Cargando…
Exploring Diversity of COVID‑19 Based on Substitution Distance
BACKGROUND: The number of COVID-19 infections worldwide has reached 10 million. COVID‑19 caused by SARS-CoV-2 is more contagious than SARS-CoV-1. There is a dispute about the origin of COVID-19. Study results showed that all SARS-CoV-2 sequences around the world share a common ancestor towards the e...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Dove
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605616/ https://www.ncbi.nlm.nih.gov/pubmed/33149633 http://dx.doi.org/10.2147/IDR.S277620 |
_version_ | 1783604338706350080 |
---|---|
author | Chen, Yi-Hau Wang, Hsiuying |
author_facet | Chen, Yi-Hau Wang, Hsiuying |
author_sort | Chen, Yi-Hau |
collection | PubMed |
description | BACKGROUND: The number of COVID-19 infections worldwide has reached 10 million. COVID‑19 caused by SARS-CoV-2 is more contagious than SARS-CoV-1. There is a dispute about the origin of COVID-19. Study results showed that all SARS-CoV-2 sequences around the world share a common ancestor towards the end of 2019. METHODS: Virus sequences from COVID-19 samples at the early time should be less diversifiable than those from samples at the later time because there might be more mutations when the virus evolutes over time. The diversity of virus nucleotide sequences can be measured by the nucleotide substitution distance. To explore the diversity of SARS-CoV-2, we use different nucleotide substitution models to calculate the distances of SARS-CoV-2 samples from 3 different areas, China, Europe, and the USA. Then, we use these distances to infer the origin of COVID-19. RESULTS: It is known that COVID-19 originated in Wuhan China and then spread to Europe and the USA. By using different substitution models, the distances of SARS-CoV-2 samples from these areas are significantly different. By ANOVA testing, the p-value is less than 2.2e-16. The analyzed results in most substitution models show that China has the lowest diversity, followed by Europe and lastly by the USA. This outcome coincides with the virus transmission time order that SARS-CoV-2 starts in China, then outbreaks in Europe and finally in the USA. CONCLUSION: The magnitude of nucleotide substitution distance of SARS-CoV-2 is closely related to the transmission time order of SARS-CoV-2. This outcome reveals that the nucleotide substitution distance of SARS-CoV-2 may be used to infer the origin of COVID-19. |
format | Online Article Text |
id | pubmed-7605616 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Dove |
record_format | MEDLINE/PubMed |
spelling | pubmed-76056162020-11-03 Exploring Diversity of COVID‑19 Based on Substitution Distance Chen, Yi-Hau Wang, Hsiuying Infect Drug Resist Methodology BACKGROUND: The number of COVID-19 infections worldwide has reached 10 million. COVID‑19 caused by SARS-CoV-2 is more contagious than SARS-CoV-1. There is a dispute about the origin of COVID-19. Study results showed that all SARS-CoV-2 sequences around the world share a common ancestor towards the end of 2019. METHODS: Virus sequences from COVID-19 samples at the early time should be less diversifiable than those from samples at the later time because there might be more mutations when the virus evolutes over time. The diversity of virus nucleotide sequences can be measured by the nucleotide substitution distance. To explore the diversity of SARS-CoV-2, we use different nucleotide substitution models to calculate the distances of SARS-CoV-2 samples from 3 different areas, China, Europe, and the USA. Then, we use these distances to infer the origin of COVID-19. RESULTS: It is known that COVID-19 originated in Wuhan China and then spread to Europe and the USA. By using different substitution models, the distances of SARS-CoV-2 samples from these areas are significantly different. By ANOVA testing, the p-value is less than 2.2e-16. The analyzed results in most substitution models show that China has the lowest diversity, followed by Europe and lastly by the USA. This outcome coincides with the virus transmission time order that SARS-CoV-2 starts in China, then outbreaks in Europe and finally in the USA. CONCLUSION: The magnitude of nucleotide substitution distance of SARS-CoV-2 is closely related to the transmission time order of SARS-CoV-2. This outcome reveals that the nucleotide substitution distance of SARS-CoV-2 may be used to infer the origin of COVID-19. Dove 2020-10-29 /pmc/articles/PMC7605616/ /pubmed/33149633 http://dx.doi.org/10.2147/IDR.S277620 Text en © 2020 Chen and Wang. http://creativecommons.org/licenses/by-nc/3.0/ This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution – Non Commercial (unported, v3.0) License (http://creativecommons.org/licenses/by-nc/3.0/). By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms (https://www.dovepress.com/terms.php). |
spellingShingle | Methodology Chen, Yi-Hau Wang, Hsiuying Exploring Diversity of COVID‑19 Based on Substitution Distance |
title | Exploring Diversity of COVID‑19 Based on Substitution Distance |
title_full | Exploring Diversity of COVID‑19 Based on Substitution Distance |
title_fullStr | Exploring Diversity of COVID‑19 Based on Substitution Distance |
title_full_unstemmed | Exploring Diversity of COVID‑19 Based on Substitution Distance |
title_short | Exploring Diversity of COVID‑19 Based on Substitution Distance |
title_sort | exploring diversity of covid‑19 based on substitution distance |
topic | Methodology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605616/ https://www.ncbi.nlm.nih.gov/pubmed/33149633 http://dx.doi.org/10.2147/IDR.S277620 |
work_keys_str_mv | AT chenyihau exploringdiversityofcovid19basedonsubstitutiondistance AT wanghsiuying exploringdiversityofcovid19basedonsubstitutiondistance |