Isolation and Characterization of a Novel Bat Coronavirus Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coronavirus

Abstract

We report the isolation and characterization of a novel bat coronavirus which is much closer to the severe acute respiratory syndrome coronavirus (SARS-CoV) in genomic sequence than others previously reported, particularly in its S gene. Cell entry and susceptibility studies indicated that this virus can use ACE2 as a receptor and infect animal and human cell lines. Our results provide further evidence of the bat origin of the SARS-CoV and highlight the likelihood of future bat coronavirus emergence in humans.T he 2002-2003 outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV) was a significant public health threat at the beginning of the 21st century (1). Initial evidences showed that the masked palm civet (Paguma larvata) was the primary suspect in the animal origin of SARS-CoV (2, 3). Later studies suggested that Chinese horseshoe bats are natural reservoirs and that the masked palm civet most likely served as an intermediate amplification host for SARS-CoV (4, 5). From our longitudinal surveillance of bat SARS-like coronavirus (SL-CoV) in a single bat colony of the species Rhinolophus sinicus in Kunming, Yunnan Province, China, we found a high prevalence of diverse SL-CoVs (6). Whole-genome sequence comparison revealed that these SL-CoVs have 78% to 95% nucleotide sequence identities to SARS-CoV, with the major differences located in the spike protein (S) genes and the region of open reading frame 8 (ORF8). We recently isolated a bat SL-CoV strain (WIV1) and constructed an infectious clone of another strain (SHC014); significantly, these strains are closely related to SARS-CoV and capable of using the same cellular receptor (angiotensin-converting enzyme 2 [ACE2]) as SARS-CoV (6, 7). Despite the high similarity in genomic sequences and receptor usage of these two strains, there is still some difference between the N-terminal domains of the S proteins of SARS-CoV and other SL-CoVs, indicating that other unknown SL-CoVs are circulating in bats.Here we report the isolation of a new SL-CoV strain, named bat SL-CoV WIV16. SL-CoV WIV16 was isolated from a single fecal sample of Rhinolophus sinicus, which was collected in Kunming, Yunnan Province, in July 2013. The full genomic sequence of SLCoV WIV16 (GenBank accession number KT444582) was determined and contained 30,290 nucleotides (nt) and a poly(A) tail which is slightly larger than those of SARS-CoVs and other bat SL-CoVs (6, 8-13). The WIV16 genome has a 40.9% GϩC content and short untranslated regions (UTRs) of 264 and 339 nt at the 5= and 3= termini, respectively. Its gene organization is identical to that of WIV1 and slightly different from that of the civet SARS-CoV and other bat SL-CoVs due to an additional ORF (name ORFx) detected between the ORF6 and ORF7 genes of the WIV1 and WIV16 genomes (data not shown). The conserved transcriptional regulatory sequence was identified upstream of ORFx, indicating that this is likely to be a potential functional gene. The overall nucleotide sequence of WIV16 has 96% identity (higher than that of any p...

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

“…MERS-CoV was suggested to originate from bats, but the reservoir host fueling spillover to humans is unequivocally dromedary camels (Haagmans et al, 2014;Memish et al, 2013). Both SARS-CoV and SARS-CoV-2 are closely related and originated in bats, who most likely serve as reservoir host for these two viruses (Ge et al, 2013;Hu et al, 2017;Li et al, 2005b;Yang et al, 2015a;Zhou et al, 2020). Whereas palm civets and racoon dogs have been recognized as intermediate hosts for zoonotic transmission of SARS-CoV between bats and humans (Guan et al, 2003;Kan et al, 2005;Wang et al, 2005), the SARS-CoV-2 intermediate host remains unknown.…”

“…Whereas palm civets and racoon dogs have been recognized as intermediate hosts for zoonotic transmission of SARS-CoV between bats and humans (Guan et al, 2003;Kan et al, 2005;Wang et al, 2005), the SARS-CoV-2 intermediate host remains unknown. The recurrent spillovers of coronaviruses in humans along with detection of numerous coronaviruses in bats, including many SARS-related coronaviruses (SARSr-CoVs), suggest that future zoonotic transmission events may continue (Anthony et al, 2017;Ge et al, 2013;Hu et al, 2017;Li et al, 2005b;Menachery et al, 2015;Menachery et al, 2016;Yang et al, 2015a;Zhou et al, 2020). In addition to the highly pathogenic zoonotic pathogens SARS-CoV, MERS-CoV, and SARS-CoV-2, all belonging to the b-coronavirus genus, four low-pathogenicity coronaviruses are endemic in humans: HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E.…”

“…MERS-CoV S, however, uses domain A to recognize non-acetylated sialoside attachment receptors Park et al, 2019), which likely promote subsequent binding of domain B (S B ) to the entry receptor, dipeptidyl-peptidase 4 (Lu et al, 2013;Raj et al, 2013). SARS-CoV and several SARS-related coronaviruses (SARSr-CoV) interact directly with angiotensin-converting enzyme 2 (ACE2) via S B to enter target cells (Ge et al, 2013;Kirchdoerfer et al, 2018;Li et al, 2005a;Li et al, 2003;Song et al, 2018;Yang et al, 2015a).…”

Hosts and Sources of Endemic Human Coronaviruses

“…Intermediary adaptation was strongly suspected for the SARS-CoV whose zoonotic source is in carnivores, in which the virus would have evolved human-compatible receptor tropism Guan et al, 2003;Song et al, 2005;Wang et al, 2005;Xu et al, 2004). However, viruses directly infecting human cells have later been found in rhinolophid bats, the primordial natural host of the species SARS-related CoV Ge et al, 2013;Yang et al, 2015). Of note, these viruses are conspecific with SARS-CoV but do not fall into the viral clade that was transferred from carnivores to humans and initiated the epidemic.…”

Genomic characterization of a novel poxvirus from a flying fox: evidence for a new genus?

“…For example, diverse Coronavirus species (Ge et al, 2016;Yang et al, 2015b) and Reovirus species (Yang et al, 2015c) have been isolated and characterized from bats showing no signs of clinical disease. Indeed, aside from the lyssavirus species infecting bats, few other viruses to date appear associated with clinical disease.…”