Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes

@article{Simmonds2005ConsensusPF,
  title={Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes},
  author={Peter Simmonds and Jens Bukh and Christophe Combet and Gilbert Del{\'e}age and Nobuyuki Enomoto and Stephen M. Feinstone and Phillippe Halfon and Geneviève Inchauspé and Carla Kuiken and Geert Maertens and Masashi Mizokami and Donald G. Murphy and Hiroaki Okamoto and Jean Michel Pawlotsky and François Penin and Erwin Sablon and Tadasu Shin-I and Lieven J Stuyver and H. J. Thiel and Sergei Viazov and Amy J. Weiner and Anders Widell},
  journal={Hepatology},
  year={2005},
  volume={42}
}
International standardization and coordination of the nomenclature of variants of hepatitis C virus (HCV) is increasingly needed as more is discovered about the scale of HCV‐related liver disease and important biological and antigenic differences that exist between variants. A group of scientists expert in the field of HCV genetic variability, and those involved in development of HCV sequence databases, the Hepatitis Virus Database (Japan), euHCVdb (France), and Los Alamos (United States), met… 
Nomenclature and numbering of the hepatitis C virus.
TLDR
A group of experts in the field of HCV genetic variability, and those involved in development ofHCV sequence databases, drew up revised criteria for the assignment of new genotypes as they are discovered in the future and discussed how HCV sequences databases could introduce and facilitate a standardized numbering system.
Expanded Classification of Hepatitis C Virus Into 7 Genotypes and 67 Subtypes: Updated Criteria and Genotype Assignment Web Resource
TLDR
This study represents a major update to the previous consensus HCV classification, incorporating additional sequence information derived from over 1,300 (near‐)complete genome sequences of HCV available on public databases in May 2013.
Classification, Genetic Diversity and Global Distribution of Hepatitis C Virus (HCV) Genotypes and Subtypes
TLDR
The genetic diversity of HCV is higher than that of the human immunodeficiency virus type 1 (HIV-1) and hepatitis B virus (HBV), because HCV has been infecting humans for a longer time period compared to HIV-1 and does not have the overlapping reading frames present in HBV, which constrain the molecular evolution of HBV.
Hepatitis C Virus Genotypes and Their Evolution
TLDR
Analysis of the hepatitis C virus genome showed that the viruses evolved along with their hosts and that, worldwide, HCV should be classified into seven major genotypes with their serial subtypes.
A New Subtype of Hepatitis C Virus Genotype 3: Analysis of Available Evidence
TLDR
Assessment of the relatedness of isolate FM165 together with several sequences retrieved from the database to the new HCV-3 subtype reported from Iran in 2006 suggests that the new subtype has a vast geographical distribution in Iran.
A new subtype of hepatitis C virus genotype 1: complete genome and phylogenetic relationships of an Equatorial Guinea isolate.
TLDR
The complete genome sequence of an HCV genotype 1 isolate from Equatorial Guinea is reported, the first complete HCV-1 genome of African origin and it is proposed that this isolate is a representative of a new, distinct variant of HCV subtype 1.
Genetic Variability and the Classification of Hepatitis E Virus
TLDR
Analysis of complete genome sequences or concatenated ORF1/ORF2 amino acid sequences indicated that HEV variants most closely related to those infecting humans can be consistently divided into six genotypes, which may form the basis for a future genetic classification of HEV into four species.
euHCVdb: the European hepatitis C virus database
TLDR
The European Hepatitis C Virus Database is described, a collection of computer-annotated sequences based on reference genomes, mainly dedicated to HCV protein sequences, 3D structures and functional analyses.
Recombination in Hepatitis C Virus
TLDR
The literature considering the reasons underlying the difficulties for unequivocally establishing recombination in this virus along with the analytical methods necessary to do it is reviewed and the potential consequences, especially in clinical practice, of HCV recombination are analyzed in light of the coming new therapeutic approaches against this virus.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 101 REFERENCES
Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization
TLDR
Recommendations are presented that existing subtype designations are reassigned within these clades based upon publication priority, the existence of a complete genome sequence and prevalence, and the assignment of isolates to new clades and subtypes should be confined to isolates characterized from epidemiologically unlinked individuals.
Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: comparison with classifications based upon sequence similarity.
Variants of hepatitis C virus (HCV) have been classified by nucleotide sequence comparisons in different regions of the genome. Many investigators have defined the ranges of sequence similarity
Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region.
TLDR
A new nomenclature for HCV variants is proposed in this communication that reflects the two-tiered nature of sequence differences between different viral isolates and describes criteria that would enable new variants to be assigned within the classification as they are discovered.
Genotype determination of hepatitis C virus from Northern India: Identification of a new subtype
TLDR
The type 3 variants including a new subtype (3g) to be the major cause of HCV infection in India are demonstrated.
Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: implications for virus classification. The International HCV Collaborative Study Group.
TLDR
The existence of great diversity within a single genotype was also found amongst type 3 sequences in the Indian subcontinent, amongst type 4 variants in Central Africa and the Middle East, and amongst type variants in Nigeria.
Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants.
TLDR
Phylogenetic analysis revealed the existence of three distinct groups of sequences that corresponded to the recently described HCV types 1 and 2 variants, while viral sequences detected in around a third of the blood donors formed a separate phylogenetic group that probably represents infection with a novel virus species.
Evidence of intratypic recombination in natural populations of hepatitis C virus.
TLDR
Three different genomic regions of four HCV strains isolated from Peruvian patients were sequenced in order to investigate the congruence of HCV genotyping for these three genomic regions, revealing that a crossover event had taken place in the NS5B protein.
A novel hepatitis C virus (HCV) subtype from Somalia and its classification into HCV clade 3.
TLDR
Phylogenetic analysis of the sequences of the core, envelope 1 and part of the non- structural 5b regions suggests that all three isolates belong to a distinct HCV genetic group, tentatively classified as subtype 3h, which shows the highest sequence similarity with HCV isolates from Indonesia.
The origin and evolution of hepatitis viruses in humans.
  • P. Simmonds
  • Biology, Medicine
    The Journal of general virology
  • 2001
TLDR
The spread and origins of hepatitis C virus (HCV) in human populations have been the subject of extensive investigations, but the relatively recent times predicted for the origin of these viruses fit poorly with their epidemiological distributions and the recent evidence for species-associated variants of HBV and HGV/GBV-C in a wide range of non-human primates.
...
1
2
3
4
5
...