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Tettamanti Boshier FA, Reeves DB, Duke ER, Swan DA, Prlic M, Cardozo-Ojeda EF, Schiffer JT. Substantial uneven proliferation of CD4 + T cells during recovery from acute HIV infection is sufficient to explain the observed expanded clones in the HIV reservoir. J Virus Erad 2022; 8:100091. [PMID: 36582473 PMCID: PMC9792356 DOI: 10.1016/j.jve.2022.100091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 09/08/2022] [Accepted: 10/10/2022] [Indexed: 12/03/2022] Open
Abstract
The HIV reservoir is a population of 1-10 million anatomically dispersed, latently infected memory CD4+ T cells in which HIV DNA is quiescently integrated into human chromosomal DNA. When antiretroviral therapy (ART) is stopped and HIV replication initiates in one of these cells, systemic viral spread resumes, rekindling progression to AIDS. Therefore, HIV latency prevents cure. The detection of many populations of identical HIV sequences at unique integration sites implicates CD4+ T cell proliferation as the critical driver of reservoir sustainment after a prolonged period of effective ART. Initial reservoir formation occurs during the first week of primary infection usually before ART is started. While empirical data indicates that both de novo infection and cellular proliferation generate latently infected cells during early untreated infection, it is not known which of these mechanisms is predominant. We developed a mathematical model that recapitulates the profound depletion and brisk recovery of CD4+ T cells, reservoir creation, and viral load trajectory during primary HIV infection. We extended the model to stochastically simulate individual HIV reservoir clones. This model predicts the first detection of HIV infected clones approximately 5 weeks after infection as has recently been shown in vivo and suggests that substantial, uneven proliferation among clones during the recovery from CD4+ lymphopenia is the most plausible explanation for the observed clonal reservoir distribution during the first year of infection.
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Affiliation(s)
- Florencia A. Tettamanti Boshier
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
| | - Daniel B. Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
| | - Elizabeth R. Duke
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
- Department of Medicine, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - David A. Swan
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
| | - Martin Prlic
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
- Department of Global Health, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - E. Fabian Cardozo-Ojeda
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
- Department of Medicine, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
- Clinical Research Division, University of Washington, 1959 NE Pacific St., Seattle, WA, USA
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Bracis C, Moore M, Swan DA, Matrajt L, Anderson L, Reeves DB, Burns E, Schiffer JT, Dimitrov D. Improving vaccination coverage and offering vaccine to all school-age children allowed uninterrupted in-person schooling in King County, WA: Modeling analysis. Math Biosci Eng 2022; 19:5699-5716. [PMID: 35603374 PMCID: PMC9553324 DOI: 10.3934/mbe.2022266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rapid spread of highly transmissible SARS-CoV-2 variants combined with slowing pace of vaccination in Fall 2021 created uncertainty around the future trajectory of the epidemic in King County, Washington, USA. We analyzed the benefits of offering vaccination to children ages 5-11 and expanding the overall vaccination coverage using mathematical modeling. We adapted a mathematical model of SARS-CoV-2 transmission, calibrated to data from King County, Washington, to simulate scenarios of vaccinating children aged 5-11 with different starting dates and different proportions of physical interactions (PPI) in schools being restored. Dynamic social distancing was implemented in response to changes in weekly hospitalizations. Reduction of hospitalizations and estimated time under additional social distancing measures are reported over the 2021-2022 school year. In the scenario with 85% vaccination coverage of 12+ year-olds, offering early vaccination to children aged 5-11 with 75% PPI was predicted to prevent 756 (median, IQR 301-1434) hospitalizations cutting youth hospitalizations in half compared to no vaccination and largely reducing the need for additional social distancing measures over the school year. If, in addition, 90% overall vaccination coverage was reached, 60% of remaining hospitalizations would be averted and the need for increased social distancing would almost certainly be avoided. Our work suggests that uninterrupted in-person schooling in King County was partly possible because reasonable precaution measures were taken at schools to reduce infectious contacts. Rapid vaccination of all school-aged children provides meaningful reduction of the COVID-19 health burden over this school year but only if implemented early. It remains critical to vaccinate as many people as possible to limit the morbidity and mortality associated with future epidemic waves.
