Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences

Area of Science:

• Veterinary Virology
• Molecular Epidemiology
• Bioinformatics

Background:

• Molecular epidemiology is crucial for controlling classical swine fever (CSF).
• Current phylogenetic analyses often use short viral gene fragments (5´NTR, E2), limiting differentiation of closely related isolates.
• Accurate virus tracing requires robust phylogenetic methods for effective control.

Purpose of the Study:

• To compare the variability and phylogenetic suitability of different classical swine fever virus (CSFV) genomic regions.
• To identify optimal viral genomic regions for reliable molecular epidemiology and virus tracing.
• To enhance phylogenetic resolution for differentiating closely related CSFV isolates.

Main Methods:

• Sequencing of a 3508-3510 nt region in the 5´ terminal third of the viral genome from 33 CSFV isolates.
• Comparative analysis of nucleotide sequences from various genomic regions (5´NTR, E2, Npro, C, Erns, E1) including 22 additional GenBank sequences.
• Phylogenetic analysis to assess variability and suitability for differentiating CSFV isolates.

Main Results:

• Full-length E2 gene sequences (1119 nt) demonstrated the highest suitability for reliable and statistically significant phylogenetic analysis.
• Phylogenetic results using full-length E2 sequences were comparable to those obtained with much longer 5´NTR-E2 sequences.
• The study identified full-length E2 sequences as an improved basis for CSFV molecular epidemiology.

Conclusions:

• Full-length E2 gene sequencing is recommended for robust CSFV molecular epidemiology and virus tracing.
• This approach provides a solid foundation for enhanced control measures against classical swine fever.
• The method's efficacy is demonstrated by analyzing closely related CSFV isolates from a recent Lithuanian outbreak.