Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats

Hu, Dan; Zhu, Chen; Ai, Lele; He, Ting; Wang, Yi; Ye, Fuqiang; Yang, Lu; Ding, Chenxi; Zhu, Xuhui; Lv, Ruicheng; Zhu, Jingyuan; Hassan, Bachar H.; Feng, Youjun; Tan, Weilong; Wang, Changjun

doi:10.1038/s41426-018-0155-5

Cited by 272 publications

(263 citation statements)

References 39 publications

(43 reference statements)

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“…Moreover, bat-derived coronaviruses fell in basal positions in the subgenus Sarbecovirus, with 2019-nCoV most closely related to bat-SL-CoVZC45 and bat-SL-CoVZXC21, which were also sampled from bats. 23 These data are consistent with a bat reservoir for coronaviruses in general and for 2019-nCoV in particular. However, despite the importance of bats, several facts suggest that another animal is acting as an intermediate host between bats and humans.…”

Section: Sars-covsupporting

confidence: 76%

“…Some contigs identified in all the samples were closely related to the bat SARS-like betacoronavirus bat-SL-CoVZC45 betacoronavirus. 23 Bat-SL-CoVZC45 was then used as the reference genome and reads from each pool were mapped to it, generating consensus sequences corresponding to all the pools. These consensus sequences were then used as new reference genomes.…”

Section: Resultsmentioning

confidence: 99%

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Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

et al. 2020

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Background In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed. MethodsWe did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus.Findings The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues.Interpretation 2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensinconverting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation.

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Section: Sars-covsupporting

confidence: 76%

Section: Resultsmentioning

confidence: 99%

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

et al. 2020

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“…The bat CoV to which 2019_nCoV has the highest similarity was isolated from Rhinolophus sinicus (MG772933, described in Hu et al 2018), which might indicate that this species may also have been the original source of Figure 2 Phylogenetic tree of the 253 5'-end noncoding sequences of Sarbecovirus species from bats. A Merbecovirus was included as an outlier.…”

Section: Resultsmentioning

confidence: 99%

2019_nCoV/SARS-CoV-2: rapid classification of betacoronaviruses and identification of Traditional Chinese Medicine as potential origin of zoonotic coronaviruses

Wassenaar

Zou²

2020

Letters in Applied Microbiology

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Significance and Impact of the Study: The noncoding upstream and downstream flanks of coronavirus genomes allow for rapid classification of novel Betacoronavirus species and correct identification of genetic relationships. Although bats are the likely natural host of 2019_nCoV, the exact bat species that serves as the natural host of the virus remains as yet unknown. Chinese bat species with commercial value were identified as natural reservoirs of coronaviruses and are used in Traditional Chinese Medicine. Since their trading provides a potential risk for spreading zoonoses, a change in these practices is highly recommended. AbstractThe current outbreak of a novel severe acute respiratory syndrome-like coronavirus, 2019_nCoV (now named SARS-CoV-2), illustrated difficulties in identifying a novel coronavirus and its natural host, as the coding sequences of various Betacoronavirus species can be highly diverse. By means of wholegenome sequence comparisons, we demonstrate that the noncoding flanks of the viral genome can be used to correctly separate the recognized four betacoronavirus subspecies. The conservation would be sufficient to define target sequences that could, in theory, classify novel virus species into their subspecies. Only 253 upstream noncoding sequences of Sarbecovirus are sufficient to identify genetic similarities between species of this subgenus. Furthermore, it was investigated which bat species have commercial value in China, and would thus likely be handled for trading purposes. A number of coronavirus genomes have been published that were obtained from such bat species. These bats are used in Traditional Chinese Medicine, and their handling poses a potential risk to cause zoonotic coronavirus epidemics.1

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“…Previous reports showed that species from the bat genera Rhinolophus in southern China are a rich pool of SARS-like-CoVs, which belong to the subgenera Sarbecovirus. These viruses exhibit rich genetic diversity and frequent recombination events, which may increase the potential for cross-species transmission [7,42,[51][52][53][54][55]. Here, we reconstructed the evolutionary history of the 2019-nCoV cluster (Box Box 1.…”

Section: Trends In Molecular Medicinementioning

confidence: 99%

COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives

Sun

Wang

et al. 2020

Trends in Molecular Medicine

546

502

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Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats

Cited by 272 publications

References 39 publications

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

2019_nCoV/SARS-CoV-2: rapid classification of betacoronaviruses and identification of Traditional Chinese Medicine as potential origin of zoonotic coronaviruses

COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives

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