1
|
Wang L, Huang AT, Katzelnick LC, Lefrancq N, Escoto AC, Duret L, Chowdhury N, Jarman R, Conte MA, Berry IM, Fernandez S, Klungthong C, Thaisomboonsuk B, Suntarattiwong P, Vandepitte W, Whitehead SS, Cauchemez S, Cummings DAT, Salje H. Antigenic distance between primary and secondary dengue infections correlates with disease risk. Sci Transl Med 2024; 16:eadk3259. [PMID: 38657027 DOI: 10.1126/scitranslmed.adk3259] [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] [Received: 08/17/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Many pathogens continuously change their protein structure in response to immune-driven selection, resulting in weakened protection even in previously exposed individuals. In addition, for some pathogens, such as dengue virus, poorly targeted immunity is associated with increased risk of severe disease through a mechanism known as antibody-dependent enhancement. However, it remains unclear whether the antigenic distances between an individual's first infection and subsequent exposures dictate disease risk, explaining the observed large-scale differences in dengue hospitalizations across years. Here, we develop a framework that combines detailed antigenic and genetic characterization of viruses with details on hospitalized cases from 21 years of dengue surveillance in Bangkok, Thailand, to identify the role of the antigenic profile of circulating viruses in determining disease risk. We found that the risk of hospitalization depended on both the specific order of infecting serotypes and the antigenic distance between an individual's primary and secondary infections, with risk maximized at intermediate antigenic distances. These findings suggest that immune imprinting helps determine dengue disease risk and provide a pathway to monitor the changing risk profile of populations and to quantifying risk profiles of candidate vaccines.
Collapse
Affiliation(s)
- Lin Wang
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Angkana T Huang
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Leah C Katzelnick
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noémie Lefrancq
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Ana Coello Escoto
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Loréna Duret
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Nayeem Chowdhury
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Jarman
- Coalition for Epidemic Preparedness Initiative, Washington, DC 20006, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | | | - Warunee Vandepitte
- Queen Sirikit National Institute of Child Health, Bangkok 10400, Thailand
| | - Stephen S Whitehead
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Paris 75015, France
| | - Derek A T Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
2
|
Katzelnick L, Odio C, Daag J, Crisostomo MV, Voirin C, Escoto AC, Adams C, Hein LD, Aogo R, Mpingabo P, Rodriguez GR, Firdous S, Fernandez MA, White L, Agrupis KA, Deen J, de Silva A, Ylade M. Dengue virus IgG and serotype-specific neutralizing antibody titers measured with standard and mature viruses are associated with protection. Res Sq 2024:rs.3.rs-4145863. [PMID: 38659845 PMCID: PMC11042401 DOI: 10.21203/rs.3.rs-4145863/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Recent work demonstrates the limitations of the standard dengue virus (DENV) neutralization assay to predict protection against dengue. We perform studies to compare how a commercial IgG ELISA, envelope domain III (EDIII) or non-structural protein 1 (NS1) binding antibodies, and titers from plaque reduction neutralization tests (PRNTs) using reference standard and clinical mature viruses are associated with dengue disease. Healthy children (n = 1,206) in Cebu, Philippines were followed for 5 years. High ELISA values (≥3) were associated with reduced dengue probability relative to naïve children (3% vs. 10%, p = 0.008), but antibody binding EDIII or NS1 from each serotype had no association. High standard and mature geometric mean PRNT titers were associated with reduced dengue disease overall (p < 0.01), and high DENV2 and DENV3 titers in both assays provided protection against the matched serotype (p < 0.02). However, while 52% of dengue cases had standard virus PRNT titers > 100, only 2% of cases had mature virus PRNT titers > 100 (p < 0.001), indicating a lower, more consistent threshold for protection. Each assay may be useful for different purposes as correlates of protection in population and vaccine trials.
