1
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Mariniello A, Nasti TH, Chang DY, Hashimoto M, Malik S, McManus DT, Lee J, McGuire DJ, Cardenas MA, Umana P, Nicolini V, Antia R, Saha A, Buchwald Z, Kissick H, Ghorani E, Novello S, Sangiolo D, Scagliotti GV, Ramalingam SS, Ahmed R. Platinum-Based Chemotherapy Attenuates the Effector Response of CD8 T Cells to Concomitant PD-1 Blockade. Clin Cancer Res 2024; 30:1833-1845. [PMID: 37992307 PMCID: PMC11061601 DOI: 10.1158/1078-0432.ccr-23-1316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/27/2023] [Accepted: 11/20/2023] [Indexed: 11/24/2023]
Abstract
PURPOSE Combination of chemotherapy with programmed cell death 1 (PD-1) blockade is a front-line treatment for lung cancer. However, it remains unknown whether and how chemotherapy affects the response of exhausted CD8 T cells to PD-1 blockade. EXPERIMENTAL DESIGN We used the well-established mouse model of T-cell exhaustion with chronic lymphocytic choriomeningitis virus (LCMV) infection to assess the effect of chemotherapy (cisplatin+pemetrexed) on T-cell response to PD-1 blockade, in the absence of the impact of chemotherapy on antigen release and presentation observed in tumor models. RESULTS When concomitantly administered with PD-1 blockade, chemotherapy affected the differentiation path of LCMV-specific CD8 T cells from stem-like to transitory effector cells, thereby reducing their expansion and production of IFNγ. After combination treatment, these restrained effector responses resulted in impaired viral control, compared with PD-1 blockade alone. The sequential combination strategy, where PD-1 blockade followed chemotherapy, proved to be superior to the concomitant combination, preserving the proliferative response of exhausted CD8 T cells to PD-1 blockade. Our findings suggest that the stem-like CD8 T cells themselves are relatively unaffected by chemotherapy partly because they are quiescent and maintained by slow self-renewal at the steady state. However, upon the proliferative burst mediated by PD-1 blockade, the accelerated differentiation and self-renewal of stem-like cells may be curbed by concomitant chemotherapy, ultimately resulting in impaired overall CD8 T-cell effector functions. CONCLUSIONS In a translational context, we provide a proof-of-concept to consider optimizing the timing of chemo-immunotherapy strategies for improved CD8 T-cell functions. See related commentary by Vignali and Luke, p. 1705.
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Affiliation(s)
- Annapaola Mariniello
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Department of Oncology, University of Torino, Turin, Italy
- Winship Cancer Institute, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Tahseen H. Nasti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
| | - Daniel Y. Chang
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
| | - Masao Hashimoto
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
| | - Sakshi Malik
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
| | - Daniel T. McManus
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
| | - Judong Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
| | - Donald J. McGuire
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
| | - Maria A. Cardenas
- Department of Urology, Emory University School of Medicine, Atlanta, Georgia
| | - Pablo Umana
- Roche Pharma Research and Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Valeria Nicolini
- Roche Pharma Research and Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia
| | - Ananya Saha
- Department of Biology, Emory University, Atlanta, Georgia
| | - Zachary Buchwald
- Winship Cancer Institute, Winship Cancer Institute of Emory University, Atlanta, Georgia
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia
| | - Hayden Kissick
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Winship Cancer Institute, Winship Cancer Institute of Emory University, Atlanta, Georgia
- Department of Urology, Emory University School of Medicine, Atlanta, Georgia
| | - Ehsan Ghorani
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Cancer Immunology and Immunotherapy Unit, Imperial College London, Department of Surgery and Cancer, London, United Kingdom
| | - Silvia Novello
- Department of Oncology, University of Torino, Turin, Italy
| | - Dario Sangiolo
- Department of Oncology, University of Torino, Turin, Italy
| | | | - Suresh S. Ramalingam
- Winship Cancer Institute, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Winship Cancer Institute, Winship Cancer Institute of Emory University, Atlanta, Georgia
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2
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Streicker DG, Griffiths ME, Antia R, Bergner L, Bowman P, de Moraes MVDS, Esvelt K, Famulare M, Gilbert A, He B, Jarvis MA, Kennedy DA, Kuzma J, Wanyonyi CN, Remien C, Rocke T, Rosenke K, Schreiner C, Sheen J, Simons D, Yordanova IA, Bull JJ, Nuismer SL. Developing transmissible vaccines for animal infections. Science 2024; 384:275-277. [PMID: 38669579 DOI: 10.1126/science.adn3231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Intrinsically safe designs and a staged transparent development process will be essential.
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Affiliation(s)
| | | | - Rustom Antia
- Author affiliations are listed in the supplementary materials
| | - Laura Bergner
- Author affiliations are listed in the supplementary materials
| | - Peter Bowman
- Author affiliations are listed in the supplementary materials
| | | | - Kevin Esvelt
- Author affiliations are listed in the supplementary materials
| | - Mike Famulare
- Author affiliations are listed in the supplementary materials
| | - Amy Gilbert
- Author affiliations are listed in the supplementary materials
| | - Biao He
- Author affiliations are listed in the supplementary materials
| | | | - David A Kennedy
- Author affiliations are listed in the supplementary materials
| | - Jennifer Kuzma
- Author affiliations are listed in the supplementary materials
| | | | | | - Tonie Rocke
- Author affiliations are listed in the supplementary materials
| | - Kyle Rosenke
- Author affiliations are listed in the supplementary materials
| | | | - Justin Sheen
- Author affiliations are listed in the supplementary materials
| | - David Simons
- Author affiliations are listed in the supplementary materials
| | | | - James J Bull
- Author affiliations are listed in the supplementary materials
| | - Scott L Nuismer
- Author affiliations are listed in the supplementary materials
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3
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Aggarwal C, Ahmed H, Sharma P, Reddy ES, Nayak K, Singla M, Maheshwari D, Chawla YM, Panda H, Rai RC, Gunisetty S, Priyamvada L, Bhaumik SK, Ahamed SF, Vivek R, Bhatnagar P, Singh P, Kaur M, Dixit K, Kumar S, Gottimukkala K, Saini K, Bajpai P, Sreekanth GP, Mammen S, Rajan A, Verghese VP, Abraham AM, Shah P, Alagarasu K, Yu T, Davis CW, Wrammert J, Ansari A, Antia R, Kabra SK, Medigeshi GR, Ahmed R, Lodha R, Shet A, Chandele A, Murali-Krishna K. Severe disease during both primary and secondary dengue virus infections in pediatric populations. Nat Med 2024; 30:670-674. [PMID: 38321219 DOI: 10.1038/s41591-024-02798-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/02/2024] [Indexed: 02/08/2024]
Abstract
Dengue is a global epidemic causing over 100 million cases annually. The clinical symptoms range from mild fever to severe hemorrhage and shock, including some fatalities. The current paradigm is that these severe dengue cases occur mostly during secondary infections due to antibody-dependent enhancement after infection with a different dengue virus serotype. India has the highest dengue burden worldwide, but little is known about disease severity and its association with primary and secondary dengue infections. To address this issue, we examined 619 children with febrile dengue-confirmed infection from three hospitals in different regions of India. We classified primary and secondary infections based on IgM:IgG ratios using a dengue-specific enzyme-linked immunosorbent assay according to the World Health Organization guidelines. We found that primary dengue infections accounted for more than half of total clinical cases (344 of 619), severe dengue cases (112 of 202) and fatalities (5 of 7). Consistent with the classification based on binding antibody data, dengue neutralizing antibody titers were also significantly lower in primary infections compared to secondary infections (P ≤ 0.0001). Our findings question the currently widely held belief that severe dengue is associated predominantly with secondary infections and emphasizes the importance of developing vaccines or treatments to protect dengue-naive populations.
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Affiliation(s)
- Charu Aggarwal
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Pragati Sharma
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Elluri Seetharami Reddy
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Kaustuv Nayak
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mohit Singla
- Division of Pediatric Pulmonology and Intensive Care, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Deepti Maheshwari
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Yadya M Chawla
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Harekrushna Panda
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ramesh Chandra Rai
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sivaram Gunisetty
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Lalita Priyamvada
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Siddhartha Kumar Bhaumik
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Syed Fazil Ahamed
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bengaluru, India
| | - Rosario Vivek
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bengaluru, India
- The University of Trans-Disciplinary Health Sciences & Technology, Bengaluru, India
| | - Priya Bhatnagar
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- TERI school of advanced studies, New Delhi, India
| | - Prabhat Singh
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Manpreet Kaur
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kritika Dixit
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sanjeev Kumar
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kamal Gottimukkala
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Keshav Saini
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Prashant Bajpai
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Gopinathan Pillai Sreekanth
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shobha Mammen
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - Anand Rajan
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - Valsan Philip Verghese
- Pediatric Infectious Diseases, Department of Pediatrics, Christian Medical College, Vellore, India
| | - Asha Mary Abraham
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - Paresh Shah
- Department of Molecular Virology, National Institute of Virology, Pune, India
| | - Kalichamy Alagarasu
- Department of Molecular Virology, National Institute of Virology, Pune, India
| | - Tianwei Yu
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Shenzhen Research Institute of Big Data, School of Data Science, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Carl W Davis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Aftab Ansari
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Sushil Kumar Kabra
- Division of Pediatric Pulmonology and Intensive Care, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Guruprasad R Medigeshi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Rakesh Lodha
- Division of Pediatric Pulmonology and Intensive Care, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India.
| | - Anita Shet
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bengaluru, India.
- International Vaccine Access Centre, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Anmol Chandele
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Kaja Murali-Krishna
- ICGEB Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
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4
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Uddbäck I, Michalets SE, Saha A, Mattingly C, Kost KN, Williams ME, Lawrence LA, Hicks SL, Lowen AC, Ahmed H, Thomsen AR, Russell CJ, Scharer CD, Boss JM, Koelle K, Antia R, Christensen JP, Kohlmeier JE. Prevention of respiratory virus transmission by resident memory CD8 + T cells. Nature 2024; 626:392-400. [PMID: 38086420 PMCID: PMC11040656 DOI: 10.1038/s41586-023-06937-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
An ideal vaccine both attenuates virus growth and disease in infected individuals and reduces the spread of infections in the population, thereby generating herd immunity. Although this strategy has proved successful by generating humoral immunity to measles, yellow fever and polio, many respiratory viruses evolve to evade pre-existing antibodies1. One approach for improving the breadth of antiviral immunity against escape variants is through the generation of memory T cells in the respiratory tract, which are positioned to respond rapidly to respiratory virus infections2-6. However, it is unknown whether memory T cells alone can effectively surveil the respiratory tract to the extent that they eliminate or greatly reduce viral transmission following exposure of an individual to infection. Here we use a mouse model of natural parainfluenza virus transmission to quantify the extent to which memory CD8+ T cells resident in the respiratory tract can provide herd immunity by reducing both the susceptibility of acquiring infection and the extent of transmission, even in the absence of virus-specific antibodies. We demonstrate that protection by resident memory CD8+ T cells requires the antiviral cytokine interferon-γ (IFNγ) and leads to altered transcriptional programming of epithelial cells within the respiratory tract. These results suggest that tissue-resident CD8+ T cells in the respiratory tract can have important roles in protecting the host against viral disease and limiting viral spread throughout the population.
