| Autor: |
Guang, August, Howison, Mark, Ledingham, Lauren, D'Antuono, Matthew, Chan, Philip A., Lawrence, Charles, Dunn, Casey W., Kantor, Rami |
| Předmět: |
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| Zdroj: |
Frontiers in Microbiology; 2/17/2022, Vol. 12, p1-13, 13p |
| Abstrakt: |
Background: Phylogenetic analyses of HIV sequences are used to detect clusters and inform public health interventions. Conventional approaches summarize within-host HIV diversity with a single consensus sequence per host of the pol gene, obtained from Sanger or next-generation sequencing (NGS). There is growing recognition that this approach discards potentially important information about within-host sequence variation, which can impact phylogenetic inference. However, whether alternative summary methods that incorporate intra-host variation impact phylogenetic inference of transmission network features is unknown. Methods: We introduce profile sampling , a method to incorporate within-host NGS sequence diversity into phylogenetic HIV cluster inference. We compare this approach to Sanger- and NGS-derived pol and near-whole-genome consensus sequences and evaluate its potential benefits in identifying molecular clusters among all newly-HIV-diagnosed individuals over six months at the largest HIV center in Rhode Island. Results: Profile sampling cluster inference demonstrated that within-host viral diversity impacts phylogenetic inference across individuals, and that consensus sequence approaches can obscure both magnitude and effect of these impacts. Clustering differed between Sanger- and NGS-derived consensus and profile sampling sequences, and across gene regions. Discussion: Profile sampling can incorporate within-host HIV diversity captured by NGS into phylogenetic analyses. This additional information can improve robustness of cluster detection. [ABSTRACT FROM AUTHOR] |
| Databáze: |
Complementary Index |
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