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Analysis of Bat Coronavirus Indicates Similarity to Human SARS-Causing Virus

NEW YORK (GenomeWeb News) – Genomic and other analyses indicate that two newly identified bat coronaviruses are highly similar to the coronavirus behind the 2002 to 2003 outbreak of severe acute respiratory syndrome, according to a Nature study appearing online yesterday.

An international research team led by Zheng-Li Shi, a professor at Wuhan Institute of Virology of the Chinese Academy of Sciences, and Peter Daszak, the president of EcoHealth Alliance, uncovered the new viruses by digging through bat fecal samples obtained from a bat colony in Yunnan Province, China. The genome sequences of those viruses closely resembled the virus from the earlier human outbreak, even in the key receptor binding domain region of the viral spike protein. In addition, they isolated and grew the virus in cell culture, allowing further analyses, which indicated that the virus could directly infect human cells.

"Our discovery that bats carrying SARS-CoV may be able to directly infect humans has enormous implications for public health control measures," Daszak said in a statement.

According to the US Centers for Disease Control and Prevention, nearly 8,100 people worldwide became ill during the 2002 to 2003 SARS pandemic, and 774 died. Infection is marked by a high fever, and other symptoms include headache and mild respiratory problem. The CDC added that some patients came down with a dry cough and most patients went on to develop pneumonia. The virus appeared to spread through close contact.

Over the course of a year-long survey searching for SARS-like coronaviruses in Chinese horseshoe bats, the team of investigators collected 117 fecal samples. Using a one-step reverse transcription-nested PCR approach followed by sequencing, the group confirmed that 27 samples contained coronaviruses. By examining the S protein RBD sequences, the team found that those samples comprise some seven different strains, two of which were novel.

Those novel strains, dubbed SL-CoV RsSHC014 and SL-CoV Rs3367, were then fully sequenced and found to be 29,787 basepairs long. The investigators noted that these two strains showed 95 percent nucleotide sequence identity with the Tor2 strain of the human SARS-CoV, higher than other bat SARS-like coronaviruses.

Phylogenetic analysis of the novel bat virus strains coupled with other bat and human and civet SARS-CoV strains indicated that Rs3367 or RsSHC014 is a descendent of a recombination of lineages that also led to SARS-CoV as well as a previously identified bat SARS-like coronavirus.

In addition, the researchers reported that the two new SL-CoVs have 96 percent and 85 percent amino acid sequence identity with SARS-CoV, and a number of residues on the receptor binding domain, which mediates viral entry, were conserved between the new viruses and the human pathogen.

Shi, Daszak, and their colleagues were also able to isolate and passage one of the strains in Vero cells. The purified virions, they noted, had typical coronavirus morphology, had 99.9 percent nucleotide genome sequence identity, and had 100 percent amino acid sequence identity with the SL-CoV Rs3367 virus S1 region. They named the new isolate SL-CoV WIVI.

Through viral infectivity studies, the investigators found that SL-CoV WIVI could use ACE2 from humans, civets, and Chinese horseshoe bats to act as the receptor to enter cells and that it could grow in a range of cell lines from a number of different species, including humans, pigs, and bats. Real-time RT-PCR analysis, though, indicated that it was more efficient in some cell types than in others.

In addition, they found that seven of nine sera from SARS patients collected in 2003 that they tested could neutralize tissue cultures infected with SL-CoV WIVI, indicating to the researchers that there is a "close relationship" between the viruses.

"Since 2003 there has been disagreement about the origin of the virus that directly evolved into human SARS-CoV, the causative agent of the first emerging pandemic threat of the 21st century," Shi said in a statement. "Even though our team reported that bats are natural reservoirs of SARS­-like coronaviruses in 2005, we have been searching for this missing link for 10 years, and finally we've found it."

Ian Lipkin, a professor at Columbia University, tempered that idea. "This paper hasn't resolved the provenance of SARS-CoV; nonetheless, it does provide compelling evidence that an intermediate host was not necessary," he said in a statement.

The investigators also noted that the diversity of bat coronaviruses appeared to be higher than previous estimates. Together with the hints that the Middle East respiratory syndrome coronavirus could also be derived from bats, they cautioned that coronaviruses could represent a serious global public health threat.

"Our findings suggest that SARS-like coronaviruses are diverse and abundant in bats in Asia, and the potential for future spillover remains high," Daszak added. "If we add this to the recent finding that Middle East respiratory syndrome coronavirus originates in Saudi Arabian bats, it's strong evidence that bat coronaviruses remain a substantial global threat to public health."