Updated HIV-1 Consensus Sequences Change but Stay Within Similar Distance From Worldwide Samples [electronic resource]

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Tác giả:

Ngôn ngữ: eng

Ký hiệu phân loại: 574.5 [Unassigned]

Thông tin xuất bản: Los Alamos, N.M. : Oak Ridge, Tenn. : Los Alamos National Laboratory ; Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy, 2022

Mô tả vật lý: Size: Article No. 828765 : , digital, PDF file.

Bộ sưu tập: Metadata

ID: 259623

HIV consensus sequences are used in various bioinformatic, evolutionary, and vaccine related research. Since the previous HIV-1 subtype and CRF consensus sequences were constructed in 2002, the number of publicly available HIV-1 sequences have grown exponentially, especially from non-EU and US countries. Here, we reconstruct 90 new HIV-1 subtype and CRF consensus sequences from 3,470 high-quality, representative, full genome sequences in the LANL HIV database. While subtypes and CRFs are unevenly spread across the world, in total 89 countries were represented. For consensus sequences that were based on at least 20 genomes, we found that on average 2.3% (range 0.8?10%) of the consensus genome site states changed from 2002 to 2021, of which about half were nucleotide state differences and the rest insertions and deletions. Interestingly, the 2021 consensus sequences were shorter than in 2002, and compared to 4,674 HIV-1 worldwide genome sequences, the 2021 consensuses were somewhat closer to the worldwide genome sequences, i.e., showing on average fewer nucleotide state differences. Some subtypes/CRFs have had limited geographical spread, and thus sampling of subtypes/CRFs is uneven, at least in part, due to the epidemiological dynamics. Thus, taken as a whole, the 2021 consensus sequences likely are good representations of the typical subtype/CRF genome nucleotide states. The new consensus sequences are available at the LANL HIV database.
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