The DOI matches its Crossref record; 49 of the 49 references it cites were found in a registry or an index.
Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses
Open accessAbstract
Although a variety of SARS-CoV-2 related coronaviruses have been identified, the evolutionary origins of this virus remain elusive. We describe a meta-transcriptomic study of 411 samples collected from 23 bat species in a small (~1100 hectare) region in Yunnan province, China, from May 2019 to November 2020. We identified coronavirus contigs in 40 of 100 sequencing libraries, including seven representing SARS-CoV-2-like contigs. From these data we obtained 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV related genomes. Of these viruses, RpYN06 exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome and was the closest relative of SARS-CoV-2 in the ORF1ab, ORF7a, ORF8, N, and ORF10 genes. The other three SARS-CoV-2 related coronaviruses were nearly identical in sequence and clustered closely with a virus previously identified in pangolins from Guangxi, China, although with a genetically distinct spike gene sequence. We also identified 17 alphacoronavirus genomes, including those closely related to swine acute diarrhea syndrome virus and porcine epidemic diarrhea virus. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species in Southeast Asia and southern China, with the largest contiguous hotspots extending from South Lao and Vietnam to southern China. Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China. These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.
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1 retracted
RETRACTED ARTICLE: Origin and cross-species transmission of bat coronaviruses in China
Latinne, A., Hu, B., Olival, K. J., Zhu, G., Zhang, L., Li, H., Chmura, A. A., Field, H. E., Zambrana-Torrelio, C., Epstein, J. H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17687-3 · Cited by 339
RetractedThe Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
fastp: an ultra-fast all-in-one FASTQ preprocessor
Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty560 · Cited by 29,721
Self-citationA novel coronavirus from patients with pneumonia in China, 2019
Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2001017 · Cited by 28,244
Self-citationBLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
A pneumonia outbreak associated with a new coronavirus of probable bat origin
Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., et al. (2020) · Nature · doi:10.1038/s41586-020-2012-7 · Cited by 21,969
Self-citationFast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.75 · Cited by 15,355
SWISS-MODEL: homology modelling of protein structures and complexes
Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky427 · Cited by 13,067
Cited by
Sarbecovirus RBD indels and specific residues dictating multi-species ACE2 adaptiveness
Si, J.-Y., Chen, Y.-M., Sun, Y.-H., Gu, M.-X., Huang, M.-L., Shi, L.-L., Yu, X., Yang, X., Xiong, Q., Ma, C.-B., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53029-3 · Cited by 25
Self-citationSARS-CoV-2's origin should be investigated worldwide for pandemic prevention
Wu, Z., Jin, Q., Wu, G., Lu, J., Li, M., Guo, D., Lan, K., Feng, L., Qian, Z., Ren, L., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)02020-1 · Cited by 23
Du, W., Debski-Antoniak, O., Drabek, D., van Haperen, R., van Dortmondt, M., van der Lee, J., Drulyte, I., van Kuppeveld, F. J. M., Grosveld, F., Hurdiss, D. L., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49693-0 · Cited by 19
Kaushik, R., Kumar, N., Zhang, K. Y. J., Srivastava, P., Bhatia, S., & Malik, Y. S. (2022) · Environmental Research · doi:10.1016/j.envres.2022.113303 · Cited by 13
(2024) · doi:10.1371/journal.ppat.1012704 · Cited by 10
Metadata
- Authors
- Zhou, H., Ji, J., Chen, X., Bi, Y., Li, J., Wang, Q., Hu, T., Song, H., Zhao, R., Chen, Y., Cui, M., Zhang, Y., Hughes, A. C., Holmes, E. C., & Shi, W.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2021-08
- Volume
- 184
- Issue
- 17
- Pages
- 4380-4391.e14
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W3170734619
- Cited by
- 380
- References
- 49
- FWCI
- 46.57
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Zhou, H., Ji, J., Chen, X., Bi, Y., Li, J., Wang, Q., Hu, T., Song, H., Zhao, R., Chen, Y., Cui, M., Zhang, Y., Hughes, A. C., Holmes, E. C., & Shi, W. (2021). Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. Cell. https://doi.org/10.1016/j.cell.2021.06.008
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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