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Cárdenas P, Corredor V, Santos-Vega M. Genomic epidemiological models describe pathogen evolution across fitness valleys. SCIENCE ADVANCES 2022; 8:eabo0173. [PMID: 35857510 PMCID: PMC9278859 DOI: 10.1126/sciadv.abo0173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Genomics is fundamentally changing epidemiological research. However, systematically exploring hypotheses in pathogen evolution requires new modeling tools. Models intertwining pathogen epidemiology and genomic evolution can help understand processes such as the emergence of novel pathogen genotypes with higher transmissibility or resistance to treatment. In this work, we present Opqua, a flexible simulation framework that explicitly links epidemiology to sequence evolution and selection. We use Opqua to study determinants of evolution across fitness valleys. We confirm that competition can limit evolution in high-transmission environments and find that low transmission, host mobility, and complex pathogen life cycles facilitate reaching new adaptive peaks through population bottlenecks and decoupling of selective pressures. The results show the potential of genomic epidemiological modeling as a tool in infectious disease research.
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Affiliation(s)
- Pablo Cárdenas
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vladimir Corredor
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
| | - Mauricio Santos-Vega
- Grupo Biología Matemática y Computacional, Departamento Ingeniería Biomédica, Universidad de los Andes, Bogotá, D.C., Colombia
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Lourenço J, Obolski U, Swarthout TD, Gori A, Bar-Zeev N, Everett D, Kamng'ona AW, Mwalukomo TS, Mataya AA, Mwansambo C, Banda M, Gupta S, French N, Heyderman RS. Determinants of high residual post-PCV13 pneumococcal vaccine-type carriage in Blantyre, Malawi: a modelling study. BMC Med 2019; 17:219. [PMID: 31801542 PMCID: PMC6894346 DOI: 10.1186/s12916-019-1450-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/24/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND In November 2011, Malawi introduced the 13-valent pneumococcal conjugate vaccine (PCV13) into the routine infant schedule. Four to 7 years after introduction (2015-2018), rolling prospective nasopharyngeal carriage surveys were performed in the city of Blantyre. Carriage of Streptococcus pneumoniae vaccine serotypes (VT) remained higher than reported in high-income countries, and impact was asymmetric across age groups. METHODS A dynamic transmission model was fit to survey data using a Bayesian Markov-chain Monte Carlo approach, to obtain insights into the determinants of post-PCV13 age-specific VT carriage. RESULTS Accumulation of naturally acquired immunity with age and age-specific transmission potential were both key to reproducing the observed data. VT carriage reduction peaked sequentially over time, earlier in younger and later in older age groups. Estimated vaccine efficacy (protection against carriage) was 66.87% (95% CI 50.49-82.26%), similar to previous estimates. Ten-year projected vaccine impact (VT carriage reduction) among 0-9 years old was lower than observed in other settings, at 76.23% (CI 95% 68.02-81.96%), with sensitivity analyses demonstrating this to be mainly driven by a high local force of infection. CONCLUSIONS There are both vaccine-related and host-related determinants of post-PCV13 pneumococcal VT transmission in Blantyre with vaccine impact determined by an age-specific, local force of infection. These findings are likely to be generalisable to other Sub-Saharan African countries in which PCV impact on carriage (and therefore herd protection) has been lower than desired, and have implications for the interpretation of post-PCV carriage studies and future vaccination programs.
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Affiliation(s)
- J Lourenço
- Department of Zoology, University of Oxford, Oxford, UK.
