Subgenotype IB Research Articles

Phylogenetic analysis of hepatitis A virus in Thailand

Human hepatitis A virus (HAV) is a major causative agent of acute hepatitis, and the isolates are categorised into four genotypes: I (GI), II (GII), III (GIII), and VII (GVII). Although viral hepatitis has been detected under a nationwide surveillance system in Thailand, the genetic variation of HAV has not yet been determined. In the present study, serum specimens were collected from acute hepatitis patients in Thailand from 1998-2002. The IgM-class antibody to HAV was detected in 156 out of 394 sera, counting as many as 39.6% of acute viral hepatitis cases. HAV RNA in the serum specimens was amplified by reverse-transcription polymerase chain reaction (RT-PCR), and a phylogenetic analysis of the putative VP1/2A junction of the genome was performed. The isolates were grouped into two genetic groups, GIA and GIB. This is the first report to identify subgenotype IB (GIB) in Thailand. The genetic segregation was closely related to the province where hepatitis A occurred and the serum specimens were collected. In addition, genetically similar strains were identified in both 1998 and 2001-2002 isolates from two close provinces in the southern part of Thailand, suggesting that a strain indigenous to the province or district has been circulating in southern Thailand.

Genetic analysis of hepatitis A virus isolates from Brazil.

A limited number of hepatitis A virus (HAV) isolates from South America have been characterised at the genomic level. IgM anti-HAV positive serum samples collected from patients with hepatitis A living in the five geographical regions of Brazil (North, Northeast, Central, South, and Southeast) were used to obtain HAV isolates and determine their genetic relatedness. Of the 232 case isolates, sequence data were obtained from the VP1/2A junction region of the HAV genome. All isolates were classified in genotype I; 231 belonged to subgenotype IA, and one to subgenotype IB. HAV isolates from four States formed distinct clusters of highly related sequences. However, isolates from other states did not cluster and the sequences from those states were intermingled with sequences found in the other states. The amino acid sequences of all but two isolates showed a Leu --> Ile substitution at position 42 in the 2A protein. This substitution appeared to be a characteristic geographic fingerprint of HAV sequences within Brazil.

Evidence of recombination in natural populations of hepatitis A virus

Genetic analysis of selected genome regions of hepatitis A virus (HAV) suggested that distinct genotypes of HAV could be found in different geographical regions. At least seven HAV genotypes have been identified all over the world, including four human genotypes (I, II, III, and VII) and three simian strains (IV, V, and VI). Phylogenetic analysis using full-length VP1 sequences revealed that human strain 9F94 has a close genetic relation with strain SLF-88 (sub-genotype VII). Nevertheless, the same analysis using full-length VP2 or VP3 sequences revealed that strain 9F94 has a close genetic relation with strain MBB (sub-genotype IB). To test the possibility of genetic recombination, phylogenetic studies were carried out, revealing that a crossing over had taken place in the VP1 capsid protein. These findings indicate that capsid-recombination can play a significant role in shaping the genetic diversity of HAV and, as such, can have important implications for its evolution, biology, and control.

Analysis of the genotype-determining region of hepatitis A viral RNA in relation to disease severities

Although hepatitis A is still a considerable problem in Japan, correlation of genomic differences of hepatitis A virus (HAV) and the clinical status of hepatitis A has not been studied. To examine whether the HAV genotype is associated with the disease severity, we analyzed the HAV genotype-determining region in sera from patients with hepatitis A of various clinical degrees. Serum samples from 47 Japanese patients with sporadic hepatitis A from 4 different areas in Japan, including 8 with fulminant hepatitis, 11 with severe acute hepatitis (AHs), and 28 with AHs, were examined for HAV RNA. The 168 base pair sequence of the genotype-determining region, which is located at the VP1/2A junction, was amplified by reverse transcription-polymerase chain reaction, and the nucleotide sequence was determined by direct sequencing. By comparing sequences for VP1/2A, we determined that 44 of 47 cases examined were of subgenotype IA, two were of subgenotype IB, and one was of subgenotype IIIA. With respect to subgenotype IA strains, individuals who were infected between 1990 and 1996 tended to show similar sequences, whereas those infected between 1997 and 1999 showed sequences slightly different from those of the 1990–1996 cases. There were no apparent associations between disease severity and sequences of the genotype-determining region. Hepatitis A of our study was caused by a variety of subgenotype IA strains, consistent with the sporadic spread of infection. Disease severity was not associated with the nucleotide sequence of the HAV genotype-determining region.

Characterization of hepatitis A virus isolates from subgenotypes IA and IB in Rio de Janeiro, Brazil.

Hepatitis A virus (HAV) isolates from around the world have been classified into seven genotypes (I-VII). Most human strains belong to genotype I, which has been divided into two subgenotypes, A and B. South America has provided a small number of strains studied at the genome level. In the present study, IgM anti-HAV antibodies were detected in 116 out of 250 (46%) serum samples collected from consecutive patients with acute hepatitis referred to the Brazilian Reference Center for Viral Hepatitis, Rio de Janeiro. Viral RNA were extracted from all 250 samples and submitted to a reverse transcription-polymerase chain reaction (RT-PCR) assay designed to amplify a genome segment in the VP1/2A junction region. HAV RNA was detected in 54/116 (47%) and 17/134 (13%) IgM anti-HAV-positive and -negative sera, respectively. In addition, HAV RNA was detected in 17/35 (49%) IgM anti-HAV-positive sera that had been collected at a day care center where cases of acute hepatitis were being observed for 3 months. Nucleotide sequences (168 bp) of PCR products were determined for 30 HAV isolates. Phylogenetic analysis showed that 21 belonged to subgenotype IB, while 9 were of subgenotype IA. Interestingly, a concomitant circulation of isolates from subgenotypes IA and IB was observed in the day care center.

Molecular epidemiology of South African strains of hepatitis A virus: 1982-1996.

Isolates of hepatitis A virus (HAV) are of a single serotype, with human isolates being categorised within four genotypes. In addition, there are three genotypes exclusively associated with Old World monkeys. In some geographical regions, related isolates cluster suggesting endemic spread of the virus, while in other regions several genotypes circulate. Virtually no data are available with regard to the genetic relatedness of South African (SA) strains of HAV. A 177 base segment within the VP1 region and a 168 base segment encompassing the putative VP1/P2A junction of 20 clinical and one environmental wild-type isolate(s) of HAV from SA were amplified by reverse transcriptase-polymerase chain reaction. The nucleotide sequences from the SA isolates showed > 85% nucleic acid sequence identity with published sequences for HAV strains from genotype I, with the majority of strains (81%) clustering within subgenotype IB and the remainder in subgenotype IA. A high degree of conservation was noted between the predicted amino acid sequences from SA clinical isolates and isolates from the rest of the world. Data presented indicate that in SA there is a circulating population of endemic HAVs from two distinct subgenotypes. This study provides valuable new data on the genetic relatedness of HAVs from southern Africa and the distribution of subgenotype IB.