The Nucleotide Sequence of the Hepatitis B Viral Genome and the Identification of the Major Viral Genes

Effect of frameshift mutation in the pre-C region of hepatitis B virus on the X and C genes

“…2a). These results confirm that our mutant HBV has a defective pre-C region, and hence cannot synthesize (Valenzuela et al, 1980); mutant HBV (ad O ; HBV-71 ; DHBV (Mandart et aL, 1984).…”

Secretion of Particles of Hepatitis B Surface Antigen from Insect Cells Using a Baculovirus Vector

“…It has been claimed that the HBV pre-S2 region (Milich et al, 1985;Valenzuela et al, 1985) enhances the immunogenicity of the HBsAg. A recombinant baculovirus (AcNPV-PsSYK27) has therefore been constructed containing the coding region of the pre-S2 region (55 amino acids) as well as the HBsAg gene.…”

Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame

“…Many viruses, including f X174 (Sanger et al+, 1977), HBV (Valenzuela et al+, 1980), and HEV (Tam et al+, 1991) have overlapping genes and/or regions in which a nucleic acid signal is embedded in a coding sequence+ The HCV genome almost certainly contains multifunctional regions and may have overlapping reading frames; however to date, no proteins encoded in overlapping genes have been described from this virus+ We combined conventional sequence analysis methods and a new program called Framesplitter to search for multifunctional regions in the main ORF of HCV (see Materials and Methods)+ In an initial analysis, eight highly divergent HCV sequences were studied+ Synonymous codons with exceptionally conserved third-position nucleotides were identified throughout the main ORF+ Figure 1A shows the tabulated results of the analysis carried out on a small portion of the coreencoding region+ In the first codon in this region (amino acid 33 of the main ORF), all eight sequences contain the same glycine codon, GGA (see Fig+ 1B)+ This is noteworthy because the genetic code contains four glycine codons (GGA, GGC, GGG, and GGU)+ The probability that all eight sequences would contain the same glycine codon is one in 16,384 (i+e+, 4 7 )+ Three such unusually conserved codons occur in the segment of the HCV core-encoding region shown in Figure 1B+ These codons form part of a larger cluster (#1; see Fig+ 2)+ Clusters of such conserved codons very rarely occur by chance in a sequence with only a single ORF+ Any region in which such a cluster occurs is likely to contain more genetic information than a single coding sequence+ Five clusters of codons with unusual conservation of third-position nucleotides were detected in the main ORF of HCV (Fig+ 2): a prominent cluster occurs in the core-encoding region (amino acids 11-175); a small cluster is located near the E2 (amino acids 672-728); and three clusters are distributed across NS5b (amino acids 2565-3034)+ Earlier studies detected an unusual degree of conservation in the regions containing several of these clusters (Ina et al+, 1994;Smith & Simmonds, 1997); however, the site near the terminus of E2 has not been noted previously+ Based on our results, we reexamined the issue of possible reading frames overlapping the main ORF+ Alternate open reading frames, defined here as 50 or more consecutive codons without an in-frame stop codon, were sought in and around the five clusters of excessive codon conservation noted in the main ORF+ A potential overlapping and open alternate reading frame (ARF) was found in the first cluster, in the ϩ1 reading frame relative to the main ORF (see Fig+ 2, lower insert; "X" identifies stop codons)+ The ϩ1 reading frame is open for at least 124 codons in the vast majority (89%) of the 214 full-length core sequences available for analysis+ This ARF is open for at least 142 codons in 93% of 90 genotype 1 sequences, and for at least 124 codons in 89% of 37 genotype 2 sequences, 84% of 25 genotype 3 and genotype 10 sequences, 80% of 15 genotype 4 sequences, 100% of 11 genotype 5 sequences, and 81% of 36 sequences of the genotypes 6, 7, 8, 9, and 11+ In contrast, the ϩ2 reading frame has numerous stop codons in this region of the genome+ Figure 3 depicts the standard reading frame (the main ORF), the ϩ1 reading frame, and the ϩ2 reading frame of three HCV sequences that are known to be infectious+ These infectious sequences have a potential coding region in the ϩ1 frame that is...…”