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Complete genome sequences of hepatitis C virus subtype 3i and 3a subtype isolates from India
Gouri M Gupte1, Ashwini Y Ramdasi, Anupriya S Kulkarni
1National Institute of Virology, Pashan, Pune, India.
Insights
Full genome sequences of Indian Hepatitis C virus (HCV) subtypes 3i and 3a were determined. This provides crucial data for understanding HCV evolution and developing new treatments for genotype 3 infections.
Area of Science:
- Virology
- Genomics
- Hepatology
Background:
- Hepatitis C virus (HCV) causes chronic hepatitis and is classified into six genotypes.
- Genotype 3 HCV is more responsive to interferon therapy.
- Subtypes 3a, 3g, 3j, and 3i are prevalent in India.
Purpose of the Study:
- To determine the complete genome sequences of Indian HCV subtypes 3i and 3a.
- To analyze the genomic characteristics and phylogenetic relationships of these isolates.
Main Methods:
- Serum samples with HCV RNA (subtypes 3i and 3a) were used.
- Complete HCV genomes were amplified using 11 overlapping PCR fragments.
- Sequencing of the amplified fragments was performed.
Main Results:
- The Indian HCV 3i isolate's genome clustered with genotype 3, confirming it as a distinct subtype.
- Nucleotide identity was highest in the core region (86.1-88.7%) and lowest in the E2 region (69.4-70.7%) for the 3i isolate.
- The Indian HCV 3a isolate's genome showed 91.1% similarity to known genotype 3a sequences.
- No evidence of recombination between different HCV genotypes was found in either isolate.
Conclusions:
- Complete genomic sequences of genotype 3 HCV isolates are valuable for studying HCV evolution and classification.
- This data can aid in developing novel therapeutic and preventive strategies for HCV infections.
Aim:
Hepatitis C virus (HCV), a major causative agent of chronic hepatitis, is classified into six major genotypes. Genotype 3 HCV infection is more sensitive to interferon therapy. In India, genotype 3, particularly subtype 3a, HCV infections are common. Three novel HCV subtypes i.e., 3g, 3j, and 3i were identified from India based on partial genomic sequences. This report provides full genome sequences of one isolate each of subtypes 3i and 3a.
Methods:
Serum samples positive for subtype 3i and 3a HCV RNA based on core region genomic sequences were studied. Complete HCV genomes were amplified as 11 overlapping PCR fragments and sequenced.
Results:
The complete genomic sequence of Indian HCV 3i isolate clustered with other genotype 3 sequences, and was closer to subtypes 3b and 3a (80.5% and 79.1% [SD 0.4%] nucleotide identity). Nucleotide similarities were the highest in the core region (86.1-88.7%), and the least in the E2 region (69.4-70.7%). Phylogenetic tree analysis confirmed the existence of a separate subtype 3i. The Indian HCV 3a isolate's complete genomic sequences clustered with previously known genotype 3a sequences with a nucleotide similarity of 91.1% (SD 0.2%). Neither isolates showed evidence of recombination of different HCV genotypes.
Conclusion:
The information on complete genomic sequences of the genotype 3 HCV isolates should be helpful in future studies on HCV evolution and classification, and for development of newer therapeutic and preventive strategies against this infection.
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