Proline-Rich Hypervariable Region of Hepatitis E Virus: Arranging the Disorder

Abstract

The hepatitis E virus (HEV) hypervariable region (HVR) presents the highest divergence of the entire HEV genome. It is characteristically rich in proline, and so is also known as the “polyproline region” (PPR). HEV genotype 3 (HEV-3) exhibits different PPR lengths due to insertions, PPR and/or RNA-dependent RNA polymerase (RdRp) duplications and deletions. A total of 723 PPR-HEV sequences were analyzed, of which 137 HEV-3 sequences were obtained from clinical specimens (from acute and chronic infection) by Sanger sequencing. Eight swine stool/liver samples were also analyzed. N- and C-terminal fragments were confirmed as being conserved, but they harbored differences between genotypes and were not proline-plentiful regions. The genuine PPR is the intermediate region between them. HEV-3 PPR contains a higher percentage (30.4%) of prolines than other genotypes. We describe for the first time: (1) the specific placement of HEV-3 PPR rearrangements in sites 1 to 14 of the PPR, noting that duplications are more frequently attached to sites 11 and 12 (AAs 74–79 and 113–118, respectively); (2) the cadence of repetitions follows a circular-like pattern of blocks A to J, with F, G, H, and I being the most frequent; (3) a previously unreported insertion homologous to apolipoprotein C1; and (4) the increase in frequency of potential N-glycosylation sites and differences in AAs composition related to duplications.

Processing and Subcellular Localization of the Hepatitis E Virus Replicase: Identification of Candidate Viral Factories

“…We aligned 44 aa sequences from different HEV genotypes to identify variable regions which are generally more prone to accept epitope insertions without impacting viral replication. Indeed, the HVR stood out as the region with the highest divergence of the entire HEV genome, thus confirming previous reports ( Muñoz-Chimeno et al, 2020 ). Focusing on the HVR, we next aligned several epitope aa sequences with that of HEV in an aim to identify similar aa and to ease epitope insertion with the least disruption.…”

“…After aligning 44 HEV strains, the HVR appeared as the least conserved domain in the ORF1 sequence. In addition, while presenting the highest divergence of the entire HEV genome ( Muñoz-Chimeno et al, 2020 ), the HVR is known to tolerate inserted fragments arising either from duplication of viral genome or from human genes which were reported to confer better replication efficacies or adaptation to cell culture ( Shukla et al, 2011 , 2012 ; Nguyen et al, 2012 ; Johne et al, 2014 ; Lhomme et al, 2014 ).…”

The Translated Amino Acid Sequence of an Insertion in the Hepatitis E Virus Strain 47832c Genome, But Not the RNA Sequence, Is Essential for Efficient Cell Culture Replication

“…Insertions within the HVR have been described for several HEV strains detected in chronically infected patients [ 18 , 19 ]. However, the distinct function and mechanism of action of the insertions has not been elucidated thus far, although an involvement in the ability to efficiently replicate in cell culture has been assumed and already demonstrated for some of the strains [ 21 , 22 ].…”

“…Several properties of the insertions in the HVR have been suggested to be responsible for the replication-enhancing effect [ 18 , 19 ]. One observation is that the insertions often lead to a higher charge of the translated protein, because charged amino acids are more often present than non-charged [ 18 , 19 ]. However, the drastic negative effect observed in mutant p47832/Ins-Change, where only the order of the two parts of the insertion were changed, but not the overall amino acid composition, argues against a general role of overall charging.…”

“…It has been suggested to be involved in host range adaptation [ 16 ] and efficiency of RNA replication [ 17 ]. In addition, several insertions have been described within the HVR of strains derived from chronically infected patients [ 18 ]. These insertions originate from human host genes or from the HEV genome and can vary in length resulting in longer HVRs that range between 228 and 315 nt [ 19 ].…”