NEW YORK (GenomeWeb) – Viruses isolated from bats living in a cave in southwest China harbor all the genetic piecesof the coronavirus behind the human severe acute respiratory syndrome epidemic that occurred about 15 years ago.
The 2002 to 2003 SARS outbreak began in southern China, and eventually sickened about 8,100 people worldwide and killed 774 people in a dozen different countries, according to the US Centers for Disease Control and Prevention.
Subsequent sequencing analyses traced the virus to bats and civets. In 2013, an international team of researchers found that horseshoe bats in a cave in China's Yunnan Province harbored coronaviruses that resembled the human SARS-coronavirus, but with some key differences.
That team, led by the Chinese Academy of Sciences' Zheng-Li Shi, has monitored the cave for five years, collecting bat viral samples. As they reported in PLOS Pathogens today, they found distinct bat coronaviruses within that cave that — when put together — had all the genetic pieces of the human SARS-CoV. This suggested to the team that the ancestor of the human SARS-CoV arose through recombination of the bat viruses before spilling over into an intermediate host, possibly the civet.
"As a whole, our findings from a five-year longitudinal study conclusively demonstrate that all building blocks of the pandemic SARS-CoV genome are present in bat SARSr-CoVs from a single location in Yunnan," Shi and her colleagues wrote in their paper.
Over the course of their surveillance of the cave, the researchers collected 602 bat anal swabs or fecal samples and tested them for the presence of coronaviruses using Pan-CoV RT-PCR. Of those samples, 84 tested positive for a coronavirus and underwent sequencing. Sixty-four of the coronavirus-positive samples contained SARS related-CoVs (SARSr-CoVs). Most of the SARSr-CoV samples came from the horseshoe bat, Rhinolophus sinicus. All the bat SARSr-CoV samples were highly similar to one another as well as to previously reported bat, civet, and human samples.
The researchers sequenced the full genomes of 11 of the novel SARSr-CoV strains they found in the cave. These genomes ranged in size from 29,694 nucleotides to 30,291 nucleotides. When combined with the four viruses the researchers previously uncovered in this cave, they calculated that the SARSr-CoVs circulating there shared between 92 percent and 99.9 percent sequence identity. Similarly, they were between 93.2 percent and 96 percent similar to human and civet viruses.
To delve further into the genetic diversity of the bat viruses, the researchers focused on the variable region of the SARSr-CoV S gene, which corresponds to the receptor-binding domain of SARS-CoV. This region, the researchers noted, largely distinguishes between SARS-CoVs and SARSr-CoVs.
Sequencing analysis of the region split the viruses into two clades: one that is the same size and overlaps with the amino acid sequence of the SARS-CoV RBD and one that is smaller than the SARSr-CoV S gene due to two deletions.
While no one SARSr-CoV strain was same as the SARS-CoV strain, all the pieces that made up the human strain were present in the cave, scattered in different bat strains. Some strains, for instance, had S gene N-terminal domains similar to that of SARS-CoV, but RBDs that differed, while others have similar RBDs, but differing NTDs.
Likewise, most ORF8 regions of SARSr-CoVs differed from those found in SARS-CoV — even the SARSr-CoVs with similar S genes — but one strain had an ORF8 region similar to that of civet SARS-CoV, while another that had start and stop codons like those in human strains. Yet another strain, meanwhile, had an ORF3 region resembling that from SARS-CoV.
These bat SARSr-CoV further exhibited signs of frequent recombination, suggesting that recombination events among these strains could have shaped the evolution of human SARS-CoV.
Based on their findings, the researchers suggested that SARS-CoV arose through the recombination of SARSr-CoV within horseshoe bats in Yunnan Province before spilling over into civets or people in the region.