中国禽传染性支气管炎病毒的遗传演化及时空传播分析

doi:10.11843/j.issn.0366-6964.2023.06.032

Abstract

Abstract: The aim of this study was to explore the rules of the genetic variation and spatio-temporal transmission of the Chinese IBV isolates, all the sequences of N gene from GenBank database were downloaded. Bioinformatic software including MEGA 6.0, RDP 4.95, SimPlot 3.5.1, BEAST v1.10.4, jmodeltest 2.1.7, Tracer v1.7.1, TempEst v1.5.1, FigTree v1.4.3 and SpreaD3 v0.9.7 were respectively used to analyze the characteristics of phylogenetic tree, recombination events, origin,population dynamics and spatio-temporal transmission of the IBV isolates. The phylogenetic tree analysis showed that a total of six genotypes were identified, and the LX4-type was the predominant genotype. The recombination analysis showed that recombination event was found in N gene in one of isolate from Sichuan province. The maximum clade credibi-lity tree showed that the Chinese IBVs were most likely to be originated in Liaoning province in the early 1930s. Bayesian phylogeographic analyses indicated that multiple transmission routes and three epicenters in China were found, including the Northeastern Region (Heilongjiang, Liaoning, and Jilin), the Northern and Eastern Region (Hebei, Shandong and Jiangsu) and the Southern Region (Guangdong and Guangxi). Shandong has been the source of spreads in China. Our study revealed that the IBVs' origin, transmission routes and a recombination event occurred in N gene in China, suggesting that it is necessary to continue to carry out the molecular epidemiology study and strengthen the analysis of the N gene of IBV.

Key words: infectious bronchitis virus, genetic variation, recombination, origin, spatial transmission

CLC Number:

S851.31

FAN Wensheng, LIU Sijia, QIU Shenben, HUANG Aifang, WANG Yan, LIU Minfang, MEI Minmin, CHEN Xinliang, WEI Ping, MO Meilan. Genetic Evolution and Spatio-temporal Transmission Analysis of the Chinese Infectious Bronchitis Virus[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2543-2554.

