Hepatitis C Virus (HCV) Genotyping Assays for Identification of HCV Genotype 2/1 Chimeras

2019 ◽  
Vol 57 (7) ◽  
Author(s):  
Kai-Henrik Peiffer ◽  
Lisa Kuhnhenn ◽  
Evelyn Stelzl ◽  
Julia Dietz ◽  
Simone Susser ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Real Time ◽  
Real Time Pcr ◽  
Hcv Genotype ◽  
Hcv Genotypes ◽  
The Real ◽  
Genotype 2 ◽  
Hcv Genotype 2 ◽  
Genotype Ii

ABSTRACT Besides seven major hepatitis C virus (HCV) genotypes (GT), a number of intergenotypic recombinant strains have been described. These so-called chimeras combine genetic characteristics of different HCV genotypes. However, correct genotype classification is important, as choice and duration of direct-acting antiviral (DAA) treatment is mainly based on the viral genotype. Therefore, misclassification of chimeras might lead to suboptimal treatment of patients infected with these strains. For example, 2k/1b chimeras are typically described as HCV genotype 2 strains by commercially available hybridization assays, but real-time PCR-based tests recognizing another HCV region might be more suitable for correct chimera detection. In this study, the analytic capacity of the hybridization-assay Versant HCV Genotype 2.0 (LiPA 2.0) and the real-time PCR-based-assays cobas HCV GT and Abbott RealTime HCV Genotype II were tested in a selected cohort of 230 patients infected with HCV genotype 1 (n = 53) and 2 (n = 177) and 48 patients infected with HCV 2/1 chimeric strains. While the Versant HCV Genotype 2.0 (LiPA 2.0) assay failed to identify chimeras in all of the patients (48/48, 100%), cobas HCV GT and Abbott HCV Genotype II assays identified chimeras correctly in 90% (43/48) and 65% (31/48) of the cases, respectively. In conclusion, while the hybridization-based Versant HCV Genotype 2.0 (LiPA 2.0) assay seems to be unsuitable for detection of HCV 2/1 chimeras, use of the real-time PCR-based assays cobas HCV GT and Abbott RealTime HCV Genotype II led to a higher rate of chimera detection.

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