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Affiliation(s)
- Chloe Bracis
- Université Grenoble Alpes, TIMC-IMAG/MAGE, Grenoble 38000, France
| | - Mia Moore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David A. Swan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laura Matrajt
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Larissa Anderson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel B. Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dobromir Dimitrov
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
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3
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Swan DA, Goyal A, Bracis C, Moore M, Krantz E, Brown E, Cardozo-Ojeda F, Reeves DB, Gao F, Gilbert PB, Corey L, Cohen MS, Janes H, Dimitrov D, Schiffer JT. Mathematical Modeling of Vaccines That Prevent SARS-CoV-2 Transmission. Viruses 2021; 13:1921. [PMID: 34696352 PMCID: PMC8539635 DOI: 10.3390/v13101921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/01/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 vaccine clinical trials assess efficacy against disease (VEDIS), the ability to block symptomatic COVID-19. They only partially discriminate whether VEDIS is mediated by preventing infection completely, which is defined as detection of virus in the airways (VESUSC), or by preventing symptoms despite infection (VESYMP). Vaccine efficacy against transmissibility given infection (VEINF), the decrease in secondary transmissions from infected vaccine recipients, is also not measured. Using mathematical modeling of data from King County Washington, we demonstrate that if the Moderna (mRNA-1273QS) and Pfizer-BioNTech (BNT162b2) vaccines, which demonstrated VEDIS > 90% in clinical trials, mediate VEDIS by VESUSC, then a limited fourth epidemic wave of infections with the highly infectious B.1.1.7 variant would have been predicted in spring 2021 assuming rapid vaccine roll out. If high VEDIS is explained by VESYMP, then high VEINF would have also been necessary to limit the extent of this fourth wave. Vaccines which completely protect against infection or secondary transmission also substantially lower the number of people who must be vaccinated before the herd immunity threshold is reached. The limited extent of the fourth wave suggests that the vaccines have either high VESUSC or both high VESYMP and high VEINF against B.1.1.7. Finally, using a separate intra-host mathematical model of viral kinetics, we demonstrate that a 0.6 log vaccine-mediated reduction in average peak viral load might be sufficient to achieve 50% VEINF, which suggests that human challenge studies with a relatively low number of infected participants could be employed to estimate all three vaccine efficacy metrics.
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Affiliation(s)
- David A. Swan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
| | - Ashish Goyal
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
| | - Chloe Bracis
- TIMC-IMAG/BCM, Université Grenoble Alpes, 38000 Grenoble, France;
| | - Mia Moore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
| | - Elizabeth Krantz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
| | - Elizabeth Brown
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Fabian Cardozo-Ojeda
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
| | - Daniel B. Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
| | - Fei Gao
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Myron S. Cohen
- Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Dobromir Dimitrov
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
- Department of Applied Mathematics, University of Washington, Seattle, WA 98195, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (D.A.S.); (A.G.); (M.M.); (E.K.); (E.B.); (F.C.-O.); (D.B.R.); (F.G.); (P.B.G.); (L.C.); (H.J.); (D.D.)
