Potentially infectious novel hepatitis a virus strains detected in selected treated wastewater discharge sources, South Africa

Hepatitis A virus (HAV) is a waterborne pathogen of public health importance. In South Africa (SA), unique HAV subgenotype IB strains have been detected in surface and wastewater samples, as well as on fresh produce at the point of retail. However, due to the use of molecular-based assays, the infectivity of the detected strains was unknown. Considering the potential shift of HAV endemicity from high to intermediate, which could increase the risk of severe symptomatic disease, this study investigated the identity of HAV strains detected before and after viability treatment of selected wastewater discharge samples. For one year, 118 samples consisting of sewage, treated wastewater discharge and downstream dam water were collected from five wastewater treatment plants (WWTP 1, 2, 3, 4 and 5). Unique HAV IB strains were detected in samples from all five WWTPs, with 11 of these strains carrying amino acid mutations at the immunodominant and neutralisation epitopes. A quasispecies dynamic of HAV has also been detected in sewage samples. The subsequent application of viability PCR revealed that potentially infectious HAV strains were discharged from WWTP 1, 2, 4 and 5 into the dam. Therefore, there is a potential risk of HAV exposure to communities using water sources downstream the WWTPs.Supplementary file 1 of Figure 1: Fasta file of the sequence alignment used to infer phylogenetic analysis targeting the VP1 region of hepatitis A virus (HAV) strains detected in samples from all five wastewater treatment plants (WWTPs). Supplementary file 2 of Figure 3: Fasta file of the sequence alignment used to infer phylogenetic analysis targeting the VP1/P2B junction of hepatitis A virus (HAV) strains detected in samples from all five wastewater treatment plants (WWTPs). Supplementary file 3 of Figure 5: Graphic view of the complete protein alignment (from position 1 to 300) of the deduced amino acid sequences of the VP1 region of the HM175 strain and hepatitis A virus (HAV) strains carrying mutations at immunodominant and neutralisation epitopes. Supplementary file 4 of Figure 5: Fasta file of the sequence alignment of the VP1 region of the HM175 strain and hepatitis A virus (HAV) strains carrying mutations at immunodominant and neutralisation epitopes. Supplementary file 5 of Figure 6: Fasta file of the sequence alignment of the VP1 region of the HM175 strain and hepatitis A virus (HAV) strains carrying in-frame deletions. Supplementary file 6 of Figure 7: Graphic view of the amino acid sequence alignment of the VP1/P2B junction of the HM175 strain and 47 hepatitis A virus (HAV) strains carrying the C70S and/or M104I changes. Supplementary file 7 of Figure 7: Fasta file of the sequence alignment of the VP1/P2B junction of the HM175 strain and 47 hepatitis A virus (HAV) strains carrying the C70S and/or M104I changes.The Rand Water Chair in Public Health; the Poliomyelitis Research Foundation (PRF); University of Pretoria and National Research Foundation (NRF).http://www.mdpi.com/journal/virusesam2021Medical VirologySchool of Health Systems and Public Health (SHSPH