Group 5: GBV‐C/HGV isolates from South Africa

Journal of Medical Virology 65:121±122 (2001) Brief Communication Group 5: GBV-C/HGV Isolates From South Africa Mahomed A. Sathar1* and Denis F. York2 1 Department of Medicine, Nelson R Mandela School of Medicine, Faculty of Health Sciences, University of Natal, Durban, South Africa 2 Department of Virology, Nelson R Mandela School of Medicine, Faculty of Health Sciences, University of Natal, Durban, South Africa It was assumed initially that analysis of the 50 NCR allowed the discrimination of three major groups that correlated with the geographic origins of the isolates and with the analysis of the complete genome sequences. Based on this assumption, sequence and phylogenetic analysis of the 50 non-coding region (50 NCR) of GBV-C/HGV isolates from the Western and Eastern Cape Provinces [Tucker et al., 1999] and the province of KwaZulu Natal [Sathar et al., 1999] of South Africa demonstrated the presence of new variants of GBV-C/ HGV in South Africa. Unlike Tucker et al. [1999] neither major deletions nor additional bands to the predicted 344bp PCR fragment were observed in any of the isolates from KwaZulu Natal [Sathar et al., 1999]. Recent evidence suggests that phylogenetic analysis of the 50 NCR may not always provide an accurate guide to the relationship of complete genome sequences [Smith et al., 2000]. In their thorough analysis of 33 epidemiologically distinct complete or near complete genomic sequences of GBV-C/HGV, Smith et al. [2000] provided evidence of the existence of four major geographically distinct phylogenetic groups that were equally divergent from the chimpanzee isolate, GBVCtrop [Birkenmeyer et al., 1998]. Group 1 included isolates from Ghana, West Africa, and a single Japanese isolate; Group 2 included isolates from Europe, North and South America, and Japan; Group 3 included isolates from Japan and China; and Group 4 included isolates from southeast Asia [Smith et al., 2000]. Analysis of 50 NCR (positions ÿ388 to ÿ1) and subfragments of this region, including those previously identi®ed as reproducing the phylogenetic relationships of group 1 and 2 isolates, provided <70% bootstrap support for either groups 3 or 4 [Smith et al., 1997]. However, the variants from KwaZulu Natal grouped separately from the 50 -NCR sequences of complete genome sequences for the region ÿ388 to ÿ1 [Smith et al., 2000]. When 50 NCR sequences of complete genome sequences for the region 143±442 were analyzed, Group 3 (bootstrap support 83%) and Group 4 (bootstrap support 71%) isolates are not clearly differentiated by the phylogenetic analysis of this ß 2001 WILEY-LISS, INC. region; only the South African isolates grouped separately (Fig. 1). In contrast, analysis of a 200-nt fragment from the center of the E2 gene (positions 1,344±1,543) provides>70% bootstrap support for all four phylogenetic groupings, while a 600-nt region (position 994±1,594) provided >98% bootstrap support. GBV-C/HGV isolates from KwaZulu Natal form an additional ®fth group when E2 sequences for the 350 nt region (positions 1,146 to 1,495) are compared with the corresponding region from the complete genome sequences of all four phylogenetic groups [Smith et al., 2000]. With the sole exception of E2 gene, phylogenetic analysis of individual genes and subgenomic regions, including the 50 NCR, failed to consistently produce congruent phylogenetic trees of the four major groups that correlate with the geographic origin of the isolates [Smits et al., 2000]. Phylogenetic analysis of the E2 gene segment of KZN isolates was shown to be consistent with previous analysis of the 50 NCR [Sathar et al., 1999], suggesting that these belong to a ®fth group [Smith et al., 2000]. In their proposal that South African GBV-C/HGV isolates be classi®ed as ``Genotype 5,'' Tucker and Smuts [2000] did not make reference to the ®ndings of Smith et al. [2000] nor did they include in their analysis GBV-C/HGV isolates from the province of KwaZulu Natal, South Africa [Sathar et al., 1999]. Phylogenetic analysis of 50 NCR sequences of the ``novel'' South African GBV-C/HGV isolates from the provinces of the Western, and Eastern Cape (excluding the deletants) [Tucker et al., 1999] and from KwaZulu Natal [Sathar et al., 1999], grouped South African isolates as Grant sponsor: University of Natal, Durban, South Africa. *Correspondence to: Mahomed A. Sathar, Department of Medicine, Nelson R Mandela School of Medicine, Faculty of Health Sciences, University of Natal, PO Box 7 Congella 4013 South Africa. E-mail: sathar@med.und.ac.za Accepted 8 January 2001 122 Sathar and York Fig. 1. Consensus phylogenetic tree of 50 NCR sequences of GBV-C/ HGV isolates from South Africa and representative published sequences from GenBank/EMBL. Phylogenetic analysis was carried out on a 311-bp fragment, positions 143±442 in the GBV-C prototype isolate (U36380). Maximum likelihood distances between sequences were calculated using Phylip DNADIST (ts:tv ˆ 3, assuming no rate an additional ®fth group (Fig. 1). The inclusion of GBV-C/HGV isolates from KwaZulu Natal in the proposal made by Tucker and Smuts [2000] that South African isolates be classi®ed as Group 5 or Genotype 5, will be more representative of isolates from South Africa. It would certainly be interesting to obtain the E2 sequences of additional South African isolates. However, the complete sequence of one or more of the novel South African isolates would indeed settle the question of whether or not this is in fact a new phylogenetic variant. ACKNOWLEDGMENTS We acknowledge Tulio de Oliveira for the phylogenetic analysis. variation between sites), and used to produce a neighbour joining tree using Phylip NEIGHBOR. Bootstrap values (100 replicates) were obtained with the SEQBOOT and CONSENSE options of Phylip. The tree was produced using Treeview version 1.5. KZN ˆ KwaZulu Natal; A-H ˆ 8 geographical health regions of KwaZulu Natal. REFERENCES Birkenmeyer LG, Desai SM, Muerhoff AS, Leary TP, Simons JN, Montes CC, Mushahwar IK. 1998. Isolation of a GB virus-related genome from a chimpanzee. J Med Virol 56:44±51. Sathar MA, Soni PN, Pegoraro R, Simmonds P, Smith DB, Dhillon AP, Dusheiko GM. 1999. A new variant of GB virus C/hepatitis G virus (GBV-C/HGV) from South Africa. Virus Res 64:151±160. Smith DB, Guceanu N, Davidson F, Jarvis LM, Mokili JLK, Hamid S, Ludlam CA, Simmonds P. 1997. Discrimination of hepatitis G virus/GBV-C geographical variants by analysis of the 50 noncoding region. J Gen Virol 78:1533±1542. Smith DB, Basaras M, Simon F, Haydon D, Cuceanu N, Prescott L, Kamenka C, Millband D, Sathar MA, Simmonds P. 2000. Phylogenetic analysis of GBV-C/Hepatitis G virus. 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