Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.
- Publisher:
- MDPI
- Publication Type:
- Journal Article
- Citation:
- Viruses, 2023, 15, (5), pp. 1065
- Issue Date:
- 2023-04-26
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Full metadata record
Field | Value | Language |
---|---|---|
dc.contributor.author | Cai, X | |
dc.contributor.author | Lan, T | |
dc.contributor.author |
Ping, P https://orcid.org/0000-0002-1829-3273 |
|
dc.contributor.author |
Oliver, B https://orcid.org/0000-0002-7122-9262 |
|
dc.contributor.author | Li, J | |
dc.date.accessioned | 2024-02-12T06:35:33Z | |
dc.date.available | 2023-04-24 | |
dc.date.available | 2024-02-12T06:35:33Z | |
dc.date.issued | 2023-04-26 | |
dc.identifier.citation | Viruses, 2023, 15, (5), pp. 1065 | |
dc.identifier.issn | 1999-4915 | |
dc.identifier.issn | 1999-4915 | |
dc.identifier.uri | http://hdl.handle.net/10453/175591 | |
dc.description.abstract | The COVID-19 pandemic caused by SARS-CoV-2 has had a severe impact on people worldwide. The reference genome of the virus has been widely used as a template for designing mRNA vaccines to combat the disease. In this study, we present a computational method aimed at identifying co-existing intra-host strains of the virus from RNA-sequencing data of short reads that were used to assemble the original reference genome. Our method consisted of five key steps: extraction of relevant reads, error correction for the reads, identification of within-host diversity, phylogenetic study, and protein binding affinity analysis. Our study revealed that multiple strains of SARS-CoV-2 can coexist in both the viral sample used to produce the reference sequence and a wastewater sample from California. Additionally, our workflow demonstrated its capability to identify within-host diversity in foot-and-mouth disease virus (FMDV). Through our research, we were able to shed light on the binding affinity and phylogenetic relationships of these strains with the published SARS-CoV-2 reference genome, SARS-CoV, variants of concern (VOC) of SARS-CoV-2, and some closely related coronaviruses. These insights have important implications for future research efforts aimed at identifying within-host diversity, understanding the evolution and spread of these viruses, as well as the development of effective treatments and vaccines against them. | |
dc.format | Electronic | |
dc.language | eng | |
dc.publisher | MDPI | |
dc.relation | http://purl.org/au-research/grants/arc/DP180100120 | |
dc.relation.ispartof | Viruses | |
dc.relation.isbasedon | 10.3390/v15051065 | |
dc.rights | info:eu-repo/semantics/openAccess | |
dc.subject | 0605 Microbiology | |
dc.subject.classification | 3107 Microbiology | |
dc.subject.mesh | Animals | |
dc.subject.mesh | Humans | |
dc.subject.mesh | SARS-CoV-2 | |
dc.subject.mesh | COVID-19 | |
dc.subject.mesh | Phylogeny | |
dc.subject.mesh | Pandemics | |
dc.subject.mesh | Genome, Viral | |
dc.subject.mesh | Spike Glycoprotein, Coronavirus | |
dc.subject.mesh | Animals | |
dc.subject.mesh | Humans | |
dc.subject.mesh | Phylogeny | |
dc.subject.mesh | Genome, Viral | |
dc.subject.mesh | Pandemics | |
dc.subject.mesh | Spike Glycoprotein, Coronavirus | |
dc.subject.mesh | COVID-19 | |
dc.subject.mesh | SARS-CoV-2 | |
dc.subject.mesh | Animals | |
dc.subject.mesh | Humans | |
dc.subject.mesh | SARS-CoV-2 | |
dc.subject.mesh | COVID-19 | |
dc.subject.mesh | Phylogeny | |
dc.subject.mesh | Pandemics | |
dc.subject.mesh | Genome, Viral | |
dc.subject.mesh | Spike Glycoprotein, Coronavirus | |
dc.title | Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search. | |
dc.type | Journal Article | |
utslib.citation.volume | 15 | |
utslib.location.activity | Switzerland | |
utslib.for | 0605 Microbiology | |
pubs.organisational-group | University of Technology Sydney | |
pubs.organisational-group | University of Technology Sydney/Faculty of Engineering and Information Technology | |
pubs.organisational-group | University of Technology Sydney/Faculty of Science | |
pubs.organisational-group | University of Technology Sydney/Strength - CHT - Health Technologies | |
pubs.organisational-group | University of Technology Sydney/Faculty of Science/School of Life Sciences | |
pubs.organisational-group | University of Technology Sydney/Faculty of Engineering and Information Technology/School of Computer Science | |
pubs.organisational-group | University of Technology Sydney/Centre for Health Technologies (CHT) | |
utslib.copyright.status | open_access | * |
dc.date.updated | 2024-02-12T06:35:30Z | |
pubs.issue | 5 | |
pubs.publication-status | Published online | |
pubs.volume | 15 | |
utslib.citation.issue | 5 |
Abstract:
The COVID-19 pandemic caused by SARS-CoV-2 has had a severe impact on people worldwide. The reference genome of the virus has been widely used as a template for designing mRNA vaccines to combat the disease. In this study, we present a computational method aimed at identifying co-existing intra-host strains of the virus from RNA-sequencing data of short reads that were used to assemble the original reference genome. Our method consisted of five key steps: extraction of relevant reads, error correction for the reads, identification of within-host diversity, phylogenetic study, and protein binding affinity analysis. Our study revealed that multiple strains of SARS-CoV-2 can coexist in both the viral sample used to produce the reference sequence and a wastewater sample from California. Additionally, our workflow demonstrated its capability to identify within-host diversity in foot-and-mouth disease virus (FMDV). Through our research, we were able to shed light on the binding affinity and phylogenetic relationships of these strains with the published SARS-CoV-2 reference genome, SARS-CoV, variants of concern (VOC) of SARS-CoV-2, and some closely related coronaviruses. These insights have important implications for future research efforts aimed at identifying within-host diversity, understanding the evolution and spread of these viruses, as well as the development of effective treatments and vaccines against them.
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