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Swan DA, Bracis C, Janes H, Moore M, Matrajt L, Reeves DB, Burns E, Donnell D, Cohen MS, Schiffer JT, Dimitrov D. COVID-19 vaccines that reduce symptoms but do not block infection need higher coverage and faster rollout to achieve population impact. Sci Rep 2021; 11:15531. [PMID: 34330945 PMCID: PMC8324774 DOI: 10.1038/s41598-021-94719-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/08/2021] [Indexed: 01/11/2023] Open
Abstract
Trial results for two COVID-19 vaccines suggest at least 90% efficacy against symptomatic disease (VEDIS). It remains unknown whether this efficacy is mediated by lowering SARS-CoV-2 infection susceptibility (VESUSC) or development of symptoms after infection (VESYMP). We aim to assess and compare the population impact of vaccines with different efficacy profiles (VESYMP and VESUSC) satisfying licensure criteria. We developed a mathematical model of SARS-CoV-2 transmission, calibrated to data from King County, Washington. Rollout scenarios starting December 2020 were simulated with combinations of VESUSC and VESYMP resulting in up to 100% VEDIS. We assumed no reduction of infectivity upon infection conditional on presence of symptoms. Proportions of cumulative infections, hospitalizations and deaths prevented over 1 year from vaccination start are reported. Rollouts of 1 M vaccinations (5000 daily) using vaccines with 50% VEDIS are projected to prevent 23-46% of infections and 31-46% of deaths over 1 year. In comparison, vaccines with 90% VEDIS are projected to prevent 37-64% of infections and 46-64% of deaths over 1 year. In both cases, there is a greater reduction if VEDIS is mediated mostly by VESUSC. The use of a "symptom reducing" vaccine will require twice as many people vaccinated than a "susceptibility reducing" vaccine with the same 90% VEDIS to prevent 50% of the infections and death over 1 year. Delaying the start of the vaccination by 3 months decreases the expected population impact by more than 50%. Vaccines which prevent COVID-19 disease but not SARS-CoV-2 infection, and thereby shift symptomatic infections to asymptomatic infections, will prevent fewer infections and require larger and faster vaccination rollouts to have population impact, compared to vaccines that reduce susceptibility to infection. If uncontrolled transmission across the U.S. continues, then expected vaccination in Spring 2021 will provide only limited benefit.
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Affiliation(s)
- David A Swan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M2-C200, P.O. Box 19024, Seattle, WA, 98109-1024, USA
| | - Chloe Bracis
- Université Grenoble Alpes, TIMC-IMAG/BCM, 38000, Grenoble, France
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M2-C200, P.O. Box 19024, Seattle, WA, 98109-1024, USA
| | - Mia Moore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M2-C200, P.O. Box 19024, Seattle, WA, 98109-1024, USA
| | - Laura Matrajt
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M2-C200, P.O. Box 19024, Seattle, WA, 98109-1024, USA
| | - Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M2-C200, P.O. Box 19024, Seattle, WA, 98109-1024, USA
| | | | - Deborah Donnell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M2-C200, P.O. Box 19024, Seattle, WA, 98109-1024, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Myron S Cohen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M2-C200, P.O. Box 19024, Seattle, WA, 98109-1024, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dobromir Dimitrov
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M2-C200, P.O. Box 19024, Seattle, WA, 98109-1024, USA.
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
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5
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Matrajt L, Eaton J, Leung T, Dimitrov D, Schiffer JT, Swan DA, Janes H. Optimizing vaccine allocation for COVID-19 vaccines shows the potential role of single-dose vaccination. Nat Commun 2021; 12:3449. [PMID: 34103510 PMCID: PMC8187351 DOI: 10.1038/s41467-021-23761-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/13/2021] [Indexed: 01/17/2023] Open
Abstract
Most COVID-19 vaccines require two doses, however with limited vaccine supply, policymakers are considering single-dose vaccination as an alternative strategy. Using a mathematical model combined with optimization algorithms, we determined optimal allocation strategies with one and two doses of vaccine under various degrees of viral transmission. Under low transmission, we show that the optimal allocation of vaccine vitally depends on the single-dose efficacy. With high single-dose efficacy, single-dose vaccination is optimal, preventing up to 22% more deaths than a strategy prioritizing two-dose vaccination for older adults. With low or moderate single-dose efficacy, mixed vaccination campaigns with complete coverage of older adults are optimal. However, with modest or high transmission, vaccinating older adults first with two doses is best, preventing up to 41% more deaths than a single-dose vaccination given across all adult populations. Our work suggests that it is imperative to determine the efficacy and durability of single-dose vaccines, as mixed or single-dose vaccination campaigns may have the potential to contain the pandemic much more quickly.
