Influenza virus is not known to affect wild felids. We demonstrate that avian influenza A (H5N1) virus caused severe pneumonia in tigers and leopards that fed on infected poultry carcasses. This finding extends the host range of influenza virus and has implications for influenza virus epidemiology and wildlife conservation.

Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently classified into six genotypes and an increasing number of subtypes. Most likely, this heterogeneity is caused by genetic drift; evidence for recombination is scarce. To study the molecular heterogeneity of HCV in Vietnam, we analyzed 58 HCV RNA-positive sera from Vietnamese blood donors by sequence analysis of the CORE and NS5B regions. Phylogenetic analyses revealed the presence of genotype 1 (38%), genotype 2 (10.3%), and genotype 6 viruses (51.7%). All samples showed concordant results except for two (D3 and D54). Sample D54 was a mixed infection of genotype 2i and 6h viruses. Whole-genome analysis and bootscan analysis of sample D3, on the other hand, revealed a recombinant virus with genotype 2i and genotype 6p sequences at the 5 and 3 ends, respectively. The crossover point was located between nucleotide positions 3405 to 3464 (numbering according to prototype strain HCV-H, M67463) at the NS2/NS3 junction. The identification of this naturally occurring recombinant virus strengthens the concept that recombination may play a role in HCV epidemiology and evolution. Furthermore, the location of the recombination breakpoint may be relevant for constructing infectious chimeric viruses.

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Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently divided into six genotypes. A line probe assay (LiPA), which targets the 5 untranslated region (5UTR) of the HCV genome, is widely used for genotyping. However, this assay cannot distinguish many genotype 6 subtypes from genotype 1 due to high sequence similarity in the 5UTR. We investigated the accuracy of a new generation LiPA (VERSANT HCV genotype 2.0 assay), in which genotyping is based on 5UTR and core sequences, by testing 75 selected HCV RNA-positive sera from Southeast Asia (Vietnam and Thailand). For comparison, sera were tested on the 5UTR based VERSANT HCV genotype assay and processed for sequence analysis of the 5UTR-to-core and NS5b regions as well. Phylogenetic analysis of both regions revealed the presence of genotype 1, 2, 3, and 6 viruses. Using the new LiPA assay, genotypes 6c to 6l and 1a/b samples were more accurately genotyped than with the previous test only targeting the 5UTR (96% versus 71%, respectively). These results indicate that the VERSANT HCV genotype 2.0 assay is able to discriminate genotypes 6c to 6l from genotype 1 and allows a more accurate identification of genotype 1a from 1b by using the genotype-specific core information.

Hepatitis C virus (HCV) has a linear positive-stranded RNA genome of ϳ9,600 nucleotides in length and displays a high level of sequence diversity caused by high mutation rates and recombination. However, when we performed long distance reverse transcription-PCRs on HCV RNA isolated from serum of chronic HCV patients, not only full-length HCV genomes but also HCV RNAs which varied in size from 7,600 to 8,346 nucleotides and contained large in-frame deletions between E1 and NS2 were amplified. Carefully designed control experiments indicated that these deletion mutants are a bona fide natural RNA species, most likely packaged in virions. Moreover, deletion mutants were detected in sera of patients infected with different HCV genotypes. We observed that 7/37 (18.9%) of genotype 1, 5/43 (11.6%) of genotype 3, and 4/13 (30.7%) of genotype 6 samples contained HCV deletion mutant genomes. These observations further exemplify HCV's huge genetic diversity and warrant studies to explore their biological relevance.Hepatitis C virus (HCV) is an enveloped virus that belongs to the family Flaviviridae. Its linear positive-stranded RNA genome of approximately 9.6 kb in length encodes both structural (core, E1, and E2) and nonstructural (p7, N2, NS3, NS4a/b, and NS5a/b) proteins in a single open reading frame, flanked by short conserved untranslated regions (UTRs) located at the 5Ј and 3Ј ends of the genome that are required for viral replication and protein translation (5,7,8). One of the most striking characteristics of HCV is its capacity to cause a chronic liver disease in a high percentage of individuals (24). To do so, HCV encodes proteins which promote persistence, and sequence variation, especially in the envelope genes (E1 and E2), results in escape from adaptive immune responses (9, 27).Lack of proofreading ability of the viral RNA-dependent RNA polymerase is the driving force behind HCV's genetic diversity. As a result of the large amount (10 12 ) of virions produced each day in chronic hepatitis C patients and the rate of incorrect nucleotide insertions, which reaches the order of 10 Ϫ3 to 10 Ϫ4 base substitutions per site per year, HCV quasispecies are generated (22,26). Recombination may be another mechanism by which genetic diversity is driven, given the recent identification of naturally occurring intergenotypic recombinant viruses (13, 21). Because of the huge genetic diversity, HCVs are currently categorized into six major genotypes and more than 80 subtypes (25).HCV genetic variation has been studied in relation to epidemiology, response to antiviral therapy, and clinical parameters, using different techniques that have focused on short genomic regions. However, analysis of full-length viral genomes may be necessary to better understand the characteristics of HCV. Previously, we analyzed sera from HCV RNA-positive blood donors from Ho Chi Minh City, Vietnam, in order to analyze the molecular heterogeneity of HCV in Southeast Asia (21). Based on sequence analysis of core and NS5b regions in a set of sera, two ...