Preliminary molecular epidemiological investigation of hepatitis E virus sequences from Québec, Canada

Our study objective was to describe the Canadian Hepatitis E virus (HEV) sequences currently cataloged in GenBank from three populations: commercially raised pigs, retail pork, and locally acquired Hepatitis E cases, and to interpret the molecular evidence they provide. We searched the GenBank for any/all Canadian HEV sequences from these populations, and identified highly similar matches using the Basic Local Alignment Search Tool (BLAST) algorithm, studying sequences of the partial ORF2 gene. We validated the findings made using Multiple Sequence Comparison by Log-Expectation (MUSCLE) and Clustal 2 programs for multiple sequence alignments, as inputs to estimate dendrograms using both neighbour-joining and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) methods. The GenBank search yielded 47 sequences collected from pigs: 32 sequences from two to four month old commercial pigs in Québec, one from three to four month old pigs at a research station in Ontario, one from two month old pigs in a commercial Saskatchewan herd, and 13 collected from finisher pigs in a national survey. Additionally, 14 sequences were collected from a national survey of Canadian retail pork livers, and seven sequences from two Canadian pediatric patients with locally acquired Hepatitis E, both from the province of Québec. All sequences belonged to genotype 3. Eight of the 14 sequences from retail pork livers had human-derived sequences in their top ten BLAST matches; six did not. Those eight sequences having close human BLAST matches clustered within a dendrogram, as did those with no close human BLAST matches. Human sequences with close matches to the eight retail sequences included both of the Québec Hepatitis E cases, as well as sequences from Japanese Hepatitis E cases, and Japanese blood donors. Seven of the eight HEV sequences from retail liver with close human BLAST matches originated in Québec. Kulldorff's spatial scan statistic showed a significant (P<0.05) spatial cluster of these sequences, but not of the overall dataset of 12 HEV sequences collected from Québec retail livers. All seven retail liver sequences with close human matches were processed in-store. We conclude that some Canadian sequences of HEV collected from pigs/pork are more closely related to human sequences than others, and hypothesize that detection of some HEV sequences recovered from Canadian retail pork livers may be associated with exposure to human shedding. More research needs to be conducted at the processing level to help understand the molecular epidemiology of HEV in Canadian retail pork.