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Affiliation(s)
- Laura Matrajt
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Julia Eaton
- School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA, USA
| | - Tiffany Leung
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dobromir Dimitrov
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David A Swan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Matrajt L, Eaton J, Leung T, Dimitrov D, Schiffer JT, Swan DA, Janes H. Optimizing vaccine allocation for COVID-19 vaccines: potential role of single-dose vaccination. medRxiv 2021:2020.12.31.20249099. [PMID: 33469590 PMCID: PMC7814836 DOI: 10.1101/2020.12.31.20249099] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Most COVID-19 vaccines require two doses, however with limited vaccine supply, policymakers are considering single-dose vaccination as an alternative strategy. Using a mathematical model combined with optimization algorithms, we determined optimal allocation strategies with one and two doses of vaccine under various degrees of viral transmission. Under low transmission, we show that the optimal allocation of vaccine vitally depends on the single-dose efficacy (SDE). With high SDE, single-dose vaccination is optimal, preventing up to 22% more deaths than a strategy prioritizing two-dose vaccination for older adults. With low or moderate SDE, mixed vaccination campaigns with complete coverage of older adults are optimal. However, with modest or high transmission, vaccinating older adults first with two doses is best, preventing up to 41% more deaths than a single-dose vaccination given across all adult populations. Our work suggests that it is imperative to determine the efficacy and durability of single-dose vaccines, as mixed or single-dose vaccination campaigns may have the potential to contain the pandemic much more quickly.
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Affiliation(s)
- Laura Matrajt
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Julia Eaton
- School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, USA
| | - Tiffany Leung
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dobromir Dimitrov
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - David A. Swan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Roychoudhury P, Swan DA, Duke E, Corey L, Zhu J, Davé V, Spuhler LR, Lund JM, Prlic M, Schiffer JT. Tissue-resident T cell-derived cytokines eliminate herpes simplex virus-2-infected cells. J Clin Invest 2020; 130:2903-2919. [PMID: 32125285 PMCID: PMC7260013 DOI: 10.1172/jci132583] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/11/2020] [Indexed: 01/19/2023] Open
Abstract
The mechanisms underlying rapid elimination of herpes simplex virus-2 (HSV-2) in the human genital tract despite low CD8+ and CD4+ tissue-resident T cell (Trm cell) density are unknown. We analyzed shedding episodes during chronic HSV-2 infection; viral clearance always predominated within 24 hours of detection even when viral load exceeded 1 × 107 HSV DNA copies, and surges in granzyme B and IFN-γ occurred within the early hours after reactivation and correlated with local viral load. We next developed an agent-based mathematical model of an HSV-2 genital ulcer to integrate mechanistic observations of Trm cells in in situ proliferation, trafficking, cytolytic effects, and cytokine alarm signaling from murine studies with viral kinetics, histopathology, and lesion size data from humans. A sufficiently high density of HSV-2-specific Trm cells predicted rapid elimination of infected cells, but our data suggest that such Trm cell densities are relatively uncommon in infected tissues. At lower, more commonly observed Trm cell densities, Trm cells must initiate a rapidly diffusing, polyfunctional cytokine response with activation of bystander T cells in order to eliminate a majority of infected cells and eradicate briskly spreading HSV-2 infection.
