Tion was less than one (Table 3), indicating that purifying selection was

Tion was less than one (Table 3), indicating that purifying selection was the dominant force in the evolution and divergence of GB virus C within respective hosts. To determine whether any of the amino acid sites in E2 gene in each patient are under positive selection, we performed site-specific substitution analysis. The hypothesis of neutral evolution could not be rejected by the LRT (Table 4), thus indicating none of the amino acid sites in each patient are under positive selection.Phylogenetic analysisPrior to the genetic analysis, we performed six different recombination detection tests to identify whether any of the cloned sequences were recombinant. Four sequences, two from patient ZX_M_15 and the others from patient JL_M_29, were Z-360 recombinant (Table 2; Fig. 2). Therefore, these recombinant sequences were excluded from further genetic analysis. To evaluate the possible emergence of recombinant sequences, we performed the PCR based experiment by mixing two isolates representing different genotypes. GBV-C E2 clone QC_5_21 (genotype III) and XA_16_001 (genotype II) were physically mixed with the same ratio to use as a template and the E2 gene was PCR amplified, cloned and sequenced under identical conditions. Recombination analysis on those PCR-base recombinant sequences showed there were three recombinant sequences in a total of 10 clones. However, 4 recombinant sequences were detected in a total of 196 E2 sequences. Nevertheless, these results are consistent with the fact that recombination in natural population is less frequent than in the experimental condition [48]. Phylogenetic analysis has revealed that while eight HIV patients were infected with GBV-C genotype 3, two patients were infected with GBV-C genotype 2 (Fig. 2). GBV-C E2 sequences from the respective patients formed a patient-specific unique cluster with strong bootstrap support (Fig. 2). GBV-C viral strains from patients XA_M_20, QC_M_05, and JZ_M_26 appeared to be monophyletic (Fig. 2). Although patients YXX_M_11 and JL_M_29 clustered together, GBV-C sequences from YXX_M_11 were basal to the GBV-C sequences from JL_M_29, indicating that the GBV-C in YXX_M_11 was likely the founding population for JL_M_29. The observation of low branching pattern (Fig. 2), low nucleotide diversity (p) (Table 3), and mean pairwise differences (d) (Table 3) in JL_M_29 further indicated that patient JL_M_29 was relatively recently infected and the viralDiscussionThe present study investigated the prevalence and population dynamics of GB virus C in HIV infected individuals representing 13 geographic regions in Hubei Province of China. Intravenous drug abuse, paid blood donation, and unsafe sex practice (hetero sexual and homo sexual) are the major route of HIV transmission among the susceptible individuals in Hubei Province of China.n p 0.00145660.000988 25.9375 211.637 210.997 213.602 215.734 0.140 0.020 0.009 22.0025 22.2332 1.54914 0.001 0.950 28.194 29.5448 213.369 0.26629 23.4866 0.00307660.001815 20.4936 21.6038 21.8122 22.1745 21.0874 21.7883 0.001 0.023 0.034 0.00292460.001727 0.52232-67-4 web 00704360.003789 0.00565360.003095 0.00530160.002920 0.00861860.004651 0.00551960.003048 0.00330760.001941 0.00886060.004695 10.9947365.217300 0.671 3.78947461.991743 0.624 6.84967363.382386 0.777 9.66911864.662595 0.651 6.58421163.246829 0.891 7.02105363.442320 0.712 8.74736864.213996 0.589 3.63157961.920425 0.444 3.72514661.967228 0.203 0.326 1.80882461.095936 0.167 0.06437 0.560 17 19 20 20 20 20 17 18.Tion was less than one (Table 3), indicating that purifying selection was the dominant force in the evolution and divergence of GB virus C within respective hosts. To determine whether any of the amino acid sites in E2 gene in each patient are under positive selection, we performed site-specific substitution analysis. The hypothesis of neutral evolution could not be rejected by the LRT (Table 4), thus indicating none of the amino acid sites in each patient are under positive selection.Phylogenetic analysisPrior to the genetic analysis, we performed six different recombination detection tests to identify whether any of the cloned sequences were recombinant. Four sequences, two from patient ZX_M_15 and the others from patient JL_M_29, were recombinant (Table 2; Fig. 2). Therefore, these recombinant sequences were excluded from further genetic analysis. To evaluate the possible emergence of recombinant sequences, we performed the PCR based experiment by mixing two isolates representing different genotypes. GBV-C E2 clone QC_5_21 (genotype III) and XA_16_001 (genotype II) were physically mixed with the same ratio to use as a template and the E2 gene was PCR amplified, cloned and sequenced under identical conditions. Recombination analysis on those PCR-base recombinant sequences showed there were three recombinant sequences in a total of 10 clones. However, 4 recombinant sequences were detected in a total of 196 E2 sequences. Nevertheless, these results are consistent with the fact that recombination in natural population is less frequent than in the experimental condition [48]. Phylogenetic analysis has revealed that while eight HIV patients were infected with GBV-C genotype 3, two patients were infected with GBV-C genotype 2 (Fig. 2). GBV-C E2 sequences from the respective patients formed a patient-specific unique cluster with strong bootstrap support (Fig. 2). GBV-C viral strains from patients XA_M_20, QC_M_05, and JZ_M_26 appeared to be monophyletic (Fig. 2). Although patients YXX_M_11 and JL_M_29 clustered together, GBV-C sequences from YXX_M_11 were basal to the GBV-C sequences from JL_M_29, indicating that the GBV-C in YXX_M_11 was likely the founding population for JL_M_29. The observation of low branching pattern (Fig. 2), low nucleotide diversity (p) (Table 3), and mean pairwise differences (d) (Table 3) in JL_M_29 further indicated that patient JL_M_29 was relatively recently infected and the viralDiscussionThe present study investigated the prevalence and population dynamics of GB virus C in HIV infected individuals representing 13 geographic regions in Hubei Province of China. Intravenous drug abuse, paid blood donation, and unsafe sex practice (hetero sexual and homo sexual) are the major route of HIV transmission among the susceptible individuals in Hubei Province of China.n p 0.00145660.000988 25.9375 211.637 210.997 213.602 215.734 0.140 0.020 0.009 22.0025 22.2332 1.54914 0.001 0.950 28.194 29.5448 213.369 0.26629 23.4866 0.00307660.001815 20.4936 21.6038 21.8122 22.1745 21.0874 21.7883 0.001 0.023 0.034 0.00292460.001727 0.00704360.003789 0.00565360.003095 0.00530160.002920 0.00861860.004651 0.00551960.003048 0.00330760.001941 0.00886060.004695 10.9947365.217300 0.671 3.78947461.991743 0.624 6.84967363.382386 0.777 9.66911864.662595 0.651 6.58421163.246829 0.891 7.02105363.442320 0.712 8.74736864.213996 0.589 3.63157961.920425 0.444 3.72514661.967228 0.203 0.326 1.80882461.095936 0.167 0.06437 0.560 17 19 20 20 20 20 17 18.