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Affiliation(s)
- Ida Uddbäck
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Sarah E Michalets
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Ananya Saha
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Cameron Mattingly
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Kirsten N Kost
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - M Elliott Williams
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Laurel A Lawrence
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Allan R Thomsen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Charles J Russell
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Jan P Christensen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jacob E Kohlmeier
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
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5
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Elliott Williams M, Hardnett FP, Sheth AN, Wein AN, Li ZRT, Radzio-Basu J, Dinh C, Haddad LB, Collins EMB, Ofotokun I, Antia R, Scharer CD, Garcia-Lerma JG, Kohlmeier JE, Swaims-Kohlmeier A. The menstrual cycle regulates migratory CD4 T-cell surveillance in the female reproductive tract via CCR5 signaling. Mucosal Immunol 2024; 17:41-53. [PMID: 37866719 PMCID: PMC10990418 DOI: 10.1016/j.mucimm.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
Despite their importance for immunity against sexually transmitted infections, the composition of female reproductive tract (FRT) memory T-cell populations in response to changes within the local tissue environment under the regulation of the menstrual cycle remains poorly defined. Here, we show that in humans and pig-tailed macaques, the cycle determines distinct clusters of differentiation 4 T-cell surveillance behaviors by subsets corresponding to migratory memory (TMM) and resident memory T cells. TMM displays tissue-itinerant trafficking characteristics, restricted distribution within the FRT microenvironment, and distinct effector responses to infection. Gene pathway analysis by RNA sequencing identified TMM-specific enrichment of genes involved in hormonal regulation and inflammatory responses. FRT T-cell subset fluctuations were discovered that synchronized to cycle-driven CCR5 signaling. Notably, oral administration of a CCR5 antagonist drug blocked TMM trafficking. Taken together, this study provides novel insights into the dynamic nature of FRT memory CD4 T cells and identifies the menstrual cycle as a key regulator of immune surveillance at the site of STI pathogen exposure.
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Affiliation(s)
- M Elliott Williams
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Felica P Hardnett
- Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anandi N Sheth
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine and Grady Health System, Atlanta, GA, USA
| | - Alexander N Wein
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Zheng-Rong Tiger Li
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jessica Radzio-Basu
- Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chuong Dinh
- Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lisa B Haddad
- Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Elizabeth M B Collins
- Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Igho Ofotokun
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine and Grady Health System, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Christopher D Scharer
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - J Gerardo Garcia-Lerma
- Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jacob E Kohlmeier
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Alison Swaims-Kohlmeier
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA; Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA; Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA, USA.
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6
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Bull JJ, Nuismer SL, Remien CH, Griffiths ME, Antia R. Recombinant transmissible vaccines will be intrinsically contained despite the ability to superinfect. Expert Rev Vaccines 2024; 23:294-302. [PMID: 38372241 PMCID: PMC11003445 DOI: 10.1080/14760584.2024.2320845] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/19/2023] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
INTRODUCTION Transmissible vaccines offer a novel approach to suppressing viruses in wildlife populations, with possible applications against viruses that infect humans as zoonoses - Lassa, Ebola, rabies. To ensure safety, current designs propose a recombinant vector platform in which the vector is isolated from the target wildlife population. Because using an endemic vector creates the potential for preexisting immunity to block vaccine transmission, these designs focus on vector viruses capable of superinfection, spreading throughout the host population following vaccination of few individuals. AREAS COVERED We present original theoretical arguments that, regardless of its R0 value, a recombinant vaccine using a superinfecting vector is not expected to expand its active infection coverage when released into a wildlife population that already carries the vector. However, if superinfection occurs at a high rate such that individuals are repeatedly infected throughout their lives, the immunity footprint in the population can be high despite a low incidence of active vaccine infections. Yet we provide reasons that the above expectation is optimistic. EXPERT OPINION High vaccine coverage will typically require repeated releases or release into a population lacking the vector, but careful attention to vector choice and vaccine engineering should also help improve transmissible vaccine utility.
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Affiliation(s)
- James J Bull
- Department of Biological Sciences, U. Idaho, Moscow, ID 83844 USA
| | - Scott L Nuismer
- Department of Biological Sciences. University of Idaho. Moscow, ID 83844
- Department of Mathematics. University of Idaho. Moscow, ID 83844
| | | | - Megan E Griffiths
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia, 30322 USA
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7
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Nikas A, Ahmed H, Moore MR, Zarnitsyna VI, Antia R. When does humoral memory enhance infection? PLoS Comput Biol 2023; 19:e1011377. [PMID: 37603552 PMCID: PMC10470880 DOI: 10.1371/journal.pcbi.1011377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/31/2023] [Accepted: 07/20/2023] [Indexed: 08/23/2023] Open
Abstract
Antibodies and humoral memory are key components of the adaptive immune system. We consider and computationally model mechanisms by which humoral memory present at baseline might increase rather than decrease infection load; we refer to this effect as EI-HM (enhancement of infection by humoral memory). We first consider antibody dependent enhancement (ADE) in which antibody enhances the growth of the pathogen, typically a virus, and typically at intermediate 'Goldilocks' levels of antibody. Our ADE model reproduces ADE in vitro and enhancement of infection in vivo from passive antibody transfer. But notably the simplest implementation of our ADE model never results in EI-HM. Adding complexity, by making the cross-reactive antibody much less neutralizing than the de novo generated antibody or by including a sufficiently strong non-antibody immune response, allows for ADE-mediated EI-HM. We next consider the possibility that cross-reactive memory causes EI-HM by crowding out a possibly superior de novo immune response. We show that, even without ADE, EI-HM can occur when the cross-reactive response is both less potent and 'directly' (i.e. independently of infection load) suppressive with regard to the de novo response. In this case adding a non-antibody immune response to our computational model greatly reduces or completely eliminates EI-HM, which suggests that 'crowding out' is unlikely to cause substantial EI-HM. Hence, our results provide examples in which simple models give qualitatively opposite results compared to models with plausible complexity. Our results may be helpful in interpreting and reconciling disparate experimental findings, especially from dengue, and for vaccination.
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Affiliation(s)
- Ariel Nikas
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Mia R. Moore
- Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Veronika I. Zarnitsyna
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
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8
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Faliti CE, Anam FA, Cheedarla N, Woodruff MC, Usman SY, Runnstrom MC, Van TT, Kyu S, Ahmed H, Morrison-Porter A, Quehl H, Haddad NS, Chen W, Cheedarla S, Neish AS, Roback JD, Antia R, Khosroshahi A, Lee FEH, Sanz I. Poor immunogenicity upon SARS-CoV-2 mRNA vaccinations in autoimmune SLE patients is associated with pronounced EF-mediated responses and anti-BAFF/Belimumab treatment. medRxiv 2023:2023.06.08.23291159. [PMID: 37398319 PMCID: PMC10312827 DOI: 10.1101/2023.06.08.23291159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Novel mRNA vaccines have resulted in a reduced number of SARS-CoV-2 infections and hospitalizations. Yet, there is a paucity of studies regarding their effectiveness on immunocompromised autoimmune subjects. In this study, we enrolled subjects naïve to SARS-CoV-2 infections from two cohorts of healthy donors (HD, n=56) and systemic lupus erythematosus (SLE, n=69). Serological assessments of their circulating antibodies revealed a significant reduction of potency and breadth of neutralization in the SLE group, only partially rescued by a 3rd booster dose. Immunological memory responses in the SLE cohort were characterized by a reduced magnitude of spike-reactive B and T cell responses that were strongly associated with poor seroconversion. Vaccinated SLE subjects were defined by a distinct expansion and persistence of a DN2 spike-reactive memory B cell pool and a contraction of spike-specific memory cTfh cells, contrasting with the sustained germinal center (GC)-driven activity mediated by mRNA vaccination in the healthy population. Among the SLE-associated factors that dampened the vaccine responses, treatment with the monoclonal antibody anti-BAFF/Belimumab (a lupus FDA-approved B cell targeting agent) profoundly affected the vaccine responsiveness by restricting the de novo B cell responses and promoting stronger extra-follicular (EF)-mediated responses that were associated with poor immunogenicity and impaired immunological memory. In summary, this study interrogates antigen-specific responses and characterized the immune cell landscape associated with mRNA vaccination in SLE. The identification of factors associated with reduced vaccine efficacy illustrates the impact of SLE B cell biology on mRNA vaccine responses and provides guidance for the management of boosters and recall vaccinations in SLE patients according to their disease endotype and modality of treatment.
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Affiliation(s)
- Caterina E. Faliti
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Fabliha A. Anam
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Matthew C. Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Sabeena Y. Usman
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Martin C. Runnstrom
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Trinh T.P. Van
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Shuya Kyu
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Andrea Morrison-Porter
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hannah Quehl
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Natalie S. Haddad
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
- MicroB-plex, Atlanta, GA, USA
| | | | - Suneethamma Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Arezou Khosroshahi
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - F. Eun-Hyung Lee
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
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9
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Valanparambil RM, Carlisle J, Linderman SL, Akthar A, Millett RL, Lai L, Chang A, McCook-Veal AA, Switchenko J, Nasti TH, Saini M, Wieland A, Manning KE, Ellis M, Moore KM, Foster SL, Floyd K, Davis-Gardner ME, Edara VV, Patel M, Steur C, Nooka AK, Green F, Johns MA, O'Brein F, Shanmugasundaram U, Zarnitsyna VI, Ahmed H, Nyhoff LE, Mantus G, Garett M, Edupuganti S, Behra M, Antia R, Wrammert J, Suthar MS, Dhodapkar MV, Ramalingam S, Ahmed R. Antibody Response to COVID-19 mRNA Vaccine in Patients With Lung Cancer After Primary Immunization and Booster: Reactivity to the SARS-CoV-2 WT Virus and Omicron Variant. J Clin Oncol 2022; 40:3808-3816. [PMID: 35759727 PMCID: PMC9671759 DOI: 10.1200/jco.21.02986] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/15/2022] [Accepted: 04/27/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE To examine COVID-19 mRNA vaccine-induced binding and neutralizing antibody responses in patients with non-small-cell lung cancer (NSCLC) to SARS-CoV-2 614D (wild type [WT]) strain and variants of concern after the primary 2-dose and booster vaccination. METHODS Eighty-two patients with NSCLC and 53 healthy volunteers who received SARS-CoV-2 mRNA vaccines were included in the study. Blood was collected longitudinally, and SARS-CoV-2-specific binding and neutralizing antibody responses were evaluated by Meso Scale Discovery assay and live virus Focus Reduction Neutralization Assay, respectively. RESULTS A majority of patients with NSCLC generated binding and neutralizing antibody titers comparable with the healthy vaccinees after mRNA vaccination, but a subset of patients with NSCLC (25%) made poor responses, resulting in overall lower (six- to seven-fold) titers compared with the healthy cohort (P = < .0001). Although patients age > 70 years had lower immunoglobulin G titers (P = < .01), patients receiving programmed death-1 monotherapy, chemotherapy, or a combination of both did not have a significant impact on the antibody response. Neutralizing antibody titers to the B.1.617.2 (Delta), B.1.351 (Beta), and in particular, B.1.1.529 (Omicron) variants were significantly lower (P = < .0001) compared with the 614D (WT) strain. Booster vaccination led to a significant increase (P = .0001) in the binding and neutralizing antibody titers to the WT and Omicron variant. However, 2-4 months after the booster, we observed a five- to seven-fold decrease in neutralizing titers to WT and Omicron viruses. CONCLUSION A subset of patients with NSCLC responded poorly to the SARS-CoV-2 mRNA vaccination and had low neutralizing antibodies to the B.1.1.529 Omicron variant. Booster vaccination increased binding and neutralizing antibody titers to Omicron, but antibody titers declined after 3 months. These data highlight the concern for patients with cancer given the rapid spread of SARS-CoV-2 Omicron variant.
