Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing

As one of the main influenza antigens, neuraminidase (NA) in H3N2 virus has evolved extensively for more than 50 years due to continuous immune pressure. While NA has recently emerged as an effective vaccine target, biophysical constraints on the antigenic evolution of NA remain largely elusive. Here, we apply combinatorial mutagenesis and next-generation sequencing to characterize the local fitness landscape in an antigenic region of NA in six different human H3N2 strains that were isolated around 10 years apart. The local fitness landscape correlates well among strains and the pairwise epistasis is highly conserved. Our analysis further demonstrates that local net charge governs the pairwise epistasis in this antigenic region. In addition, we show that residue coevolution in this antigenic region is correlated with the pairwise epistasis between charge states. Overall, this study demonstrates the importance of quantifying epistasis and the underlying biophysical constraint for building a model of influenza evolution.

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Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing

10.1101/2021.07.10.451918 ◽

2021 ◽

Author(s):

Yiquan Wang ◽

Ruipeng Lei ◽

Armita Nourmohammad ◽

Nicholas C. Wu

Keyword(s):

Fitness Landscape ◽

H3n2 Virus ◽

Effective Vaccine ◽

Human Influenza ◽

Net Charge ◽

Antigenic Region ◽

Immune Pressure ◽

Antigenic Evolution ◽

Charge Balancing ◽

Influenza H3n2

As one of the main influenza antigens, neuraminidase (NA) in H3N2 virus has evolved extensively for more than 50 years due to continuous immune pressure. While NA has emerged as an effective vaccine target recently, biophysical constraints on the antigenic evolution of NA remain largely elusive. Here, we apply deep mutational scanning to characterize the local fitness landscape in an antigenic region of NA in six different human H3N2 strains that were isolated around 10 years apart. The local fitness landscape correlates well among strains and the pairwise epistasis is highly conserved. Our analysis further demonstrates that local net charge governs the pairwise epistasis in this antigenic region. In addition, we show that residue coevolution in this antigenic region can be predicted by charge states and pairwise epistasis. Overall, this study demonstrates the importance of quantifying epistasis and the underlying biophysical constraint for building a predictive model of influenza evolution.

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Mutational networks of escape from transmitted HIV-1 infection

PLoS ONE ◽

10.1371/journal.pone.0243391 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243391

Author(s):

Elma H. Akand ◽

Stephen J. Maher ◽

John M. Murray

Keyword(s):

Immune Response ◽

Effective Vaccine ◽

Subtype C ◽

Hub And Spoke ◽

Binding Domains ◽

Immune Pressure ◽

Subtype B ◽

Combined Operations ◽

Founder Virus ◽

Coreceptor Binding

Human immunodeficiency virus (HIV) is subject to immune selective pressure soon after it establishes infection at the founder stage. As an individual progresses from the founder to chronic stage of infection, immune pressure forces a history of mutations that are embedded in envelope sequences. Determining this pathway of coevolving mutations can assist in understanding what is different with the founder virus and the essential pathways it takes to maintain infection. We have combined operations research and bioinformatics methods to extract key networks of mutations that differentiate founder and chronic stages for 156 subtype B and 107 subtype C envelope (gp160) sequences. The chronic networks for both subtypes revealed strikingly different hub-and-spoke topologies compared to the less structured transmission networks. This suggests that the hub nodes are impacted by the immune response and the resulting loss of fitness is compensated by mutations at the spoke positions. The major hubs in the chronic C network occur at positions 12, 137 (within the N136 glycan), and 822, and at position 306 for subtype B. While both founder networks had a more heterogeneous connected network structure, interestingly founder B subnetworks around positions 640 and 837 preferentially contained CD4 and coreceptor binding domains. Finally, we observed a differential effect of glycosylation between founder and chronic subtype B where the latter had mutational pathways significantly driven by N-glycosylation. Our study provides insights into the mutational pathways HIV takes to evade the immune response, and presents features more likely to establish founder infection, valuable for effective vaccine design.

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Charge Balancing of Model Gold-Nanoparticle-Peptide Conjugates Controlled by the Peptide’s Net Charge and the Ligand to Nanoparticle Ratio

The Journal of Physical Chemistry C ◽

10.1021/jp501489t ◽

2014 ◽

Vol 118 (19) ◽

pp. 10302-10313 ◽

Cited By ~ 26

Author(s):

L. Gamrad ◽

C. Rehbock ◽

J. Krawinkel ◽

B. Tumursukh ◽

A. Heisterkamp ◽

...