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Affiliation(s)
- Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and
| | - David A. Swan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Elizabeth Duke
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jia Zhu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and
| | - Veronica Davé
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Global Health and
| | - Laura Richert Spuhler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jennifer M. Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Global Health and
| | - Martin Prlic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Global Health and
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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8
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Reeves DB, Huang Y, Duke ER, Mayer BT, Cardozo-Ojeda EF, Boshier FA, Swan DA, Rolland M, Robb ML, Mascola JR, Cohen MS, Corey L, Gilbert PB, Schiffer JT. Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials. PLoS Comput Biol 2020; 16:e1007626. [PMID: 32084132 PMCID: PMC7055956 DOI: 10.1371/journal.pcbi.1007626] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 03/04/2020] [Accepted: 12/22/2019] [Indexed: 12/19/2022] Open
Abstract
The ongoing Antibody Mediated Prevention (AMP) trials will uncover whether passive infusion of the broadly neutralizing antibody (bNAb) VRC01 can protect against HIV acquisition. Previous statistical simulations indicate these trials may be partially protective. In that case, it will be crucial to identify the mechanism of breakthrough infections. To that end, we developed a mathematical modeling framework to simulate the AMP trials and infer the breakthrough mechanisms using measurable trial outcomes. This framework combines viral dynamics with antibody pharmacokinetics and pharmacodynamics, and will be generally applicable to forthcoming bNAb prevention trials. We fit our model to human viral load data (RV217). Then, we incorporated VRC01 neutralization using serum pharmacokinetics (HVTN 104) and in vitro pharmacodynamics (LANL CATNAP database). We systematically explored trial outcomes by reducing in vivo potency and varying the distribution of sensitivity to VRC01 in circulating strains. We found trial outcomes could be used in a clinical trial regression model (CTRM) to reveal whether partially protective trials were caused by large fractions of VRC01-resistant (IC50>50 μg/mL) circulating strains or rather a global reduction in VRC01 potency against all strains. The former mechanism suggests the need to enhance neutralizing antibody breadth; the latter suggests the need to enhance VRC01 delivery and/or in vivo binding. We will apply the clinical trial regression model to data from the completed trials to help optimize future approaches for passive delivery of anti-HIV neutralizing antibodies. Infusions of broadly neutralizing antibodies are currently being tested as a novel HIV prevention modality. To help interpret the results of these antibody mediated prevention (AMP) studies we developed a mathematical modeling framework. The approach combines antibody potency and drug levels with models of HIV viral dynamics, which will be generally applicable to future studies. Through simulating these clinical trials, we found trial outcomes can be used in combination to infer whether breakthrough infections are caused by large fractions of antibody-resistant circulating strains or some reduction in potency against all strains. This distinction helps to focus future trials on enhancing neutralizing antibody breadth or antibody delivery and/or in vivo binding.
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Affiliation(s)
- Daniel B. Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Yunda Huang
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Elizabeth R. Duke
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Bryan T. Mayer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - E. Fabian Cardozo-Ojeda
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Florencia A. Boshier
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David A. Swan
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD USA and Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Merlin L. Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD USA and Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Myron S. Cohen
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lawrence Corey
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Joshua T. Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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9
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Schiffer JT, Swan DA, Prlic M, Lund JM. Herpes simplex virus-2 dynamics as a probe to measure the extremely rapid and spatially localized tissue-resident T-cell response. Immunol Rev 2019; 285:113-133. [PMID: 30129205 DOI: 10.1111/imr.12672] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Herpes simplex virus-2 infection is characterized by frequent episodic shedding in the genital tract. Expansion in HSV-2 viral load early during episodes is extremely rapid. However, the virus invariably peaks within 18 hours and is eliminated nearly as quickly. A critical feature of HSV-2 shedding episodes is their heterogeneity. Some episodes peak at 108 HSV DNA copies, last for weeks due to frequent viral re-expansion, and lead to painful ulcers, while others only reach 103 HSV DNA copies and are eliminated within hours and without symptoms. Within single micro-environments of infection, tissue-resident CD8+ T cells (TRM ) appear to contain infection within a few days. Here, we review components of TRM biology relevant to immune surveillance between HSV-2 shedding episodes and containment of infection upon detection of HSV-2 cognate antigen. We then describe the use of mathematical models to correlate large spatial gradients in TRM density with the heterogeneity of observed shedding within a single person. We describe how models have been leveraged for clinical trial simulation, as well as future plans to model the interactions of multiple cellular subtypes within mucosa, predict the mechanism of action of therapeutic vaccines, and describe the dynamics of 3-dimensional infection environment during the natural evolution of an HSV-2 lesion.
