Full-genome nucleotide sequence and analysis of a Chinese swine hepatitis E virus isolate of genotype 4 identified in the Guangxi Zhuang autonomous region: evidence of zoonotic risk from swine to human in South China

Alignment-free method for DNA sequence clustering using Fuzzy integral similarity

A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence analysis algorithms. In this study, we developed an alignment-free algorithm for faster sequence analysis. The novelty of our approach is the inclusion of fuzzy integral with Markov chain for sequence analysis in the alignment-free model. The method estimate the parameters of a Markov chain by considering the frequencies of occurrence of all possible nucleotide pairs from each DNA sequence. These estimated Markov chain parameters were used to calculate similarity among all pairwise combinations of DNA sequences based on a fuzzy integral algorithm. This matrix is used as an input for the neighbor program in the PHYLIP package for phylogenetic tree construction. Our method was tested on eight benchmark datasets and on in-house generated datasets (18 s rDNA sequences from 11 arbuscular mycorrhizal fungi (AMF) and 16 s rDNA sequences of 40 bacterial isolates from plant interior). The results indicate that the fuzzy integral algorithm is an efficient and feasible alignment-free method for sequence analysis on the genomic scale.

Infection by Brazilian and Dutch swine hepatitis E virus strains induces haematological changes in Macaca fascicularis

BACKGROUND

Hepatitis E virus (HEV) has been described as an emerging pathogen in Brazil and seems to be widely disseminated among swine herds. An autochthonous human case of acute hepatitis E was recently reported. To obtain a better understanding of the phenotypic profiles of both human and swine HEV strains, a experimental study was conducted using the animal model, Macaca fascicularis.

METHODS

Six cynomolgus monkeys (Macaca fascicularis) were inoculated intravenously with swine HEV genotype 3 that was isolated from naturally and experimentally infected pigs in Brazil and the Netherlands. Two other monkeys were inoculated with HEV genotype 3 that was recovered from Brazilian and Argentinean patients with locally acquired acute and fulminant hepatitis E. The haematological, biochemical, and virological parameters of all animals were monitored for 67 days.

RESULTS

Subclinical hepatitis was observed in all monkeys after inoculation with HEV genotype 3 that was recovered from the infected swine and human patients. HEV RNA was detected in the serum and/or faeces of 6 out of the 8 cynomolgus monkeys between 5 and 53 days after inoculation. The mild inflammation of liver tissues and elevations of discrete liver enzymes were observed. Seroconversions to anti-HEV IgM and/or IgG were detected in 7 animals. Reactivities to anti-HEV IgA were also detected in the salivary samples of 3 animals. Interestingly, all of the infected monkeys showed severe lymphopenia and a trend toward monocytosis, which coincided with elevations in alanine aminotransferase and antibody titres.

CONCLUSIONS

The ability of HEV to cross the species barrier was confirmed for both the swine (Brazilian and Dutch) and human (Argentinean) strains, thus reinforcing the zoonotic risk of hepatitis E in South America. Cynomolgus monkeys that were infected with HEV genotype 3 developed subclinical hepatitis that was associated with haematological changes. Haematological approaches should be considered in future studies of HEV infection.

Study on prevalence and genotype of hepatitis E virus isolated from Rex Rabbits in Beijing, China

A novel genotype of hepatitis E virus (HEV) isolated from rabbits is reported. The aim of this study was to confirm and further investigate the prevalence of the novel HEV genotype in rabbits in China. Sera and faecal samples were collected from farmed rex rabbits in Beijing, China. All serum samples were tested for anti-HEV antibody by EIA. Both the serum and the faecal samples were evaluated for detection of HEV RNA using a nested RT-PCR assay. The nucleotide sequences of rabbit HEV were then analysed, and sequence homology of rabbit HEV compared against human HEV genotypes 1-4, and avian HEV.

RESULTS

The prevalence of positive serum anti-HEV from rex rabbits was 54.62% (65/119). The detection rate of HEV RNA using ORF2 primers was 6.96% (8/115) amongst rabbit faecal samples. All eight amplicons shared 98.3-100% nucleotide homology with each other and had identities of 75.8-78.6%, 73.9-75.0%, 77.5-81.0%, 74.2-78.6% and 54.8-57.6% with the corresponding regions of genotypes 1-4 and avian HEV, respectively. Phylogenetic analysis showed that the eight sequences formed one individual branch and were on the same branch with GDC9 and GDC46, both of which were reported to be a novel genotype of HEV isolated from rabbits. The conclusion is that this study provides further information about HEV infecting rabbits, which may be a new animal host of HEV, as well as genetical evidence of a new mammalian genotype of HEV.

Analysing complete genome sequence of swine hepatitis E virus (HEV), strain CHN-XJ-SW13 isolated from Xinjiang, China: putative host range, and disease severity determinants in HEV

Hepatitis E is a worldwide public health problem, particular in areas where hygiene conditions are poor. Hepatitis E virus (HEV) has at least four genotypes: genotypes 1 and 2 exclusively infect human; while genotypes 3 and 4, are considered to be a zoonotic agent, infecting both humans and animals. This study was aimed at determining why genotype 3 and 4 HEV strains isolated from swine are able to cross species borders, whereas genotype1 and 2 strains isolated from humans are not. The full length genome of the swine HEV isolate CHN-XJ-SW13 was amplified as overlapping fragments using reverse-transcription-nested polymerase chain reaction (RT-nPCR) and rapid amplification of cDNA ends (RACE). The sequence of CHN-XJ-SW13 was compared with those of 90 HEV strains covering genotype 1-4 retrieved from GenBank. Possible regions of the viral genome, specifying the host range of HEV or associated with the severity of hepatitis E disease, were then screened for with the aid of the ALIGNX sequences alignment software package. The CHN-XJ-SW13 swine HEV isolate was determined to be a novel subtype of genotype 4, whose sequence provided several valuable clues for tracing the sources of human HEV infection. 25 specific nucleotide positions were identified to possibly being involved specifying the host range of HEV or determining the severity of hepatitis E disease.

Hepatitis E virus infection among animals and humans in Xinjiang, China: possibility of swine to human transmission of sporadic hepatitis E in an endemic area

Hepatitis E is a worldwide public health problem, especially in areas with poor sanitation. This study examines the potential hepatitis E virus (HEV) animal reservoirs and the current status of HEV infection among animals and humans in an endemic area of Xinjiang, China. One thousand five hundred twenty-one serum samples from 12 different animal species and 296 sera from humans were detected for anti-HEV with an in-house enzyme immunoassay, and partial HEV RNA was amplified with a reverse transcription-nested polymerase chain reaction (RT-nPCR). All these distinct animal species, except jerboa and hoptoad, were positive for anti-HEV. However, HEV RNA was only amplified from pigs and a sporadic hepatitis E case in humans. The human HEV strain (CHN-XJ-HE29) shared 100% nucleotide identity with the swine HEV strain (CHN-XJ-SW50), both of which were collected from the same district; this indicates the possibility of HEV transmission from swine to humans in an endemic area.