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Affiliation(s)
- Rajesh M. Valanparambil
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA
| | | | - Susanne L. Linderman
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA
| | - Akil Akthar
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA
| | | | - Lilin Lai
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Yerkes National Primate Center, Atlanta, GA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Andres Chang
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA
- Winship Cancer Institute, Atlanta, GA
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA
| | - Ashley A. McCook-Veal
- Biostatistics Shared Resource, Winship Cancer Institute, Emory University, Atlanta, GA
| | - Jeffrey Switchenko
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA
| | - Tahseen H. Nasti
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA
| | - Manpreet Saini
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Andreas Wieland
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA
- Department of Otolaryngology, The Ohio State University, Columbus, OH
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH
| | - Kelly E. Manning
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Yerkes National Primate Center, Atlanta, GA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Madison Ellis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Yerkes National Primate Center, Atlanta, GA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Kathryn M. Moore
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Yerkes National Primate Center, Atlanta, GA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Stephanie L. Foster
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Yerkes National Primate Center, Atlanta, GA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Katharine Floyd
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Yerkes National Primate Center, Atlanta, GA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Meredith E. Davis-Gardner
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Yerkes National Primate Center, Atlanta, GA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Venkata-Viswanadh Edara
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Yerkes National Primate Center, Atlanta, GA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Mit Patel
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Yerkes National Primate Center, Atlanta, GA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Conor Steur
- Winship Cancer Institute, Atlanta, GA
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA
| | - Ajay K. Nooka
- Winship Cancer Institute, Atlanta, GA
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA
| | | | | | | | - Uma Shanmugasundaram
- Winship Cancer Institute, Atlanta, GA
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA
| | - Veronika I. Zarnitsyna
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Biology, Emory University, Atlanta, GA
| | - Hasan Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Biology, Emory University, Atlanta, GA
| | - Lindsay E. Nyhoff
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Pediatrics, Emory University, Atlanta, GA
| | - Grace Mantus
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Pediatrics, Emory University, Atlanta, GA
| | - Michael Garett
- Department of Microbiology and Immunology, Emory University, Atlanta, GA
- Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
| | - Srilatha Edupuganti
- Department of Microbiology and Immunology, Emory University, Atlanta, GA
- Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
| | | | - Rustom Antia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Biology, Emory University, Atlanta, GA
| | - Jens Wrammert
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Pediatrics, Emory University, Atlanta, GA
| | - Mehul S. Suthar
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Yerkes National Primate Center, Atlanta, GA
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Madhav V. Dhodapkar
- Winship Cancer Institute, Atlanta, GA
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA
| | | | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA
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10
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Johnson PLF, Bergstrom CT, Regoes RR, Longini IM, Halloran ME, Antia R. Evolutionary consequences of delaying intervention for monkeypox. Lancet 2022; 400:1191-1193. [PMID: 36152668 PMCID: PMC9534010 DOI: 10.1016/s0140-6736(22)01789-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/05/2022] [Indexed: 01/06/2023]
Affiliation(s)
- Philip L F Johnson
- Department of Biology, University of Maryland, College Park, MA, 20742, USA.
| | - Carl T Bergstrom
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Roland R Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, WA, USA; Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
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11
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Desikan R, Linderman SL, Davis C, Zarnitsyna VI, Ahmed H, Antia R. Vaccine models predict rules for updating vaccines against evolving pathogens such as SARS-CoV-2 and influenza in the context of pre-existing immunity. Front Immunol 2022; 13:985478. [PMID: 36263031 PMCID: PMC9574365 DOI: 10.3389/fimmu.2022.985478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/03/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Currently, vaccines for SARS-CoV-2 and influenza viruses are updated if the new vaccine induces higher antibody-titers to circulating variants than current vaccines. This approach does not account for complex dynamics of how prior immunity skews recall responses to the updated vaccine. We: (i) use computational models to mechanistically dissect how prior immunity influences recall responses; (ii) explore how this affects the rules for evaluating and deploying updated vaccines; and (iii) apply this to SARS-CoV-2. Our analysis of existing data suggests that there is a strong benefit to updating the current SARS-CoV-2 vaccines to match the currently circulating variants. We propose a general two-dose strategy for determining if vaccines need updating as well as for vaccinating high-risk individuals. Finally, we directly validate our model by reanalysis of earlier human H5N1 influenza vaccine studies.
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Affiliation(s)
- Rajat Desikan
- Clinical Pharmacology Modeling & Simulation, GlaxoSmithKline (GSK), Stevenage, Hertfordshire, United Kingdom
- *Correspondence: Rajat Desikan, ; Rustom Antia,
| | - Susanne L. Linderman
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Carl Davis
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | | | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, United States
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, United States
- *Correspondence: Rajat Desikan, ; Rustom Antia,
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12
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Chang A, Akhtar A, Linderman SL, Lai L, Orellana-Noia VM, Valanparambil R, Ahmed H, Zarnitsyna VI, McCook-Veal AA, Switchenko JM, Koff JL, Blum KA, Ayers AA, O'Leary CB, Churnetski MC, Sulaiman S, Kives M, Sheng P, Davis CW, Nooka AK, Antia R, Dhodapkar MV, Suthar MS, Cohen JB, Ahmed R. Humoral Responses Against SARS-CoV-2 and Variants of Concern After mRNA Vaccines in Patients With Non-Hodgkin Lymphoma and Chronic Lymphocytic Leukemia. J Clin Oncol 2022; 40:3020-3031. [PMID: 35436146 PMCID: PMC9470134 DOI: 10.1200/jco.22.00088] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/22/2022] [Accepted: 03/25/2022] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Patients with non-Hodgkin lymphoma including chronic lymphocytic leukemia (NHL/CLL) are at higher risk of severe SARS-CoV-2 infection. We investigated vaccine-induced antibody responses in patients with NHL/CLL against the original SARS-CoV-2 strain and variants of concern including B.1.167.2 (Delta) and B.1.1.529 (Omicron). MATERIALS AND METHODS Blood from 121 patients with NHL/CLL receiving two doses of vaccine were collected longitudinally. Antibody binding against the full-length spike protein, the receptor-binding, and N-terminal domains of the original strain and of variants was measured using a multiplex assay. Live-virus neutralization against Delta, Omicron, and the early WA1/2020 strains was measured using a focus reduction neutralization test. B cells were measured by flow cytometry. Correlation between vaccine response and clinical factors was determined. RESULTS Mean anti-SARS-CoV-2 spike immunoglobulin G-binding titers were 85-fold lower in patients with NHL/CLL compared with healthy controls, with seroconversion occurring in only 67% of patients. Neutralization titers were also lower and correlated with binding titers (P < .0001). Treatment with anti-CD20-directed therapies within 1 year resulted in 136-fold lower binding titers. Peripheral blood B-cell count also correlated with vaccine response. At 3 months from last anti-CD20-directed therapy, B-cell count ≥ 4.31/μL blood around the time of vaccination predicted response (OR 7.46, P = .04). Antibody responses also correlated with age. Importantly, neutralization titers against Delta and Omicron were reduced six- and 42-fold, respectively, with 67% of patients seropositive for WA1/2020 exhibiting seronegativity for Omicron. CONCLUSION Antibody binding and live-virus neutralization against SARS-CoV-2 and its variants of concern including Delta and Omicron were substantially lower in patients with NHL/CLL compared with healthy vaccinees. Anti-CD20-directed therapy < 1 year before vaccination and number of circulating B cells strongly predict vaccine response.
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Affiliation(s)
- Andres Chang
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Akil Akhtar
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Susanne L. Linderman
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Lilin Lai
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
- Department of Pediatrics, Emory University Schools of Medicine, Atlanta, GA
- Yerkes National Primate Research Center, Atlanta, GA
| | - Victor M. Orellana-Noia
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Rajesh Valanparambil
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Hasan Ahmed
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
- Department of Biology, Emory University, Atlanta, GA
| | - Veronika I. Zarnitsyna
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
- Department of Biology, Emory University, Atlanta, GA
| | - Ashley A. McCook-Veal
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA
| | - Jeffrey M. Switchenko
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA
| | - Jean L. Koff
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Kristie A. Blum
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Amy A. Ayers
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Colin B. O'Leary
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Michael C. Churnetski
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Shahana Sulaiman
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Melissa Kives
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Preston Sheng
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Carl W. Davis
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Ajay K. Nooka
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Rustom Antia
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
- Department of Biology, Emory University, Atlanta, GA
| | - Madhav V. Dhodapkar
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Mehul S. Suthar
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
- Department of Pediatrics, Emory University Schools of Medicine, Atlanta, GA
| | - Jonathon B. Cohen
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Rafi Ahmed
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
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13
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Desikan R, Linderman SL, Davis C, Zarnitsyna V, Ahmed H, Antia R. Modeling suggests that multiple immunizations or infections will reveal the benefits of updating SARS-CoV-2 vaccines. bioRxiv 2022:2022.05.21.492928. [PMID: 35665010 PMCID: PMC9164442 DOI: 10.1101/2022.05.21.492928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
When should vaccines to evolving pathogens such as SARS-CoV-2 be updated? Our computational models address this focusing on updating SARS-CoV-2 vaccines to the currently circulating Omicron variant. Current studies typically compare the antibody titers to the new variant following a single dose of the original-vaccine versus the updated-vaccine in previously immunized individuals. These studies find that the updated-vaccine does not induce higher titers to the vaccine-variant compared with the original-vaccine, suggesting that updating may not be needed. Our models recapitulate this observation but suggest that vaccination with the updated-vaccine generates qualitatively different humoral immunity, a small fraction of which is specific for unique epitopes to the new variant. Our simulations suggest that these new variant-specific responses could dominate following subsequent vaccination or infection with either the currently circulating or future variants. We suggest a two-dose strategy for determining if the vaccine needs updating and for vaccinating high-risk individuals.
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Affiliation(s)
- Rajat Desikan
- Clinical Pharmacology Modeling & Simulation, GlaxoSmithKline (GSK), Gunnels Wood Rd, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
- These authors contributed equally
| | - Susanne L. Linderman
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Carl Davis
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Veronika Zarnitsyna
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- These authors contributed equally
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14
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Abstract
Background and objectives Theory suggests that some types of vaccines against infectious pathogens may lead to the evolution of variants that cause increased harm, particularly when they infect unvaccinated individuals. This theory was supported by the observation that the use of an imperfect vaccine to control Marek's disease virus in chickens resulted in the virus evolving to be more lethal to unvaccinated birds. This raises the concern that the use of some other vaccines may lead to similar pernicious outcomes. We examine that theory with a focus on considering the regimes in which such outcomes are expected. Methodology We evaluate the plausibility of assumptions in the original theory. The previous theory rested heavily on a particular form of transmission-mortality-recovery trade-off and invoked other assumptions about the pathways of evolution. We review alternatives to mortality in limiting transmission and consider evolutionary pathways that were omitted in the original theory. Results The regime where the pernicious evolutionary outcome occurs is narrowed by our analysis but remains possible in various scenarios. We propose a more nuanced consideration of alternative models for the within-host dynamics of infections and for factors that limit virulence. Our analysis suggests imperfect vaccines against many pathogens will not lead to the evolution of pathogens with increased virulence in unvaccinated individuals. Conclusions and implications Evolution of greater pathogen mortality driven by vaccination remains difficult to predict, but the scope for such outcomes appears limited. Incorporation of mechanistic details into the framework, especially regarding immunity, may be requisite for prediction accuracy. Lay Summary A virus of chickens appears to have evolved high mortality in response to a vaccine that merely prevented disease symptoms. Theory has predicted this type of evolution in response to a variety of vaccines and other interventions such as drug treatment. Under what circumstances is this pernicious result likely to occur? Analysis of the theory in light of recent changes in our understanding of viral biology raises doubts that medicine-driven, pernicious evolution is likely to be common. But we are far from a mechanistic understanding of the interaction between pathogen and host that can predict when vaccines and other medical interventions will lead to the unwanted evolution of more virulent pathogens. So, while the regime where a pernicious result obtains may be limited, caution remains warranted in designing many types of interventions.
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Affiliation(s)
- James J Bull
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA,Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA. E-mail:
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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15
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Abstract
We have come a long way since the start of the COVID-19 pandemic-from hoarding toilet paper and wiping down groceries to sending our children back to school and vaccinating billions. Over this period, the global community of epidemiologists and evolutionary biologists has also come a long way in understanding the complex and changing dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19. In this Review, we retrace our steps through the questions that this community faced as the pandemic unfolded. We focus on the key roles that mathematical modeling and quantitative analyses of empirical data have played in allowing us to address these questions and ultimately to better understand and control the pandemic.
