Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide. Therefore, this study aimed to build a phylogenetic tree of complete genomes of SARS-CoV-2 and other species of Gamma coronavirus to explore the pos...
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| Format: | Article |
| Language: | English |
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College of science, university of Diyala
2024-04-01
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| Series: | Academic Science Journal |
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| Online Access: | https://acadscij.uodiyala.edu.iq/index.php/Home/article/view/426 |
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| author | Alaa Khudair Abbas Al-Khafaji Bashar Talib Al-Nuaimi |
| author_facet | Alaa Khudair Abbas Al-Khafaji Bashar Talib Al-Nuaimi |
| author_sort | Alaa Khudair Abbas Al-Khafaji |
| collection | DOAJ |
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The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide. Therefore, this study aimed to build a phylogenetic tree of complete genomes of SARS-CoV-2 and other species of Gamma coronavirus to explore the possibility of finding the evolutionary relationships between them and wished to analyze them in order to forecast the best trees illustrating the sequences' evolutionary relationships and obtain a well-supported phylogenetic tree by using the Neighbor-Joining (NJ) and Maximum Likelihood (ML) methods after performing multiple sequence alignment (MSA). This study utilized 16 isolates of Gamma coronavirus species and SARS-CoV-2 retrieved from the NCBI (National Center for Biotechnology Information) database for this investigation. The experimental outcomes when applying the two methods to the same dataset show that a well-supported and trustworthy phylogenetic tree was obtained with a bootstrapping value of 100% for all branches of the tree when applying the ML method. Additionally, a well-supported and fast-constructing phylogenetic tree was obtained through the NJ method for all branches except one, where the bootstrapping value appeared to be 56%. The research was conducted in 2022 at the College of Science, Diyala University.
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| format | Article |
| id | doaj-art-cb45528037d24d338e0b58a649fb481f |
| institution | Kabale University |
| issn | 2958-4612 2959-5568 |
| language | English |
| publishDate | 2024-04-01 |
| publisher | College of science, university of Diyala |
| record_format | Article |
| series | Academic Science Journal |
| spelling | doaj-art-cb45528037d24d338e0b58a649fb481f2024-11-19T10:00:17ZengCollege of science, university of DiyalaAcademic Science Journal2958-46122959-55682024-04-012210.24237/ASJ.02.02.695BPhylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2Alaa Khudair Abbas Al-KhafajiBashar Talib Al-Nuaimi The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide. Therefore, this study aimed to build a phylogenetic tree of complete genomes of SARS-CoV-2 and other species of Gamma coronavirus to explore the possibility of finding the evolutionary relationships between them and wished to analyze them in order to forecast the best trees illustrating the sequences' evolutionary relationships and obtain a well-supported phylogenetic tree by using the Neighbor-Joining (NJ) and Maximum Likelihood (ML) methods after performing multiple sequence alignment (MSA). This study utilized 16 isolates of Gamma coronavirus species and SARS-CoV-2 retrieved from the NCBI (National Center for Biotechnology Information) database for this investigation. The experimental outcomes when applying the two methods to the same dataset show that a well-supported and trustworthy phylogenetic tree was obtained with a bootstrapping value of 100% for all branches of the tree when applying the ML method. Additionally, a well-supported and fast-constructing phylogenetic tree was obtained through the NJ method for all branches except one, where the bootstrapping value appeared to be 56%. The research was conducted in 2022 at the College of Science, Diyala University. https://acadscij.uodiyala.edu.iq/index.php/Home/article/view/426SARS-CoV-2, phylogenetic tree construction, Maximum-Likelihood, COVID-19, phylogenetic inference, Neighbor-Joining. |
| spellingShingle | Alaa Khudair Abbas Al-Khafaji Bashar Talib Al-Nuaimi Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2 Academic Science Journal SARS-CoV-2, phylogenetic tree construction, Maximum-Likelihood, COVID-19, phylogenetic inference, Neighbor-Joining. |
| title | Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2 |
| title_full | Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2 |
| title_fullStr | Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2 |
| title_full_unstemmed | Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2 |
| title_short | Phylogenetic Tree Construction of Gamma Coronavirus Genera and SARS-CoV-2 |
| title_sort | phylogenetic tree construction of gamma coronavirus genera and sars cov 2 |
| topic | SARS-CoV-2, phylogenetic tree construction, Maximum-Likelihood, COVID-19, phylogenetic inference, Neighbor-Joining. |
| url | https://acadscij.uodiyala.edu.iq/index.php/Home/article/view/426 |
| work_keys_str_mv | AT alaakhudairabbasalkhafaji phylogenetictreeconstructionofgammacoronavirusgeneraandsarscov2 AT bashartalibalnuaimi phylogenetictreeconstructionofgammacoronavirusgeneraandsarscov2 |