Identification of a novel hepatitis E virus in Nigeria

Sporadic cases of acute hepatitis E among ten native Nigerian adults were reported in Port-Harcourt (Nigeria). Hepatitis E virus (HEV) was detected in serum and/or faecal samples of seven patients by RT–PCR of the open reading frame (ORF)-1 polymerase region and the 3′-end of ORF2. Restriction analysis widely used to distinguish genotypes I and III showed that all Nigerian strains have a pattern similar to the Mexican strain (NotI, nt 286; SmaI, nt 397; no KpnI restriction site) but displayed a BsmI restriction site at nt 213 as do most African HEV strains sequenced so far. Sequence analysis performed from internal ORF1 and ORF2 PCR products displayed strong homogeneity between the HEV isolates, determining a regional cluster. Phylogenetic analysis of nucleotide sequences revealed that these strains were more related to the Mexican prototype genotype III (87% homology in ORF1, 80% homology in ORF2) than to either the African strain genotype I (74% homology in ORF1, 77% homology in ORF2) or the USA strain genotype II (75% homology in ORF1, 77% homology in ORF2). Genetic divergence up to 15% in ORF2 with the Mexican genotype clearly defined a new subgenotype within genotype III. At the amino acid level, Nigerian strains showed more homology with genotype III (96%) than with genotype I (92%). This study clearly determined the co-existence of genotypes I and III in Africa. These Nigerian HEV strains belonging to genotype III, but sharing some properties with genotype I, could be one of the missing links between African and Latin American HEV and could help us to determine the phylogenetic evolution of HEV from the ancestral virus.