Pairwise diversity and tMRCA as potential markers for HIV infection recency
| Autor: | Vladimir Novitsky, Susan Engelbrecht, Simani Gaseitsiwe, Joseph Makhema, Jia Weng, Sikhulile Moyo, Eduan Wilkinson, Rosemary Musonda, Alain Vandormael, Rui Wang, Max Essex, Kenanao P. Kotokwe, Tulio de Oliveira |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Most recent common ancestor R software Time Factors Phylogenetic inference HIV recency pairwise distances Bayesian probability Human immunodeficiency virus (HIV) Observational Study HIV Infections Genome amplification medicine.disease_cause HIV incidence 03 medical and health sciences Bayes' theorem Medicine Humans business.industry virus diseases Bayes Theorem General Medicine Virology 3. Good health 030104 developmental biology Cross-Sectional Studies HIV-1C Evolutionary biology HIV-1 Pairwise comparison tMRCA business Research Article |
| Zdroj: | Medicine |
| ISSN: | 1536-5964 0025-7974 |
| Popis: | Intrahost human immunodeficiency virus (HIV)-1 diversity increases linearly over time. We assessed the extent to which mean pairwise distances and the time to the most recent common ancestor (tMRCA) inferred from intrahost HIV-1C env sequences were associated with the estimated time of HIV infection. Data from a primary HIV-1C infection study in Botswana were used for this analysis (N = 42). A total of 2540 HIV-1C env gp120 variable loop region 1 to conserved region 5 (V1C5) of the HIV-1 envelope gp120 viral sequences were generated by single genome amplification and sequencing, with an average of 61 viral sequences per participant and 11 sequences per time point per participant. Raw pairwise distances were calculated for each time point and participant using the ape package in R software. The tMRCA was estimated using phylogenetic inference implemented in Bayesian Evolutionary Analysis by Sampling Trees v1.8.2. Pairwise distances and tMRCA were significantly associated with the estimated time since HIV infection (both P |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|