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Affiliation(s)
- Katia Koelle
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, GA 30322, USA
| | - Michael A. Martin
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, GA 30322, USA
- Graduate Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA 30322, USA
| | - Rustom Antia
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, GA 30322, USA
| | - Ben Lopman
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Natalie E. Dean
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
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16
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Valanparambil R, Carlisle J, Linderman S, Akthar A, Millett RL, Lai L, Chang A, McCook A, Switchenko J, Nasti T, Saini M, Andreas Wieland AW, Manning K, Ellis M, Moore K, Foster S, Floyd K, Davis-Gardner M, Viswanadh Edara V, Patel M, Steur C, Nooka A, Green F, Johns M, O Brein F, Shanmugasundaram U, Zarnitsyna V, Ahmed H, Nyhoff L, Mantus G, Garett M, Edupuganti S, Behra M, Antia R, Wrammert J, Suthar M, Dhodapkar M, Ramalingam S, Ahmed R. Antibody response to SARS-CoV-2 mRNA vaccine in lung cancer patients: Reactivity to vaccine antigen and variants of concern. medRxiv 2022. [PMID: 35018383 DOI: 10.1101/2022.01.03.22268599] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
PURPOSE We investigated SARS-CoV-2 mRNA vaccine-induced binding and live-virus neutralizing antibody response in NSCLC patients to the SARS-CoV-2 wild type strain and the emerging Delta and Omicron variants. METHODS 82 NSCLC patients and 53 healthy adult volunteers who received SARS-CoV-2 mRNA vaccines were included in the study. Blood was collected longitudinally, and SARS-CoV-2-specific binding and live-virus neutralization response to 614D (WT), B.1.617.2 (Delta), B.1.351 (Beta) and B.1.1.529 (Omicron) variants were evaluated by Meso Scale Discovery (MSD) assay and Focus Reduction Neutralization Assay (FRNT) respectively. We determined the longevity and persistence of vaccine-induced antibody response in NSCLC patients. The effect of vaccine-type, age, gender, race and cancer therapy on the antibody response was evaluated. RESULTS Binding antibody titer to the mRNA vaccines were lower in the NSCLC patients compared to the healthy volunteers (P=<0.0001). More importantly, NSCLC patients had reduced live-virus neutralizing activity compared to the healthy vaccinees (P=<0.0001). Spike and RBD-specific binding IgG titers peaked after a week following the second vaccine dose and declined after six months (P=<0.001). While patients >70 years had lower IgG titers (P=<0.01), patients receiving either PD-1 monotherapy, chemotherapy or a combination of both did not have a significant impact on the antibody response. Binding antibody titers to the Delta and Beta variants were lower compared to the WT strain (P=<0.0001). Importantly, we observed significantly lower FRNT50 titers to Delta (6-fold), and Omicron (79-fold) variants (P=<0.0001) in NSCLC patients. CONCLUSIONS Binding and live-virus neutralizing antibody titers to SARS-CoV-2 mRNA vaccines in NSCLC patients were lower than the healthy vaccinees, with significantly lower live-virus neutralization of B.1.617.2 (Delta), and more importantly, the B.1.1.529 (Omicron) variant compared to the wild-type strain. These data highlight the concern for cancer patients given the rapid spread of SARS-CoV-2 Omicron variant.
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17
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Linderman SL, Ellebedy AH, Davis C, Eberhardt CS, Antia R, Ahmed R, Zarnitsyna VI. Influenza Immunization in the Context of Preexisting Immunity. Cold Spring Harb Perspect Med 2021; 11:a040964. [PMID: 32988981 PMCID: PMC8559541 DOI: 10.1101/cshperspect.a040964] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Although we develop influenza immunity from an early age, it is insufficient to prevent future infection with antigenically novel strains. One proposed way to generate long-term protective immunity against a broad range of influenza virus strains is to boost responses to the conserved epitopes on the hemagglutinin, the major surface glycoprotein on the influenza virus. Influenza-specific humoral immunity comprises a large fraction of the overall immune memory in humans, and it has been long recognized that preexisting immunity to influenza shapes the response to subsequent influenza infections and vaccinations. However, the mechanisms by which preexisting immunity modulates the response to influenza vaccination are still not completely understood. Using a set of mathematical models, we explore several hypotheses that may contribute to diminished boosting of antibodies to conserved epitopes after repeated vaccinations.
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Affiliation(s)
- Susanne L Linderman
- Emory Vaccine Center and Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, Georgia 30322, USA
| | - Ali H Ellebedy
- Emory Vaccine Center and Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, Georgia 30322, USA
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - Carl Davis
- Emory Vaccine Center and Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, Georgia 30322, USA
| | - Christiane S Eberhardt
- Emory Vaccine Center and Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, Georgia 30322, USA
- Centre for Vaccinology and Department of Pediatrics, University Hospitals of Geneva and Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Rafi Ahmed
- Emory Vaccine Center and Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, Georgia 30322, USA
| | - Veronika I Zarnitsyna
- Emory Vaccine Center and Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, Georgia 30322, USA
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18
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Zarnitsyna VI, Akondy RS, Ahmed H, McGuire DJ, Zarnitsyn VG, Moore M, Johnson PLF, Ahmed R, Li KW, Hellerstein MK, Antia R. Dynamics and turnover of memory CD8 T cell responses following yellow fever vaccination. PLoS Comput Biol 2021; 17:e1009468. [PMID: 34648489 PMCID: PMC8568194 DOI: 10.1371/journal.pcbi.1009468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/09/2020] [Revised: 11/04/2021] [Accepted: 09/21/2021] [Indexed: 11/18/2022] Open
Abstract
Understanding how immunological memory lasts a lifetime requires quantifying changes in the number of memory cells as well as how their division and death rates change over time. We address these questions by using a statistically powerful mixed-effects differential equations framework to analyze data from two human studies that follow CD8 T cell responses to the yellow fever vaccine (YFV-17D). Models were first fit to the frequency of YFV-specific memory CD8 T cells and deuterium enrichment in those cells 42 days to 1 year post-vaccination. A different dataset, on the loss of YFV-specific CD8 T cells over three decades, was used to assess out of sample predictions of our models. The commonly used exponential and bi-exponential decline models performed relatively poorly. Models with the cell loss following a power law (exactly or approximately) were most predictive. Notably, using only the first year of data, these models accurately predicted T cell frequencies up to 30 years post-vaccination. Our analyses suggest that division rates of these cells drop and plateau at a low level (0.1% per day, ∼ double the estimated values for naive T cells) within one year following vaccination, whereas death rates continue to decline for much longer. Our results show that power laws can be predictive for T cell memory, a finding that may be useful for vaccine evaluation and epidemiological modeling. Moreover, since power laws asymptotically decline more slowly than any exponential decline, our results help explain the longevity of immune memory phenomenologically. Immunological memory, generated in response to infection or vaccination, may provide complete or partial protection from antigenically similar infections for the lifetime. Memory CD8 T cells are important players in protection from secondary viral infections but quantitative understanding of their dynamics in humans is limited. We analyze data from two studies where immunization with the yellow fever virus vaccine (YFV-17D) generates a mild acute infection and long-term memory. We find that: (i) the division rate of YFV-17D-specific CD8 T cells drops and stabilizes at ∼ 0.1% per day during the first year following vaccination whereas the death rate declines more gradually, and (ii) the number of these cells declines approximately in accordance with a power law (∝ time−0.75) for at least several decades following vaccination.
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Affiliation(s)
- Veronika I. Zarnitsyna
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- * E-mail: (VIZ); (RAn)
| | - Rama S. Akondy
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana, India
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Donald J. McGuire
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
| | | | - Mia Moore
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Philip L. F. Johnson
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Kelvin W. Li
- Department of Nutritional Sciences and Toxicology, UC Berkeley, Berkeley, California, United States of America
| | - Marc K. Hellerstein
- Department of Nutritional Sciences and Toxicology, UC Berkeley, Berkeley, California, United States of America
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- * E-mail: (VIZ); (RAn)
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19
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Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its associated disease, coronavirus disease 2019 (COVID-19), has caused a devastating pandemic worldwide. Here, we explain basic concepts underlying the transition from an epidemic to an endemic state, where a pathogen is stably maintained in a population. We discuss how the number of infections and the severity of disease change in the transition from the epidemic to the endemic phase and consider the implications of this transition in the context of COVID-19.
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Affiliation(s)
| | - M Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA; University of Washington, Seattle, WA, USA
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20
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Cohen KW, Linderman SL, Moodie Z, Czartoski J, Lai L, Mantus G, Norwood C, Nyhoff LE, Edara VV, Floyd K, De Rosa SC, Ahmed H, Whaley R, Patel SN, Prigmore B, Lemos MP, Davis CW, Furth S, O’Keefe JB, Gharpure MP, Gunisetty S, Stephens K, Antia R, Zarnitsyna VI, Stephens DS, Edupuganti S, Rouphael N, Anderson EJ, Mehta AK, Wrammert J, Suthar MS, Ahmed R, McElrath MJ. Longitudinal analysis shows durable and broad immune memory after SARS-CoV-2 infection with persisting antibody responses and memory B and T cells. Cell Rep Med 2021; 2:100354. [PMID: 34250512 PMCID: PMC8253687 DOI: 10.1016/j.xcrm.2021.100354] [Citation(s) in RCA: 231] [Impact Index Per Article: 77.0] [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: 04/17/2021] [Revised: 05/27/2021] [Accepted: 06/24/2021] [Indexed: 01/10/2023]
Abstract
Ending the COVID-19 pandemic will require long-lived immunity to SARS-CoV-2. Here, we evaluate 254 COVID-19 patients longitudinally up to 8 months and find durable broad-based immune responses. SARS-CoV-2 spike binding and neutralizing antibodies exhibit a bi-phasic decay with an extended half-life of >200 days suggesting the generation of longer-lived plasma cells. SARS-CoV-2 infection also boosts antibody titers to SARS-CoV-1 and common betacoronaviruses. In addition, spike-specific IgG+ memory B cells persist, which bodes well for a rapid antibody response upon virus re-exposure or vaccination. Virus-specific CD4+ and CD8+ T cells are polyfunctional and maintained with an estimated half-life of 200 days. Interestingly, CD4+ T cell responses equally target several SARS-CoV-2 proteins, whereas the CD8+ T cell responses preferentially target the nucleoprotein, highlighting the potential importance of including the nucleoprotein in future vaccines. Taken together, these results suggest that broad and effective immunity may persist long-term in recovered COVID-19 patients.
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Affiliation(s)
- Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Susanne L. Linderman
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Julie Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Lilin Lai
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Grace Mantus
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Carson Norwood
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Lindsay E. Nyhoff
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Venkata Viswanadh Edara
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Katharine Floyd
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Rachael Whaley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shivan N. Patel
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Brittany Prigmore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Maria P. Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Carl W. Davis
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Sarah Furth
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - James B. O’Keefe
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Mohini P. Gharpure
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Sivaram Gunisetty
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Kathy Stephens
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Veronika I. Zarnitsyna
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - David S. Stephens
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Srilatha Edupuganti
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
- Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30330, USA
| | - Nadine Rouphael
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
- Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30330, USA
| | - Evan J. Anderson
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Aneesh K. Mehta
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Jens Wrammert
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Mehul S. Suthar
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, WA 98195, USA
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21
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Cohen KW, Linderman SL, Moodie Z, Czartoski J, Lai L, Mantus G, Norwood C, Nyhoff LE, Edara VV, Floyd K, De Rosa SC, Ahmed H, Whaley R, Patel SN, Prigmore B, Lemos MP, Davis CW, Furth S, O’Keefe J, Gharpure MP, Gunisetty S, Stephens KA, Antia R, Zarnitsyna VI, Stephens DS, Edupuganti S, Rouphael N, Anderson EJ, Mehta AK, Wrammert J, Suthar MS, Ahmed R, McElrath MJ. Longitudinal analysis shows durable and broad immune memory after SARS-CoV-2 infection with persisting antibody responses and memory B and T cells. medRxiv 2021:2021.04.19.21255739. [PMID: 33948610 PMCID: PMC8095229 DOI: 10.1101/2021.04.19.21255739] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Ending the COVID-19 pandemic will require long-lived immunity to SARS-CoV-2. Here, we evaluate 254 COVID-19 patients longitudinally up to eight months and find durable broad-based immune responses. SARS-CoV-2 spike binding and neutralizing antibodies exhibit a bi-phasic decay with an extended half-life of >200 days suggesting the generation of longer-lived plasma cells. SARS-CoV-2 infection also boosts antibody titers to SARS-CoV-1 and common betacoronaviruses. In addition, spike-specific IgG+ memory B cells persist, which bodes well for a rapid antibody response upon virus re-exposure or vaccination. Virus-specific CD4+ and CD8+ T cells are polyfunctional and maintained with an estimated half-life of 200 days. Interestingly, CD4+ T cell responses equally target several SARS-CoV-2 proteins, whereas the CD8+ T cell responses preferentially target the nucleoprotein, highlighting the potential importance of including the nucleoprotein in future vaccines. Taken together, these results suggest that broad and effective immunity may persist long-term in recovered COVID-19 patients.