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Affiliation(s)
- Joshua T Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - David A Swan
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Martin Prlic
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jennifer M Lund
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
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10
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Dimitrov D, Wood D, Ulrich A, Swan DA, Adamson B, Lama JR, Sanchez J, Duerr A. Projected effectiveness of HIV detection during early infection and rapid ART initiation among MSM and transgender women in Peru: A modeling study. Infect Dis Model 2019; 4:73-82. [PMID: 31025025 PMCID: PMC6475714 DOI: 10.1016/j.idm.2019.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 12/01/2022] Open
Abstract
Background The Sabes study, a treatment as prevention intervention in Peru, tested the hypothesis that initiating antiretroviral therapy (ART) early in HIV infection when viral load is high, would markedly reduce onward HIV transmission among high-risk men who have sex with men (MSM) and transgender women (TW). We investigated the potential population-level benefits of detection of HIV early after acquisition and rapid initiation of ART. Methods We designed a transmission dynamic model to simulate the HIV epidemic among MSM and TW in Peru, calibrated to data on HIV prevalence and ART coverage from 2004 to 2011. We assessed the impact of an intervention starting in 2018 in which up to 50% of the new infections were diagnosed within three months of acquisition and initiated on ART within 1 month of diagnosis. We estimated the impact of the intervention over 20 years using the cumulative prevented fraction of new HIV infections compared to scenarios without intervention. Findings Our model suggests that only 19% of the infected MSM and TW are virally suppressed in 2018 and 35%-40% of the new HIV infections are transmitted from contacts with acutely-infected partners. An intervention reaching 10% of all acutely infected MSM and TW is projected to prevent 13.3% [Uncertainty interval: 11.9%-14.3%] of the new infections over 20 years and reduce HIV incidence in 2038 by 24%. Reaching 50% of all acutely infected MSM and TW will increase the prevalence of viral suppression in 2038 to 59% and prevent 41% of expected infections over 20 years. Reaching 50% of the high-risk MSM and TW in acute phase would reduce HIV incidence in 2038 by 60% and prevent 36% of new infections between 2018 and 2038. Conclusions Early detection of HIV infections and rapid initiation of ART among MSM is desirable as it would increase the effectiveness of the HIV prevention program in Peru. Targeting high-risk MSM and TW will be highly efficient.
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Affiliation(s)
- Dobromir Dimitrov
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel Wood
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Angela Ulrich
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
| | - David A Swan
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Blythe Adamson
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Comparative Health Outcomes, Policy, & Economics (CHOICE) Institute, University of Washington, Seattle, WA, USA
| | - Javier R Lama
- Asociación Civil Impacta Salud y Educación, Lima, Peru
| | - Jorge Sanchez
- Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Universidad Mayor de San Marcos, Lima, Peru
| | - Ann Duerr
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
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11
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Schiffer JT, Swan DA, Magaret A, Corey L, Wald A, Ossig J, Ruebsamen-Schaeff H, Stoelben S, Timmler B, Zimmermann H, Melhem MR, Van Wart SA, Rubino CM, Birkmann A. Mathematical modeling of herpes simplex virus-2 suppression with pritelivir predicts trial outcomes. Sci Transl Med 2016; 8:324ra15. [PMID: 26843190 DOI: 10.1126/scitranslmed.aad6654] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pharmacokinetic and pharmacodynamic models estimate the potency of antiviral agents but do not capture viral and immunologic factors that drive the natural dynamics of infection. We designed a mathematical model that synthesizes pharmacokinetics, pharmacodynamics, and viral pathogenesis concepts to simulate the activity of pritelivir, a DNA helicase-primase inhibitor that targets herpes simplex virus. Our simulations recapitulate detailed viral kinetic shedding features in five dosage arms of a phase 2 clinical trial. We identify that in vitro estimates of median effective concentration (EC50) are lower than in vivo values for the drug. Nevertheless, pritelivir potently decreases shedding at appropriate doses based on its mode of action and long half-life. Although pritelivir directly inhibits replication in epithelial cells, our model indicates that pritelivir also indirectly limits downstream viral spread from neurons to genital keratinocytes, within genital ulcers, and from ulcer to new mucosal sites of infection. We validate our model based on its ability to predict outcomes in a subsequent trial with a higher dose. The model can therefore be used to optimize dose selection in clinical practice.
