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Shipley MM, Renner DW, Ott M, Bloom DC, Koelle DM, Johnston C, Szpara ML. Genome-Wide Surveillance of Genital Herpes Simplex Virus Type 1 From Multiple Anatomic Sites Over Time. J Infect Dis 2018; 218:595-605. [PMID: 29920588 PMCID: PMC6047417 DOI: 10.1093/infdis/jiy216] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/26/2018] [Indexed: 12/12/2022] Open
Abstract
Here we present genomic and in vitro analyses of temporally separated episodes of herpes simplex virus type 1 (HSV-1) shedding by an HSV-1-seropositive and human immunodeficiency virus (HIV)/HSV-2-seronegative individual who has frequent recurrences of genital HSV-1. Using oligonucleotide enrichment, we compared viral genomes from uncultured swab specimens collected on different days and from distinct genital sites. We found that viral genomes from 7 swab specimens and 3 cultured specimens collected over a 4-month period from the same individual were 98.5% identical. We observed a >2-fold difference in the number of minority variants between swab specimens from lesions, swab specimens from nonlesion sites, and cultured specimens. This virus appeared distinct in its phylogenetic relationship to other strains, and it contained novel coding variations in 21 viral proteins. This included a truncation in the UL11 tegument protein, which is involved in viral egress and spread. Normal immune responses were identified, suggesting that unique viral genomic features may contribute to the recurrent genital infection that this participant experiences.
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Affiliation(s)
- Mackenzie M Shipley
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park
| | - Daniel W Renner
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park
| | - Mariliis Ott
- Department of Medicine, University of Washington, Seattle, Washington
| | - David C Bloom
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
- Department of Global Health, University of Washington, Seattle, Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Benaroya Research Institute, Seattle, Washington
| | - Christine Johnston
- Department of Medicine, University of Washington, Seattle, Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Moriah L Szpara
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park
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Moody MA, Gao F, Gurley TC, Amos JD, Kumar A, Hora B, Marshall DJ, Whitesides JF, Xia SM, Parks R, Lloyd KE, Hwang KK, Lu X, Bonsignori M, Finzi A, Vandergrift NA, Alam SM, Ferrari G, Shen X, Tomaras GD, Kamanga G, Cohen MS, Sam NE, Kapiga S, Gray ES, Tumba NL, Morris L, Zolla-Pazner S, Gorny MK, Mascola JR, Hahn BH, Shaw GM, Sodroski JG, Liao HX, Montefiori DC, Hraber PT, Korber BT, Haynes BF. Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses. Cell Host Microbe 2016; 18:354-62. [PMID: 26355218 DOI: 10.1016/j.chom.2015.08.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/14/2015] [Accepted: 08/14/2015] [Indexed: 11/19/2022]
Abstract
The third variable (V3) loop and the CD4 binding site (CD4bs) of the HIV-1 envelope are frequently targeted by neutralizing antibodies (nAbs) in infected individuals. In chronic infection, HIV-1 escape mutants repopulate the plasma, and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3 and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tier 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses.
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Affiliation(s)
- M Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA; Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
| | - Thaddeus C Gurley
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Joshua D Amos
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Amit Kumar
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Dawn J Marshall
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - John F Whitesides
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Krissey E Lloyd
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kwan-Ki Hwang
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM and Department of Microbiology, Infectology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada and Department of Microbiology and Immunology, McGill University, Montreal, QC H2X 1P1, Canada
| | - Nathan A Vandergrift
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Gift Kamanga
- University of North Carolina Project, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Myron S Cohen
- Departments of Medicine, Epidemiology, Microbiology, and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Noel E Sam
- Kilimanjaro Christian Medical Center, Moshi 25102, Tanzania
| | - Saidi Kapiga
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Elin S Gray
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Nancy L Tumba
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Lynn Morris
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Susan Zolla-Pazner
- Department of Pathology, New York University School of Medicine, New York, NY 10010, USA; Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA
| | - Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY 10010, USA
| | - John R Mascola
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Beatrice H Hahn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph G Sodroski
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - David C Montefiori
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Peter T Hraber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Bette T Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
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OuYang Y, Sun J, Huang Y, Lu L, Xu W, Hu X, Hong K, Jiang S, Shao Y, Ma L. Neutralization sensitivity of HIV-1 subtype B' clinical isolates from former plasma donors in China. Virol J 2013; 10:10. [PMID: 23289760 PMCID: PMC3599083 DOI: 10.1186/1743-422x-10-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 12/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HIV-1 subtype B' isolates have been predominantly circulating in China. Their intra- and inter-subtype neutralization sensitivity to autologous and heterologous plasmas has not been well studied. RESULTS Twelve HIV-1 B' clinical isolates obtained from patients were tested for their intra- and inter-subtype neutralization sensitivity to the neutralization antibodies in the plasmas from patients infected by HIV-1 B' and CRF07_BC subtypes, respectively. We found that the plasmas from the HIV-1 B'-infected patients could potently neutralize heterologous viruses of subtype B' with mean ID50 titer (1/x) of about 67, but they were not effective in neutralizing autologous viruses of subtype B' with mean ID50 titer (1/x) of about 8. The plasmas from HIV-1 CRF07_BC-infected patients exhibited weak inter-subtype neutralization activity against subtype B' viruses with ID50 titer (1/x) is about 22. The neutralization sensitivity of HIV-1 B' isolates was inversely correlated with the neutralizing activity of plasmas from HIV-1 B'-infected patients (Spearman's r = -0.657, P = 0.020), and with the number of potential N-glycosylation site (PNGS) in V1-V5 region (Spearman's r = -0.493, P = 0.034), but positively correlated with the viral load (Spearman's r = 0.629, P = 0.028). It had no correlation with the length of V1-V5 regions or the CD4+ T cell count. Virus AH259V has low intra-subtype neutralization sensitivity, it can be neutralized by 17b (IC50: 10μg/ml) and 447-52D (IC50: 1.6μg/ml), and the neutralizing antibodies (nAbs) in plasma AH259P are effective in neutralizing infection by the primary HIV-1 isolates with different subtypes with ID50 titers (1/x) in the range of 32-396. CONCLUSIONS These findings suggest that the HIV-1 subtype B' viruses may mutate under the immune pressure, thus becoming resistant to the autologous nAbs, possibly by changing the number of PNGS in the V1-V5 region of the viral gp120. Some of primary HIV-1 isolates are able to induce both intra- and inter-subtype cross-neutralizing antibody responses.
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Affiliation(s)
- Yabo OuYang
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
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