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Affiliation(s)
- Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Susanne L. Linderman
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Julie Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Lilin Lai
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Grace Mantus
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Carson Norwood
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Lindsay E. Nyhoff
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Venkata Viswanadh Edara
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Katharine Floyd
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Rachael Whaley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shivan N. Patel
- Department of Medicine, Division of Infectious Diseases, Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Brittany Prigmore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Maria P. Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Carl W. Davis
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Sarah Furth
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - James O’Keefe
- Emory University School of Medicine, Department of Medicine, Atlanta, GA 30322, USA
| | - Mohini P. Gharpure
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Sivaram Gunisetty
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | | | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Veronika I. Zarnitsyna
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA,Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - David S. Stephens
- Emory University School of Medicine, Department of Medicine, Atlanta, GA 30322, USA
| | - Srilatha Edupuganti
- Department of Medicine, Division of Infectious Diseases, Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Nadine Rouphael
- Department of Medicine, Division of Infectious Diseases, Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Evan J. Anderson
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Emory University School of Medicine, Department of Medicine, Atlanta, GA 30322, USA
| | - Aneesh K. Mehta
- Emory University School of Medicine, Department of Medicine, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Mehul S. Suthar
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Rafi Ahmed
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, WA 98195, USA
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22
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Pan YG, Aiamkitsumrit B, Bartolo L, Wang Y, Lavery C, Marc A, Holec PV, Rappazzo CG, Eilola T, Gimotty PA, Hensley SE, Antia R, Zarnitsyna VI, Birnbaum ME, Su LF. Vaccination reshapes the virus-specific T cell repertoire in unexposed adults. Immunity 2021; 54:1245-1256.e5. [PMID: 34004140 PMCID: PMC8192456 DOI: 10.1016/j.immuni.2021.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 09/20/2020] [Revised: 02/01/2021] [Accepted: 04/21/2021] [Indexed: 11/30/2022]
Abstract
We examined how baseline CD4+ T cell repertoire and precursor states impact responses to pathogen infection in humans using primary immunization with yellow fever virus (YFV) vaccine. YFV-specific T cells in unexposed individuals were identified by peptide-MHC tetramer staining and tracked pre- and post-vaccination by tetramers and TCR sequencing. A substantial number of YFV-reactive T cells expressed memory phenotype markers and contained expanded clones in the absence of exposure to YFV. After vaccination, pre-existing YFV-specific T cell populations with low clonal diversity underwent limited expansion, but rare populations with a reservoir of unexpanded TCRs generated robust responses. These altered dynamics reorganized the immunodominance hierarchy and resulted in an overall increase in higher avidity T cells. Thus, instead of further increasing the representation of dominant clones, YFV vaccination recruits rare and more responsive T cells. Our findings illustrate the impact of vaccines in prioritizing T cell responses and reveal repertoire reorganization as a key component of effective vaccination.
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Affiliation(s)
- Yi-Gen Pan
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamas Aiamkitsumrit
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laurent Bartolo
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yifeng Wang
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Criswell Lavery
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA 19104, USA
| | - Adam Marc
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA 19104, USA
| | - Patrick V Holec
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Garrett Rappazzo
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Theresa Eilola
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phyllis A Gimotty
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | | | - Michael E Birnbaum
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laura F Su
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA 19104, USA.
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23
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Affiliation(s)
| | - Ottar Bjornstad
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta GA, USA
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24
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Lavine JS, Bjornstad ON, Antia R. Immunological characteristics govern the transition of COVID-19 to endemicity. Science 2021; 371:741-745. [PMID: 33436525 PMCID: PMC7932103 DOI: 10.1126/science.abe6522] [Citation(s) in RCA: 229] [Impact Index Per Article: 76.3] [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: 09/04/2020] [Revised: 11/10/2020] [Accepted: 01/07/2021] [Indexed: 12/14/2022]
Abstract
We are currently faced with the question of how the severity of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may change in the years ahead. Our analysis of immunological and epidemiological data on endemic human coronaviruses (HCoVs) shows that infection-blocking immunity wanes rapidly but that disease-reducing immunity is long-lived. Our model, incorporating these components of immunity, recapitulates both the current severity of SARS-CoV-2 infection and the benign nature of HCoVs, suggesting that once the endemic phase is reached and primary exposure is in childhood, SARS-CoV-2 may be no more virulent than the common cold. We predict a different outcome for an emergent coronavirus that causes severe disease in children. These results reinforce the importance of behavioral containment during pandemic vaccine rollout, while prompting us to evaluate scenarios for continuing vaccination in the endemic phase.
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Affiliation(s)
- Jennie S Lavine
- Department of Biology, Emory University, Atlanta, GA 30322, USA.
| | - Ottar N Bjornstad
- Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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25
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Desikan R, Antia R, Dixit NM. Physical 'strength' of the multi-protein chain connecting immune cells: Does the weakest link limit antibody affinity maturation?: The weakest link in the multi-protein chain facilitating antigen acquisition by B cells in germinal centres limits antibody affinity maturation. Bioessays 2021; 43:e2000159. [PMID: 33448042 DOI: 10.1002/bies.202000159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022]
Abstract
The affinities of antibodies (Abs) for their target antigens (Ags) gradually increase in vivo following an infection or vaccination, but reach saturation at values well below those realisable in vitro. This 'affinity ceiling' could in many cases restrict our ability to fight infections and compromise vaccines. What determines the affinity ceiling has been an unresolved question for decades. Here, we argue that it arises from the strength of the chain of protein complexes that is pulled by B cells during the process of Ag acquisition. The affinity ceiling is determined by the strength of the weakest link in the chain. We identify the weakest link and show that the resulting affinity ceiling can explain the Ab affinities realized in vivo, providing a conceptual understanding of Ab affinity maturation. We explore plausible evolutionary underpinnings of the affinity ceiling, examine supporting evidence and alternative hypotheses and discuss implications for vaccination strategies.
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Affiliation(s)
- Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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26
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Matrajt L, Halloran ME, Antia R. Successes and Failures of the Live-attenuated Influenza Vaccine: Can We Do Better? Clin Infect Dis 2021; 70:1029-1037. [PMID: 31056675 PMCID: PMC7319054 DOI: 10.1093/cid/ciz358] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 10/18/2018] [Accepted: 04/30/2019] [Indexed: 11/17/2022] Open
Abstract
Background The effectiveness of the live-attenuated influenza vaccine (LAIV) can vary widely, ranging from 0% to 50%. The reasons for these discrepancies remain largely unclear. Methods We use mathematical models to explore how the efficacy of LAIV is affected by the degree of mismatch with the currently circulating influenza strain and interference with pre-existing immunity. The models incorporate 3 key antigenic distances: the distances between the vaccine strain, pre-existing immunity, and the challenge strain. Results Our models show that an LAIV that is matched with the currently circulating strain is likely to have only modest efficacy. Our results suggest that the efficacy of the vaccine would be increased (optimized) if, rather than being matched to the circulating strain, it is antigenically slightly further from pre-existing immunity than the circulating strain. The models also suggest 2 regimes in which LAIV that is matched to circulating strains may be protective: in children before they have built immunity to circulating strains and in response to novel strains (such as antigenic shifts) which are at substantial antigenic distance from previously circulating strains. We provide an explanation for the variation in vaccine effectiveness between studies and countries of vaccine effectiveness observed during the 2014–2015 influenza season. Conclusions LAIV is offered to children across the world; however, its effectiveness significantly varies between studies. Here, we propose a mechanistic explanation to understand these differences. We further propose a way to select the LAIV strain that would have a higher chance of being protective.
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Affiliation(s)
- Laura Matrajt
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center.,Department of Biostatistics, University of Washington, Seattle
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia
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27
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Matrajt L, Halloran ME, Antia R. Reply to Lindsey, Höschler, and de Silva. Clin Infect Dis 2020; 70:2236-2237. [PMID: 31412101 DOI: 10.1093/cid/ciz774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Laura Matrajt
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle.,Department of Biostatistics, University of Washington, Seattle
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia
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28
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Moore JR, Ahmed H, Manicassamy B, Garcia-Sastre A, Handel A, Antia R. Varying Inoculum Dose to Assess the Roles of the Immune Response and Target Cell Depletion by the Pathogen in Control of Acute Viral Infections. Bull Math Biol 2020; 82:35. [PMID: 32125535 DOI: 10.1007/s11538-020-00711-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/19/2020] [Indexed: 02/05/2023]
Abstract
It is difficult to determine whether an immune response or target cell depletion by the infectious agent is most responsible for the control of acute primary infection. Both mechanisms can explain the basic dynamics of an acute infection-exponential growth of the pathogen followed by control and clearance-and can also be represented by many different differential equation models. Consequently, traditional model comparison techniques using time series data can be ambiguous or inconclusive. We propose that varying the inoculum dose and measuring the subsequent infectious load can rule out target cell depletion by the pathogen as the main control mechanism. Infectious load can be any measure that is proportional to the number of infected cells, such as viraemia. We show that a twofold or greater change in infectious load is unlikely when target cell depletion controls infection, regardless of the model details. Analyzing previously published data from mice infected with influenza, we find the proportion of lung epithelial cells infected was 21-fold greater (95% confidence interval 14-32) in the highest dose group than in the lowest. This provides evidence in favor of an alternative to target cell depletion, such as innate immunity, in controlling influenza infections in this experimental system. Data from other experimental animal models of acute primary infection have a similar pattern.
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Affiliation(s)
- James R Moore
- Division of Vaccines and Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, USA.
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, USA
| | - Balaji Manicassamy
- Department of Microbiology and Immunology, University of Iowa School College of Medicine, Iowa City, USA
| | | | - Andreas Handel
- Epidemiology and Biostatistics, University of Georgia, Athens, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, USA
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29
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Bhaumik SK, Kulkarni RR, Weldon WC, Silveira ELV, Ahmed H, Gunisetty S, Chandele A, Antia R, Verma H, Sutter R, Pallansch MA, Oberste MS, Villinger F, Orenstein W, Murali-Krishna K. Immune Priming and Long-term Persistence of Memory B Cells After Inactivated Poliovirus Vaccine in Macaque Models: Support for at least 2 Doses. Clin Infect Dis 2019; 67:S66-S77. [PMID: 30376091 PMCID: PMC6206122 DOI: 10.1093/cid/ciy634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background As a risk-mitigation strategy to minimize paralytic polio following withdrawal of Sabin type 2 from the oral poliovirus vaccine in April 2016, a single full dose or 2 fractional doses of inactivated poliovirus vaccine (IPV) are recommended. However, limited knowledge exists on long-term persistence of immune memory following 1- or 2-dose IPV schedules. Methods We examined induction and maintenance of immune memory following single- vs 2-dose IPV schedules, either full-dose intramuscular or fractional-dose intradermal, in rhesus macaques. Humoral responses, bone marrow–homing antibody-secreting plasma cells, and blood-circulating/lymph node–homing memory B cells were examined longitudinally. Results A single dose of IPV, either full or fractional, induced binding antibodies and memory B cells in all vaccinated macaques, despite failing to induce neutralizing antibodies (NT Abs) in many of them. However, these memory B cells declined rapidly, reaching below detection in the systemic circulation by 5 months; although a low frequency of memory B cells was detectable in draining lymph nodes of some, but not all, animals. By contrast, a 2-dose vaccination schedule, either full or fractional, efficiently induced NT Abs in all animals along with bone marrow–homing plasma cells and memory B cells. These memory B cells persisted in the systemic circulation for up to 16 months, the maximum duration tested after the second dose of vaccination. Conclusions Two doses of IPV, regardless of whether fractional or full, are more effective than a single dose for inducing long-lasting memory B cells.
