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Barzilai LP, Schrago CG. Signatures of natural selection in tree topology shape of serially sampled viral phylogenies. Mol Phylogenet Evol 2023; 183:107776. [PMID: 36990305 DOI: 10.1016/j.ympev.2023.107776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/24/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Tree shape metrics can be computed fast for trees of any size, which makes them promising alternatives to intensive statistical methods and parameter-rich evolutionary models in the era of massive data availability. Previous studies have demonstrated their effectiveness in unveiling important parameters in viral evolutionary dynamics, although the impact of natural selection on the shape of tree topologies has not been thoroughly investigated. We carried out a forward-time and individual-based simulation to investigate whether tree shape metrics of several kinds could predict the selection regime employed to generate the data. To examine the impact of the genetic diversity of the founder viral population, simulations were run under two opposing starting configurations of the genetic diversity of the infecting viral population. We found that four evolutionary regimes, namely, negative, positive, and frequency-dependent selection, as well as neutral evolution, were successfully distinguished by tree topology shape metrics. Two metrics from the Laplacian spectral density profile (principal eigenvalue and peakedness) and the number of cherries were the most informative for indicating selection type. The genetic diversity of the founder population had an impact on differentiating evolutionary scenarios. Tree imbalance, which has been frequently associated with the action of natural selection on intrahost viral diversity, was also characteristic of neutrally evolving serially sampled data. Metrics calculated from empirical analysis of HIV datasets indicated that most tree topologies exhibited shapes closer to the frequency-dependent selection or neutral evolution regimes.
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Patel V, Spouge JL. Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects. PLoS One 2020; 15:e0227127. [PMID: 31923263 PMCID: PMC6953795 DOI: 10.1371/journal.pone.0227127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 12/12/2019] [Indexed: 11/27/2022] Open
Abstract
If viruses or other pathogens infect a single host, the outcome of infection may depend on the initial basic reproduction number R0, the expected number of host cells infected by a single infected cell. This article shows that sometimes, phylogenetic models can estimate the initial R0, using only sequences sampled from the pathogenic population during its exponential growth or shortly thereafter. When evaluated by simulations mimicking the bursting viral reproduction of HIV and simultaneous sampling of HIV gp120 sequences during early viremia, the estimated R0 displayed useful accuracies in achievable experimental designs. Estimates of R0 have several potential applications to investigators interested in the progress of infection in single hosts, including: (1) timing a pathogen’s movement through different microenvironments; (2) timing the change points in a pathogen’s mode of spread (e.g., timing the change from cell-free spread to cell-to-cell spread, or vice versa, in an HIV infection); (3) quantifying the impact different initial microenvironments have on pathogens (e.g., in mucosal challenge with HIV, quantifying the impact that the presence or absence of mucosal infection has on R0); (4) quantifying subtle changes in infectability in therapeutic trials (either human or animal), even when therapies do not produce total sterilizing immunity; and (5) providing a variable predictive of the clinical efficacy of prophylactic therapies.
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Affiliation(s)
- Vruj Patel
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John L. Spouge
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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RifeMagalis B, Strickland SL, Shank SD, Autissier P, Schuetz A, Sithinamsuwan P, Lerdlum S, Fletcher JLK, de Souza M, Ananworanich J, Valcour V, Williams KC, Kosakovsky Pond SL, RattoKim S, Salemi M. Phyloanatomic characterization of the distinct T cell and monocyte contributions to the peripheral blood HIV population within the host. Virus Evol 2020; 6:veaa005. [PMID: 32355568 PMCID: PMC7185683 DOI: 10.1093/ve/veaa005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Human immunodeficiency virus (HIV) is a rapidly evolving virus, allowing its genetic sequence to act as a fingerprint for epidemiological processes among, as well as within, individual infected hosts. Though primarily infecting the CD4+ T-cell population, HIV can also be found in monocytes, an immune cell population that differs in several aspects from the canonical T-cell viral target. Using single genome viral sequencing and statistical phylogenetic inference, we investigated the viral RNA diversity and relative contribution of each of these immune cell types to the viral population within the peripheral blood. Results provide evidence of an increased prevalence of circulating monocytes harboring virus in individuals with high viral load in the absence of suppressive antiretroviral therapy. Bayesian phyloanatomic analysis of three of these individuals demonstrated a measurable role for these cells, but not the circulating T-cell population, as a source of cell-free virus in the plasma, supporting the hypothesis that these cells can act as an additional conduit of virus spread.
