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RAPID COMMUNICATION ORF3a deletion in field strains of porcine transmissible gastroenteritis virus in China A hint of association with porcine respiratory coronavirus X Zhang 1 Y Zhu 1 X Zhu 1 J Chen 1 H Shi 1 D Shi 1 H Dong 1 2 L Feng 1 1 State Key Laboratory of Veterinary Biotechnology Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences Harbin Heilongjiang China 2 Molecular Biology Gembloux Agro Bio Tech University of LiC18ege LiC18ege Belgium Correspondence L Feng State Key Laboratory of Veterinary Biotechnology Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences Harbin Heilongjiang China Emails fl fengli h Funding information National Key Technology Support Program Grant Award Number 2015BAD12B02 National Natural Science Foundation of China Grant Award Number 31572541 31502092 Summary Porcine transmissible gastroenteritis virus TGEV is a pathogenic coronavirus responsible for high diarrhoea associated morbidity and mortality in suckling piglets We analysed the TGEV ORF3 gene using nested polymerase chain reaction and identified an ORF3a deletion in three field strains of TGEV collected from piglets in China in 2015 Eight TGEV ORF3 sequences were obtained in this study Phyloge netic tree analysis of ORF3 showed that the eight TGEV ORF3 genes all belonged to the Miller cluster CH LNCT and CH MZL were closely correlated with Miller M6 while CH SH was correlated with Miller M60 These results thus indicate that the existence of Miller as well as the Purdue cluster in Chinese field strains of TGEV Furthermore we found the first evidence for a large deletion in ORF3 result ing in the loss of ORF3a previously reported in porcine respiratory coronavirus in three field strains CH LNCT CH MZL and CH SH of TGEV The results of the present study thus provide important information regarding the underlying evolution mechanisms of coronaviruses KEYWORDS deletion ORF3a transmissible gastroenteritis virus 1 INTRODUCTION Porcine diarrhoea can lead to weight loss and death in piglets Coronaviruses CoVs are a major cause of porcine diarrhoea in pig herds worldwide leading to important economic losses Zuniga Pas cual Iglesias Sanchez Sola 1 5 2017 Blackwell Verlag GmbH 1 five non structural proteins polyprotein 1a polyprotein 1ab ORF3a ORF3b and 7 Porcine respiratory virus is an S gene deletion mutant of TGEV first identified in Belgium in 1984 Pensaert Calle baut lane 2 CH SDRZ lane 3 CH SY lane 4 CH ZB lane 5 CH BJ lane 6 CH NM2 lane 7 CH LNCT lane 8 CH SH lane 9 CH MZL lane 10 Positive control attenuated H lane 11 negative control ZHANG ET AL 3 Previous reports detected a series of large deletions downstream of the TGEV S gene resulting in loss of the transcription signal and the initiation codon of ORF3a McGoldrick Lowings gene loss in 96 1933 was due to a disconti nuity in ORF3a while the deletion of TGEV ORF3a in the current study was continuous which has not previously been reported in TGEV Some TGEV viruses belonging to the Miller group have been found in China attenuated H and TS Li et al 2010 Wang et al 2010 while Purdue strains such as TGEV HX and SHXB strains are also prevalent in China Hu et al 2015 Weiwei et al 2014 thus providing increased opportunities for reorganization The leader RNA binding site and ORF3a start site were included in the deleted region identified in TGEV the current study Figure 3 and in the sequences of PRCV ISU 1 Lai Welter Zhang et al 2007 Previous studies on the genetic structures of PRCV and TGEV revealed two unique characteristics First the PRCV S gene lacks nt 621 681 resulting in a smaller S glycoprotein in PRCV than TGEV Second TGEV and PRCV differ in the ORF3 region the leader RNA binding site CTAAAC in PRCV is altered or partially deleted before the ORF3a gene Wang 00 1 5 https doi org 10 1111 tbed 12634 ZHANG ET AL 5