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Affiliation(s)
- Siddhartha Kumar Bhaumik
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
| | - Raveendra R Kulkarni
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
| | - William C Weldon
- Division of Viral Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | | | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, Georgia
| | - Sivaram Gunisetty
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Rustom Antia
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
| | - Harish Verma
- Polio Eradication Department, World Health Organization, Geneva, Switzerland
| | - Roland Sutter
- Polio Eradication Department, World Health Organization, Geneva, Switzerland
| | - Mark A Pallansch
- Division of Viral Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Francois Villinger
- Yerkes Primate Center, Emory University School of Medicine, Atlanta, Georgia
| | - Walter Orenstein
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Kaja Murali-Krishna
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia.,ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.,Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
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30
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Dale GA, Wilkins DJ, Bohannon CD, Dilernia D, Hunter E, Bedford T, Antia R, Sanz I, Jacob J. Clustered Mutations at the Murine and Human IgH Locus Exhibit Significant Linkage Consistent with Templated Mutagenesis. J Immunol 2019; 203:1252-1264. [PMID: 31375545 PMCID: PMC6702052 DOI: 10.4049/jimmunol.1801615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 06/18/2019] [Indexed: 01/21/2023]
Abstract
Somatic hypermutation generates a myriad of Ab mutants in Ag-specific B cells, from which high-affinity mutants are selected. Chickens, sheep, and rabbits use nontemplated point mutations and templated mutations via gene conversion to diversify their expressed Ig loci, whereas mice and humans rely solely on untemplated somatic point mutations. In this study, we demonstrate that, in addition to untemplated point mutations, templated mutagenesis readily occurs at the murine and human Ig loci. We provide two distinct lines of evidence that are not explained by the Neuberger model of somatic hypermutation: 1) across multiple data sets there is significant linkage disequilibrium between individual mutations, especially among close mutations, and 2) among those mutations, those <8 bp apart are significantly more likely to match microhomologous regions in the IgHV repertoire than predicted by the mutation profiles of somatic hypermutation. Together, this supports the role of templated mutagenesis during somatic diversification of Ag-activated B cells.
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Affiliation(s)
- Gordon A Dale
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Daniel J Wilkins
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Caitlin D Bohannon
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Dario Dilernia
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Trevor Bedford
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322; and
| | - Ignacio Sanz
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA 30322
| | - Joshy Jacob
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329;
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31
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Jacobs NT, Onuoha NO, Antia A, Steel J, Antia R, Lowen AC. Incomplete influenza A virus genomes occur frequently but are readily complemented during localized viral spread. Nat Commun 2019; 10:3526. [PMID: 31387995 PMCID: PMC6684657 DOI: 10.1038/s41467-019-11428-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [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: 12/22/2018] [Accepted: 07/15/2019] [Indexed: 11/09/2022] Open
Abstract
Segmentation of viral genomes into multiple RNAs creates the potential for replication of incomplete viral genomes (IVGs). Here we use a single-cell approach to quantify influenza A virus IVGs and examine their fitness implications. We find that each segment of influenza A/Panama/2007/99 (H3N2) virus has a 58% probability of being replicated in a cell infected with a single virion. Theoretical methods predict that IVGs carry high costs in a well-mixed system, as 3.6 virions are required for replication of a full genome. Spatial structure is predicted to mitigate these costs, however, and experimental manipulations of spatial structure indicate that local spread facilitates complementation. A virus entirely dependent on co-infection was used to assess relevance of IVGs in vivo. This virus grows robustly in guinea pigs, but is less infectious and does not transmit. Thus, co-infection allows IVGs to contribute to within-host spread, but complete genomes may be critical for transmission.
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Affiliation(s)
- Nathan T Jacobs
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nina O Onuoha
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Alice Antia
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - John Steel
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
- Emory-UGA Center of Excellence for Influenza Research and Surveillance, Emory University School of Medicine, Atlanta, GA, USA.
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32
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Abstract
Replicating recombinant vector vaccines consist of a fully competent viral vector backbone engineered to express an antigen from a foreign transgene. From the perspective of viral replication, the transgene is not only dispensable but may even be detrimental. Thus vaccine revertants that delete or inactivate the transgene may evolve to dominate the vaccine virus population both during the process of manufacture of the vaccine as well as during the course of host infection. A particular concern is that this vaccine evolution could reduce its antigenicity—the immunity elicited to the transgene. We use mathematical and computational models to study vaccine evolution and immunity. These models include evolution arising during the process of manufacture, the dynamics of vaccine and revertant growth, plus innate and adaptive immunity elicited during the course of infection. Although the selective basis of vaccine evolution is easy to comprehend, the immunological consequences are not. One complication is that the opportunity for vaccine evolution is limited by the short period of within-host growth before the viral population is cleared. Even less obvious, revertant growth may only weakly interfere with vaccine growth in the host and thus have a limited effect on immunity to vaccine. Overall, we find that within-host vaccine evolution can sometimes compromise vaccine immunity, but only when the extent of evolution during vaccine manufacture is severe, and this evolution can be easily avoided or mitigated. Recombinant vector vaccines are live replicating viruses that are engineered to carry extra genes derived from a pathogen—and these extra genes produce proteins against which we want to generate immunity. These vaccine genomes may evolve to lose the extra genes during the process of manufacture of the vaccine or during replication within an individual, and there is a concern that this evolution might severely limit the vaccine’s efficacy. The dynamics of this process are studied here with mathematical models. The potential for vaccine evolution within the host is somewhat limited by the short-term growth of the vaccine population before it is suppressed by the immune response. We find that evolution is a problem only when the process of manufacture results in the majority of the vaccine virus being revertant. We show that increasing the vaccine inoculum size or reducing the level of revertant in the vaccine inoculum can largely avoid the loss of immunity arising from evolution.
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Affiliation(s)
- James J. Bull
- Department Integrative Biology, University of Texas, Austin, Texas, United States of America
- * E-mail:
| | - Scott L. Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Rustom Antia
- Department of Biology, Emory University, Altanta, Georgia, United States of America
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33
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Moore JR, Ahmed H, McGuire D, Akondy R, Ahmed R, Antia R. Dependence of CD8 T Cell Response upon Antigen Load During Primary Infection : Analysis of Data from Yellow Fever Vaccination. Bull Math Biol 2019; 81:2553-2568. [PMID: 31165405 PMCID: PMC6657775 DOI: 10.1007/s11538-019-00618-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 05/24/2019] [Indexed: 02/07/2023]
Abstract
A major question in immunology is what role antigen load plays in determining the size of the CD8 immune response. Is the amount of antigen important during recruitment, proliferation, and/or memory formation? Animal studies have shown that antigen is only strictly required early during activation of T cells, but the importance of antigen at later timepoints is unclear. Using data from 24 volunteers infected with the yellow fever vaccine virus (YFV), we analyzed the dependence of T cell proliferation upon viral load. We found that volunteers with high viral load initially have greater T cell responses, but by 28 days post-vaccination those with lower viral load are able to 'catch-up.' Using differential equation modeling we show that this pattern is consistent with viral load only affecting recruitment (i.e., programmed proliferation) as opposed to affecting recruitment and proliferation (i.e., antigen-dependent proliferation). A quantitative understanding of the dependence of T cell dynamics on antigen load will be of use to modelers studying not only vaccination, but also cancer immunology and autoimmune disorders.
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Affiliation(s)
- James R Moore
- Division of Vaccines and Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, USA.
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, USA
| | - Don McGuire
- Emory Vaccine Center, Emory University, Atlanta, USA
| | - Rama Akondy
- Department of Microbiology and Immunobiology, Emory University, Atlanta, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University, Atlanta, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, USA
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34
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Abstract
Theoretical models suggest that mixed-strain infections, or co-infections, are an important driver of pathogen evolution. However, the within-host dynamics of co-infections vary enormously, which complicates efforts to develop a general understanding of how co-infections affect evolution. Here, we develop a general framework which condenses the within-host dynamics of co-infections into a few key outcomes, the most important of which is the overall R0 of the co-infection. Similar to how fitness is determined by two different alleles in a heterozygote, the R0 of a co-infection is a product of the R0 values of the co-infecting strains, shaped by the interaction of those strains at the within-host level. Extending the analogy, we propose that the overall R0 reflects the dominance of the co-infecting strains, and that the ability of a mutant strain to invade a population is a function of its dominance in co-infections. To illustrate the utility of these concepts, we use a within-host model to show how dominance arises from the within-host dynamics of a co-infection, and then use an epidemiological model to demonstrate that dominance is a robust predictor of the ability of a mutant strain to save a maladapted wild-type strain from extinction (evolutionary emergence).
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Affiliation(s)
- Mary Bushman
- Department of Biology, Emory University , Atlanta, GA , USA
| | - Rustom Antia
- Department of Biology, Emory University , Atlanta, GA , USA
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35
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Li ZRT, Zarnitsyna VI, Lowen AC, Kohlmeier JE, Antia R. Quantifying the selection on influenza A virus imposed by CD8 T cells. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.76.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
An essential question regarding the T cell-inducing influenza vaccine is whether the cellular immunity may drive the virus to rapidly evolve and escape. In our previous modeling study, we have shown an CD8 T cell escape-variant of influenza A virus (IAV) invades extremely slowly given empirical HLA allele frequencies and modest selection pressure. Guided by the model, we aim to quantify the selection from CD8 T cells using a novel digital droplet PCR system under different in vivo settings.
Mice were intranasally primed with HKx31 (H3N2) and challenged with a 1:1 mixture of wild-type and mutant PR8, which harbors an N370Q escaping mutation in its NP366–374 immunodominant epitope, on day 30 post-priming. The area under the in vivo viral growth curve (AUC) is used to measure the fitness of wild-type and mutant viruses. Based on the AUCs of C57BL/6 (H-2b/b) and CF1B6 (H-2b/d), the estimated selective advantage of this mutation is 0.28 [0.20, 0.36] and 0.21 [0.10, 0.34], respectively. Interestingly, although the intramuscularly primed C57BL/6 gave a similar estimate for the advantage (0.22 [0.16, 0.30]), the advantage became much more apparent on day 6 and 8 after PR8 challenge. This implies the lung resident memory CD8 T cells may be the source of selection during the initial stage of IAV infection.
In combination with the model prediction, an escape-variant of IAV that carries a mutant immunodominant epitope may need 100 to 500 generations (corresponding to 1 to 5 years if the infection period is assumed to be 4 days) to reach 50% of prevalence given the frequency of cognate HLA alleles is 20%. We concluded that the selection from CD8 T cells may not be sufficient to drive the CD8 T cell epitopes of IAV to evolve rapidly like the antibody epitopes.