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Affiliation(s)
- Brittany RifeMagalis
- Department of Pathology, Immunology, and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32601, USA
| | - Samantha L Strickland
- Department of Pathology, Immunology, and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32601, USA
| | - Stephen D Shank
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | | | - Alexandra Schuetz
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences - United States Component, Bangkok 10400, Thailand
- SEARCH, Thai Red Cross AIDS Research Center, Bangkok 10330, Thailand
| | - Pasiri Sithinamsuwan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, MD 20850, USA
| | - Sukalaya Lerdlum
- Division of Neurology, Department of Medicine, Phramongkutklao Hospital, Bangkok 10400, Thailand
| | - James L K Fletcher
- Faculty of Medicine, Department of Radiology, Chulalongkorn University, Bangkok 10330, Thailand
| | - Mark de Souza
- Faculty of Medicine, Department of Radiology, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jintanat Ananworanich
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences - United States Component, Bangkok 10400, Thailand
- SEARCH, Thai Red Cross AIDS Research Center, Bangkok 10330, Thailand
- Faculty of Medicine, Department of Radiology, Chulalongkorn University, Bangkok 10330, Thailand
| | - Victor Valcour
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA
| | | | | | | | - Silvia RattoKim
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences - United States Component, Bangkok 10400, Thailand
- SEARCH, Thai Red Cross AIDS Research Center, Bangkok 10330, Thailand
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32601, USA
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Park SY, Love TMT, Kapoor S, Lee HY. HIITE: HIV-1 incidence and infection time estimator. Bioinformatics 2019; 34:2046-2052. [PMID: 29438560 DOI: 10.1093/bioinformatics/bty073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/08/2018] [Indexed: 01/23/2023] Open
Abstract
Motivation Around 2.1 million new HIV-1 infections were reported in 2015, alerting that the HIV-1 epidemic remains a significant global health challenge. Precise incidence assessment strengthens epidemic monitoring efforts and guides strategy optimization for prevention programs. Estimating the onset time of HIV-1 infection can facilitate optimal clinical management and identify key populations largely responsible for epidemic spread and thereby infer HIV-1 transmission chains. Our goal is to develop a genomic assay estimating the incidence and infection time in a single cross-sectional survey setting. Results We created a web-based platform, HIV-1 incidence and infection time estimator (HIITE), which processes envelope gene sequences using hierarchical clustering algorithms and informs the stage of infection, along with time since infection for incident cases. HIITE's performance was evaluated using 585 incident and 305 chronic specimens' envelope gene sequences collected from global cohorts including HIV-1 vaccine trial participants. HIITE precisely identified chronically infected individuals as being chronic with an error less than 1% and correctly classified 94% of recently infected individuals as being incident. Using a mixed-effect model, an incident specimen's time since infection was estimated from its single lineage diversity, showing 14% prediction error for time since infection. HIITE is the first algorithm to inform two key metrics from a single time point sequence sample. HIITE has the capacity for assessing not only population-level epidemic spread but also individual-level transmission events from a single survey, advancing HIV prevention and intervention programs. Availability and implementation Web-based HIITE and source code of HIITE are available at http://www.hayounlee.org/software.html. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, CA, USA
| | - Tanzy M T Love
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Shivankur Kapoor
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, CA, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, CA, USA
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HIV-1 and hepatitis C virus selection bottleneck in Chinese people who inject drugs. AIDS 2018; 32:309-320. [PMID: 29194114 DOI: 10.1097/qad.0000000000001702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES For both HIV-1 and hepatitis C virus (HCV), assessing the stringency of the transmission process is a scientific priority. Enumerations of transmitted/founder (TF) viruses have shown a strict transmission bottleneck in sexual transmission of HIV-1 and a wide range in the multiplicity of infection in HCV. Here, we aim to determine the stringency of parenteral transmission for HIV-1 and HCV in people who inject drugs (PWID). DESIGN We used molecular sequencing and several complementary analyses to enumerate the TF HIV-1 and HCV variants in a well described cohort of PWID in Xinjiang, China. METHODS We performed single genome sequencing of HIV-1 env and 5' half HCV genomes, then applied phylogenetic analysis and validated models of early virus diversification to enumerate TF viruses in 60 PWID. We used multivariate analysis to determine correlates of multivariant transmission (MVT). RESULTS We generated 1070 env region sequences from 33 HIV-1 early infected individuals and 773 5' half region sequences from 27 HCV early infected individuals. We found rates of MVT of 39 and 54%, respectively, for HIV-1 and HCV, with a limited range in the number of TF viruses in both infections. Behavioural characteristics suggested high-risk injection practices and lower risk sexual practices; we did not find an association between any specific behaviours and MVT. CONCLUSION MVT is frequent in parenteral transmission of both HIV-1 and HCV in Xinjiang PWID, indicating a less stringent transmission process than sexual transmission.
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Abstract
The human immunodeficiency virus (HIV) evolves rapidly owing to the combined activity of error-prone reverse transcriptase, recombination, and short generation times, leading to extensive viral diversity both within and between hosts. This diversity is a major contributing factor in the failure of the immune system to eradicate the virus and has important implications for the development of suitable drugs and vaccines to combat infection. This review will discuss the recent technological advances that have shed light on HIV evolution and will summarise emerging concepts in this field.
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Affiliation(s)
- Sophie M Andrews
- Nuffield Department of Clinical Medicine, University of Oxford, NDMRB, Oxford, UK
| | - Sarah Rowland-Jones
- Nuffield Department of Clinical Medicine, University of Oxford, NDMRB, Oxford, UK
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Abstract
OBJECTIVE Properly priming cytotoxic T-lymphocyte (CTL) responses is an important task in HIV-1 vaccination. However, the STEP trial showed no efficacy even though the vaccine elicited HIV-specific CTL responses. Our study is to investigate whether or not the STEP vaccine enhanced viral escape in infected volunteers. METHODS The signature of viral escape, the presence of multiple escape variants, could be falsely represented by the existence of multiple founder viruses. Therefore, we use a mathematical model to designate STEP study patients with infections from a single founder virus. We then conduct permutation tests on each of 9988 Gag, Pol, and Nef overlapping peptides to identify epitopes with significant differences in diversity between the vaccine and placebo groups using previously published STEP trial sequence data. RESULTS We identify signatures of vaccine-enhanced viral escape within HIV-1 Nef from the STEP trial. Vaccine-treated patients showed a greater level of epitope diversity in one of the immunodomiant epitopes, EVGFPVRPQVPL (Nef65-76), compared with placebo-treated patients (P = 0.0038). In the other three Nef epitopes, there is a marginally significant difference in the epitope diversity between the vaccine and placebo group (P < 0.1). This greater epitope diversity was neither due to any difference in infection duration nor overall nef gene diversity between the two groups, suggesting that the increase in viral escape was likely mediated by vaccine-induced T-cell responses. CONCLUSION Viral escape in Nef is elevated preferentially in STEP vaccine-treated individuals, suggesting that vaccination primarily modulated initial CTL responses. Our observations provide important insights into improving vaccine-primed first immune control.
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