Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin

This virus is 98.48% identical in genome sequence to a bat coronavirus detected in 2016 in bats in a cave in the vicinity of the index pig farm. The SADS-CoV originated from the same genus of horseshoe bats (Rhinolophus) as SARS-CoV. The outbreak began in Guangdong province in the vicinity of the origin of the SARS pandemic. A fatal swine disease outbreak was observed in a pig farm in Qingyuan, Guangdong province, China, on 28 October 2016. The disease caused severe and acute diarrhoea and acute vomiting, leading to death due to rapid weight loss in newborn piglets that are less than five days of age. Infected piglets died 2-6 days after disease onset, whereas infected sows suffered only mild diarrhoea and most sows recovered within two days. The mortality rate was as high as 90% in piglets that were five days or younger, whereas in piglets that were older than eight days, the mortality dropped to 5%. Subsequently, SADS-related outbreaks were found in three additional pig farms within 20-150 km of the index farm, and by 2 May 2017, the disease had caused the death of 24,693 piglets at these four farms. Measures taken to control SADS included separation of sick sows and piglets from the rest of the herd. A sample collected from the small intestine of a diseased piglet was analysed by metagenomics analysis using next-generation sequencing (NGS) to identify potential aetiological agents. Of the 15,256,565 total reads obtained, 4,225 matched sequences of the bat CoV HKU2, which was first detected in Chinese horseshoe bats in Hong Kong and Guangdong province, China. By de novo assembly and targeted PCR, a 27,173-bp CoV genome was obtained that shared 95% sequence identity to HKU2-CoV. Thirty-three full genome sequences of SADS-CoV were subsequently obtained that were 99.9% identical to each other. The virus replicated to higher titres in piglets than in sows and displayed tissue tropism of the small intestine. Retrospective PCR analysis revealed that SADS-CoV was present on farm A during the PEDV epidemic, where the first strongly positive SADS-CoV sample was detected on 6 December 2016. From mid-January onwards, SADS-CoV was the dominant viral agent detected in diseased animals. An antibody assay based on the S1 domain of the spike (S) protein was rapidly developed using a luciferase immunoprecipitation system. Among 46 recovered sows tested, 12 were seropositive for SADS-CoV within three weeks of infection. To investigate possible zoonotic transmission, serum samples from 35 farm workers who had close contact with sick pigs were also analysed using the same luciferase immunoprecipitation system approach, and none were positive for SADS-CoV. Although the overall genome identity of SADS-CoV and HKU2-CoV is 95%, the S gene sequence identity is only 86%, suggesting that the previously reported HKU2-CoV is not the direct progenitor of SADS-CoV, but that they may have originated from a common ancestor. To test this hypothesis, further studies are needed to investigate the evolutionary relationship between SADS-CoV and HKU2-CoV.