Characterization of the complete genomic sequence of genotype II hepatitis A virus (CF53/Berne isolate)

Abstract

The complete genomic sequence of hepatitis A virus (HAV) CF53/Berne strain was determined. Pairwise comparison with other complete HAV genomic sequences demonstrated that the CF53/Berne isolate is most closely related to the single genotype VII strain, SLF88. This close relationship was confirmed by phylogenetic analyses of different genomic regions, and was most pronounced within the capsid region. These data indicated that CF53/Berne and SLF88 isolates are related more closely to each other than are subtypes IA and IB. A histogram of the genetic differences between HAV strains revealed four separate peaks. The distance values for CF53/Berne and SLF88 isolates fell within the peak that contained strains of the same subtype, showing that they should be subtypes within a single genotype. The complete genomic data indicated that genotypes II and VII should be considered a single genotype, based upon the complete VP1 sequence, and it is proposed that the CF53/Berne isolate be classified as genotype IIA and strain SLF88 as genotype IIB. The CF53/Berne isolate is cell-adapted, and therefore its sequence was compared to that of two other strains adapted to cell culture, HM-175/7 grown in MK-5 and GBM grown in FRhK-4 cells. Mutations found at nucleotides 3889, 4087 and 4222 that were associated with HAV attenuation and cell adaptation in HM175/7 and GMB strains were not present in the CF53/Berne strain. Deletions found in the 59UTR and P3A regions of the CF53/Berne isolate that are common to cell-adapted HAV isolates were identified, however.

Genetic variability of hepatitis A virus strain HAF-203 isolated in Brazil and expression of the VP1 gene in Escherichia coli

“…Finally, when our isolate was compared with the AGM-27 strain, a nucleotide homology of 81.2% was observed. These results confirm previous studies in which the AGM-27 strain proved to be unique, because it differs significantly from any other HAV isolate , Tsarev et al 1991, such as the CF53/Berne, SLF88 and NOR-21 isolates (Ching et al 2002, Lu et al 2004, Stene-Johasen et al 2005). …”

“…In an attempt to better characterize the HAF-203 genotype, its nucleotide sequence was compared to 25 complete nucleotide sequences available in databanks. The HAF-203 strain displays a high degree of homology with HM-175, its attenuated derivative, IVA and MBB strains (99.7,99.5,98.8,and 94.8% respectively), confirming previous data (de Paula et al 2002, Lu et al 2004, Stene-Johansen et al 2005 in which HAF-203 was assigned to genotype IB.…”

“…(Hu et al 2002); LA (Najarian et al 1985); HAS-15 (Sverlov et al 1987); M2 (AY974170, Badillo et al unpublished); HAV-FG (Beneduce et al 1995); GBM (Graft et al 1994(Graft et al , 1997; MBB (Paul et al 1987); IVA (DQ646426, Bitchenco et al unpublished) HM-175, HM-175 attenuated and NC001489 (Cohen et al 1987a,b); CF53/Berne (Lu et al 2004); SLF88 (Ching et al 2002 ) ;NOR-21 (Stene-Johansen et al 2005); AGM-27 (Tsarev et al 1991). respectively), in the 2B protein (nucleotide 3880 was altered from T→C) and in the 3D protein (nucleotide 6232 changed from T→C and nucleotide 7206 from A→G). Mutations were also witnessed in 5'and 3' untranslated regions (UTRs).…”

Characterization of outbreak hepatitis a isolates in five Tunisian childcare centers

“…Picornaviridae family, is transmitted primarily through the fecal-oral route (14). The nucleotide analysis of the VP1/2A junction classified HAV in six different genotypes (I-VI) and six sub-genotypes (IA, IB, IIA, IIB, IIIA, and IIIB) (13,17).…”

Infección por el virus de la hepatitis A: epidemiología y diversidad genética

“…Cada uno de los subgenotipos IIA y IIB se definió por una cepa única, a saber: la CF53/Berna aislada en Francia en 1979 y la SLF88 aislada en Sierra Leona en 1988, respectivamente (18,23,66). Se han identificado eventos de recombinación del genotipo IIA con el genotipo IB en la región genómica P1, mencionada previamente.…”