| | - U Obolski
- School of Public Health, Tel Aviv University, Tel Aviv, Israel.,Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | - T D Swarthout
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | - A Gori
- NIHR Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
| | - N Bar-Zeev
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - D Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,The Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - A W Kamng'ona
- Department of Biomedical Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
| | - T S Mwalukomo
- Department of Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - A A Mataya
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | - M Banda
- Ministry of Education, Blantyre, Malawi
| | - S Gupta
- Department of Zoology, University of Oxford, Oxford, UK
| | - N French
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - R S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,NIHR Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
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Pilosof S, He Q, Tiedje KE, Ruybal-Pesántez S, Day KP, Pascual M. Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum. PLoS Biol 2019; 17:e3000336. [PMID: 31233490 PMCID: PMC6611651 DOI: 10.1371/journal.pbio.3000336] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 07/05/2019] [Accepted: 06/05/2019] [Indexed: 01/14/2023] Open
Abstract
In their competition for hosts, parasites with antigens that are novel to the host immune system will be at a competitive advantage. The resulting frequency-dependent selection can structure parasite populations into strains of limited genetic overlap. For the causative agent of malaria, Plasmodium falciparum, the high recombination rates and associated vast diversity of its highly antigenic and multicopy var genes preclude such clear clustering in endemic regions. This undermines the definition of strains as specific, temporally persisting gene variant combinations. We use temporal multilayer networks to analyze the genetic similarity of parasites in both simulated data and in an extensively and longitudinally sampled population in Ghana. When viewed over time, populations are structured into modules (i.e., groups) of parasite genomes whose var gene combinations are more similar within than between the modules and whose persistence is much longer than that of the individual genomes that compose them. Comparison to neutral models that retain parasite population dynamics but lack competition reveals that the selection imposed by host immunity promotes the persistence of these modules. The modular structure is, in turn, associated with a slower acquisition of immunity by individual hosts. Modules thus represent dynamically generated niches in host immune space, which can be interpreted as strains. Negative frequency-dependent selection therefore shapes the organization of the var diversity into parasite genomes, leaving a persistence signature over ecological time scales. Multilayer networks extend the scope of phylodynamics analyses by allowing quantification of temporal genetic structure in organisms that generate variation via recombination or other non-bifurcating processes. A strain structure similar to the one described here should apply to other pathogens with large antigenic spaces that evolve via recombination. For malaria, the temporal modular structure should enable the formulation of tractable epidemiological models that account for parasite antigenic diversity and its influence on intervention outcomes. A combination of computational modeling and empirical data reveals persistent strain structure despite vast antigenic diversity in the human malaria parasite Plasmodium falciparum, with potential consequences for the acquisition of immunity.
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Affiliation(s)
- Shai Pilosof
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Qixin He
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Kathryn E. Tiedje
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
| | | | - Karen P. Day
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
| | - Mercedes Pascual
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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Reverse immunodynamics: a new method for identifying targets of protective immunity. Sci Rep 2019; 9:2164. [PMID: 30770839 PMCID: PMC6377634 DOI: 10.1038/s41598-018-37288-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
Despite a dramatic increase in our ability to catalogue variation among pathogen genomes, we have made far fewer advances in using this information to identify targets of protective immunity. Epidemiological models predict that strong immune selection can cause antigenic variants to structure into genetically discordant sets of antigenic types (e.g. serotypes). A corollary of this theory is that targets of immunity may be identified by searching for non-overlapping associations of amino acids among co-circulating antigenic variants. We propose a novel population genetics methodology that combines such predictions with phylogenetic analyses to identify genetic loci (epitopes) under strong immune selection. We apply this concept to the AMA-1 protein of the malaria parasite Plasmodium falciparum and find evidence of epitopes among certain regions of low variability which could render them ideal vaccine candidates. The proposed method can be applied to a myriad of multi-strain pathogens for which vast amounts of genetic data has been collected in recent years.
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Lourenço J, Watkins ER, Obolski U, Peacock SJ, Morris C, Maiden MCJ, Gupta S. Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein. Sci Rep 2017; 7:9023. [PMID: 28831154 PMCID: PMC5567354 DOI: 10.1038/s41598-017-08990-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022] Open
Abstract
Populations of Streptococcus pneumoniae (SP) are typically structured into groups of closely related organisms or lineages, but it is not clear whether they are maintained by selection or neutral processes. Here, we attempt to address this question by applying a machine learning technique to SP whole genomes. Our results indicate that lineages evolved through immune selection on the groEL chaperone protein. The groEL protein is part of the groESL operon and enables a large range of proteins to fold correctly within the physical environment of the nasopharynx, thereby explaining why lineage structure is so stable within SP despite high levels of genetic transfer. SP is also antigenically diverse, exhibiting a variety of distinct capsular serotypes. Associations exist between lineage and capsular serotype but these can be easily perturbed, such as by vaccination. Overall, our analyses indicate that the evolution of SP can be conceptualized as the rearrangement of modular functional units occurring on several different timescales under different pressures: some patterns have locked in early (such as the epistatic interactions between groESL and a constellation of other genes) and preserve the differentiation of lineages, while others (such as the associations between capsular serotype and lineage) remain in continuous flux.
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Affiliation(s)
- José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
| | | | - Uri Obolski
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samuel J Peacock
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | | | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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