2017-2019年四川地区猪A群轮状病毒的分子流行病学调查

doi:10.3864/j.issn.0578-1752.2021.05.017

Abstract

Abstract:

【Objective】The aim of this study was to investigate the prevalence and molecular characterization of porcine group A rotavirus (RVA) in large-scale pig farms in Sichuan, to provid a theoretical basis for the development for porcine RVA vaccine. 【Method】 From 2017 to 2019, the 303 samples were collected from 40 pig farms in 14 regions of Sichuan province. Prevalence of RVA was detected by real-time RT-PCR method, and RVA positive samples were typed by RT-PCR. At the same time, the whole genomes of RVA VP4 and VP7 gene were amplified from some positive samples. The genotypes of the corresponding strains were determined by RotaC^2.0 classification tool. Sequence homology was analyzed by MegAlign. Phylogenetic tree was constructed by Neighbor-Joining method through MEGA 7.0. SimPlot and RDP4 softwares were applied for recombination analysis. 【Result】 Of the 303 samples examined, 32.34% (98/303, 95%CI=27.1%-37.9%) were positive for RVA. Among the 39 G types, G9 (41%) was the dominant genotype, while G4, G5, G26, and G3 were detected in 23%, 28.2%, 5.1% and 2.7%, respectively. The P[13] genotype (40.7%) was dominant among the 59 P types, followed by P[6], P[23] and P[1] in 30.5%, 23.7% and 5.1%, respectively. Furthermore, the 30 strains successfully identified the G/P combination genotype, and the dominant combination genotype was G9P[23] (23.3%), the other combinations were G4P[6] (16.7%), G9P[13] (13.3%), G5P[23] (10%), G5P[13] (10%), G9P[6] (6.7%), G26P[13] (6.7%), G4P[13] (6.7%), G4P[23] (3.3%) and G3P[13] (3.3%). Notably, the G5P[23], G4P[13], G9P[6], G26P[13] and G4P[23] were first identified in China. In addition, the recombination analysis showed that four strains had recombination on VP7 or VP4 genes. 【Conclusion】 The results demonstrated that the prevalence of RVA in diarrhea piglet feces was high and the genotypes were complex in Sichuan. The dominant genotype of RVAs was G9P[23]. The results of this study enriched the epidemiological data of RVA and provided an important reference for the prevention and control of porcine RVA in Sichuan province.

Key words: porcine group A rotavirus, molecular epidemiology, genomic research, recombination

Qun ZHOU,XiaoFei CHEN,RuiCi KAN,Yu LI,Hui CAO,YanLing PENG,Bin ZHANG. Molecular Epidemiological Investigation of Porcine Group A Rotavirus in Sichuan from 2017 to 2019[J].Scientia Agricultura Sinica, 2021, 54(5): 1063-1072.

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References 31

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地区 Region	猪场个数 Farm	样本数 Number of samples	RVA阳性数 Positive number	G型 G genotype	P 型 P genotype	G/P组合型 G/P combination genotype
眉山Meishan	6	62	14	G3,G4,G9	P[1],P[13],P[23]	G3P[13],G4P[23],G9P[23],G9P[13]
绵阳Mianyang	5	34	24	G5,G9	P[23]	G9P[23],G5P[23]
泸州Luzhou	5	13	3	G9	P[1],P[13]	G9P[13]
西昌Xichang	5	25	8		P[1],P[13]
成都Chengdu	4	49	9	G9	P[13],P[23]	G9P[13],G9P[23]
雅安Yaan	4	13	3	G9	P[13]	G9P[13]
内江Neijiang	3	18	2	G9	P[6]	G9P[6]
宜宾Yibin	2	7	5	G5	P[13],P[23]	G5P[23],G5P[13]
乐山Leshan	1	4	2	G4	P[13]	G4P[13]
遂宁Suining	1	18	4	G9,G26	P[13],P[23]	G9P[23],G26P[13]
南充Nanchong	1	3	3	G9	P[13]	G9P[13]
资阳Ziyang	1	18	2	G4	P[6]	G4P[6]
广元Guangyuan	1	36	19	G4,G5	P[6],P[13]	G4P[6],G5P[13]
攀枝花Panzhihua	1	3	0
共计Total	40	303	98