Collapse
|
3
|
Ylade M, Crisostomo MV, Daag JV, Agrupis KA, Cuachin AM, Sy AK, Kim DR, Ahn HS, Escoto AC, Katzelnick LC, Adams C, White L, de Silva AM, Deen J, Lopez AL. Effect of single-dose, live, attenuated dengue vaccine in children with or without previous dengue on risk of subsequent, virologically confirmed dengue in Cebu, the Philippines: a longitudinal, prospective, population-based cohort study. Lancet Infect Dis 2024:S1473-3099(24)00099-9. [PMID: 38527474 DOI: 10.1016/s1473-3099(24)00099-9] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND A three-dose dengue vaccine (CYD-TDV) was licensed for use in children aged 9 years and older starting in 2015 in several dengue-endemic countries. In 2016, the Philippine Department of Health implemented a dengue vaccination programme, which was discontinued because of safety concerns. We assessed the relative risk of developing virologically confirmed dengue among children who did or did not receive a single dose of CYD-TDV by previous dengue virus (DENV) infections at baseline classified as none, one, and two or more infections. METHODS In this longitudinal, prospective, population-based cohort study, we enrolled healthy children (aged 9-14 years) residing in Bogo or Balamban, Cebu, Philippines, between May 2, and June 2, 2017, before a mass dengue vaccination campaign, via the Rural Health Unit in Bogo and three Rural Health Units in Balamban. We collected demographic information and sera for baseline DENV serostatus and conducted active surveillance for acute febrile illness. Children who developed acute febrile illness were identified, clinical data were collected, and blood was drawn for confirmation of dengue by RT-PCR. The primary outcome was the relative risk of developing virologically confirmed dengue among children who received or did not receive a single dose of CYD-TDV by DENV serostatus at baseline. FINDINGS A single dose of CYD-TDV did not confer protection against virologically confirmed dengue in children who had none or one previous DENV infection at baseline. One dose conferred significant protection against hospital admission for virologically confirmed dengue among participants who had two or more previous DENV infections at baseline during the first 3 years (70%, 95% CI 20-88; p=0·017) and the entire follow-up period (67%, 19-87; p=0·016). INTERPRETATION The risk of developing virologically confirmed dengue after a single dose of CYD-TDV varied by baseline DENV serostatus. Since the study assessed the effect of only a single dose, the findings cannot inform decisions on vaccination by public health officers. However, the findings have implications for children who receive an incomplete vaccination regimen and these results should prompt more detailed analyses in future trials on dengue vaccines. FUNDING The Philippine Department of Health, Hanako Foundation, WHO, Swedish International Development Cooperation Agency, International Vaccine Institute, University of North Carolina, and US National Institute of Allergy and Infectious Diseases.
Collapse
Affiliation(s)
- Michelle Ylade
- Institute of Child Health and Human Development, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Maria Vinna Crisostomo
- Institute of Child Health and Human Development, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Jedas Veronica Daag
- Institute of Child Health and Human Development, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Kristal An Agrupis
- Institute of Child Health and Human Development, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Anna Maureen Cuachin
- Institute of Child Health and Human Development, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Ava Kristy Sy
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | | | | | - Ana Coello Escoto
- Viral Epidemiology and Immunity Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cameron Adams
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Laura White
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jacqueline Deen
- Institute of Child Health and Human Development, National Institutes of Health, University of the Philippines Manila, Manila, Philippines.
| | - Anna Lena Lopez
- Institute of Child Health and Human Development, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| |
Collapse
|
4
|
Wang L, Huang AT, Katzelnick LC, Lefrancq N, Escoto AC, Duret L, Chowdhury N, Jarman R, Conte MA, Berry IM, Fernandez S, Klungthong C, Thaisomboonsuk B, Suntarattiwong P, Vandepitte W, Whitehead S, Cauchemez S, Cummings DA, Salje H. Antigenic diversity and dengue disease risk. Res Sq 2023:rs.3.rs-3214507. [PMID: 37577717 PMCID: PMC10418532 DOI: 10.21203/rs.3.rs-3214507/v1] [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: 08/15/2023]
Abstract
Many pathogens continuously change their protein structure in response to immune-driven selection, resulting in weakened protection. In addition, for some pathogens such as dengue virus, poorly targeted immunity is associated with increased risk of severe disease, through a mechanism known as antibody-dependent enhancement. However, it remains a mystery whether the antigenic distance between an individual's first infection and subsequent exposures dictate disease risk, explaining the observed large-scale differences in dengue hospitalisations across years. Here we develop an inferential framework that combines detailed antigenic and genetic characterisation of viruses, and hospitalised cases from 21 years of surveillance in Bangkok, Thailand to identify the role of the antigenic profile of circulating viruses in determining disease risk. We find that the risk of hospitalisation depends on both the specific order of infecting serotypes and the antigenic distance between an individual's primary and secondary infections, with risk maximised at intermediate antigenic distances. These findings suggest immune imprinting helps determine dengue disease risk, and provides a pathway to monitor the changing risk profile of populations and to quantifying risk profiles of candidate vaccines.
