Classification of the Zoonotic Hepatitis E Virus Genotype 3 Into Distinct Subgenotypes

Abstract

Hepatitis E virus (HEV) genotype 3 is the most common genotype linked to HEV infections in Europe and America. Three major clades (HEV-3.1, HEV-3.2, and HEV-3.3) have been identified but the overlaps between intra-subtype and inter-subtype p-distances make subtype classification inconsistent. Reference sequences have been proposed to facilitate communication between researchers and new putative subtypes have been identified recently. We have used the full or near full-length HEV-3 genome sequences available in the Genbank database (April 2020; n = 503) and distance analyses of clades HEV-3.1 and HEV-3.2 to determine a p-distance cut-off (0.093 nt substitutions/site) in order to define subtypes. This could help to harmonize HEV-3 genotyping, facilitate molecular epidemiology studies and investigations of the biological and clinical differences between HEV-3 subtypes.

Genetic Diversity of Hepatitis E Virus Type 3 in Switzerland—From Stable to Table

“…The assignment of sequences from two meat products from Germany to subtype 3c was also confirmed, and they were shown not to be closely related. [39,41]. The evolutionary history was inferred by using the Maximum Likelihood method and Tamura-Nei model [42].…”

“…While the three sequences from the wild boars group very closely together, the sequence from the pig is a little further away, but all sequences clearly belong to the cluster of Swiss sequences within 3h, 3h_s (Figure 4). As already seen in the phylogenetic tree of the partial [39,41]. The evolutionary history was inferred by using the Maximum Likelihood method and Tamura-Nei model [42].…”

“…The pairwise distance to 3l, the most closely related subtype after 3h, is nearly identical for WB33 and KW13 and clearly above the demarcation cut-off. For the subtype 3h all official references, for all other subtypes the single recommended representatives [39,41] were included. Where necessary, genomes were shortened to identical starting and ending nucleotides (6738-7138 nt length).…”

Screening of Swiss Pig Herds for Hepatitis E Virus: A Pilot Study

“…RNA kit with DTT 32.0 3.0 3 33 1 Genome coverage in percentage relative to reference strain MG573193; 2 relative to reference MF346772; 3 relative to reference MF444119; 4 number of total reads detected regarding the best reference strain, as mentioned for the coverage. Reference sequences are labelled with their subtype according to Smith et al [30] and Nicot et al [26] in bold and with their accession number. Reference sequences from Swiss strains within subtype 3h are labelled with "3h_s".…”

“…Bootstrap values ≥ 75 are indicated. The analysis involved 33 sequences, including 32 reference sequences received from the NCBI GenBank.Reference sequences are labelled with their subtype according to Smith et al[30] and Nicot et al[26] in bold and with their accession number. Reference sequences from Swiss strains within subtype 3h are labelled with "3h_s".…”