Genomic diversity and recombination of Seneca Valley viruses emerged in pig herds in Guangdong Province during 2019
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Genomic diversity and recombination of Seneca Valley viruses emerged in pig herds in Guangdong Province during 2019 Jianxin Liu1 · Qianju Guo1 · Huizi Li1 · Xianglong Yu1 · Boyang Liu1 · Bingqian Zhao1 · Zhangyong Ning1 Received: 18 February 2020 / Accepted: 17 May 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Seneca Valley virus (SVV) is an emerging global picornavirus that causes porcine idiopathic vesicular disease. We characterized the genome and conducted evolutionary and recombination analyses of four newly identified SVV strains which were CH-GDZS-2019, CH-GDMZ-2019, CH-GDHZ01-2019, and CH-GDHZ02-2019. Sequence alignment and phylogenetic analysis showed that strains circulating in swine herds in China were genetically diverse and complex. Recombination analyses indicated that strain CH-GDZS-2019 was derived from strains USA-IA44662-2015-P1 and USA-GBI29-2015, which were both isolated in the USA in 2015, while CH-GDMZ-2019 was derived from the Chinese field strains 1-2018-BH-China and CH-GDQC-2017. Our results provided important insights into the molecular characterization of the SVV strains co-circulating in Guangdong Province in China in 2019 and demonstrated the importance of additional SVV surveillance in China. Keywords Seneca valley virus · Genetic evolution · Recombination
Introduction Seneca Valley virus (SVV) is an emerging virus in the genus Senecavirus of the family Picornaviridae. SVV is a nonsegmented, positive-sense RNA virus that was first identified accidentally in contaminated cells in the USA (US) in 2002 [1, 2]. Its pathogenicity in pigs has drawn much attention since the first outbreak of SVV-associated porcine idiopathic vesicular disease (PIVD) in Brazil in 2015 [3]. Since then, SVV associated with PIVD has shown increasing geographic distribution and, to date, has occurred in a number of major pig-raising countries [4–7]. Guangdong Province is a major pig-producing region in China that has experienced significant damage from SVV since its first identified case in 2015 with additional outbreaks since then [6, 8, 9].
Edited by Takeshi Noda. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11262-020-01769-x) contains supplementary material, which is available to authorized users. * Zhangyong Ning [email protected] 1
College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
SVV’s genome consists of a 5′-untranslated region (UTR), an open reading frame encoding a single large polyprotein, and a polyadenylated 3′-UTR. In the virus’s life cycle, its polyprotein is cleaved into a leader protein (L) and structural (VP1-VP2-VP3-VP4) and non-structural proteins (2A-2B-2C-3A-3B-3C-3D) with different physiological functions [1]. SVV has also been shown to have recombination characteristics similar to other viruses in the Picornaviridae family, including enterovirus, poliovirus, aphthoviruses, and cardioviruses [10, 11]. For example, one study found th
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