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Affiliation(s)
- Joshua T Schiffer
- Department of Medicine, University of Washington, Seattle, WA 98105, USA. Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - David A Swan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Amalia Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Department of Laboratory Medicine, University of Washington, Seattle, WA 98105, USA
| | - Lawrence Corey
- Department of Medicine, University of Washington, Seattle, WA 98105, USA. Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Department of Laboratory Medicine, University of Washington, Seattle, WA 98105, USA
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, WA 98105, USA. Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Department of Laboratory Medicine, University of Washington, Seattle, WA 98105, USA. Department of Epidemiology, University of Washington, Seattle, WA 98105, USA
| | | | | | | | | | | | - Murad R Melhem
- Institute for Clinical Pharmacodynamics, Latham, NY 12307, USA
| | - Scott A Van Wart
- Institute for Clinical Pharmacodynamics, Latham, NY 12307, USA. School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Christopher M Rubino
- Institute for Clinical Pharmacodynamics, Latham, NY 12307, USA. School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
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12
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Schiffer JT, Swan DA, Magaret A, Wald A. O17.5 Increased herpes simplex virus-2 shedding in hiv-1 infected persons is due to poor immunologic control in both ganglia and genital mucosa. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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13
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Schiffer JT, Mayer BT, Fong Y, Swan DA, Wald A. Herpes simplex virus-2 transmission probability estimates based on quantity of viral shedding. J R Soc Interface 2014; 11:20140160. [PMID: 24671939 DOI: 10.1098/rsif.2014.0160] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Herpes simplex virus (HSV)-2 is periodically shed in the human genital tract, most often asymptomatically, and most sexual transmissions occur during asymptomatic shedding. It would be helpful to identify a genital viral load threshold necessary for transmission, as clinical interventions that maintain viral quantity below this level would be of high utility. However, because viral expansion, decay and re-expansion kinetics are extremely rapid during shedding episodes, it is impossible to directly measure genital viral load at the time of sexual activity. We developed a mathematical model based on reproducing shedding patterns in transmitting partners, and median number of sex acts prior to transmission in discordant couples, to estimate infectivity of single viral particles in the negative partner's genital tract. We then inferred probability estimates for transmission at different levels of genital tract viral load in the transmitting partner. We predict that transmission is unlikely at viral loads less than 10(4) HSV DNA copies. Moreover, most transmissions occur during prolonged episodes with high viral copy numbers. Many shedding episodes that result in transmission do not reach the threshold of clinical detection, because the ulcer remains very small, highlighting one reason why HSV-2 spreads so effectively within populations.
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Affiliation(s)
- Joshua T Schiffer
- Department of Medicine, University of Washington, , Seattle, WA, USA
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14
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Kunwar P, Hawkins N, Dinges WL, Liu Y, Gabriel EE, Swan DA, Stevens CE, Maenza J, Collier AC, Mullins JI, Hertz T, Yu X, Horton H. Superior control of HIV-1 replication by CD8+ T cells targeting conserved epitopes: implications for HIV vaccine design. PLoS One 2013; 8:e64405. [PMID: 23741326 PMCID: PMC3669284 DOI: 10.1371/journal.pone.0064405] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/12/2013] [Indexed: 12/21/2022] Open
Abstract
A successful HIV vaccine will likely induce both humoral and cell-mediated immunity, however, the enormous diversity of HIV has hampered the development of a vaccine that effectively elicits both arms of the adaptive immune response. To tackle the problem of viral diversity, T cell-based vaccine approaches have focused on two main strategies (i) increasing the breadth of vaccine-induced responses or (ii) increasing vaccine-induced responses targeting only conserved regions of the virus. The relative extent to which set-point viremia is impacted by epitope-conservation of CD8+ T cell responses elicited during early HIV-infection is unknown but has important implications for vaccine design. To address this question, we comprehensively mapped HIV-1 CD8+ T cell epitope-specificities in 23 ART-naïve individuals during early infection and computed their conservation score (CS) by three different methods (prevalence, entropy and conseq) on clade-B and group-M sequence alignments. The majority of CD8+ T cell responses were directed against variable epitopes (p<0.01). Interestingly, increasing breadth of CD8+ T cell responses specifically recognizing conserved epitopes was associated with lower set-point viremia (r = - 0.65, p = 0.009). Moreover, subjects possessing CD8+ T cells recognizing at least one conserved epitope had 1.4 log10 lower set-point viremia compared to those recognizing only variable epitopes (p = 0.021). The association between viral control and the breadth of conserved CD8+ T cell responses may be influenced by the method of CS definition and sequences used to determine conservation levels. Strikingly, targeting variable versus conserved epitopes was independent of HLA type (p = 0.215). The associations with viral control were independent of functional avidity of CD8+ T cell responses elicited during early infection. Taken together, these data suggest that the next-generation of T-cell based HIV-1 vaccines should focus on strategies that can elicit CD8+ T cell responses to multiple conserved epitopes of HIV-1.
