Molecular Characterization of Lapinized Classical Swine Fever Vaccine Strain by Full-Length Genome Sequencing and Analysis

Abstract

The complete genome of a lapinized classical swine fever virus (CSFV) vaccine strain was amplified into nine overlapping fragments by RT-PCR, and nucleotide sequences were determined. Complete genome sequence alignment and phylogenetic analysis indicated 92.6–98.6% identities at the nucleotide level with other reported CSFV strains and could be grouped into subgroup 1.1 along with other attenuated strains of CSFV. The 5′-UTR demonstrated >97.0% nucleotide similarity with most of vaccine CSFV strains from China. Further, its 3′-UTR sequence indicated a length similar to all the CSFV strains from China with >98.0% nucleotide similarity, although high length heterogeneity of 3′-UTR was reported among different CSFV strains. There was 12 nt (TTTTCTTTTTTT) insertion in 3′-UTR similar to other reported attenuated vaccine strains. However, secondary structure of 3′-UTR indicated that Indian CSFV strain requires further passage to obtain a 3′-UTR structure similar to most of the attenuated strains.

Keywords:

• Classical swine fever virus
• Complete genome sequence
• Lapinized vaccine
• Phylogenetics
• Sequence alignment
• UTR

Acknowledgments

This study was generously supported, in part, by a project “Development of RNA replicon-based vaccine vector for enhanced expression and immune responses,” Grant No. BT/PR6442/AAQ/01/239/2005 from the Department of Biotechnology (DBT), Government of India. This work also received financial support from the Indian Council of Agricultural Research (ICAR), India.