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Handel A, Li Y, McKay B, Pawelek KA, Zarnitsyna V, Antia R. Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design. PLoS Comput Biol 2018; 14:e1006505. [PMID: 30273336 PMCID: PMC6181424 DOI: 10.1371/journal.pcbi.1006505] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 04/30/2018] [Revised: 10/11/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Vaccination is an effective method to protect against infectious diseases. An important consideration in any vaccine formulation is the inoculum dose, i.e., amount of antigen or live attenuated pathogen that is used. Higher levels generally lead to better stimulation of the immune response but might cause more severe side effects and allow for less population coverage in the presence of vaccine shortages. Determining the optimal amount of inoculum dose is an important component of rational vaccine design. A combination of mathematical models with experimental data can help determine the impact of the inoculum dose. We illustrate the concept of using data and models to inform inoculum dose determination for vaccines, wby fitting a mathematical model to data from influenza A virus (IAV) infection of mice and human parainfluenza virus (HPIV) infection of cotton rats at different inoculum doses. We use the model to map inoculum dose to the level of immune protection and morbidity and to explore how such a framework might be used to determine an optimal inoculum dose. We show how a framework that combines mathematical models with experimental data can be used to study the impact of inoculum dose on important outcomes such as immune protection and morbidity. Our findings illustrate that the impact of inoculum dose on immune protection and morbidity can depend on the specific pathogen and that both protection and morbidity do not necessarily increase monotonically with increasing inoculum dose. Once vaccine design goals are specified with required levels of protection and acceptable levels of morbidity, our proposed framework can help in the rational design of vaccines and determination of the optimal amount of inoculum. An important component of vaccines is the amount of pathogen inoculum, dead or alive, that is included in the vaccine. This inoculum dose, sometimes also referred to as antigen dose, needs to be large enough to induce good protective immunity. However, one usually also wants to keep the dose low to reduce costs, maximize the number of vaccine doses available, and minimize potential vaccine side effects. The inoculum dose is currently chosen based on limited data from clinical trials. In this study, we set up a framework that combines data with mathematical models to illustrate how such a combination could lead to better and more efficient determination of an optimal inoculum dose for vaccines.
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Affiliation(s)
- Andreas Handel
- Department of Epidemiology and Biostatistics and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| | - Yan Li
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Brian McKay
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
| | - Kasia A. Pawelek
- Department of Mathematics and Computational Science, University of South Carolina Beaufort, Bluffton, South Carolina, United States of America
| | - Veronika Zarnitsyna
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
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37
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Bushman M, Antia R, Udhayakumar V, de Roode JC. Within-host competition can delay evolution of drug resistance in malaria. PLoS Biol 2018; 16:e2005712. [PMID: 30130363 PMCID: PMC6103507 DOI: 10.1371/journal.pbio.2005712] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
In the malaria parasite P. falciparum, drug resistance generally evolves first in low-transmission settings, such as Southeast Asia and South America. Resistance takes noticeably longer to appear in the high-transmission settings of sub-Saharan Africa, although it may spread rapidly thereafter. Here, we test the hypothesis that competitive suppression of drug-resistant parasites by drug-sensitive parasites may inhibit evolution of resistance in high-transmission settings, where mixed-strain infections are common. We employ a cross-scale model, which simulates within-host (infection) dynamics and between-host (transmission) dynamics of sensitive and resistant parasites for a population of humans and mosquitoes. Using this model, we examine the effects of transmission intensity, selection pressure, fitness costs of resistance, and cross-reactivity between strains on the establishment and spread of resistant parasites. We find that resistant parasites, introduced into the population at a low frequency, are more likely to go extinct in high-transmission settings, where drug-sensitive competitors and high levels of acquired immunity reduce the absolute fitness of the resistant parasites. Under strong selection from antimalarial drug use, however, resistance spreads faster in high-transmission settings than low-transmission ones. These contrasting results highlight the distinction between establishment and spread of resistance and suggest that the former but not the latter may be inhibited in high-transmission settings. Our results suggest that within-host competition is a key factor shaping the evolution of drug resistance in P. falciparum. The malaria parasite Plasmodium falciparum has evolved resistance to most antimalarial drugs, greatly complicating treatment and control of the disease. Curiously, although sub-Saharan Africa accounts for the majority of the global burden of malaria, the evolution of drug resistance in Africa has been markedly delayed compared to Asia and the Americas. One reason might be that, in a population in which the prevalence of infection is high, a newly emerged drug-resistant strain faces a high risk of extinction due to competition from drug-sensitive parasites that already “occupy” most of the host population. Using a mathematical model, we confirm that drug-resistant parasites face a much greater risk of extinction in a “high-transmission” setting like sub-Saharan Africa than in a “low-transmission” setting like Southeast Asia. However, we also find that when drug-resistant parasites manage to avoid extinction, their subsequent spread may be more rapid in high-transmission settings than in low-transmission settings, especially when selection is strong. These results offer a novel explanation for global patterns of drug resistance evolution in malaria and suggest a new dimension to consider in resistance prevention and containment efforts: namely, the intrinsic favorability of low- and high-transmission settings for establishment and spread of drug resistance.
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Affiliation(s)
- Mary Bushman
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jacobus C. de Roode
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
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38
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Adekola A, Antia R, Emikpe B, Jubril A, Ohore O. Hepatitis E virus infection seroprevalence and associated pathological changes in pigs slaughtered at the Bodija municipal abattoir, Ibadan, Nigeria. Int J Infect Dis 2018. [DOI: 10.1016/j.ijid.2018.04.4294] [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: 11/16/2022] Open
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39
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Zarnitsyna VI, Bulusheva I, Handel A, Longini IM, Halloran ME, Antia R. Intermediate levels of vaccination coverage may minimize seasonal influenza outbreaks. PLoS One 2018; 13:e0199674. [PMID: 29944709 PMCID: PMC6019388 DOI: 10.1371/journal.pone.0199674] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 01/24/2018] [Accepted: 06/12/2018] [Indexed: 11/30/2022] Open
Abstract
For most pathogens, vaccination reduces the spread of the infection and total number of cases; thus, public policy usually advocates maximizing vaccination coverage. We use simple mathematical models to explore how this may be different for pathogens, such as influenza, which exhibit strain variation. Our models predict that the total number of seasonal influenza infections is minimized at an intermediate (rather than maximal) level of vaccination, and, somewhat counter-intuitively, further increasing the level of the vaccination coverage may lead to higher number of influenza infections and be detrimental to the public interest. This arises due to the combined effects of: competition between multiple co-circulating strains; limited breadth of protection afforded by the vaccine; and short-term strain-transcending immunity following natural infection. The study highlights the need for better quantification of the components of vaccine efficacy and longevity of strain-transcending cross-immunity in order to generate nuanced recommendations for influenza vaccine coverage levels.
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Affiliation(s)
- Veronika I. Zarnitsyna
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, 30322, United States of America
- * E-mail: (VZ); (RA)
| | - Irina Bulusheva
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Andreas Handel
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, 30602, United States of America
| | - Ira M. Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, 32611, United States of America
| | - M. Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, United States of America
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, 30322, United States of America
- * E-mail: (VZ); (RA)
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40
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Moore J, Ahmed H, Antia R. High dimensional random walks can appear low dimensional: Application to influenza H3N2 evolution. J Theor Biol 2018; 447:56-64. [PMID: 29571708 DOI: 10.1016/j.jtbi.2018.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 08/22/2017] [Revised: 02/26/2018] [Accepted: 03/15/2018] [Indexed: 11/19/2022]
Abstract
One important feature of the mammalian immune system is the highly specific binding of antigens to antibodies. Antibodies generated in response to one infection may also provide some level of cross immunity to other infections. One model to describe this cross immunity is the notion of antigenic space, which assigns each antibody and each virus a point in Rn. Past studies using hemagglutination data have suggested the dimensionality of antigenic space, n, is low. We propose that influenza evolution may be modeled as a Gaussian random walk. We then show that hemagluttination data would be consistent with a walk in very high dimensions. The discrepancy between our result and prior studies is due to the fact that random walks can appear low dimensional according to a variety of analyses including principal component analysis (PCA) and multidimensional scaling (MDS). A high dimensionality of antigenic space is of importance to modelers, as it suggests a smaller role for pre-existing immunity within the host population.
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Affiliation(s)
- James Moore
- Department of Biology, Emory University, Atlanta, GA, USA.
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
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41
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Emikpe O, Omobowale T, Jarikre T, Otuh P, Oyebanji V, Antia R. High grade lymphoma in a six-year old boerboel: a case report. BJVM 2018. [DOI: 10.15547/bjvm.1021] [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: 11/12/2022] Open
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42
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Youngblood B, Hale JS, Kissick HT, Ahn E, Xu X, Wieland A, Araki K, West EE, Ghoneim HE, Fan Y, Dogra P, Davis CW, Konieczny BT, Antia R, Cheng X, Ahmed R. Effector CD8 T cells dedifferentiate into long-lived memory cells. Nature 2017; 552:404-409. [PMID: 29236683 PMCID: PMC5965677 DOI: 10.1038/nature25144] [Citation(s) in RCA: 315] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/17/2017] [Indexed: 01/20/2023]
Abstract
Memory CD8 T cells that circulate in the blood and are present in lymphoid organs are an essential component of long-lived T cell immunity. These memory CD8 T cells remain poised to rapidly elaborate effector functions upon re-exposure to pathogens, but also have many properties in common with naive cells, including pluripotency and the ability to migrate to the lymph nodes and spleen. Thus, memory cells embody features of both naive and effector cells, fuelling a long-standing debate centred on whether memory T cells develop from effector cells or directly from naive cells. Here we show that long-lived memory CD8 T cells are derived from a subset of effector T cells through a process of dedifferentiation. To assess the developmental origin of memory CD8 T cells, we investigated changes in DNA methylation programming at naive and effector cell-associated genes in virus-specific CD8 T cells during acute lymphocytic choriomeningitis virus infection in mice. Methylation profiling of terminal effector versus memory-precursor CD8 T cell subsets showed that, rather than retaining a naive epigenetic state, the subset of cells that gives rise to memory cells acquired de novo DNA methylation programs at naive-associated genes and became demethylated at the loci of classically defined effector molecules. Conditional deletion of the de novo methyltransferase Dnmt3a at an early stage of effector differentiation resulted in reduced methylation and faster re-expression of naive-associated genes, thereby accelerating the development of memory cells. Longitudinal phenotypic and epigenetic characterization of the memory-precursor effector subset of virus-specific CD8 T cells transferred into antigen-free mice revealed that differentiation to memory cells was coupled to erasure of de novo methylation programs and re-expression of naive-associated genes. Thus, epigenetic repression of naive-associated genes in effector CD8 T cells can be reversed in cells that develop into long-lived memory CD8 T cells while key effector genes remain demethylated, demonstrating that memory T cells arise from a subset of fate-permissive effector T cells.
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Affiliation(s)
- Ben Youngblood
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - J Scott Hale
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Haydn T Kissick
- Department of Urology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Eunseon Ahn
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Xiaojin Xu
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Andreas Wieland
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Koichi Araki
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Erin E West
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Pranay Dogra
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Carl W Davis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Bogumila T Konieczny
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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43
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Nuismer SL, Althouse BM, May R, Bull JJ, Stromberg SP, Antia R. Eradicating infectious disease using weakly transmissible vaccines. Proc Biol Sci 2017; 283:rspb.2016.1903. [PMID: 27798311 DOI: 10.1098/rspb.2016.1903] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/04/2016] [Indexed: 01/23/2023] Open
Abstract
Viral vaccines have had remarkable positive impacts on human health as well as the health of domestic animal populations. Despite impressive vaccine successes, however, many infectious diseases cannot yet be efficiently controlled or eradicated through vaccination, often because it is impossible to vaccinate a sufficient proportion of the population. Recent advances in molecular biology suggest that the centuries-old method of individual-based vaccine delivery may be on the cusp of a major revolution. Specifically, genetic engineering brings to life the possibility of a live, transmissible vaccine. Unfortunately, releasing a highly transmissible vaccine poses substantial evolutionary risks, including reversion to high virulence as has been documented for the oral polio vaccine. An alternative, and far safer approach, is to rely on genetically engineered and weakly transmissible vaccines that have reduced scope for evolutionary reversion. Here, we use mathematical models to evaluate the potential efficacy of such weakly transmissible vaccines. Our results demonstrate that vaccines with even a modest ability to transmit can significantly lower the incidence of infectious disease and facilitate eradication efforts. Consequently, weakly transmissible vaccines could provide an important tool for controlling infectious disease in wild and domestic animal populations and for reducing the risks of emerging infectious disease in humans.
