Development of computational sequence analysis for the characterization of Hepatitis E in Catalonia

Abstract

Hepatitis E virus (HEV) is a zoonotic virus that causes acute hepatitis with increasing incidence in humans in Europe which is mainly transmitted by the consumption of undercooked pig meat. Zoonotic genotypes HEV-3 and HEV-4 are zoonotic and predominant in Europe. The use of animal collective environmental samples (slurry from farms and wastewater from slaughterhouses and wastewater treatment plants (WWTP)) to study the circulation of HEV genotypes in Catalonia. Samples have been concentrated and analyzed by (RT)qPCR and n(RT)PCR. HEV genotypes have been subtyped using amplicon-deep sequencing (ADS) with minION by an optimized bioinformatic pipeline. The impact of several parameters in the bioinformatic pipeline such as trimming, clustering, and subsampling have been evaluated. A quality score of 7 with clustering the sequences at 90% of homology were selected for the bioinformatic pipeline. In total, 14 HEV subtypes were detected in the study. HEV-3f and HEV-3e are predominant in environmental samples near areas impacted by the pig industry. HEV-3c is the majoritarian genotype in WWTP with low contact to the branch sector. Samples had a minoritarian presence of HEV-3oni. These results are part of a pilot study which combines ADS and computational analysis to elucidate the HEV genotypes and their zoonotic potential.