scholarly journals Learning the language of viral evolution and escape

Science ◽  
2021 ◽  
Vol 371 (6526) ◽  
pp. 284-288 ◽  
Author(s):  
Brian Hie ◽  
Ellen D. Zhong ◽  
Bonnie Berger ◽  
Bryan Bryson
Keyword(s):  
Immune System ◽  
Natural Language ◽  
Vaccine Development ◽  
Sequence Data ◽  
Viral Evolution ◽  
Machine Learning Algorithms ◽  
Language Models ◽  
Viral Escape ◽  
Human Immune System ◽  
Influenza Hemagglutinin

The ability for viruses to mutate and evade the human immune system and cause infection, called viral escape, remains an obstacle to antiviral and vaccine development. Understanding the complex rules that govern escape could inform therapeutic design. We modeled viral escape with machine learning algorithms originally developed for human natural language. We identified escape mutations as those that preserve viral infectivity but cause a virus to look different to the immune system, akin to word changes that preserve a sentence’s grammaticality but change its meaning. With this approach, language models of influenza hemagglutinin, HIV-1 envelope glycoprotein (HIV Env), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike viral proteins can accurately predict structural escape patterns using sequence data alone. Our study represents a promising conceptual bridge between natural language and viral evolution.

scholarly journals Learning the language of viral evolution and escape

2020 ◽  
Author(s):  
Brian Hie ◽  
Ellen Zhong ◽  
Bonnie Berger ◽  
Bryan Bryson
Keyword(s):  
Natural Language ◽  
Vaccine Development ◽  
Viral Evolution ◽  
Machine Learning Algorithms ◽  
Viral Fitness ◽  
Language Models ◽  
Viral Escape ◽  
Semantic Change ◽  
Influenza Hemagglutinin ◽  
Escape Mutants

AbstractViral mutation that escapes from human immunity remains a major obstacle to antiviral and vaccine development. While anticipating escape could aid rational therapeutic design, the complex rules governing viral escape are challenging to model. Here, we demonstrate an unprecedented ability to predict viral escape by using machine learning algorithms originally developed to model the complexity of human natural language. Our key conceptual advance is that predicting escape requires identifying mutations that preserve viral fitness, or “grammaticality,” and also induce high antigenic change, or “semantic change.” We develop viral language models for influenza hemagglutinin, HIV Env, and SARS-CoV-2 Spike that we use to construct antigenically meaningful semantic landscapes, perform completely unsupervised prediction of escape mutants, and learn structural escape patterns from sequence alone. More profoundly, we lay a promising conceptual bridge between natural language and viral evolution.One sentence summaryNeural language models of semantic change and grammaticality enable unprecedented prediction of viral escape mutations.

scholarly journals Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Juhye M Lee ◽  
Rachel Eguia ◽  
Seth J Zost ◽  
Saket Choudhary ◽  
Patrick C Wilson ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Viral Evolution ◽  
Surface Protein ◽  
Viral Escape ◽  
Viral Neutralization ◽  
Influenza Hemagglutinin ◽  
Human Sera ◽  
Order Of Magnitude ◽  
Amino Acid Mutations ◽  
Major Surface

A longstanding question is how influenza virus evolves to escape human immunity, which is polyclonal and can target many distinct epitopes. Here, we map how all amino-acid mutations to influenza’s major surface protein affect viral neutralization by polyclonal human sera. The serum of some individuals is so focused that it selects single mutations that reduce viral neutralization by over an order of magnitude. However, different viral mutations escape the sera of different individuals. This individual-to-individual variation in viral escape mutations is not present among ferrets that have been infected just once with a defined viral strain. Our results show how different single mutations help influenza virus escape the immunity of different members of the human population, a phenomenon that could shape viral evolution and disease susceptibility.

scholarly journals Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin

2019 ◽  
Author(s):  
Juhye M. Lee ◽  
Rachel Eguia ◽  
Seth J. Zost ◽  
Saket Choudhary ◽  
Patrick C. Wilson ◽  
...  
Keyword(s):  
Viral Evolution ◽  
Surface Protein ◽  
Viral Escape ◽  
Viral Neutralization ◽  
Influenza Hemagglutinin ◽  
Human Sera ◽  
Order Of Magnitude ◽  
Amino Acid Mutations ◽  
Major Surface ◽  
Polyclonal Serum

AbstractA longstanding question is how influenza evolves to escape human immunity, which is polyclonal and can target many distinct epitopes on the virus. Here we map how all amino-acid mutations to influenza’s major surface protein affect viral neutralization by polyclonal human sera. The serum of some individuals is so focused that it selects single mutations that reduce viral neutralization by over an order of magnitude. However, different viral mutations escape the sera of different individuals. This individual-to-individual variation in viral escape mutations isnotpresent among ferrets, which are frequently used as a model in influenza studies. Our results show how different single mutations help influenza escape the immunity of different members of the human population, a phenomenon that could shape viral evolution and disease susceptibility.

