Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, yet limi...

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Autores principales:	Tingting Li, Dongxia Liu, Yadi Yang, Jiali Guo, Yujie Feng, Xinmo Zhang, Shilong Cheng, Jie Feng
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/85246d66bbd24bccb85ea2292d60c732
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spelling	oai:doaj.org-article:85246d66bbd24bccb85ea2292d60c7322021-12-02T13:57:01ZPhylogenetic supertree reveals detailed evolution of SARS-CoV-210.1038/s41598-020-79484-82045-2322https://doaj.org/article/85246d66bbd24bccb85ea2292d60c7322020-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-79484-8https://doaj.org/toc/2045-2322Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, yet limited progress was obtained, principally owing to the disability of these methods to reasonably integrate phylogenetic information from all genes of SARS-CoV-2. Supertree method based on multiple trees can produce the overall reasonable phylogenetic tree. However, the supertree method has been barely used for phylogenetic analysis of viruses. Here we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. Compared with other phylogenetic analysis methods, the supertree method showed more resolution power for phylogenetic analysis of coronaviruses. In particular, the MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences. Furthermore, the discovery of evolution and mutation in SARS-CoV-2 was achieved by MRP pseudo-sequence supertree analysis. Taken together, the MRP pseudo-sequence supertree provided more information on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.Tingting LiDongxia LiuYadi YangJiali GuoYujie FengXinmo ZhangShilong ChengJie FengNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-9 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tingting Li Dongxia Liu Yadi Yang Jiali Guo Yujie Feng Xinmo Zhang Shilong Cheng Jie Feng Phylogenetic supertree reveals detailed evolution of SARS-CoV-2
description	Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, yet limited progress was obtained, principally owing to the disability of these methods to reasonably integrate phylogenetic information from all genes of SARS-CoV-2. Supertree method based on multiple trees can produce the overall reasonable phylogenetic tree. However, the supertree method has been barely used for phylogenetic analysis of viruses. Here we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. Compared with other phylogenetic analysis methods, the supertree method showed more resolution power for phylogenetic analysis of coronaviruses. In particular, the MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences. Furthermore, the discovery of evolution and mutation in SARS-CoV-2 was achieved by MRP pseudo-sequence supertree analysis. Taken together, the MRP pseudo-sequence supertree provided more information on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.
format	article
author	Tingting Li Dongxia Liu Yadi Yang Jiali Guo Yujie Feng Xinmo Zhang Shilong Cheng Jie Feng
author_facet	Tingting Li Dongxia Liu Yadi Yang Jiali Guo Yujie Feng Xinmo Zhang Shilong Cheng Jie Feng
author_sort	Tingting Li
title	Phylogenetic supertree reveals detailed evolution of SARS-CoV-2
title_short	Phylogenetic supertree reveals detailed evolution of SARS-CoV-2
title_full	Phylogenetic supertree reveals detailed evolution of SARS-CoV-2
title_fullStr	Phylogenetic supertree reveals detailed evolution of SARS-CoV-2
title_full_unstemmed	Phylogenetic supertree reveals detailed evolution of SARS-CoV-2
title_sort	phylogenetic supertree reveals detailed evolution of sars-cov-2
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/85246d66bbd24bccb85ea2292d60c732
work_keys_str_mv	AT tingtingli phylogeneticsupertreerevealsdetailedevolutionofsarscov2 AT dongxialiu phylogeneticsupertreerevealsdetailedevolutionofsarscov2 AT yadiyang phylogeneticsupertreerevealsdetailedevolutionofsarscov2 AT jialiguo phylogeneticsupertreerevealsdetailedevolutionofsarscov2 AT yujiefeng phylogeneticsupertreerevealsdetailedevolutionofsarscov2 AT xinmozhang phylogeneticsupertreerevealsdetailedevolutionofsarscov2 AT shilongcheng phylogeneticsupertreerevealsdetailedevolutionofsarscov2 AT jiefeng phylogeneticsupertreerevealsdetailedevolutionofsarscov2
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Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

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