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- Publisher Website: 10.1186/s13073-021-00847-5
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Article: Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients
Title | Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients |
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Authors | |
Keywords | SARS-CoV-2 COVID-19 Intra-host Variation Dynamics |
Issue Date | 2021 |
Publisher | BioMed Central Ltd. The Journal's web site is located at http://genomemedicine.com/ |
Citation | Genome Medicine, 2021, v. 13, article no. 30 How to Cite? |
Abstract | Background:
Since early February 2021, the causative agent of COVID-19, SARS-CoV-2, has infected over 104 million people with more than 2 million deaths according to official reports. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown.
Methods:
Using high-throughput sequencing of metatranscriptomic and hybrid captured libraries, we characterized consensus genomes and intra-host single nucleotide variations (iSNVs) of serial samples collected from eight patients with COVID-19. The distribution of iSNVs along the SARS-CoV-2 genome was analyzed and co-occurring iSNVs among COVID-19 patients were identified. We also compared the evolutionary dynamics of SARS-CoV-2 population in the respiratory tract (RT) and gastrointestinal tract (GIT).
Results:
The 32 consensus genomes revealed the co-existence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in a single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparing allele frequencies of the iSNVs revealed a clear genetic differentiation between intra-host populations from the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events during intra-host migrations. Compared to RT populations, the GIT populations showed a better maintenance and rapid development of viral genetic diversity following the suspected intra-host bottlenecks.
Conclusions:
Our findings here illustrate the intra-host bottlenecks and evolutionary dynamics of SARS-CoV-2 in different anatomic sites and may provide new insights to understand the virus-host interactions of coronaviruses and other RNA viruses. |
Persistent Identifier | http://hdl.handle.net/10722/305243 |
ISSN | 2023 Impact Factor: 10.4 2023 SCImago Journal Rankings: 4.975 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Wang, Y | - |
dc.contributor.author | Wang, D | - |
dc.contributor.author | Zhang, L | - |
dc.contributor.author | Sun, W | - |
dc.contributor.author | Zhang, Z | - |
dc.contributor.author | Chen, W | - |
dc.contributor.author | Zhu, A | - |
dc.contributor.author | Huang, Y | - |
dc.contributor.author | Xiao, F | - |
dc.contributor.author | Yao, J | - |
dc.contributor.author | Gan, M | - |
dc.contributor.author | Li, F | - |
dc.contributor.author | Luo, L | - |
dc.contributor.author | Huang, X | - |
dc.contributor.author | Zhang, Y | - |
dc.contributor.author | Wong, SS | - |
dc.contributor.author | Chen, X | - |
dc.contributor.author | Ji, J | - |
dc.contributor.author | Ou, Z | - |
dc.contributor.author | Xiao, M | - |
dc.contributor.author | Li, M | - |
dc.contributor.author | Li, J | - |
dc.contributor.author | Ren, P | - |
dc.contributor.author | Deng, Z | - |
dc.contributor.author | Zhong, H | - |
dc.contributor.author | Xu, X | - |
dc.contributor.author | Song, T | - |
dc.contributor.author | Mok, CKP | - |
dc.contributor.author | Peiris, M | - |
dc.contributor.author | Zhong, N | - |
dc.contributor.author | Zhao, J | - |
dc.contributor.author | Li, Y | - |
dc.contributor.author | Li, J | - |
dc.contributor.author | Zhao, J | - |
dc.date.accessioned | 2021-10-20T10:06:40Z | - |
dc.date.available | 2021-10-20T10:06:40Z | - |
dc.date.issued | 2021 | - |
dc.identifier.citation | Genome Medicine, 2021, v. 13, article no. 30 | - |
dc.identifier.issn | 1756-994X | - |
dc.identifier.uri | http://hdl.handle.net/10722/305243 | - |
dc.description.abstract | Background: Since early February 2021, the causative agent of COVID-19, SARS-CoV-2, has infected over 104 million people with more than 2 million deaths according to official reports. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. Methods: Using high-throughput sequencing of metatranscriptomic and hybrid captured libraries, we characterized consensus genomes and intra-host single nucleotide variations (iSNVs) of serial samples collected from eight patients with COVID-19. The distribution of iSNVs along the SARS-CoV-2 genome was analyzed and co-occurring iSNVs among COVID-19 patients were identified. We also compared the evolutionary dynamics of SARS-CoV-2 population in the respiratory tract (RT) and gastrointestinal tract (GIT). Results: The 32 consensus genomes revealed the co-existence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in a single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparing allele frequencies of the iSNVs revealed a clear genetic differentiation between intra-host populations from the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events during intra-host migrations. Compared to RT populations, the GIT populations showed a better maintenance and rapid development of viral genetic diversity following the suspected intra-host bottlenecks. Conclusions: Our findings here illustrate the intra-host bottlenecks and evolutionary dynamics of SARS-CoV-2 in different anatomic sites and may provide new insights to understand the virus-host interactions of coronaviruses and other RNA viruses. | - |
dc.language | eng | - |
dc.publisher | BioMed Central Ltd. The Journal's web site is located at http://genomemedicine.com/ | - |
dc.relation.ispartof | Genome Medicine | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | SARS-CoV-2 | - |
dc.subject | COVID-19 | - |
dc.subject | Intra-host | - |
dc.subject | Variation | - |
dc.subject | Dynamics | - |
dc.title | Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients | - |
dc.type | Article | - |
dc.identifier.email | Peiris, M: malik@hkucc.hku.hk | - |
dc.identifier.authority | Mok, CKP=rp01805 | - |
dc.identifier.authority | Peiris, M=rp00410 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1186/s13073-021-00847-5 | - |
dc.identifier.pmid | 33618765 | - |
dc.identifier.pmcid | PMC7898256 | - |
dc.identifier.scopus | eid_2-s2.0-85101394477 | - |
dc.identifier.hkuros | 327403 | - |
dc.identifier.volume | 13 | - |
dc.identifier.spage | article no. 30 | - |
dc.identifier.epage | article no. 30 | - |
dc.identifier.isi | WOS:000623225400002 | - |
dc.publisher.place | United Kingdom | - |