COVIEdb: A database for potential immune epitopes of coronaviruses

2020 ◽  
Author(s):  
Jingcheng Wu ◽  
Wenfan Chen ◽  
Jingjing Zhou ◽  
Wenyi Zhao ◽  
Shuqing Chen ◽  
...  
Keyword(s):  
Immune System ◽  
Large Scale ◽  
Vaccine Development ◽  
Protein Sequences ◽  
T Cell Epitopes ◽  
Human Immune System ◽  
The World ◽  
Human Immune ◽  
Human Coronaviruses ◽  
Novel Coronavirus

Abstract2019 novel coronavirus (2019-nCoV) has caused large-scale pandemic COVID-19 all over the world. It’s essential to find out which parts of the 2019-nCoV sequence are recognized by human immune system for vaccine development. And for the prevention of the potential outbreak of similar coronaviruses in the future, vaccines against immunogenic epitopes shared by different human coronaviruses are essential. Here we predict all the potential B/T-cell epitopes for SARS-CoV, MERS-CoV, 2019-nCoV and RaTG13-CoV based on the protein sequences. We found YFKYWDQTY in ORF1ab protein, VYDPLQPEL and TVYDPLQPEL in spike (S) protein might be pan-coronavirus targets for vaccine development. All the predicted results are stored in a database COVIEdb (http://biopharm.zju.edu.cn/coviedb/).

scholarly journals Cooperation between Strain-Specific and Broadly Neutralizing Responses Limited Viral Escape and Prolonged the Exposure of the Broadly Neutralizing Epitope

2017 ◽  
Vol 91 (18) ◽  
Author(s):  
Colin Anthony ◽  
Talita York ◽  
Valerie Bekker ◽  
David Matten ◽  
Philippe Selhorst ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Prolonged Exposure ◽  
Vaccine Development ◽  
Viral Evolution ◽  
Neutralizing Antibody ◽  
Viral Escape ◽  
Broadly Neutralizing Antibodies ◽  
Immunogen Design ◽  
Early Strain ◽  
Hiv 1

ABSTRACT V3-glycan-targeting broadly neutralizing antibodies (bNAbs) are a focus of HIV-1 vaccine development. Understanding the viral dynamics that stimulate the development of these antibodies can provide insights for immunogen design. We used a deep-sequencing approach, together with neutralization phenotyping, to investigate the rate and complexity of escape from V3-glycan-directed bNAbs compared to overlapping early strain-specific neutralizing antibody (ssNAb) responses to the V3/C3 region in donor CAP177. Escape from the ssNAb response occurred rapidly via an N334-to-N332 glycan switch, which took just 7.5 weeks to reach >50% frequency. In contrast, escape from the bNAbs was mediated via multiple pathways and took longer, with escape first occurring through an increase in V1 loop length, which took 46 weeks to reach 50% frequency, followed by an N332-to-N334 reversion, which took 66 weeks. Importantly, bNAb escape was incomplete, with contemporaneous neutralization observed up to 3 years postinfection. Both the ssNAb response and the bNAb response were modulated by the presence/absence of the N332 glycan, indicating an overlap between the two epitopes. Thus, selective pressure by ssNAbs to maintain the N332 glycan may have constrained the bNAb escape pathway. This slower and incomplete viral escape resulted in prolonged exposure of the bNAb epitope, which may in turn have aided the maturation of the bNAb lineage. IMPORTANCE The development of an HIV-1 vaccine is of paramount importance, and broadly neutralizing antibodies are likely to be a key component of a protective vaccine. The V3-glycan-targeting bNAb responses are among the most promising vaccine targets, as they are commonly elicited during infection. Understanding the interplay between viral evolution and the development of these antibodies provides insights that may guide immunogen design. Our work contrasted the dynamics of the early strain-specific antibodies and the later broadly neutralizing responses to a common Env target (V3C3), showing slower and more complex escape from bNAbs. Constrained bNAb escape, together with evidence of contemporaneous autologous virus neutralization, supports the proposal that prolonged exposure of the bNAb epitope enabled the maturation of the bNAb lineage.

scholarly journals The Interplay between Dengue Virus and the Human Innate Immune System: A Game of Hide and Seek

Vaccines ◽  
2019 ◽  
Vol 7 (4) ◽  
pp. 145 ◽  
Author(s):  
Nicolas Tremblay ◽  
Wesley Freppel ◽  
Aïssatou Aïcha Sow ◽  
Laurent Chatel-Chaix
Keyword(s):  
Immune System ◽  
Dengue Virus ◽  
Innate Immune System ◽  
Vaccine Development ◽  
Immunological Response ◽  
Innate Immune ◽  
Special Focus ◽  
World Population ◽  
Human Immune System ◽  
System A

