Patterns of mutation within an emerging endemic lineage of HEV‐3a

Abstract

Summary The hepatitis E virus can cause chronic infections in immuno‐suppressed patients, and cases have been on the rise globally. Viral mutations during such infections are difficult to characterize. We deep‐sequenced viral populations from 15 immunocompromised patients with chronic HEV to identify the viral lineage and describe viral mutational hotspots within and across patients. A total of 21 viral RNA samples were collected between 2012 and 2017 from a single hospital in Singapore. Sequences covering a total of 3894 bp of the HEV genome were obtained. Phylogenetic analyses identified all sequences as belonging to the HEV‐3a sub‐clade and clearly indicate a unique local lineage. Deep sequencing reveals variable viral population complexity during infections. Comparisons of viral samples from the same patients spaced 2‐19 months apart revealed rapid nucleotide replacements in the dominant viral sequence in both ribavirin treated and treatment‐naive patients. Mutational hotspots were identified within ORF3 and the PCP/HVR domain of ORF1.

Seroepidemiology and genotyping of hepatitis E virus in Singapore reveal rise in number of cases and similarity of human strains to those detected in pig livers

“…Phylogenetic analyses of concatenated ORF1 and ORF2 sequences from 59 HEV samples revealed that most of the strains belong to genotype 3a (44/59, 75%; shaded, Figure a). When compared with selected strains previously reported in Singapore, our genotype 3a strains clustered closely with four (KT447526, KT447528, AHB282, AHB300) but not with another strain (AH284) that was believed to have been imported (Zhu et al, ) (Figure a). Notably, only one of the genotype 3a strains was from a non‐resident, and the other 43 samples were from Singapore residents.…”

“…Molecular analyses of sequences in our study of human sera revealed genotype 3 to be distinctly the most prevalent (121/143, 84.6%), with genotype 3a as the main circulating strain. Although Teo et al () and Zhu et al () have previously described the identification of genotype 3a in Singapore, the number of their cases (3 and 15, respectively) was small. Our study detected genotype 3a in 44 of 59 patient samples with concatenated ORF1 and ORF2 sequences (74.6%).…”

“…Singapore. This rise in the number of HEV cases and recent reports of chronic HEV in solid organ transplant recipients (Teo et al, 2017) and immunocompromised patients (Zhu et al, 2019) (Albano et al, 2019;Wallace et al, ). Being asymptomatic or not having raised ALTs to prompt follow-up investigations for hepatitis, these silent HEV-infected persons may pose a risk for transmission, spreading the virus unawares when they donate blood, or passing it to others faecal-orally particularly if they are engaged in the food industry.…”

“…The rise in the rate and the almost 10‐fold increase in the number of positive HEV IgG cases over 10 years among residents are similar to findings in Europe (European Centre for Disease Prevention & Control, ), which is suggestive of a growing hepatitis E burden in Singapore. This rise in the number of HEV cases and recent reports of chronic HEV in solid organ transplant recipients (Teo et al, ) and immunocompromised patients (Zhu et al, ) raise considerable concerns. A pertinent question would be whether blood donors in Singapore should be screened for hepatitis E.…”

“…The phylogenetic trees were constructed using concatenated sequences from ORF1 and ORF2. Genotypes of HEV reference strains (Lu, Li, & Hagedorn, 2006;Smith et al, 2016), selected strains previously reported in Singapore (Teo et al, 2017;Zhu et al, 2019) and selected reference strains from previous studies (Nishizawa et al, 2017) were downloaded from GenBank (Clark, Karsch-Mizrachi, Lipman, Ostell, & Sayer, 2016). Males formed the majority of hepatitis E-infected persons among both residents (56%-70%, Figure 1c) and non-residents (72%-100%, Figure 1d).…”