Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones

Benkő, Mária and Harrach, Balázs and Kaján, Győző L. (2023) Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones. HELIYON, 9 (1). ArtNo: e12895. ISSN 2405-8440

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Abstract

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.

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