Abstract

Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and network inferences, drug resistant mutations (DRMs), subtypes and HIV-1 diversity estimations were completed. Haplotypes were reconstructed to infer transmission clusters. Phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared. Higher HIV-1 diversity (n.s.) was seen in men who have sex with men, heterosexual, and male participants in DC. 54.0% of the participants contained at least one DRM. The 40–49 year-olds showed the highest prevalence of DRMs (22.9%). Phylogenetic analysis of pol and env sequences grouped 31.9–33.8% of the participants into clusters. HIV-TRACE grouped 2.9–12.8% of participants when using consensus sequences and 9.0–64.2% when using haplotypes. NGS allowed us to characterize the local phylodynamics of HIV-1 in DC more broadly and accurately, given a better representation of its diversity and dynamics. Reconstructed haplotypes provided novel and deeper phylodynamic insights, which led to networks linking a higher number of participants. Our understanding of the HIV-1 epidemic was expanded with the powerful coupling of HIV-1 NGS data with epidemiological data.

Details

Title
A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing
Author
Gibson, Keylie M 1   VIAFID ORCID Logo  ; Kamwing, Jair 2 ; Castel, Amanda D 2 ; Bendall, Matthew L 1   VIAFID ORCID Logo  ; Wilbourn Brittany 2 ; Jordan, Jeanne A 2 ; Crandall, Keith A 3   VIAFID ORCID Logo  ; Pérez-Losada Marcos 4   VIAFID ORCID Logo  ; Subramanian Thilakavathy 5 ; Binkley, Jeffery 5 ; Taylor, Rob 5 ; Rayeed Nabil 5 ; Akridge, Cheryl 5 ; Purinton Stacey 5 ; Naughton, Jeff 5 ; Natella, Rakhmanina 6 ; D’Angelo Larry 7 ; Kharfen, Michael 8 ; Wood, Angela 9 ; Serlin, Michael 9 ; Kumar, Princy 10 ; Parenti, David 11 ; Greenberg, Alan 12 ; Monroe, Anne 12 ; Happ Lindsey Powers 12 ; Jaurretche, Maria 12 ; Peterson, James 12 ; Wilcox, Ronald D 13 ; Rana Sohail 14 ; Horberg, Michael A 15 ; Fernández, Ricardo 16 ; Hebou Annick 17 ; Dieffenbach, Carl 18 ; Masur, Henry 18 ; Bordon, Jose 19 ; Gebeyehu, Teferi 20 ; Benator, Debra 21 ; Ruiz, Maria Elena 22 ; Goldstein, Deborah 23 ; Hardy, David 23 

1  The George Washington University, Computational Biology Institute, The Milken Institute School of Public Health, Washington, USA (GRID:grid.253615.6) (ISNI:0000 0004 1936 9510) 
2  The George Washington University, Department of Epidemiology, The Milken Institute School of Public Health, Washington, USA (GRID:grid.253615.6) (ISNI:0000 0004 1936 9510) 
3  The George Washington University, Computational Biology Institute, The Milken Institute School of Public Health, Washington, USA (GRID:grid.253615.6) (ISNI:0000 0004 1936 9510); The George Washington University, Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, Washington, USA (GRID:grid.253615.6) (ISNI:0000 0004 1936 9510) 
4  The George Washington University, Computational Biology Institute, The Milken Institute School of Public Health, Washington, USA (GRID:grid.253615.6) (ISNI:0000 0004 1936 9510); The George Washington University, Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, Washington, USA (GRID:grid.253615.6) (ISNI:0000 0004 1936 9510); Universidade do Porto, Campus Agrário de Vairão, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal (GRID:grid.5808.5) (ISNI:0000 0001 1503 7226) 
5  Cerner Corporation, Arlington, USA (GRID:grid.418415.d) (ISNI:0000 0004 0507 1772) 
6  Children’s National Medical Center Pediatric Clinic, Washington, USA (GRID:grid.239560.b) (ISNI:0000 0004 0482 1586) 
7  Children’s National Medical Center Adolescent Clinic, Washington, USA (GRID:grid.239560.b) (ISNI:0000 0004 0482 1586) 
8  DC Department of Health HAHSTA, Washington, USA (GRID:grid.410330.5) (ISNI:0000 0004 0510 3826) 
9  Family and Medical Counseling Service, Washington, USA (GRID:grid.421315.0) 
10  Georgetown University, Washington, USA (GRID:grid.213910.8) (ISNI:0000 0001 1955 1644) 
11  George Washington Medical Faculty Associates, Washington, USA (GRID:grid.213910.8) 
12  The George Washington University, Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, Washington, USA (GRID:grid.253615.6) (ISNI:0000 0004 1936 9510) 
13  Howard University Hospital Adult Clinic, Washington, USA (GRID:grid.411399.7) (ISNI:0000 0004 0427 2775) 
14  Howard University Hospital Pediatric Clinic, Washington, USA (GRID:grid.411399.7) (ISNI:0000 0004 0427 2775) 
15  Kaiser Permanente, Rockville, USA (GRID:grid.280062.e) (ISNI:0000 0000 9957 7758) 
16  La Clinica Del Pueblo, Washington, USA (GRID:grid.420752.6) (ISNI:0000 0004 0396 1798) 
17  MetroHealth, Washington, USA (GRID:grid.430779.e) (ISNI:0000 0000 8614 884X) 
18  National Institutes of Health, Bethesda, USA (GRID:grid.94365.3d) (ISNI:0000 0001 2297 5165) 
19  Washington Health Institute, Washington, USA (GRID:grid.94365.3d) 
20  Unity Health Care, Washington, USA (GRID:grid.94365.3d) 
21  Veterans Affairs Medical Center, Washington, USA (GRID:grid.413721.2) (ISNI:0000 0004 0419 317X) 
22  Washington Hospital Center, Washington, USA (GRID:grid.415235.4) (ISNI:0000 0000 8585 5745) 
23  Whitman-Walker Health, Washington, USA (GRID:grid.429506.c) (ISNI:0000 0004 4670 6287) 
Publication year
2020
Publication date
2020
Publisher
Nature Publishing Group
e-ISSN
20452322
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41598-020-58410-y
ProQuest document ID
2352044408
Copyright
© The Author(s) 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.