Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand

Autor:	Raabya Rossenkhan, Lydia Bonar, Jan P.L. Labuschagne, Meera Bose, Kultida Poltavee, Elizabeth A. Harbolick, Daniel B. Reeves, Morgane Rolland, Jerome H. Kim, Bethany L. Dearlove, Leigh Anne Eller, Merlin L. Robb, Gustavo H. Kijak, Hannah Kibuuka, Paul T. Edlefsen, Eric Lewitus, Phuc Pham, Bahar Ahani, Annemarie O'Sullivan, Shana Miller, Eric Sanders-Buell, Sorachai Nitayaphan, Fred Sawe, Jenica Lee, Christopher L. Owen, Yifan Li, Robert Gramzinski, Lucas Maganga, Nelson L. Michael, Sodsai Tovanabutra
Jazyk:	angličtina
Rok vydání:	2020
Předmět:	Male RNA viruses Time Factors Human immunodeficiency virus (HIV) HIV Infections medicine.disease_cause Pathology and Laboratory Medicine Database and Informatics Methods Immunodeficiency Viruses Medicine and Health Sciences Medicine Prospective Studies Biology (General) Data Management 0303 health sciences Vaccines Molecular dating 030302 biochemistry & molecular biology Phylogenetic Analysis Africa Eastern Viral Load Thailand Phylogenetics Infectious Diseases Method comparison Molecular Diagnostic Techniques Medical Microbiology Viral Pathogens Cohort Viruses Physical Sciences Female Pathogens Viral load Sequence Analysis Research Article Adult medicine.medical_specialty Computer and Information Sciences Infectious Disease Control Bioinformatics QH301-705.5 Immunology Viremia Genome Viral Research and Analysis Methods Microbiology Drug levels 03 medical and health sciences Internal medicine Virology Retroviruses Genetics East africa Humans Evolutionary Systematics Molecular Biology Microbial Pathogens 030304 developmental biology Taxonomy Evolutionary Biology business.industry Lentivirus Organisms Biology and Life Sciences HIV Eigenvalues RC581-607 medicine.disease Algebra Linear Algebra HIV-1 Parasitology Immunologic diseases. Allergy business Sequence Alignment Viral Transmission and Infection Mathematics
Zdroj:	PLoS Pathogens, Vol 16, Iss 2, p e1008179 (2020) PLoS Pathogens
ISSN:	1553-7374 1553-7366
Popis:	Most HIV-1 infected individuals do not know their infection dates. Precise infection timing is crucial information for studies that document transmission networks or drug levels at infection. To improve infection timing, we used the prospective RV217 cohort where the window when plasma viremia becomes detectable is narrow: the last negative visit occurred a median of four days before the first detectable HIV-1 viremia with an RNA test, referred below as diagnosis. We sequenced 1,280 HIV-1 genomes from 39 participants at a median of 4, 32 and 170 days post-diagnosis. HIV-1 infections were dated by using sequence-based methods and a viral load regression method. Bayesian coalescent and viral load regression estimated that infections occurred a median of 6 days prior to diagnosis (IQR: 9–3 and 11–4 days prior, respectively). Poisson-Fitter, which analyzes the distribution of hamming distances among sequences, estimated a median of 7 days prior to diagnosis (IQR: 15–4 days) based on sequences sampled 4 days post-diagnosis, but it did not yield plausible results using sequences sampled at 32 days. Fourteen participants reported a high-risk exposure event at a median of 8 days prior to diagnosis (IQR: 12 to 6 days prior). These different methods concurred that HIV-1 infection occurred about a week before detectable viremia, corresponding to 20 days (IQR: 34–15 days) before peak viral load. Together, our methods comparison helps define a framework for future dating studies in early HIV-1 infection. Author summary HIV-1 infected individuals rarely know when they became infected but knowing when an infection occurred provides critical information regarding HIV-1 pathogenesis and epidemiology. Using a unique cohort in which infection was known to have occurred in a narrow interval, we investigated methods to estimate the timing of infections. Several methods suggested that HIV-1 infection typically occurs a median of one week before the infection can be detected by HIV-1 RNA testing. Going forward, we provide a strategy that can be used to elucidate the origin of an acute/early infection.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::11231a76c5d47375b0321412c813401d https://doaj.org/article/4eba0f9f21794581ba1e24b1058d88ef Zobrazit plný text záznamu Plný text ve formátu PDF Plný text ve formátu HTML
Nepřihlášeným uživatelům se plný text nezobrazuje	K zobrazení výsledku je třeba se přihlásit.