Collapse
Affiliation(s)
- Lin Wang
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Angkana T. Huang
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Leah C. Katzelnick
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noémie Lefrancq
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Ana Coello Escoto
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Loréna Duret
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Nayeem Chowdhury
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Jarman
- Coalition for Epidemic Preparedness Initiative, Washington DC, USA
| | - Matthew A. Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | - Stephen Whitehead
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Paris, France
| | - Derek A.T. Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
5
|
Huang AT, Salje H, Escoto AC, Chowdhury N, Chávez C, Garcia-Carreras B, Rutvisuttinunt W, Maljkovic Berry I, Gromowski GD, Wang L, Klungthong C, Thaisomboonsuk B, Nisalak A, Trimmer-Smith LM, Rodriguez-Barraquer I, Ellison DW, Jones AR, Fernandez S, Thomas SJ, Smith DJ, Jarman R, Whitehead SS, Cummings DAT, Katzelnick LC. Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand. PLoS Pathog 2022; 18:e1010500. [PMID: 35500035 PMCID: PMC9098070 DOI: 10.1371/journal.ppat.1010500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 11/02/2021] [Revised: 05/12/2022] [Accepted: 04/05/2022] [Indexed: 11/19/2022] Open
Abstract
Neutralizing antibodies are important correlates of protection against dengue. Yet, determinants of variation in neutralization across strains within the four dengue virus serotypes (DENV1-4) is imperfectly understood. Studies focus on structural DENV proteins, especially the envelope (E), the primary target of anti-DENV antibodies. Although changes in immune recognition (antigenicity) are often attributed to variation in epitope residues, viral processes influencing conformation and epitope accessibility also affect neutralizability, suggesting possible modulating roles of nonstructural proteins. We estimated effects of residue changes in all 10 DENV proteins on antigenic distances between 348 DENV collected from individuals living in Bangkok, Thailand (1994-2014). Antigenic distances were derived from response of each virus to a panel of twenty non-human primate antisera. Across 100 estimations, excluding 10% of virus pairs each time, 77 of 295 positions with residue variability in E consistently conferred antigenic effects; 52 were within ±3 sites of known binding sites of neutralizing human monoclonal antibodies, exceeding expectations from random assignments of effects to sites (p = 0.037). Effects were also identified for 16 sites on the stem/anchor of E which were only recently shown to become exposed under physiological conditions. For all proteins, except nonstructural protein 2A (NS2A), root-mean-squared-error (RMSE) in predicting distances between pairs held out in each estimation did not outperform sequences of equal length derived from all proteins or E, suggesting that antigenic signals present were likely through linkage with E. Adjusted for E, we identified 62/219 sites embedding the excess signals in NS2A. Concatenating these sites to E additionally explained 3.4% to 4.0% of observed variance in antigenic distances compared to E alone (50.5% to 50.8%); RMSE outperformed concatenating E with sites from any protein of the virus (ΔRMSE, 95%IQR: 0.01, 0.05). Our results support examining antigenic determinants beyond the DENV surface. Dengue viruses, even of the same serotype, are differentially recognized by preexisting antibodies of individuals. With antibody levels being an important indicator of infection risk and pathogenicity, understanding mechanisms underlying these differences are crucial for vaccine design and development. Investigations have primarily targeted surface regions of the envelope protein (E) where virus-antibody interactions were thought to primarily occur. However, the roles of non-surface regions of the E protein as well as nonstructural proteins has been limited. We looked at the entire virus to identify associations between specific changes in the protein sequence and differences in how viruses were recognized by antibodies. In addition to recovering known determinants on the surface, we found signals in other areas on the structural building blocks of the virus. We also identified additional signals on specific areas of a protein that does not form structures of the virus but orchestrate virus formation. Our results point towards broadening the frame of investigation to gain a more comprehensive understanding of mechanisms giving rise to antibody recognition of dengue viruses, and may aid the design and evaluation of vaccines and/or assays to characterize dengue immunity.
