Ultra-Deep Sequencing Analysis of the Hepatitis A Virus 5'-Untranslated Region among Cases of the Same Outbreak from a Single Source

Abstract

Hepatitis A virus (HAV) is a causative agent of acute viral hepatitis for which an effective vaccine has been developed. Here we describe ultra-deep pyrosequences (UDPSs) of HAV 5'-untranslated region (5'UTR) among cases of the same outbreak, which arose from a single source, associated with a revolving sushi bar. We determined the reference sequence from HAV-derived clone from an attendant by the Sanger method. Sixteen UDPSs from this outbreak and one from another sporadic case were compared with this reference. Nucleotide errors yielded a UDPS error rate of < 1%. This study confirmed that nucleotide substitutions of this region are transition mutations in outbreak cases, that insertion was observed only in non-severe cases, and that these nucleotide substitutions were different from those of the sporadic case. Analysis of UDPSs detected low-prevalence HAV variations in 5'UTR, but no specific mutations associated with severity in these outbreak cases. To our surprise, HAV strains in this outbreak conserved HAV IRES sequence even if we performed analysis of UDPSs. UDPS analysis of HAV 5'UTR gave us no association between the disease severity of hepatitis A and HAV 5'UTR substitutions. It might be more interesting to perform ultra-deep sequencing of full length HAV genome in order to reveal possible unknown genomic determinants associated with disease severity. Further studies will be needed.

Direct-acting Antivirals and Host-targeting Agents against the Hepatitis A Virus

“… 9 Therefore, the possibility of an outbreak of an HAV epidemic exists. 10 , 11 A similar situation exists in South Korea. 12 Although there are safe and effective vaccines against HAV, it is also important to discover new host cell targets and to develop potential drugs for the treatment of HAV.…”

“… 64 The influence of HAV genotypes and sequence variations on the effects of amantadine should be explored. 10 , 11 , 17 The combinations of amantadine with interferon-alpha or IL-29 resulted in stronger inhibitory effects on HAV replication compared with amantadine alone. 47 , 53 Broad-target HTAs, such as interferon, ribavirin and amantadine, may suppress HAV replication in certain HAV patients.…”

Improving virus production through quasispecies genomic selection and molecular breeding

“…While no clear relationship between the severity of hepatitis A infection and mutations in the IRES has never been reported2142, their role in increasing virus replication in cell culture is well documented43. However, the replication rise observed in the HM175-HP population has no paragon among the HAV strains, and is due to the combined effect of an efficient IRES with codon usage modifications in a context of cellular shut-off.…”

Suppression of La Antigen Exerts Potential Antiviral Effects against Hepatitis A Virus

“…The nucleotide sequences of 5′NTR are one of the most conserved in HAV genomes [8], [26]. These facts suggest that HAV IRES is one of the attractive targets of antiviral agents against HAV.…”

“…HAV is still a major cause of acute hepatitis [3] , [4] . Although acute liver failure due to HAV is not common, it is still occasionally fatal [5] , despite HAV vaccine having become available [6] – [8] . This emphasizes the importance of the development of antiviral agents against HAV.…”