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Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach
Published on: December 1, 2011
Phylogenetic analysis of 3C protease (3C(pro)) coding region of Foot-and-mouth disease virus type A
J K Mohapatra1, P Priyadarshini, L Pandey
1Project Directorate on Foot and Mouth Disease, Indian Veterinary Research Institute Campus, Mukteswar-Kumaon, Nainital 263138, Uttarakhand, India. jajatil@gmail.com
Abstract:
Nucleotide sequence analysis of the 3C protease (3C(pro)) region of Foot-and-mouth disease virus type A (FMDV-A) isolates from India has revealed incongruous phylogenetic grouping between 3C(pro) and VP1 region possibly due to the genetic recombination or independent evolution of non-structural and structural protein coding regions. Similar to the VP1 region, the emerging VP3(59)-deletion group maintained its genetic distinctiveness at 3C(pro) region and was found to be diverging with time. Two lineage specific signature aa residues were detected for the deletion group in proof of lineage specific drift or selection events. 3C(pro) region exhibited high degree of conservation as evident from low dN/dS ratio (0.036) and percentage of variable aa positions (20%). A transmembrane domain from aa 27 to 44 could be predicted that possibly anchors 3C to intracellular membranes for better interaction with RNA replication complex. On the basis of sequence conservation, the likelihood that the region aa 121-150 was carrying a vaccine exploitable T-cell epitope was very high.
Insights
Phylogenetic analysis of Foot-and-mouth disease virus type A (FMDV-A) 3C protease (3C(pro)) revealed distinct evolutionary patterns and conserved regions. This suggests potential vaccine targets and insights into viral evolution.
Area of Science:
- Virology and Molecular Evolution
- Structural Biology and Bioinformatics
Background:
- Foot-and-mouth disease virus type A (FMDV-A) poses a significant threat to livestock globally.
- Understanding the genetic diversity and evolutionary dynamics of FMDV-A is crucial for effective control strategies.
- The 3C protease (3C(pro)) plays a vital role in viral replication and polyprotein processing.
Purpose of the Study:
- To analyze the nucleotide sequence and phylogenetic relationships of the FMDV-A 3C(pro) region from Indian isolates.
- To investigate potential genetic recombination or independent evolution between non-structural and structural protein coding regions.
- To identify conserved regions and potential targets for vaccine development.
Main Methods:
- Nucleotide sequence analysis of the 3C(pro) region from FMDV-A isolates.
- Phylogenetic analysis to compare 3C(pro) and VP1 regions.
- Identification of lineage-specific amino acid residues and conserved domains.
- Prediction of transmembrane domains and potential T-cell epitopes.
Main Results:
- Incongruous phylogenetic grouping between 3C(pro) and VP1 regions suggests recombination or independent evolution.
- The emerging VP3(59)-deletion group shows distinct genetic characteristics in the 3C(pro) region.
- High conservation of the 3C(pro) region (low dN/dS ratio, 20% variable amino acid positions) was observed.
- A potential transmembrane domain (aa 27-44) and a highly conserved region (aa 121-150) with vaccine-exploitable T-cell epitope potential were identified.
Conclusions:
- The 3C(pro) region of FMDV-A exhibits distinct evolutionary patterns compared to the VP1 region.
- The 3C(pro) region's high conservation and identified epitopes present promising avenues for FMDV vaccine development.
- Understanding these evolutionary dynamics is key to managing FMDV-A outbreaks.