Collapse
Affiliation(s)
- Angkana T. Huang
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Henrik Salje
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ana Coello Escoto
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nayeem Chowdhury
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Christian Chávez
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Bernardo Garcia-Carreras
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Gregory D. Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Lin Wang
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Ananda Nisalak
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Luke M. Trimmer-Smith
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Isabel Rodriguez-Barraquer
- School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Damon W. Ellison
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Anthony R. Jones
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stephen J. Thomas
- State University of New York Upstate Medical University, Syracuse, New York, United States of America
| | - Derek J. Smith
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Stephen S. Whitehead
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Derek A. T. Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (DATC); (LCK)
| | - Leah C. Katzelnick
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (DATC); (LCK)
| |
Collapse
|
6
|
Katzelnick LC, Escoto AC, Huang AT, Garcia-Carreras B, Chowdhury N, Berry IM, Chavez C, Buchy P, Duong V, Dussart P, Gromowski G, Macareo L, Thaisomboonsuk B, Fernandez S, Smith DJ, Jarman R, Whitehead SS, Salje H, Cummings DA. Antigenic evolution of dengue viruses over 20 years. Science 2021; 374:999-1004. [PMID: 34793238 PMCID: PMC8693836 DOI: 10.1126/science.abk0058] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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] [Indexed: 12/25/2022]
Abstract
Infection with one of dengue viruses 1 to 4 (DENV1-4) induces protective antibodies against homotypic infection. However, a notable feature of dengue viruses is the ability to use preexisting heterotypic antibodies to infect Fcγ receptor–bearing immune cells, leading to higher viral load and immunopathological events that augment disease. We tracked the antigenic dynamics of each DENV serotype by using 1944 sequenced isolates from Bangkok, Thailand, between 1994 and 2014 (348 strains), in comparison with regional and global DENV antigenic diversity (64 strains). Over the course of 20 years, the Thailand DENV serotypes gradually evolved away from one another. However, for brief periods, the serotypes increased in similarity, with corresponding changes in epidemic magnitude. Antigenic evolution within a genotype involved a trade-off between two types of antigenic change (within-serotype and between-serotype), whereas genotype replacement resulted in antigenic change away from all serotypes. These findings provide insights into theorized dynamics in antigenic evolution.
