Characterization of a Near Full-Length Hepatitis E Virus Genome of Subtype 3c Generated from Naturally Infected South African Backyard Pigs

Abstract

Eight genotypes of the hepatitis E virus (Orthohepevirus A; HEV) designated HEV-1 to HEV-8 have been reported from various mammalian hosts. Notably, domestic pigs and wild boars are the natural reservoirs of HEV-3 and HEV-4 genotypes with zoonotic propensity. Since HEV infection in domestic pigs is usually subclinical, it may remain undetected, facilitating zoonotic spillover of HEV to the exposed human populations. A previous study from our group in 2021, using deep sequencing of a pooled saliva sample, generated various swine enteric virus genomes, including a near full-length swine HEV genome (7040 nt; 97.7% genome coverage) from five-month-old grower pigs at a backyard pig farm in the uMgungundlovu District, KwaZulu-Natal, South Africa. In the present study, we describe the further characterization, including genotyping and subtyping of the swine HEV isolate using phylogenetics and ‘HEVnet Typing Tool’. Our analyses confirmed that the South African swine HEV genome characterized in this study belonged to HEV genotype 3 subtype 3c (HEV-3c). While HEV-3c infections in domestic pigs have been previously reported from Brazil, Germany, Italy, and the Netherlands, they only generated partial genome sequences of open reading frame 1 (ORF1) and/or ORF2. To our knowledge, this is the first near full-length swine HEV-3c genome generated from naturally infected domestic pigs (Sus scrofa domesticus) in South Africa. However, due to the gap in the information on the HEV-3c genome sequences in various geographical locations worldwide, including South Africa, the epidemiology of the South African swine HEV genome characterized in this study remains inconclusive. Molecular and genomic surveillance of HEV in domestic pig populations in South Africa would be useful to determine their prevalence, circulating subtypes, and zoonosis risk.

Keywords: HEV zoonosis; HEV-3c; Illumina sequencing; Sus scrofa domesticus; backyard pig farm; hepatitis E virus; phylogenetic analysis.

Figure 1

Schematic representation of the swine HEV genome characterized in this study. (A) The HEV reference genome (GenBank accession: NC_001434) comprises a 5′ 7-methylguanosine cap followed by a short untranslated region (UTR). It has a 3′ UTR and a polyadenylated tail. (B) The South African swine HEV genome characterized in the present study (7040 nt; GenBank accession: OM104034) extends from the nucleotide position 146 at the 5′ end to 7156 at the 3′ end compared to the reference genome. The South African swine HEV genome comprises 97.7% genome coverage (represented in green color) having complete coding sequences for the ORF2 and ORF3 and a partial coding sequence for the ORF1.

Figure 2

Molecular characterization of the swine hepatitis E virus (HEV) genome generated from the backyard pig saliva in South Africa. The PhyML tree of the full-length HEV-1 to HEV-8 genomes reported from various hosts worldwide determined that the South African swine HEV genome belonged to HEV genotype 3 (HEV-3).

Figure 3

The PhyML tree of full-length genomes of various HEV-3 subtypes available at NCBI-GenBank and the South African swine HEV genome (highlighted in red). The South African isolate clustered with the HEV-3c genomes reported from humans and wild boars in different countries, thus confirming that the South African isolate belonged to the HEV-3c subtype.

Figure 4

The PhyML tree of full-length genomes of HEV-3c reported from various geographical locations. The South African swine HEV-3c genome is highlighted in red. More HEV-3c genomes from other geographical locations, including South Africa, may be required for a conclusive epidemiological determination of the South African swine HEV-3c genome characterized in this study.