Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
Virol J. 2011 Jun 23;8:317. doi: 10.1186/1743-422X-8-317.
The 9.6 kb long RNA genome of Hepatitis C virus (HCV) is under the control of RNA dependent RNA polymerase, an error-prone enzyme, for its transcription and replication. A high rate of mutation has been found to be associated with RNA viruses like HCV. Based on genetic variability, HCV has been classified into 6 different major genotypes and 11 different subtypes. However this classification system does not provide significant information about the origin of the virus, primarily due to high mutation rate at nucleotide level. HCV genome codes for a single polyprotein of about 3011 amino acids which is processed into structural and non-structural proteins inside host cell by viral and cellular proteases.
We have identified a conserved NS4A protein sequence for HCV genotype 3a reported from four different continents of the world i.e. Europe, America, Australia and Asia. We investigated 346 sequences and compared amino acid composition of NS4A protein of different HCV genotypes through Multiple Sequence Alignment and observed amino acid substitutions C22, V29, V30, V38, Q46 and Q47 in NS4A protein of genotype 1b. Furthermore, we observed C22 and V30 as more consistent members of NS4A protein of genotype 1a. Similarly Q46 and Q47 in genotype 5, V29, V30, Q46 and Q47 in genotype 4, C22, Q46 and Q47 in genotype 6, C22, V38, Q46 and Q47 in genotype 3 and C22 in genotype 2 as more consistent members of NS4A protein of these genotypes. So the different amino acids that were introduced as substitutions in NS4A protein of genotype 1 subtype 1b have been retained as consistent members of the NS4A protein of other known genotypes.
These observations indicate that NS4A protein of different HCV genotypes originally evolved from NS4A protein of genotype 1 subtype 1b, which in turn indicate that HCV genotype 1 subtype 1b established itself earlier in human population and all other known genotypes evolved later as a result of mutations in HCV genotype 1b. These results were further confirmed through phylogenetic analysis by constructing phylogenetic tree using NS4A protein as a phylogenetic marker.
丙型肝炎病毒（HCV）的 9.6 kb 长的 RNA 基因组受 RNA 依赖性 RNA 聚合酶的控制，该酶为易错酶，用于其转录和复制。已发现高突变率与 HCV 等 RNA 病毒有关。根据遗传变异性，HCV 已分为 6 种不同的主要基因型和 11 种不同的亚型。然而，这种分类系统并不能提供关于病毒起源的重要信息，主要是由于核苷酸水平的高突变率。HCV 基因组编码约 3011 个氨基酸的单聚蛋白，该聚蛋白在宿主细胞内由病毒和细胞蛋白酶加工成结构蛋白和非结构蛋白。
我们鉴定了来自世界四大洲（欧洲、美洲、澳大利亚和亚洲）报告的 HCV 基因型 3a 的保守 NS4A 蛋白序列。我们调查了 346 个序列，并通过多重序列比对比较了不同 HCV 基因型的 NS4A 蛋白的氨基酸组成，观察到 NS4A 蛋白中 1b 基因型的氨基酸取代 C22、V29、V30、V38、Q46 和 Q47。此外，我们观察到 C22 和 V30 是 1a 基因型 NS4A 蛋白更一致的成员。同样，在基因型 5 中 Q46 和 Q47、基因型 4 中 V29、V30、Q46 和 Q47、基因型 6 中 C22、Q46 和 Q47、基因型 3 中 C22 和 V38、Q46 和 Q47 以及基因型 2 中 C22 是这些基因型 NS4A 蛋白更一致的成员。因此，引入 1b 亚型 NS4A 蛋白中的不同氨基酸已被保留为其他已知基因型 NS4A 蛋白的一致成员。
这些观察结果表明，不同 HCV 基因型的 NS4A 蛋白最初是从 1b 亚型的 NS4A 蛋白进化而来的，这反过来表明，1b 亚型的 HCV 基因型 1 较早地在人类中建立，而其他所有已知的基因型则是由于 HCV 基因型 1b 的突变而在后期进化而来的。通过使用 NS4A 蛋白作为系统发育标记构建系统发育树进行系统发育分析，进一步证实了这些结果。