References 29

[1]	CAVANAGH D. Coronavirus avian infectious bronchitis virus[J]. Vet Res, 2007, 38(2):281-297.
[2]	FAN W S, CHEN J M, ZHANG Y, et al. Phylogenetic and spatiotemporal analyses of the complete genome sequences of avian coronavirus infectious bronchitis virus in China during 1985-2020:revealing coexistence of multiple transmission chains and the origin of LX4-type virus[J]. Front Microbiol, 2022, 13:693196.
[3]	LIAN J M, WANG Z X, XU Z Y, et al. Distribution and molecular characterization of avian infectious bronchitis virus in southern China[J]. Poult Sci, 2021, 100(7):101169.
[4]	YAN W J, QIU R B, WANG F Y, et al. Genetic and pathogenic characterization of a novel recombinant avian infectious bronchitis virus derived from GI-1, GI-13, GI-28, and GI-19 strains in Southwestern China[J]. Poult Sci, 2021, 100(7):101210.
[5]	VILLALOBOS-AGVERO R A, LEÓN B, ZAMORA-SANABRIA R, et al. Molecular characterization of the S1 gene in GI-17 and GI-13 type isolates of avian infectious bronchitis virus (IBV) in Costa Rica, from 2016 to 2019[J]. VirusDisease, 2022, 33(1):84-95.
[6]	FAN W S, TANG N, DONG Z H, et al. Genetic analysis of avian coronavirus infectious bronchitis virus in Yellow chickens in Southern China over the past decade:revealing the changes of genetic diversity, dominant genotypes, and selection pressure[J]. Viruses, 2019, 11(10):898.
[7]	FINGER P F, PEPE M S, DUMMER L A, et al. Combined use of ELISA and Western blot with recombinant N protein is a powerful tool for the immunodiagnosis of avian infectious bronchitis[J]. Virol J, 2018, 15(1):189.
[8]	范文胜, 唐宁, 董志华, 等. 一株鸭源传染性支气管炎病毒的分离鉴定及结构蛋白基因和血清型分析[J]. 微生物学报, 2019, 59(3):523-532.FAN W S, TANG N, DONG Z H, et al. Identification and analysis of structural protein genes and serotype of an infectious bronchitis virus in ducks[J]. Acta Microbiologica Sinica, 2019, 59(3):523-532. (in Chinese)
[9]	THOR S W, HILT D A, KISSINGER J C, et al. Recombination in avian gamma-coronavirus infectious bronchitis virus[J]. Viruses, 2011, 3(9):1777-1799.
[10]	黄梦姣, 张芸, 薛春宜, 等. 应对日益严峻的挑战:中国禽传染性支气管炎研究[J]. 微生物学通报, 2019, 46(7):1837-1849.HUANG M J, ZHANG Y, XUE C Y, et al. To meet the growing challenge:research of avian infectious bronchitis in China[J]. Microbiology China, 2019, 46(7):1837-1849. (in Chinese)
[11]	韦平. 当前优质鸡产业面临的挑战与发展机遇——论优质鸡产业发展九大议题[J]. 中国家禽, 2019, 41(11):1-6.WEI P. Challenge and development opportunity of quality chicken industry in China:a review about 9 issues on the topic[J]. China Poultry, 2019, 41(11):1-6. (in Chinese)
[12]	KATOH K, STANDLEY D M. MAFFT multiple sequence alignment software version 7:improvements in performance and usability[J]. Mol Biol Evol, 2013, 30(4):772-780.
[13]	TAMURA K, STECHER G, PETERSON D, et al. MEGA6:molecular evolutionary genetics analysis version 6. 0[J]. Mol Biol Evol, 2013, 30(12):2725-2729.
[14]	DARRIBA D, TABOADA G L, DOALLO R, et al. jModelTest 2:more models, new heuristics and parallel computing[J]. Nat Methods, 2012, 9(8):772.
[15]	DENG Q M, SHI M Y, LI Q H, et al. Analysis of the evolution and transmission dynamics of the field MDV in China during the years 1995-2020, indicating the emergence of a unique cluster with the molecular characteristics of vv+ MDV that has become endemic in southern China[J]. Transbound Emerg Dis, 2021, 68(6):3574-3587.
[16]	SUCHARD M A, LEMEY P, BAELE G, et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1. 10[J]. Virus Evol, 2018, 4(1):vey016.
[17]	RAMBAUT A, DRUMMOND A J, XIE D, et al. Posterior summarization in Bayesian phylogenetics using tracer 1. 7[J]. Syst Biol, 2018, 67(5):901-904.
[18]	BIELEJEC F, BAELE G, VRANCKEN B, et al. SpreaD3:interactive visualization of spatiotemporal history and trait evolutionary processes[J]. Mol Biol Evol, 2016, 33(8):2167-2169.
[19]	VALASTRO V, HOLMES E C, BRITTON P, et al. S1 gene-based phylogeny of infectious bronchitis virus:an attempt to harmonize virus classification[J]. Infect Genet Evol, 2016, 39:349-364.
[20]	KUO S M, WANG C H, HOU M H, et al. Evolution of infectious bronchitis virus in Taiwan:characterisation of RNA recombination in the nucleocapsid gene[J]. Vet Microbiol, 2010, 144(3-4):293-302.
[21]	KUO S M, KAO H W, HOU M H, et al. Evolution of infectious bronchitis virus in Taiwan:positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity[J]. Vet Microbiol, 2013, 162(2-4):408-418.
[22]	吴翠兰, 何怡宁, 李和鸣, 等. 一株重组鸡传染性支气管炎病毒的分离及结构蛋白基因变异和血清型分析[J]. 畜牧兽医学报, 2015, 46(5):815-823.WU C L, HE Y N, LI H M, et al. Isolation and analysis of structural protein genes variation and serotype of a recombinant strain of chicken infectious bronchitis virus[J]. Acta Veterinaria et Zootechnica Sinica, 2015, 46(5):815-823. (in Chinese)
[23]	盛晓丹, 徐怀英, 刘霞, 等. 传染性支气管炎病毒S1和N基因遗传变异频率的分析[J]. 畜牧兽医学报, 2015, 46(6):989-997.SHENG X D, XU H Y, LIU X, et al. Genetic variation frequency of S1 and N gene of infectious bronchitis virus[J]. Acta Veterinaria et Zootechnica Sinica, 2015, 46(6):989-997. (in Chinese)
[24]	NABIL B, SABRINA B, ABDELHAKIM B. Transmission route and introduction of pandemic SARS-CoV-2 between China, Italy, and Spain[J]. J Med Virol, 2021, 93(1):564-568.
[25]	YANG Q Q, ZHAO X, LEMEY P, et al. Assessing the role of live poultry trade in community-structured transmission of avian influenza in China[J]. Proc Natl Acad Sci U S A, 2020, 117(11):5949-5954.
[26]	GAO F L, LIU X W, DU Z G, et al. Bayesianphylodynamic analysis reveals the dispersal patterns of tobacco mosaic virus in China[J]. Virology, 2019, 528:110-117.
[27]	CHEN H, SMITH G J D, ZHANG S Y, et al. Avian flu:H5N1 virus outbreak in migratory waterfowl[J]. Nature, 2005, 436(7048):191-192.
[28]	FRANZO G, NAYLOR C J, LUPINI C, et al. Continued use of IBV 793B vaccine needs reassessment after its withdrawal led to the genotype's disappearance[J]. Vaccine, 2014, 32(50):6765-6767.
[29]	FRANZO G, TUCCIARONE C M, BLANCO A, et al. Effect of different vaccination strategies on IBV QX population dynamics and clinical outbreaks[J]. Vaccine, 2016, 34(46):5670-5676.

