Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones
The present research aimed to evaluate the diversity of all monkeypox virus strains with a special focus on recently isolated ones by a comprehensive phylogenetic analysis of all available sequences, based on the concatenate of four viral genes. Almost all current strains from 2022 showed a high lev...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844023001020 |
| _version_ | 1811173327627091968 |
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| author | Mária Benkő Balázs Harrach Győző L. Kaján |
| author_facet | Mária Benkő Balázs Harrach Győző L. Kaján |
| author_sort | Mária Benkő |
| collection | DOAJ |
| description | The present research aimed to evaluate the diversity of all monkeypox virus strains with a special focus on recently isolated ones by a comprehensive phylogenetic analysis of all available sequences, based on the concatenate of four viral genes. Almost all current strains from 2022 showed a high level of similarity to each other on the analyzed stretches: 218 strains shared identical sequence. Among all analyzed strains, the highest number of differences was counted compared to a RefSeq strain (Zaire-96-I-16) on the whole concatenate. Our analysis supported the distinction between Clade I (formerly Congo Basin clade), IIa and IIb (together formerly West African clade) strains and classified all 2022 strains in the last one. The high number of differences and long branch observable concerning strain Zaire-96-I-16 is most probably caused by a sequencing error. As this strain represents one of the two available reference sequences in GenBank, it is recommendable to confirm or exclude the concerning mutation. The developed method, based on four gene sequences, reflected the established whole-genome-based intraspecies classification. Although this method provides significantly less information about the strains compared to whole genome analyses, since its resolution is much lower, it still enables the rapid subspecies classification of the strains into the established clades. The genes in the analyzed concatenate are so conserved that further differentiation of contemporary strains is impossible; these strains are identical in the analyzed sections. On the other hand, since whole genome analyses are compute-intensive, the described method offers a simpler and more accessible alternative for monitoring and preliminary typing of newly sequenced monkeypox virus strains. |
| first_indexed | 2024-04-10T17:45:05Z |
| format | Article |
| id | doaj.art-20d842ab35e647b89b15bdcf329de5f5 |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-04-10T17:45:05Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-20d842ab35e647b89b15bdcf329de5f52023-02-03T04:59:36ZengElsevierHeliyon2405-84402023-01-0191e12895Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary onesMária Benkő0Balázs Harrach1Győző L. Kaján2Veterinary Medical Research Institute, Hungária krt. 21, 1143 Budapest, HungaryVeterinary Medical Research Institute, Hungária krt. 21, 1143 Budapest, HungaryCorresponding author.; Veterinary Medical Research Institute, Hungária krt. 21, 1143 Budapest, HungaryThe present research aimed to evaluate the diversity of all monkeypox virus strains with a special focus on recently isolated ones by a comprehensive phylogenetic analysis of all available sequences, based on the concatenate of four viral genes. Almost all current strains from 2022 showed a high level of similarity to each other on the analyzed stretches: 218 strains shared identical sequence. Among all analyzed strains, the highest number of differences was counted compared to a RefSeq strain (Zaire-96-I-16) on the whole concatenate. Our analysis supported the distinction between Clade I (formerly Congo Basin clade), IIa and IIb (together formerly West African clade) strains and classified all 2022 strains in the last one. The high number of differences and long branch observable concerning strain Zaire-96-I-16 is most probably caused by a sequencing error. As this strain represents one of the two available reference sequences in GenBank, it is recommendable to confirm or exclude the concerning mutation. The developed method, based on four gene sequences, reflected the established whole-genome-based intraspecies classification. Although this method provides significantly less information about the strains compared to whole genome analyses, since its resolution is much lower, it still enables the rapid subspecies classification of the strains into the established clades. The genes in the analyzed concatenate are so conserved that further differentiation of contemporary strains is impossible; these strains are identical in the analyzed sections. On the other hand, since whole genome analyses are compute-intensive, the described method offers a simpler and more accessible alternative for monitoring and preliminary typing of newly sequenced monkeypox virus strains.http://www.sciencedirect.com/science/article/pii/S2405844023001020MonkeypoxPhylogenetic analysisRefSeq |
| spellingShingle | Mária Benkő Balázs Harrach Győző L. Kaján Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones Heliyon Monkeypox Phylogenetic analysis RefSeq |
| title | Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones |
| title_full | Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones |
| title_fullStr | Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones |
| title_full_unstemmed | Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones |
| title_short | Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones |
| title_sort | phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones |
| topic | Monkeypox Phylogenetic analysis RefSeq |
| url | http://www.sciencedirect.com/science/article/pii/S2405844023001020 |
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