LYRa11

Strain of virus

LYRa11
Virus classification
(unranked):	Virus
Realm:	Riboviria
Kingdom:	Orthornavirae
Phylum:	Pisuviricota
Class:	Pisoniviricetes
Order:	Nidovirales
Family:	Coronaviridae
Genus:	Betacoronavirus
Subgenus:	Sarbecovirus
Species:	SARS-related coronavirus
Strain:	LYRa11

LYRa11 is a SARS-like coronavirus (SL-COV) which was identified in 2011 in samples of intermediate horseshoe bats in Baoshan, Yunnan, China. The genome of this virus strain is 29805nt long, and the similarity to the whole genome sequence of SARS-CoV that caused the SARS outbreak is 91%. It was published in 2014.^[1] Like SARS-CoV and SARS-CoV-2, LYRa11 virus uses ACE2 as a receptor for infecting cells.^[2]

Phylogenetic

A phylogenetic tree based on whole-genome sequences of SARS-CoV-1 and related coronaviruses is:

SARS‑CoV‑1 related coronavirus

	16BO133, 86.3% to SARS-CoV-1, Rhinolophus ferrumequinum, North Jeolla, South Korea^[3]

	JTMC15, 86.4% to SARS-CoV-1, Rhinolophus ferrumequinum, Tonghua, Jilin^[4]

Bat SARS CoV Rf1, 87.8% to SARS-CoV-1, Rhinolophus ferrumequinum, Yichang, Hubei^[5]

	BtCoV HKU3, 87.9% to SARS-CoV-1, Rhinolophus sinicus, Hong Kong and Guangdong^[6]

LYRa11, 90.9% to SARS-CoV-1, Rhinolophus affinis, Baoshan, Yunnan^[7]

Bat SARS-CoV/Rp3, 92.6% to SARS-CoV-1, Rhinolophus pearsoni, Nanning, Guangxi^[5]

	Bat SL-CoV YNLF_31C, 93.5% to SARS-CoV-1, Rhinolophus ferrumequinum, Lufeng, Yunnan^[8]

	Bat SL-CoV YNLF_34C, 93.5% to SARS-CoV-1, Rhinolophus ferrumequinum, Lufeng, Yunnan^[8]

	SHC014-CoV, 95.4% to SARS-CoV-1, Rhinolophus sinicus, Kunming, Yunnan^[9]

	WIV1, 95.6% to SARS-CoV-1, Rhinolophus sinicus, Kunming, Yunnan^[9]

WIV16, 96.0% to SARS-CoV-1, Rhinolophus sinicus Kunming, Yunnan^[10]

	Civet SARS-CoV, 99.8% to SARS-CoV-1, Paguma larvata, market in Guangdong, China^[6]

	SARS-CoV-1

SARS-CoV-2, 79% to SARS-CoV-1^[11]

References

^ He B; Zhang Y; Xu L; Yang W; Yang F; Feng Y; et al. (2014). "Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China". J Virol. 88 (12): 7070–82. doi:10.1128/JVI.00631-14. PMC 4054348. PMID 24719429.
^ Wells, H L; Letko, M; Lasso, G; Ssebide, B; Nziza, J; Byarugaba, D K; Navarrete-Macias, I; Liang, E; et al. (2021). "The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus". Virus Evolution. 7 (1): veab007. doi:10.1093/ve/veab007. ISSN 2057-1577. PMC 7928622. PMID 33754082.
^ Kim, Yongkwan; Son, Kidong; Kim, Young-Sik; Lee, Sook-Young; Jheong, Weonhwa; Oem, Jae-Ku (2019). "Complete genome analysis of a SARS-like bat coronavirus identified in the Republic of Korea". Virus Genes. 55 (4): 545–549. doi:10.1007/s11262-019-01668-w. PMC 7089380. PMID 31076983.
^ Xu, L; Zhang, F; Yang, W; Jiang, T; Lu, G; He, B; Li, X; Hu, T; Chen, G; Feng, Y; Zhang, Y; Fan, Q; Feng, J; Zhang, H; Tu, C (February 2016). "Detection and characterization of diverse alpha- and betacoronaviruses from bats in China". Virologica Sinica. 31 (1): 69–77. doi:10.1007/s12250-016-3727-3. PMC 7090707. PMID 26847648.
^ ^a ^b Li, W. (2005). "Bats Are Natural Reservoirs of SARS-Like Coronaviruses". Science. 310 (5748): 676–679. Bibcode:2005Sci...310..676L. doi:10.1126/science.1118391. ISSN 0036-8075. PMID 16195424. S2CID 2971923.
^ ^a ^b Xing‐Yi Ge; Ben Hu; Zheng‐Li Shi (2015). "BAT CORONAVIRUSES". In Lin-Fa Wang; Christopher Cowled (eds.). Bats and Viruses: A New Frontier of Emerging Infectious Diseases (First ed.). John Wiley & Sons. pp. 127–155. doi:10.1002/9781118818824.ch5.
^ He, Biao; Zhang, Yuzhen; Xu, Lin; Yang, Weihong; Yang, Fanli; Feng, Yun; et al. (2014). "Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China". J Virol. 88 (12): 7070–82. doi:10.1128/JVI.00631-14. PMC 4054348. PMID 24719429.
^ ^a ^b Lau, Susanna K. P.; Feng, Yun; Chen, Honglin; Luk, Hayes K. H.; Yang, Wei-Hong; Li, Kenneth S. M.; Zhang, Yu-Zhen; Huang, Yi; et al. (2015). "Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination". Journal of Virology. 89 (20): 10532–10547. doi:10.1128/JVI.01048-15. ISSN 0022-538X. PMC 4580176. PMID 26269185.
^ ^a ^b Xing-Yi Ge; Jia-Lu Li; Xing-Lou Yang; et al. (2013). "Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor". Nature. 503 (7477): 535–8. Bibcode:2013Natur.503..535G. doi:10.1038/nature12711. PMC 5389864. PMID 24172901.
^ Yang, Xing-Lou; Hu, Ben; Wang, Bo; Wang, Mei-Niang; Zhang, Qian; Zhang, Wei; et al. (2016). "Isolation and Characterization of a Novel Bat Coronavirus Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coronavirus". Journal of Virology. 90 (6): 3253–6. doi:10.1128/JVI.02582-15. PMC 4810638. PMID 26719272.
^ Ben, Hu; Hua, Guo; Peng, Zhou; Zheng-Li, Shi (2020). "Characteristics of SARS-CoV-2 and COVID-19". Nature Reviews Microbiology. 19 (3): 141–154. doi:10.1038/s41579-020-00459-7. PMC 7537588. PMID 33024307.