GENOME COMPOSITION

Astroviruses have an RNA genome that is approximately 6,800 nucleotides long, without the poly (A) tail at the 3' end.

Presently, three strains of human astrovirus have been completely sequenced:

1. 1) serotype 1 Oxford reference strain maintained in LLCMK2 cells (rhesus monkey kidney epithelial cells)
2. 2) serotype 1 Newcastle strain maintained in CaC0-2 cells
3. 3) serotype 2 Oxford reference strain propagated in LLCMK2 cells

   Serotypes 4 and 5 are partially sequenced.

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Three ORFs constitute the viral genome:

• ORF 1a and ORF 1b are two ORFs found at the 5' end that encode nonstructural proteins.
• ORF 2 at the 3' end encodes a structural protein.

  During viral infection, full genomic (6.8 kb) and subgenomic (2.4kb) RNA are generated.

1) ORF 1a encodes a polypeptide that contains a serine protease motif. This astrovirus protease has features similar to other plus-stranded RNA viruses, but it has particular resemblance to the calicivirus protease. An important difference found between astrovirus and calicivirus proteases is that the astrovirus protease has serine instead of cysteine at the third catalytic amino acid residue.

2) ORF 1b encodes a polypeptide that contains a RNA-dependent RNA polymerase. The polymerase motifs are highly conserved among serotypes 1, 2, 4, and 5, with serotypes 1 and 2 being the most closely related and 4 and 5 being the least related in this region.

3) ORF 2 is a region of the largest sequence variability. In addition, it is present in both genomic and subgenomic RNA, suggesting that the role of subgenomic RNA lies in the production structural proteins. Studies on protein synthesis suggest that a single 90 kDa structural protein is produced before it is proteolytically cleaved into at least 3 smaller proteins.

Distinguishing features of astrovirus:

1) LACK OF A HELICASE DOMAIN

The astrovirus genome appears to lack a helicase domain. It is considered rather unusual for a plus-strand RNA virus of genome length larger than 6,000 nucleotides to lack a region encoding helicase.

2) RIBOSOMAL FRAMESHIFTING

ORF 1b translation is accounted for by the overlap region between ORFs 1a and 1b, a region which shows highly conserved sequences and thereby suggests a ribosomal frameshifting mechanism.