Detection of defective genomes in hepatitis A virus particles present in clinical specimens

Hepatitis A virus (HAV) particles harbouring a physically defective RNA genome have been reported to occur in all HAV-infected cell culture systems analysed so far. The most prominent defects consist of three distinct overlapping deletions in the region of the HAV genome encoding the structural proteins. By probing for the endpoints of these deletions in RNA samples using S1 nuclease and exonuclease VII mapping, we obtained suggestive evidence for the existence also of defective genomes in HAV particles present in faecal specimens, in viraemic blood collected in the course of hepatitis A virus infection in man, as well as in the liver of an experimentally infected marmoset monkey. The deletions identified extend from nucleotide (nt) 1200 to nt 3820 and from nt 1200 to nt 3240 of the HAV genome. They are compatible with two of the deletions detected in particles grown in vitro in cell cultures and shown to interfere with the replication of standard hepatitis A virions.