With 40% of the world population at risk, infections with dengue virus (DENV) constitute a serious threat to public health. While there is no antiviral therapy available against this potentially lethal disease, the efficacy of the only approved vaccine is not optimal and its safety has been recently questioned. In order to develop better vaccines based on attenuated and/or chimeric viruses, one must consider how the human immune system is engaged during DENV infection. The activation of the innate immunity through the detection of viruses by cellular sensors is the first line of defence against those pathogens. This triggers a cascade of events which establishes an antiviral state at the cell level and leads to a global immunological response. However, DENV has evolved to interfere with the innate immune signalling at multiple levels, hence dampening antiviral responses and favouring viral replication and dissemination. This review elaborates on the interplay between DENV and the innate immune system. A special focus is given on the viral countermeasure mechanisms reported over the last decade which should be taken into consideration during vaccine development.

scholarly journals Viral evolution under the pressure of an adaptive immune system: Optimal mutation rates for viral escape

Complexity ◽  
2002 ◽  
Vol 8 (2) ◽  
pp. 28-33 ◽  
Author(s):  
Christel Kamp ◽  
Claus O. Wilke ◽  
Christoph Adami ◽  
Stefan Bornholdt
Keyword(s):  
Immune System ◽  
Viral Evolution ◽  
Adaptive Immune System ◽  
Viral Escape ◽  
Mutation Rates ◽  
Adaptive Immune ◽  
System Optimal

scholarly journals Complete mapping of viral escape from neutralizing antibodies

2016 ◽  
Author(s):  
Michael B. Doud ◽  
Scott E. Hensley ◽  
Jesse D. Bloom
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Neutralizing Antibodies ◽  
Viral Evolution ◽  
The Other ◽  
Viral Escape ◽  
Amino Acid Mutation ◽  
Influenza Hemagglutinin ◽  
Complete Mapping ◽  
Protein Variants

AbstractIdentifying viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution. Here we quantify how every amino-acid mutation to influenza hemagglutinin affects neutralization by monoclonal antibodies targeting several antigenic regions. Our approach involves creating all replication-competent protein variants of the virus, selecting these variants with antibody, and using deep sequencing to identify enriched mutations. These high-throughput measurements are predictive of the effects of individual mutations in traditional neutralization assays. At many residues, only some of the possible mutations escape from an antibody. For instance, at a single residue targeted by two different antibodies, we identify some mutations that escape both antibodies and other mutations that escape only one or the other. Therefore, our approach maps how viruses can escape antibodies with mutation-level sensitivity, and shows that only some mutations at antigenic residues actually alter antigenicity.

XMODULATION IN MICEAND MEN: IL-10 PRODUCING CELLS INBLOOD AND LYMPHOID TISSUE

2008 ◽  
Vol 31 (4) ◽  
pp. 3
Author(s):  
L Barrett ◽  
M Grant ◽  
R Liwski ◽  
K West
Keyword(s):  
Immune System ◽  
Peripheral Blood ◽  
Lymphoid Tissue ◽  
Mononuclear Cells ◽  
Ex Vivo ◽  
White Blood Cells ◽  
Interleukin 10 ◽  
Healthy Individuals ◽  
Human Immune System ◽  
Healthy Humans

Background: The human immune system provides remarkable protection from a plethora of pathogens, but can cause damage when activated for a prolonged time (as inpersistent infections) or against self (autoimmunity). Therefore, mechanisms of immune system downregulation and control are imperative. There is little data on how the immune system is controlled in healthy individuals. We recently described a novel population of white blood cells that constitutively produce the immunomodulatory cytokine interleukin-10 (IL-10). Our objective was to further delineate the distribution of these cells in human and mouse models, as well as potential triggers for interleukin-10 production in vitro. Methods: Human and animal protocols were reviewed and approved by the institutional ethics board and animal care facilities, and informed consent was obtained from all human donors. The ex vivo percentage of peripheral blood CD36^+IL-10^+ mononuclear cells was assessed by intracellular flow cytometry in 10 healthy individuals. IL-10 production after exposure to twoCD36 ligands, thrombospondin and oxidized low density lipoprotein (oxLDL) was measured at 8 hours. Peripheral blood mononuclear cells and splenocytes from BL/6 (n=5) and Balb/c (n=1) micewere assessed for CD36^+IL-10^+ cells ex vivo as well. Results: The percentage of CD36^+IL-10^+ cells in peripheral blood fromhealthy individuals ranges between 0.1% and 0.9%. The percentage was similar in mouse peripheral blood, with a range of 0.4%-1.1%. These cells were also found in mouse spleen at a higher frequency than peripherally (1.1-1.5%). Human CD36^+IL-10^+ cells have more IL-10 when exposed to thrombospondin, oxLDL. Conclusions: Our novel population of IL-10 producing cells is found not only in healthy humans, but also in lymphoid tissue and blood from pathogen free mice. This highlights the evolutionary conservation of the cell across species, and suggests an important homeostatic function. The physiologic ligands for CD36 are ubiquitous in circulation, and ourin vitro data suggests a link between CD36 ligation and IL-10 production. IL-10 is a known immune system modulator, and its production by these cells may help maintain homeostaticcontrol of the immune system.

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