毒株 Strain	同源性最高的毒株 Strain with highest homology	国家及宿主 Country and host	年份 Year	同源性 Homology
SCMS-71	SCQL-5-2（MG066590）	中国/猪源China/pig	2018	99.9%
SCLS-18,SCLS-20	MOZ/21205（KP222851）	莫桑比克/人源Mozambique/human	2011	96.9%,97.4%
SCZY-165,SCZY-166	ZT-11D-T101（KM247280）	中国/人源China/human	2011	98.9%,98.3%
SCMS-69	GUB71（AB573647）	日本/猪源Japan/pig	2006	95.6%
SCGY-193,SCGY-198,SCGY-199,SCGY-201	R1954（KF726066）	中国/人源China/human	2013	95.1%
6株G5型（SCJY）,SCGY-192 6 strains of G5 （SCJY）	HLJqqhe-1（JX498960）	中国/猪源China/pig	2011	97.6%-98.1%
SCYB-Y1,SCYB-Y2	LL3354（EF159575）	中国/人源China/human	2000	93.9%,94.2%
SCYB-C2,SCYB-C3	103-P-001-1-0126（MK227837）	中国/猪源China/pig	2014	93.7%
4株G9型（SCJY） 4 strains of G9 （SCJY）	LLP48（KJ126835）	中国/猪源China/pig	2008	97.4%-97.6%
SCRS-142,SCSN-96	HBHP（KX831114）	中国/猪源China/pig	2016	98.3%
SCDY-219	GXqz-2（JX498942）	中国/猪源China/pig	2011	97.5%
SCLZ-FB,SCYA-C7	ISO31（DQ117937）	印度/人源India/human	2008	96.2%,96.5%
SCMY-28,SCMS-153,SCDY-211, SCDY-210,SCDY-209	CQ（KX831100）	中国/猪源China/pig	2016	95.9%-97.1%
SCSN-93,SCSN-94	07N1760（LC208008）	尼泊尔/猪源Nepal/pig	2007	96.1%
SCLJ-C18,SCLJ-C20	TA-1-2（KT820779）	中国/猪源China/pig	2014	85.1%

毒株 Strain	同源性最高的毒株 Strain with highest homology	国家及宿主 Country and host	年份 Year	同源性 Homology
SCMS-152,SCLZ-35,SCXC-83	A5-10（LC133517）	泰国/牛源Thailand/cow	1988	93.4%
15株P[6]型（SCGY）15 strains of P[6] （SCGY）	GUB88（AB573872）	日本/猪源Japan/pig	2006	92.6%-98.6%
SCLJ-C18,SCLJ-C20,SCZY-165	R1207（LC389888）	斯里兰卡/人源Sri Lanka/human	2009	95.7%-98.6%
SCXC-89,SCXC-85,SCXC-84,SCRS-142,SCGY-192	CMP178（DQ536362）	泰国/猪源Thailand/pig	2008	94.5%-96.8%
SCYB-Y1,SCQL-54,SCQL-55,SCMS-71,SCDY-91	SCMY（MH320795）	中国/猪源China/pig	2018	79.1%-98.8%
SCLZ-FB	FGP36（AB573878）	日本/猪源Japan/pig	2009	95.1%
SCSN-93,SCSN-94	LNCY（MF462324）	中国/猪源China/pig	2016	98.3%
SCYA-C7,SCRS-131,SCLS-18,SCLS-20, SCYA-H2,SCYA-H3,SCXC-90,SCYB-Y2	SWU-1C(MK410284)	中国/猪源China/pig	2018	92.5%-97.7%
SCDY-210,SCSN-140,SCMS-151	SCLS-R3（MK597985）	中国/人源China/human	2018	92.6%-97.0%
SCYB-C2,SCYB-C3	14175-24（KX363359）	越南/猪源Viet Nam/pig	2012	95.3%
SCSN-96	SC11（MH624176）	中国/猪源China/pig	2017	97.4%
SCMS-153,SCMS-68,SCMS-69,SCDY-211, 7株P[23]型（SCJY）7 strains of P[23] （SCJY）	HLJ/15/1（KU886316）	中国/猪源China/pig	2015	92.1-96.4%

Molecular Epidemiological Investigation of Porcine Group A Rotavirus in Sichuan from 2017 to 2019

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