Collapse
Affiliation(s)
- Leah C. Katzelnick
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Ana Coello Escoto
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Angkana T. Huang
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Bernardo Garcia-Carreras
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
| | - Nayeem Chowdhury
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States
| | - Chris Chavez
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
| | - Philippe Buchy
- GlaxoSmithKline (GSK) Vaccines, 637421 Singapore, Singapore
| | - Veasna Duong
- Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, Phnom Penh 12201, Cambodia
| | - Philippe Dussart
- Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, Phnom Penh 12201, Cambodia
| | - Gregory Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States
| | - Louis Macareo
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Derek J. Smith
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States
| | - Stephen S. Whitehead
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Henrik Salje
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Derek A.T. Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
| |
Collapse
|
7
|
Katzelnick LC, Coello Escoto A, McElvany BD, Chávez C, Salje H, Luo W, Rodriguez-Barraquer I, Jarman R, Durbin AP, Diehl SA, Smith DJ, Whitehead SS, Cummings DAT. Viridot: An automated virus plaque (immunofocus) counter for the measurement of serological neutralizing responses with application to dengue virus. PLoS Negl Trop Dis 2018; 12:e0006862. [PMID: 30356267 PMCID: PMC6226209 DOI: 10.1371/journal.pntd.0006862] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/09/2018] [Accepted: 09/20/2018] [Indexed: 12/12/2022] Open
Abstract
The gold-standard method for quantifying neutralizing antibody responses to many viruses, including dengue virus (DENV), is the plaque reduction neutralization test (PRNT, also called the immunofocus reduction neutralization test). The PRNT conducted on 96-well plates is high-throughput and requires a smaller volume of antiserum than on 6- or 24-well plates, but manual plaque counting is challenging and existing automated plaque counters are expensive or difficult to optimize. We have developed Viridot (Viridot package), a program for R with a user interface in shiny, that counts viral plaques of a variety of phenotypes, estimates neutralizing antibody titers, and performs other calculations of use to virologists. The Viridot plaque counter includes an automatic parameter identification mode (misses <10 plaques/well for 87% of diverse DENV strains [n = 1521]) and a mode that allows the user to fine-tune the parameters used for counting plaques. We compared standardized manual and Viridot plaque counting methods applied to the same wells by two analyses and found that Viridot plaque counts were as similar to the same analyst's manual count (Lin’s concordance correlation coefficient, ρc = 0.99 [95% confidence interval: 0.99–1.00]) as manual counts between analysts (ρc = 0.99 [95% CI: 0.98–0.99]). The average ratio of neutralizing antibody titers based on manual counted plaques to Viridot counted plaques was 1.05 (95% CI: 0.98–1.14), similar to the average ratio of antibody titers based on manual plaque counts by the two analysts (1.06 [95% CI: 0.84–1.34]). Across diverse DENV and ZIKV strains (n = 14), manual and Viridot plaque counts were mostly consistent (range of ρc = 0.74 to 1.00) and the average ratio of antibody titers based on manual and Viridot counted plaques was close to 1 (0.94 [0.86–1.02]). Thus, Viridot can be used for plaque counting and neutralizing antibody titer estimation of diverse DENV strains and potentially other viruses on 96-well plates as well as for formalization of plaque-counting rules for standardization across experiments and analysts. Although the plaque reduction neutralization test (PRNT) is an important assay for measuring neutralizing antibody responses against many viruses, no free, open-source programs specifically designed for virus plaque counting and neutralizing antibody titer estimation are available. We have developed Viridot, a package for R with a user-interface in shiny, which is designed for use by laboratory-based virologists and researchers with minimal coding experience. The program includes: automatic and user-specification of settings for plaque counting; saving of plaque counting settings; counting of many plates at once; and easy output of plaque counts, plaque sizes, and images with counted plaques circled. Viridot also includes programs to analyze plaque counts, including estimation of: neutralizing antibody titers, pfu/mL of a virus stock, and the dilution factor of virus needed for an experiment. Viridot can be used to standardize plaque-counting methods within and between laboratories, helping researchers formalize an important aspect of the PRNT method that is often subjective. Viridot thus provides laboratory researchers around the world with a free tool to improve the speed and consistency with which the PRNT is conducted, aiding the public health response to emerging viral diseases.
Collapse
Affiliation(s)
- Leah C. Katzelnick
- Department of Biology, University of Florida, Gainesville, FL, United States
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
- * E-mail:
| | - Ana Coello Escoto
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Benjamin D. McElvany
- Department of Medicine-Infectious Disease, Vaccine Testing Center, University of Vermont Larner College of Medicine, Burlington, VT, United States
| | - Christian Chávez
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Henrik Salje
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Wensheng Luo
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Isabel Rodriguez-Barraquer
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Anna P. Durbin
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Sean A. Diehl
- Department of Medicine-Infectious Disease, Vaccine Testing Center, University of Vermont Larner College of Medicine, Burlington, VT, United States
| | - Derek J. Smith
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Stephen S. Whitehead
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Derek A. T. Cummings
- Department of Biology, University of Florida, Gainesville, FL, United States
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| |
Collapse
|