Full-length and partial genome sequences of four members of the genus Aquareovirus, family Reoviridae (Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus) were characterized. Based on sequence comparison, the unclassified Grass carp reovirus was shown to be a member of the species Aquareovirus C. The status of golden ide reovirus, another unclassified aquareovirus, was also examined. Sequence analysis showed that it did not belong to the species Aquareovirus A or C, but assessment of its relationship to the species Aquareovirus B, D, E and F was hampered by the absence of genetic data from these species. In agreement with previous reports of ultrastructural resemblance between aquareoviruses and orthoreoviruses, genetic analysis revealed homology in the genes of the two groups. This homology concerned eight of the 11 segments of the aquareovirus genome (amino acid identity 17-42 %), and similar genetic organization was observed in two other segments. The conserved terminal sequences in the genomes of members of the two groups were also similar. These data are undoubtedly an indication of the common evolutionary origin of these viruses. This clear genetic relatedness between members of distinct genera is unique within the family Reoviridae. Such a genetic relationship is usually observed between members of a single genus. However, the current taxonomic classification of aquareoviruses and orthoreoviruses in two different genera is supported by a number of characteristics, including their distinct GMC contents, unequal numbers of genome segments, absence of an antigenic relationship, different cytopathic effects and specific econiches.

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Hepatitis C virus (HCV) isolates have been classified into six main genotypes. Genotyping methods, and especially the widely used line probe assay (LiPA), are frequently based on the 5-untranslated region (5UTR). However, this region is not appropriate for discriminating HCV strains at the subtype level and for distinguishing many genotype 6 samples from genotype 1. We investigated the capacity of a novel LiPA (Versant HCV Genotype 2.0 assay) based on the simultaneous detection of 5UTR and Core regions for genotypes 1 and 6 to provide correct HCV genotypes (characterized with a phylogenetic analysis) in a set of HCV strains mainly encountered in Western countries. The improvement was assessed by comparing the results to those obtained with the previous version of the assay. Of the 135 tested samples, 64.7% were concordant for genotype group and subtype with sequencing reference results using the Versant HCV Genotype 2.0 assay versus 37.5% with the previous version. The yield was mainly related to a better characterization of genotype 1, since the accuracy, tested in 62 genotype 1 samples, increased from 45.2% with the first version to 96.8% with the new one. However, this new version necessitates a specific PCR and could no longer be used after 5UTR PCR used for current HCV infection diagnosis. Moreover, the information provided by 5UTR hybridization is not reliable for correctly identifying the diversity within genotypes 2 and 4. Thus, the Versant HCV Genotype 2.0 assay remains a useful tool for clinical practice when only the discrimination between major HCV genotypes is necessary.

An aquareovirus was isolated from several fish species in the USA (including healthy golden shiners) that is not closely related to members of species Aquareovirus A, B and C. The virus, which is atypical (does not cause syncytia in cell cultures at neutral pH), was implicated in a winter die-off of grass carp fingerlings and has therefore been called 'American grass carp reovirus' (AGCRV). Complete nucleotide sequence analysis of the AGCRV genome and comparisons to the other aquareoviruses showed that it is closely related to golden ide reovirus (GIRV) (>92% amino acid [aa] identity in VP5(NTPase) and VP2(Pol)). However, comparisons with grass carp reovirus (Aquareovirus C) and chum salmon reovirus (Aquareovirus A) showed only 22% to 76% aa identity in different viral proteins. These findings have formed the basis for the recognition of AGCRV and GIRV as members of a new Aquareovirus species 'Aquareovirus G' by ICTV. Further sequence comparisons to other members of the family Reoviridae suggest that there has been an 'evolutionary jump,' involving a change in the number of genome segments, between the aquareoviruses (11 segments) and coltiviruses (12 segments). Segment 7 of AGRCV encodes two proteins, from two distinct ORFs, which are homologues of two Coltivirus proteins encoded by genome segments 9 and 12. A similar model has previously been reported for the rotaviruses and seadornaviruses.

The 5 noncoding region (5 NCR) of the hepatitis C virus (HCV) has become the standard for genotyping even though several reports show that its use can result in classification errors. The purpose of this study was to perform genotyping based on sequence analysis of the NS5b region in a set of 357 HCV strains isolated from blood donors in France in 2002 and 2003. Results were compared with those previously obtained using 5 NCR analysis, and HCV subtype distribution was reevaluated. Twenty-six of 120 strains (ϳ22%) initially identified as genotype 1b by 5 NCR region sequence analysis were reclassified as genotype 1a by NS5b region sequence analysis. Similarly, 14 of 23 strains (ϳ61%) initially identified as 2a/2c were reclassified as non-2a and non-2c subtypes, and 12 of 22 strains (ϳ45%) initially identified as 4c/4d subtypes were reclassified as non-4c and non-4d subtypes. Sequence analysis of the NS5b region also revealed 5 putative new subtype 2 variants and 2 putative new subtype 4 variants. Although these findings demonstrated full agreement between 5 NCR and NS5b sequence analysis with regard to type classification, genotyping based on phylogenetic analysis of the NS5b region is more accurate for subtype determination than genotyping based on analysis of the 5 NCR. Sequence analysis of the NS5b region is mandatory for epidemiologic studies.Hepatitis C virus (HCV) is a common human pathogen considered as the major cause of parenterally transmitted hepatitis (6). It is an enveloped virus with a positive-sense RNA genome containing a single large open reading frame composed of over 9,000 nucleotides (6, 11). Sequencing of HCV isolates has identified 6 genotypes and more than 70 subtypes (19,25,28,32). Accurate HCV genotyping is important for predicting response to antiviral therapy, since genotypes 1 and 4 are less likely to respond to interferon than genotypes 2 and 3 (14, 21). Genotyping is also an essential tool for epidemiological studies, since HCV genotypes vary according to epidemic history in different geographical regions (23,24,30,40). Epidemiologic studies of HCV strains from blood donors (7, 18), drug addicts (1, 12, 13), and hospital patients (22,35) have demonstrated a correlation between some subtypes and risk factors.Since the 5Ј noncoding region (5Ј NCR) is one of the most highly conserved regions of HCV, it has historically been used for virus detection and is now one of the best-characterized regions. For practical reasons, the 5Ј NCR was also chosen as the target for various genotyping methods, including the InnoLipa HCV II test (33, 34), sequencing (8,9,10,26), and the duplex mobility assay (39). However, recent studies involving NS5b region analysis (3,29,35) show that 5Ј NCR sequence analysis can lead to genotyping errors (5, 35). In this study, we used NS5b region sequence analysis to determine the HCV subtype distribution of 357 isolates collected from blood donors in France between 2002 and 2003. All samples had already been genotyped based on 5Ј NCR analysis. Results of the two seque...