上海地区鸽Ⅰ型副黏病毒F基因遗传进化及生物信息学分析

doi:10.16431/j.cnki.1671-7236.2024.12.004

Abstract

Abstract: 【Objective】 The purpose of this study was to understand the genetic variation of F gene of Pigeon paramyxovirus type Ⅰ (PPMV-1) epidemic strain in Shanghai area,analyze the bioinformatic characteristics of F protein,and provide technical support for the prevention and control of PPMV-1.【Method】 F gene of the isolate was amplified by RT-PCR,and sequencing and genetic evolution analysis were performed.The structure and function of F protein were predicted by online bioinformatics software.【Result】 The total length of the F gene coding region of the isolate was 1 662 bp,encoding 553 amino acids,and the F protein cleavage site sequence was 112R-R-Q-K-R-F117,which was consistent with the sequence structure of the virulent strain.Phylogenetic tree analysis showed that the isolate belonged to Class Ⅱ group Ⅵ.2.1.1.2.2 subtype of Newcastle disease virus (NDV).The isolate was in a different evolutionary branch from the vaccine strains La Sota and Mukteswar,and belonged to the same branch Ⅵ.2.1.1.2.2 with the domestic isolates Pi/SH/CH/0617/2013 and pigeon/Ningxia/2068/2016.The results of bioinformatics analysis showed that F protein was a hydrophilic protein with molecular mass of 59.03 ku,theoretical isoelectric point (pI) of 7.87,half-life period of 30 h,instability coefficient of 35.06 and fat coefficient of 109.73.F protein was mainly distributed in the plasma membrane and endoplasmic reticulum of the cell,and had a transmembrane structure and signaling peptides,including 6 potential N-glycosylation sites,13 cysteine residues,103 O-glycosylation sites,and 67 phosphorylation sites.In the secondary structure,alpha helix,random coil,extended chain and beta turn account for 46.11%,31.46%,18.08% and 4.34%,respectively.The predicted result of tertiary structure was consistent with the secondary structure.B-cell antigen site prediction showed that F protein contained 11 epitopes (amino acid number ≥7).【Conclusion】 The PPMV-1 isolate belonged to NDV Class Ⅱ group Ⅵ.2.1.1.2.2 subtype of NDV，and its F protein had a good epitope,which could be used as the target protein for PPMV-1 vaccine development and antiviral therapy.The results provided a certain reference for effective prevention and control of PPMV-1 infection,and also laid a foundation for further research and development of new vaccines.

Key words: Pigeon paramyxovirus type Ⅰ; F gene; phylogenetic; bioinformatics

CLC Number:

S855.3

LIU Jian, ZHOU Jinping, SHEN Liping, GUI Yaping, GE Feifei, WANG Xiaoxu, YANG Xianchao, LIU Peihong, WANG Jian. Phylogenetic and Bioinformatics Analysis of F Gene of Pigeon Paramyxovirus Type Ⅰ from Shanghai Area[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(12): 5150-5161.

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Phylogenetic and Bioinformatics Analysis of F Gene of Pigeon Paramyxovirus Type Ⅰ from Shanghai Area

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