SARS research news

11-24-20   By hunting for closely related coronaviruses, scientists can help solve the mystery of how SARS-CoV-2 jumped from bats to people, triggering the current pandemic. Now scientists have uncovered such a virus in Cambodia, virologists told Nature News…

The team found that the short segment from the new virus resembled that from SARS-CoV-2, as well as that from its closest known relative, a bat coronavirus called RaTG13. The team must now sequence the entire genome of the new virus, which likely contains about 30,000 base pairs, to find out exactly how closely related the new virus is to SARS-CoV-2.

So far the team has sequenced about 70% of the genome, but critical genes still need to be analyzed, including those that contain instructions to build the spike protein that allows the virus into cells.

RaTG13, the closest known relative of SARS-CoV-2 to date, shares 96% of its genome with the pandemic virus, and likely diverged from the pathogens' common ancestor between 40 and 70 years ago. So if the newfound virus is at least 97% similar to SAR-CoV-2, it would replace RaTG13 as the closest known relative.  If the sequences are at least 99% similar, the newfound virus may be a direct ancestor of the pandemic pathogen, Aaron Irving, an infectious-diseases researcher at Zhejiang University in Hangzhou, China, told Nature News.

"This is what we were looking for, and we found it," Dr. Veasna Duong, a virologist at the Pasteur Institute in Cambodia in Phnom Penh who led the research, told Nature News. "It was exciting and surprising at the same time." The research is still ongoing and has not yet been published in a scientific journal.   https://www.livescience.com/related-coronaviruses-cambodia-japan.html

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2-20-2020  research from a few years ago:

Olival of EHA:  “What we showed was that SARS-related viruses in these bat populations have the potential to go directly into human cells and do not need that extra mutational step [of] infecting another host.”

In other words, the path to sparking new outbreaks is potentially much more direct.  For example, one of the coronaviruses that the researchers found was a very close genetic match for the SARS virus.  So they put it in a petri dish with human cells.  The virus succeeded in infecting the cells….

Current coronavirus outbreak—as soon as it started, EcoHealth Alliance's longtime collaborators in China (principally researchers at the Wuhan Institute of Virology and the Wuhan Jinyintan Hospital) compared the new virus with the bat samples they'd collected. They found an extremely close match.    https://www.npr.org/sections/goatsandsoda/2020/02/20/807742861/new-research-bats-harbor-hundreds-of-coronaviruses-and-spillovers-arent-rare

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11-30-2017  To understand the genetic diversity of these bat SARSr-CoVs, the most variable region of the SARSr-CoV S gene, corresponding to the receptor-binding domain (RBD) of SARS-CoV, were amplified and sequenced.  Due to low viral load in some samples, RBD sequences were successfully amplified only from 49 samples.  These RBD sequences displayed high genetic diversity and could be divided into two large clades, both of which included multiple genotypes.  Clade 1 strains shared an identical size and higher amino acid (aa) sequence identity with SARS-CoV RBD, while clade 2 had a shorter size than SARS-CoV S due to two deletions (5 and 12–13 aa, respectively) (S1 Fig). Co-infections by two strains of different clades were detected in two samples, Rs3262 and Rs4087 (S1 Fig).

Based on the diversity of RBD sequences, 11 novel SARSr-CoV strains named by abbreviation of bat species and sample ID (Rs4081, Rs4084, Rs4231, Rs4237, Rs4247, Rs4255, Rs4874, Rs7327, Rs9401, Rf4092 and As6526) were selected for full-length genomic sequencing based on sample abundance, genotype of RBD as well as sampling time.  For each RBD genotype and each time of sampling, at least one representative strain was selected.  The genome size of these novel SARSr-CoVs ranged from 29694 to 30291 nucleotides (nt).  This gave a total of 15 full-length genomes of bat SARSr-CoVs from this single location (13 from R.sinicus, and one each from R. ferrumequinum and A. stoliczkanus), including our previously reported strains, Rs3367, RsSHC014, WIV1 and WIV16 [17,18].  The genomes of all 15 SARSr-CoVs circulating in this single cave shared 92.0% to 99.9% nt sequence identity.  The overall nt sequence identity between these SARSr-CoVs and human and civet SARS-CoVs is 93.2% to 96%, significantly higher than that observed for bat SARSr-CoVs reported from other locations in China (88–93%) [9,10,12,14,21,22].  The genome sequence similarity among the 15 SARSr-CoVs and SARS-CoV SZ3 strain was examined by Simplot analysis (Fig 1).  The 15 SARSr-CoVs are highly conserved and share a uniformly high sequence similarity to SARS-CoV in the non-structural gene ORF1a (96.6% to 97.1% nt sequence identity, 98.0% to 98.3% aa sequence identity) and ORF1b (96.1% to 96.6% nt sequence identity, 99.0% to 99.4% aa sequence identity).  In contrast, a considerable genetic diversity is shown in the S gene (corresponding to SZ3 genome position 21477 to 25244) and ORF8 (corresponding to SZ3 genome position 27764 to 28132) (Fig 1)….

Funding:  This work was jointly funded by National Natural Science Foundation of China (81290341, 31621061) to ZLS, China Mega-Project for Infectious Disease (2014ZX10004001-003) to ZLS, Scientific and technological basis special project (2013FY113500) to YZZ and ZLS from the Ministry of Science and Technology of China, the Strategic Priority Research Program of the Chinese Academy of Sciences (XDPB0301) to ZLS, the National Institutes of Health (NIAID R01AI110964), the USAID Emerging Pandemic Threats (EPT) PREDICT program to PD and ZLS, CAS Pioneer Hundred Talents Program to JC, NRF-CRP grant (NRF-CRP10-2012-05) to LFW and WIV “One-Three-Five” Strategic Program (WIV-135-TP1) to JC and ZLS. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript         https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006698