Epidemiology and Genetic Characterization of Hepatitis A Virus Genotype IIA

Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5′ untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored.Hepatitis A virus (HAV) is a small, nonenveloped hepatotropic virus classified in the genus Hepatovirus within the family Picornaviridae. Its genome consists of a 7,500-nucleotide linear, positive-stranded RNA with a single open reading frame (ORF) flanked by 5′ and 3′ untranslated regions (UTR) (3). The 5′ UTR is the most conserved region of the genome and contains an internal ribosome entry site (IRES). The ORF encodes a polyprotein organized into three functional regions: P1, P2, and P3. P1 is secondarily cleaved into four capsid proteins, VP1 to VP4, whereas P2 and P3 encode nonstructural proteins.Despite significant genetic variability, a single serotype has been described (13). Sequence variation of a 168-nucleotide fragment encompassing the VP1/2A junction has initially defined seven genotypes that differ by at least 15% and subtypes that differ by 7.0 to 7.5% (19). Six HAV genotypes (genotypes I to VI) are now defined based on analysis of the 900 nucleotides of the complete VP1 protein (6). Genotypes I, II, and III, divided into subtypes A and B, infect humans. The former genotype VII has been reclassified within the genotype II clade as subgenotype IIB (6, 14). Data on genotype distribution showed that genotype I was the most prevalent worldwide, with IA being reported more frequently than IB, and that subgenotype IIIA was prevalent in Central Asia (6, 16, 19). In areas of low endemicity, such as the United States and Western Europe, subgenotype IA dominates, but all genotypes and subtypes have been reported (6, 16, 23). Most HAV strains in these countries can be identified as imported strains by phylogenetic analysis thanks to growing sequence databases, which allow for the tracing of the geographic origin of a given subgenotype (16).Among HAV genotypes, subgenotypes IIA (former genotype II) and IIB (former genotype VII) were defined based on a single isolate of each: CF-53/Berne, isolated in France in 1979, and SLF88, isolated in Sierra Leone in 1988 (19). Their complete sequences are now available (4, 14). These two subgenotypes are rarely reported. Recently, sequence analysis of the P1 region allowed the identification of a recombinant IB-IIA virus in a patient returning from Morocco (7), and a second IIA strain, identified by VP1-2A analysis, was reported in a Dutch patient returning from Spain (23).From 2002 to 2007, six subgenotype IIA strains were isolated at the National Reference Centre for HAV in France (6/693 available strains [<1%]). Of these, only one was isolated from a patient reporting travel in an area of endemicity, in Benin, West Africa. Acute HAV infection has been a mandatory reportable disease in France since 2006. The mandatory notification records allowed us, first, to investigate the possible sub-Saharan origin of IIA strains by determining their prevalence among French travelers returning from Africa in 2008. Second, the genetic variability of all IIA isolates identified was characterized in order to gain insight into the molecular epidemiology of the IIA subgenotype and to elucidate the origin of autochthonous IIA cases.