Phylogenetic analysis of hepatitis E virus isolates from Egypt

Abstract

Hepatitis E virus (HEV) genome was detected by reverse transcriptase-polymerase chain reaction (RT-PCR) in fecal samples of two sporadic cases of hepatitis E in Cairo Egypt. Sequence of the complete putative structural region [open reading frame (ORF)-2] and complete region of unknown function (ORF-3) was determined for the two HEV isolates. Phylogenetic analysis of the nucleotide sequences was performed using neighbor joining or maximum parsimony methods of tree reconstruction. Direct correspondence between the HEV evolutionary trees and geographic origin of the HEV isolates was observed. Three genotypes of HEV were identified: genotype I (Asia-Africa), genotype II (US), and genotype III (Mexico). Genotype I was further divided into two subgenotypes (Asia and Africa). In the Asian subgenotype, three smaller genetic clusters were observed (China-like sequences, Burma-like sequences, and sequence from a fulminant case of HEV). The segregation of all these genetic clusters was supported by the high level of bootstrap probabilities. Four regions of the HEV genome were used for phylogenetic analysis. In all four regions, Egyptian HEV isolates were grouped in a separate African clade.

An outbreak of hepatitis E in Northern Namibia, 1983.

“…30 More recent reports of hepatitis E have emerged from many other African countries. [3][4][5][6][7][8][9][10][11] In southern Africa, surveys in South Africans and in Mozambican refugees living in Swaziland have shown serologic evidence of HEV infection, [35][36][37] but no actual disease has been documented by detection of HEV in clinical specimens. This report of hepatitis E in southern Africa is the first to unambiguously document cases by detection of HEV in patient specimens.…”

“…1 In the past decade, hepatitis E has been shown to be the cause of sporadic and epidemic hepatitis across central and south Asia, 2 and in northern and subSaharan Africa. [3][4][5][6][7][8][9][10][11] One of the largest outbreaks of hepatitis E, in Delhi, India (1955) was identified retrospectively by identification of antibodies to HEV in archived serum specimens. 12 Polymerase chain reaction (PCR) tests to detect HEV RNA 8,13,14 and improved serology for HEV [15][16][17][18] have greatly increased the ability of reference laboratories to identify hepatitis E disease.…”

Short report: phylogenetically distinct hepatitis E viruses in Pakistan.

“…To date, 15 isolates, defined as HEV contained in a specific patient specimen, have been fully sequenced; together, they comprise 5 genotypes: genotype I (Asia-Africa), genotype II (United States), genotype III (Mexico), genotype IV (Beijing, China), and genotype V (European). [2][3][4] Genotype I is the most complex, having 2 sub-genotypes: African and Asian. The Asian sub-genotype, now represented by 11 isolates, consists of 2 genetic clusters: Central Asian and South Asia.…”

“…The South Asian cluster includes isolates from Burma, India, and Nepal. 2,5 Hepatitis E is very common in Pakistan. [6][7][8] Nevertheless, only a single isolate from Sargodha has been genomically and phenotypically characterized.…”

“…10,11 We performed phylogenetic analysis of Abb-2B and all other full-length HEV genomes (n ϭ 15) in the GenBank database (Table 1) using PHYLIP and PAUP programs in GCG release 10.0 (University of Wisconsin, Madison, WI) as previously described. 2 Both methods of phylogenetic analysis placed the Abb-2B isolate in the South Asian cluster of genotype I, whereas Sar-55, the other Pakistan isolate, was placed in the Central Asia cluster of genotype I (Figure 1). The certainty of this difference is greater than 95%, as determined by 1,000 replicate bootstrap analysis.…”