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Sequencing Points to Novel Coronavirus Behind Fatal Swine Outbreak

NEW YORK (GenomeWeb) – Genomic analysis uncovered a novel coronavirus behind an outbreak that sickened and killed nearly 25,000 piglets.

The outbreak began at the end of October 2016 at a farm in Guangdong Province, China, near to where the SARS virus is thought to have emerged. Four farms in the region were eventually affected by the fatal swine disease outbreak, which disproportionally affected very young piglets.

An international team of researchers isolated and sequenced a coronavirus responsible for the outbreak — dubbed the swine acute diarrhea syndrome coronavirus (SADS-CoV) — that is highly similar to viruses found in horseshoe bats, a known reservoir of SARS-related CoVs, as the team reported today in Nature.

"The current study highlights the value of proactive viral discovery in wildlife, and targeted surveillance in response to an emerging infectious disease event, as well as the disproportionate importance of bats
 as reservoirs of viruses that threaten veterinary and public health," senior author Jing-Yun Ma from South China Agricultural University and colleagues wrote in their paper.

The outbreak was first attributed to a known coronavirus, porcine epidemic diarrhea virus (PEDV), but after mid January 2017, PEDV could no longer be detected within sick pigs, suggesting that another virus was at play.

The disease causes severe and acute diarrhea and vomiting among piglets, leading to their deaths due to rapid weight loss within days. Infected piglets five or fewer days old had a mortality rate of 90 percent, while older piglets had better outcomes with a mortality rate of 5 percent. Sows, meanwhile, had only mild diarrhea and recovered within two days. By May 2017, 24,693 piglets at four farms died.

Ma and colleagues collected a sample from the intestine of a dead piglet for metagenomic analysis. In all, they generated 15.3 million reads, of which slightly more than 4,000 matched sequences from the bat CoV HKU2, a virus first found among horseshoe bats in Hong Kong and Guangdong Province.

Through de novo assembly and targeted PCR, the researchers generated a 27,173-basepair virus that shared 95 percent sequence identity with HKU2-CoV. Thirty-three other SADS-CoV genomes were obtained from affected farms and they were 99.9 percent similar to each other, the researchers reported.

Using a qPCR test they developed, the researchers found that the SADS-CoV could be detected within sick piglets and pigs, but not in recovered or healthy pigs. Retrospective analysis of the initial samples from when PEDV was the suspected cause also found SADS-CoV in the samples, suggesting an initial co-infection. The researchers noted that as the pigs that became ill later had SADS-CoV, but not PEDV, this indicated that SADS-CoV alone could cause lethal disease.

Although HKU2-CoV and SADS-CoV were highly similar, the researchers noted that their S gene sequencing identity was only 86 percent, indicating that HKU2-CoV is not a direct progenitor of SADS-CoV.

To search for a closer relative, Ma and colleagues compared SADS-CoV to other coronaviruses obtained from bats in Guangdong Province between 2013 and 2016. From this, they found SADS-CoV had between 96 percent and 98 percent sequence identity with some of these viruses. In particular, they noted that the highest sequence similarity was found in samples obtained from the horseshoe bat Rhinolophus affinis, which has been recognized as a SARS-CoV reservoir.

In animal challenge tests, performed to fulfill Koch's postulates on the cause of disease, about half the piglets infected with SADS-CoV died, while all but one control piglet remained healthy, the researchers further reported.

The researchers noted that their findings emphasize the need to better understand coronavirus diversity and its distribution among bats to determine how it could affect livestock, public health, and the economy.