Molecular characterization of the 5? non-coding region of South African GBV-C/HGV isolates: Major deletion and evidence for a fourth genotype

Abstract

GB virus C/hepatitis G virus (GBV-C/HGV) has been characterised as a novel flavivirus, and to date three known genotypes have been cloned. Greater genetic variation of GBV-C/HGV has been demonstrated in West African isolates, but no major deletions have been shown in the 5' non-coding region (NCR). The 5'NCR regulates protein translation via an internal ribosomal entry site (IRES). We cloned, sequenced, and analysed a 344-bp polymerase chain reaction (PCR) product, representing >60% of the 5'NCR, from 32 GBV-C/HGV PCR-positive volunteers. Wild-type virus amplicons were detected in all samples. However, 5/32 (15.6%) also amplified another fragment of between 205 and 231 bp. Sequence analysis showed all cloned PCR fragments to be GBV-C/HGV-specific. A typical deletion of 113-131 bp with minor variation was detected in isolates generating the smaller bands. RNA secondary structure analysis showed the deletions to be over domains II and III. This finding suggests that nucleotides 303-444 may be non-essential for 5'NCR functioning. Phylogenetic analysis demonstrated a novel fourth South African genotype, distinct from genotypes 1-3 with DNA distances of >0.1000. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) values for the wild-type and mutant samples were normal. This study documents the first major deletion in the 5'NCR of GBV-C/HGV, and suggests that bases 303-444 may not be essential for viral replication and ribosomal entry. A fourth GBV-C/HGV genotype appears to predominate in South Africa.

A previously unrecognized sixth genotype of GB virus C revealed by analysis of 5′‐untranslated region sequences

“…Finally, an examination of GBV-C/HIV co-infection among African mothers and their infants from KwaZulu Natal province of South Africa revealed an association between co-infection and protection or delayed disease progression [Sathar et al, 2004]. Based on previous epidemiological data [Tucker et al, 1999;Sathar and York, 2001] it is likely that these individuals were infected with genotype 5. It is difficult to conclude from these few studies whether GBV-C genotype influences the clinical presentation of disease or disease outcome among GBV-C/HIV co-infected individuals.…”

“…These isolates, detected in blood donors and hepatitis patients, were designated by the authors as genotype 5-not to be confused with the novel isolates identified in South Africa in the previous year [Tucker et al, 1999] and designated subsequently genotype 5 [Tucker and Smuts, 2000]. An additional study [Mison et al, 2000] suggested the existence of a novel GBV-C genotype found among Pacific Islanders that was unlike genotype 1, 2, or 3 sequences.…”

“…In some cases, only the reported novel sequences were included to prevent overrepresentation of genotypes 1, 2, or 3. Genotype 5 sequences from South Africa reported by Tucker et al [1999] to have a major deletion within the 5 0 -UTR were not included. The aligned sequences spanned the 5 0 -UTR from nucleotides À510 to À202 of the GBV-C genome (where base þ1 is the A residue of the AUG codon at the start of the long open reading frame).…”

“…Initially, three genotypes of GBV-C were described that correlated with geographic origin [Muerhoff et al, , 1997Okamoto et al, 1997;Takahashi et al, 1997;Saito et al, 1998]; these included isolates from Africa (genotype 1), North America and Europe (genotype 2), and Japan (genotype 3). The number of genotypes expanded to include novel isolates from Myanmar and Vietnam [Naito et al, 1999] representing a fourth genotype, and isolates from South Africa were subsequently shown to represent the fifth genotype [Sathar et al, 1999;Tucker et al, 1999;Tucker and Smuts, 2000;Sathar and York, 2001]. In most studies, the identification of novel genotypes utilized phylogenetic analysis of the 5 0 -untranslated region (5 0 -UTR).…”

GB virus C/hepatitis G virus infection in dialysis patients and kidney transplant recipients in central Brazil

“…Genotype 3 is frequently observed in parts of Asia (Muerhoff et al 1996, Mukaide et al 1997, Okamoto et al 1997 Financial support: Conciteg, CNPq1998). Recent studies have identified genotype 4 in samples from Myanmar, Vietnam, and Indonesia (Naito et al 2000, Handajani et al 2000, and genotype 5 in South Africa (Tucker et al 1999, Tucker & Smuts 2000.…”