Genetic Evolution and Spatio-temporal Transmission Analysis of the Chinese Infectious Bronchitis Virus

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 29

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	XIONG Ting, HE Xianming, ZHAO Xiya, ZHUANG Tingting, HUANG Meizhen, LIANG Shijin, YU Chuanzhao, LIANG Xuejing, CHEN Ruiai. Whole Genome Analysis of Three Predominant Epidemic Strains of Chicken Infectious Bronchitis Virus and Their Pathogenicity [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2109-2122.
[2]	DENG Gunan, ZHANG Jiaqi, BAO Zhipeng, CHEN Taoyun, YU Qisheng, DING Lu, ZHU Chenxi, WANG Yi, REN Yupeng, HE Chao, ZHANG Bin. Detection of Feline Herpesvirus Type 1 and Pathogenicity of an Isolated Strain [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2253-2258.
[3]	ZHONG Zhuxia, HU Xiuzhong, XIANG Min, YU Jie, LIU Chenhui, ZHAO Shenglan, WAN Pingmin, WANG Dingfa, ZHOU Yuan, CHENG Lei. Research Progress on Biological Function and Application of Pregnancy Associated Glycoproteins in Livestock Production [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(3): 874-881.
[4]	FAN Yandi, YANG Danjiao, YE Zhongming, ZHANG Min, LAN Lan, WANG Jinghao, ZHOU Han, KANG Runmin, YU Jifeng, ZHANG Zhidong, LI Yanmin, ZHOU Long. Metagenomic Analysis of Viruses in Clinical Samples of Respiratory Diseases in Tibetan Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3836-3847.
[5]	WANG Jinglin, LIU Yangguang, XU Qilong, CHEN Shuo, DENG Zaishuang, CHENG Shiyu, DING Yueyun, ZHENG Xianrui, YIN Zongjun, ZHANG Xiaodong. Genome Structures Variant Analysis and Feature SNPs Screening of Wanyue Black Pig [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2783-2793.
[6]	LIU Jiankui, XU Ye, LIU Chen, YU Hui, YANG Yuan, HE Le, LI Jiarui, DAN Huijuan, DAI Ailing, YANG Xiaoyan, WEI Chunhua. Genomic Characteristics of Porcine Reproductive and Respiratory Syndrome Virus in Fujian Province from 2017 to 2021 based on Whole Genome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1579-1589.
[7]	MA Zhijie, WANG Shikang, ZHANG Weizhong, GUO Weixing, ZHAO Haiming, LEI Chuzhao. Y-chromosome Genomic Diversity and Paternal Origins of Qaidam Cattle and Mongolian Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1026-1033.
[8]	ZHAI Gang, GU Wenyuan, LIU Tao, LIU Ying, ZHANG Shuai, FAN Jinghui, ZUO Yuzhu. Establishment of TaqMan Detection Method of Porcine Epidemic Diarrhea Virus and Analysis of Genetic Variation based on S Gene [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 847-854.
[9]	JIA Yiquan, YU Mengting, LIU Weirong, FANG Shouguo, ZHANG Songbai. Baicalin Inhibits Infectious Bronchitis Virus Replication via Promoting the Expression of Type Ⅰ Interferon [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4839-4850.
[10]	CHEN Lu, CHANG Xinyu, SHEN Jiachen, SHEN Ruiting, ZHAO Zhenhua, HOU Xiaolin. Transcriptome Sequencing and Analysis of HD11 Cells Infected by Avian Infectious Bronchitis Virus [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4860-4865.
[11]	DAI Rongquan, LI Hui, ZHANG Bin, LI Yi, YUAN Zhankui. Computed Tomography Angiography Diagnosis and Surgery Outcome in Two Vascular Ring Anomaly Dogs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4433-4438.
[12]	ZHANG Zhengkai, LI Yefang, YE Shaohui, JIANG Lin, MA Yuehui. Research Progress of Environmental Adaptability in Goats [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(7): 2035-2046.
[13]	CAO Li, CHENG Runan, WU Zhouhui, WANG Jiawei, WANG Yu, ZHANG Yonghong, WU Qingmin, WANG Zhen. Construction and Biological Characteristics of sapC Gene Deletion Strain of Salmonella Typhimurium [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(7): 2282-2289.
[14]	TANG Xiujun, FAN Yanfeng, JIA Xiaoxu, GE Qinglian, LU Junxian, ZHOU Qian, CHEN Dawei, GAO Yushi. Studies on Mitochondrial Haplotype and Genetic Origins of Different Types Broilers [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(11): 3748-3758.
[15]	LINGHU Yuanfeng, PAN Yong, YANG Yang, DUAN Shiyu, ZHANG Jiali, ZHANG Baotai, YANG Qi. Preliminary Exploration of Binding Sites of Salmonella Typhimurium Chaperone Protein Hfq on Small RNA GcvB [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(11): 4110-4115.