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Affiliation(s)
- Scott L Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA .,Department of Mathematics, University of Idaho, Moscow, ID 83844, USA
| | - Benjamin M Althouse
- Institute for Disease Modeling, Bellevue, WA 98005, USA.,Santa Fe Institute, Santa Fe, NM 87501, USA.,New Mexico State University, Las Cruces, NM 88003, USA
| | - Ryan May
- Department of Mathematics, University of Idaho, Moscow, ID 83844, USA
| | - James J Bull
- Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Sean P Stromberg
- Bioinformatics, Omniome Inc., 10575 Roselle Street, San Diego, CA 92121, USA
| | - Rustom Antia
- Department of Biology, Emory University, Altanta, GA 30322, USA
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44
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Moore J, Ahmed H, Jia J, Akondy R, Ahmed R, Antia R. What Controls the Acute Viral Infection Following Yellow Fever Vaccination? Bull Math Biol 2017; 80:46-63. [PMID: 29110131 DOI: 10.1007/s11538-017-0365-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/16/2017] [Indexed: 12/25/2022]
Abstract
Does target cell depletion, innate immunity, or adaptive immunity play the dominant role in controlling primary acute viral infections? Why do some individuals have higher peak virus titers than others? Answering these questions is a basic problem in immunology and can be particularly difficult in humans due to limited data, heterogeneity in responses in different individuals, and limited ability for experimental manipulation. We address these questions for infections following vaccination with the live attenuated yellow fever virus (YFV-17D) by analyzing viral load data from 80 volunteers. Using a mixed effects modeling approach, we find that target cell depletion models do not fit the data as well as innate or adaptive immunity models. Examination of the fits of the innate and adaptive immunity models to the data allows us to select a minimal model that gives improved fits by widely used model selection criteria (AICc and BIC) and explains why it is hard to distinguish between the innate and adaptive immunity models. We then ask why some individuals have over 1000-fold higher virus titers than others and find that most of the variation arises from differences in the initial/maximum growth rate of the virus in different individuals.
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Affiliation(s)
- James Moore
- Department of Biology, Emory University, Atlanta, GA, USA.
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Jonathan Jia
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Rama Akondy
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
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45
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Li ZRT, Zarnitsyna VI, Lowen AC, Kohlmeier JE, Antia R. Quantifying the relative impact of influenza virus mutations on viral fitness and escape from cellular immunity. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.203.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The relative conservation of T cell epitopes in human influenza viruses compared to antibody epitopes may be explained by two mechanisms: (1) mutations of the T cell epitopes are constrained by their potential to decrease viral fitness by altering protein function, or (2) the selection benefits gained by ‘escaping’ mutations are small due to the breadth of MHC polymorphisms among human population. The level of influenza-specific cellular immunity may further complicate the relative contribution of these two mechanisms. We developed a mathematical model incorporating the mutation cost, selection benefit, and allele frequency of ‘escapable’ MHC that indicated certain combinations of these three parameters determined the fate of influenza viruses harboring mutations in T cell epitopes. To measure the mutation cost and selection benefit, we developed a novel digital droplet PCR method for the simultaneous detection of wild-type and mutant influenza viruses harboring mutations in the immunodominant NP366–374 epitope. Primary infections with WT, NP-mutated, and 1:1 mixture of WT and mutated x31 influenza viruses showed no significant difference between the two viruses, while the secondary infection of PR8-primed B6 mice with the 1:1 mixture resulted in a 10-fold decrease in the peak of viral load of WT compared to NP-mutated viruses. Together, these data show that the mutation of a single immunodominant T cell epitope provides significant selection benefit with minimal fitness cost to the virus. Future studies in mice with diverse MHC alleles are underway to quantify the impact of varying levels of cellular immune pressure on the in vivo ability of mutant influenza viruses to escape T cell immunity.
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46
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Kohlmeier A, McMaster S, Li ZR, Radzio-Basu J, Haddad LB, Sheth AN, Cong ME, Dinh C, Martin A, Hayward SL, Ofotokun I, Antia R, Garcia-Lerma JG, Kohlmeier JE. Differential localization of distinct CD4 T cell subsets in the female genital tract during the menstrual cycle is regulated by CCR5. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.149.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
CD4 T cells are essential for optimal immune responses against sexually transmitted infections, yet the composition of the CD4 T cell pool localized in the female genital tract (FGT), and the impact of the menstrual cycle on the CD4 T cell population dynamics in the FGT, remains poorly defined. Here we show the FGT CD4 T cell pool is comprised of distinct subsets of memory CD4 T cells based upon trafficking profile, anatomic regionalization, and effector responses. Based on expression of trafficking and tissue retention markers, FGT CD4 T cells are comprised of both migratory memory (TMM) and resident memory (TRM), with TMM expressing a broad array of trafficking markers that would enable their ability to perform immune surveillance in diverse tissues. Furthermore, these subsets differ in both their regionalization throughout the FGT and in their cytokine responses, notably IL-2 production. The frequency of TMM in the FGT increased during the luteal phase of the menstrual cycle and correlated with increased CCR5 expression on circulating memory CD4 T cells. Using a dual adoptive transfer mouse model, we observed that CCR5-mediated trafficking was required for the localization of memory CD4 T cells to the luminal surface of the FGT. In addition, to test cycle influence on T cell trafficking into the FGT, we administered a CCR5 antagonist to pigtail macaques at different stages of the menstrual cycle and found that inhibition of CCR5 signaling selectively reduced TMM numbers solely at luteal time points. Together, these data provide broader insight into role that distinct tissue resident CD4 T cell subsets play in barrier defenses at the FGT and also demonstrate a role for the menstrual cycle in modulating immune protection through CCR5 signaling.
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47
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Dale GA, Bohannon CD, Wilkins DJ, Dilernia D, Hunter E, Bedford T, Antia R, Sanz I, Jacob J. Gene conversion contributes significantly to IgHV somatic hypermutation in mice and humans. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.195.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
During antigen-driven affinity maturation germinal center B lymphocytes undergo multiple rounds of somatic mutagenesis in the rearranged IgHV gene segment. A direct consequence of this process is the generation of multiple antibody mutants that are, in general, specific for antigen. Survival of these mutants is contingent on preserving or improving antigen-specificity in the complementarity-determining regions (CDRs) as well as retaining a functional framework region (FWR). Broadly, somatic mutations in germinal center B cells can be classified as templated or untemplated. In animals such as rabbits and chickens, somatic mutations are mostly templated. Conversely, in mice and humans it is widely accepted that mutations are untemplated. Here, we argue in favor of the alternative, that a predominant number of somatic mutations in IgHV gene segments in mice and humans can be traced to germline IgHV genes and occur through gene conversion. Using the NP hapten model, we demonstrate that mutations in germinal center B cells and plasma cells are traceable to other germline IgHV genes. Subsequently we also demonstrate using the novel V-LAIR1-DJ antibodies described by Tan et al (Nature 2016) that mutations in human antibody IgHV rearrangements, including those in non-immunoglobulin sequences (LAIR1), are traceable to the human IgHV germline repertoire. Together, this suggests that the plethora of diversity generated in antigen specific B cells is primarily directed by the germline repertoire of IgHV genes.
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48
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Zarnitsyna VI, Handel A, McMaster SR, Hayward SL, Kohlmeier JE, Antia R. Mathematical Model Reveals the Role of Memory CD8 T Cell Populations in Recall Responses to Influenza. Front Immunol 2016; 7:165. [PMID: 27242779 PMCID: PMC4861172 DOI: 10.3389/fimmu.2016.00165] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 12/08/2015] [Accepted: 04/18/2016] [Indexed: 01/11/2023] Open
Abstract
The current influenza vaccine provides narrow protection against the strains included in the vaccine, and needs to be reformulated every few years in response to the constantly evolving new strains. Novel approaches are directed toward developing vaccines that provide broader protection by targeting B and T cell epitopes that are conserved between different strains of the virus. In this paper, we focus on developing mathematical models to explore the CD8 T cell responses to influenza, how they can be boosted, and the conditions under which they contribute to protection. Our models suggest that the interplay between spatial heterogeneity (with the virus infecting the respiratory tract and the immune response being generated in the secondary lymphoid organs) and T cell differentiation (with proliferation occurring in the lymphoid organs giving rise to a subpopulation of resident T cells in the respiratory tract) is the key to understand the dynamics of protection afforded by the CD8 T cell response to influenza. Our results suggest that the time lag for the generation of resident T cells in the respiratory tract and their rate of decay following infection are the key factors that limit the efficacy of CD8 T cell responses. The models predict that an increase in the level of central memory T cells leads to a gradual decrease in the viral load, and, in contrast, there is a sharper protection threshold for the relationship between the size of the population of resident T cells and protection. The models also suggest that repeated natural influenza infections cause the number of central memory CD8 T cells and the peak number of resident memory CD8 T cells to reach their plateaus, and while the former is maintained, the latter decays with time since the most recent infection.
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Affiliation(s)
- Veronika I Zarnitsyna
- Department of Microbiology and Immunology, Emory University School of Medicine , Atlanta, GA , USA
| | - Andreas Handel
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia , Athens, GA , USA
| | - Sean R McMaster
- Department of Microbiology and Immunology, Emory University School of Medicine , Atlanta, GA , USA
| | - Sarah L Hayward
- Department of Microbiology and Immunology, Emory University School of Medicine , Atlanta, GA , USA
| | - Jacob E Kohlmeier
- Department of Microbiology and Immunology, Emory University School of Medicine , Atlanta, GA , USA
| | - Rustom Antia
- Department of Biology, Emory University , Atlanta, GA , USA
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Zarnitsyna VI, Ellebedy AH, Davis C, Jacob J, Ahmed R, Antia R. Masking of antigenic epitopes by antibodies shapes the humoral immune response to influenza. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.80.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The immune responses to influenza, a virus that exhibits strain variation, show complex dynamics where prior immunity shapes the response to the subsequent infecting strains. Original antigenic sin (OAS) describes the observation that antibodies to the first encountered influenza strain, specifically antibodies to the epitopes on the head of influenza’s main surface glycoprotein, haemagglutinin (HA), dominate following infection with new drifted strains. OAS suggests that responses to the original strain are preferentially boosted. Recent studies also show limited boosting of the antibodies to conserved epitopes on the stem of HA, which are attractive targets for a ‘universal vaccine’. We develop multi-epitope models to explore how pre-existing immunity modulates the immune response to new strains following immunization. Our models suggest that the masking of antigenic epitopes by antibodies may play an important role in describing the complex dynamics of OAS and limited boosting of antibodies to the stem of HA. Analysis of recently published data confirms model predictions for how pre-existing antibodies to an epitope on HA decrease the magnitude of boosting of the antibody response to this epitope following immunization. We explore strategies for boosting of antibodies to conserved epitopes and generating broadly protective immunity to multiple strains.
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50
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Jacobs NT, Barra J, Antia R, Lamb TJ. Inflammatory monocytes mediate competition between genetically diverse malaria parasites during mixed-strain Plasmodium infections. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.134.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
In areas of intense malaria transmission, many individuals receive multiple infectious bites per night, leading to overlapping infections with multiple strains of Plasmodium. As the transmission likelihood of a given strain is influenced by blood-stage parasite densities, parasites that can multiply faster and avoid immune clearance mechanisms are more competitively fit and are likely to be favored by evolution. Competitive ability has previously been linked to the virulence of infection, but mechanistic details are unclear. Here, we demonstrate a role for innate phagocytic cells, specifically CD11b+ Ly6Chi inflammatory monocytes, in mediating competition between two clones of the rodent malaria parasite Plasmodium chabaudi during a mixed infection. PcAS and PcCB grow to similar densities and cause similar degrees of anemia in separate single infections, but differ in the inflammatory and immunoregulatory responses they elicit. In mixed infection, PcAS densities were more adversely impacted than those of PcCB when compared to single infections, but competitive suppression was abrogated by depletion of macrophages and monocytes prior to infection using clodronate-loaded liposomes. Flow cytometry analysis of splenic populations revealed that the CD11b+ Ly6Chi inflammatory monocyte population during mixed infection more closely resembles that of an infection with PcCB than with PcAS. Taken together, our results indicate that competition between genetically diverse malaria parasites can be mediated by innate immunity independent of parasite virulence, and that parasites gain a competitive advantage by polarizing the immune system towards a response to which they are adapted.
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