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Affiliation(s)
- Pratima Kunwar
- Viral Vaccine Program, Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Natalie Hawkins
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Warren L. Dinges
- Viral Vaccine Program, Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Polyclinic Infectious Disease, Seattle, Washington, United States of America
| | - Yi Liu
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Erin E. Gabriel
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David A. Swan
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Claire E. Stevens
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Janine Maenza
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Ann C. Collier
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - James I. Mullins
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Tomer Hertz
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Xuesong Yu
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Helen Horton
- Viral Vaccine Program, Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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Abstract
OBJECTIVE To describe a case of acute, fatal molybdenum poisoning in feedlot cattle. DESCRIPTION OF THE HERD: In total, 831 Hereford, Hereford x Angus, and Hereford x Simmental steers, aged 8 to 10 months, with an average body weight of 310 kg were fed a diet, to which sodium molybdate at a rate of 1.9% of the total ration had been accidently added. INVESTIGATION The steers lost appetite within 3 days and deaths commenced within 6 days of the diet being first offered. The error was rectified when deaths started to occur, but steers continued to die for up to 7 months afterwards. Of the 831 steers on the feedlot, 90 died and a further 5 remained in poor condition. The cause of death was periacinar to massive hepatic necrosis and acute renal tubular necrosis. Blood and tissue samples were taken from surviving steers for 76 days, by which time plasma molybdenum concentrations had returned to normal concentrations. CONCLUSION Sodium molybdate when fed at a rate of 1.9% of the diet results in acute renal tubular necrosis and periacinar to massive hepatic necrosis.
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Affiliation(s)
- D A Swan
- Swan's Veterinary Services, Esperance, Western Australia
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Penido JR, Swan DA. Disappearing intracardiac masses. J Thorac Cardiovasc Surg 1990; 99:943-5. [PMID: 2329835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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Belfort MA, Swan DA, Muñoz WP. Drainage of malignant ascites. S Afr Med J 1986; 70:65-6. [PMID: 3726694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Muñoz WP, Swan DA. Prophylactic antimicrobial agents. S Afr Med J 1986; 69:10. [PMID: 3941931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Krohn BG, Swan DA, Kay JH, Magidson O. Electrical impedance cardiogram. Measurements from hearts with acute injury. Am J Cardiol 1972. [DOI: 10.1016/0002-9149(72)90721-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Swan DA, Bell B, Oakley CM, Goodwin J. Analysis of symptomatic course and prognosis and treatment of hypertrophic obstructive cardiomyopathy. Br Heart J 1971; 33:671-85. [PMID: 5165532 PMCID: PMC487235 DOI: 10.1136/hrt.33.5.671] [Citation(s) in RCA: 132] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Abstract
The evolutionary persistence of the schizophrenia genes is discussed from the viewpoint that some beneficial attribute must be associated with the heterozygous or recessive condition to compensate for the dysgenic effects of the fully expressed disease in the homozygous schizophrenic patient. Previous hypotheses suggesting that superior creativity or greater resistance to physiological shock or stress are familial accompaniments of schizophrenia are briefly reviewed and rejected. An argument for an alternative hypothesis is offered which places the pro-survival characteristics of schizophrenia in the area of social relations and group behavior.
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