Keyword(s):

Gold Nanoparticle ◽

Peptide Conjugates ◽

Net Charge ◽

Charge Balancing

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Analysis of the Diversity of the AvBD Gene Region in Japanese Quail

Journal of Heredity ◽

10.1093/jhered/esaa035 ◽

2020 ◽

Vol 111 (5) ◽

pp. 436-443

Author(s):

Taichiro Ishige ◽

Hiromi Hara ◽

Takashi Hirano ◽

Tomohiro Kono ◽

Kei Hanzawa

Keyword(s):

Chromosomal Region ◽

Copy Number Variants ◽

Genomic Analysis ◽

Inbred Lines ◽

Innate Immune ◽

Coturnix Japonica ◽

Gene Region ◽

Functional Variation ◽

Net Charge ◽

Generation Sequencing

Abstract The avian β-defensin (AvBD) gene region is an important component of the innate immune system, encoding a variety of antimicrobial peptides. The AvBD region forms a multigene cluster in a specific chromosomal region. Comparison of the AvBD region among various birds suggests the presence of defects, duplications, and pseudogenization at many loci. The AvBD region in certain galliform birds, namely chicken, turkey, and bobwhite quail, includes AvBD3, -6, and -7, with the latter exhibiting copy number variants (CNVs) in chickens. DNA for genomic analysis was extracted from the peripheral blood of 99 randomly selected quail (Coturnix japonica) from 6 inbred lines. Nine CjAvBD1 and 8 CjAvBD12 alleles were detected. Ten haplotypes, including three that were strain specific, were found in alleles from the quail AvBD1 (CjAvBD1) and -12 (CjAvBD12) loci. Next-generation sequencing was used to determine the nucleotide sequences of the CjAvBD gene region (56–70 kb) for 7 homozygous diplotypes of these 10 haplotypes. These 7 haplotypes contained between 12 and 16 CjAvBD genes and were composed of 11 common loci: CjAvBD1, -2, -4, -5, -8, -9, -10, -11, -12, -13, and -14, but lacked CjAvBD3 and -7. Furthermore, up to 5 CjAvBD101 (AvBD6 ortholog) CNVs were observed among the 7 haplotypes. In addition, we detected amino acid substitutions causing net charge mutations that could affect antimicrobial activity in CjAvBD4, -13, -14, and -101. These results suggest that the CjAvBD region is unique among the Galliformes and that its diversity results in potential functional variation in innate immunity.

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Assessing baloxavir susceptibility of influenza viruses circulating in the United States during the 2016/17 and 2017/18 seasons

Eurosurveillance ◽

10.2807/1560-7917.es.2019.24.3.1800666 ◽

2019 ◽

Vol 24 (3) ◽

Cited By ~ 39

Author(s):

Larisa V Gubareva ◽

Vasiliy P Mishin ◽

Mira C Patel ◽

Anton Chesnokov ◽

Ha T Nguyen ◽

...

Keyword(s):

United States ◽

Influenza A ◽

The United States ◽

Influenza Viruses ◽

H3n2 Virus ◽

Amino Acid Substitutions ◽

Sequencing Analysis ◽

Dependent Endonuclease ◽

Next Generation Sequencing Analysis ◽

Generation Sequencing

The anti-influenza therapeutic baloxavir targets cap-dependent endonuclease activity of polymerase acidic (PA) protein. We monitored baloxavir susceptibility in the United States with next generation sequencing analysis supplemented by phenotypic one-cycle infection assay. Analysis of PA sequences of 6,891 influenza A and B viruses collected during 2016/17 and 2017/18 seasons showed amino acid substitutions: I38L (two A(H1N1)pdm09 viruses), E23G (two A(H1N1)pdm09 viruses) and I38M (one A(H3N2) virus); conferring 4–10-fold reduced susceptibility to baloxavir.

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Inferring the intrinsic mutational fitness landscape of influenza-like evolving antigens from temporally ordered sequence data

10.1101/2021.07.28.454153 ◽

2021 ◽

Author(s):

Julia Doelger ◽

Mehran Kardar ◽

Arup K. Chakraborty

Keyword(s):

Phylogenetic Trees ◽

Fitness Landscape ◽

Sequence Data ◽

Viral Evolution ◽

Viral Fitness ◽

Computational Method ◽

Stochastic Simulations ◽

Immune Pressure ◽

Antigenic Proteins ◽

Basic Features

There still are no effective long-term protective vaccines against viruses that continuously evolve under immune pressure such as seasonal influenza, which has caused, and can cause, devastating epidemics in the human population. For finding such a broadly protective immunization strategy it is useful to know how easily the virus can escape via mutation from specific antibody responses. This information is encoded in the fitness landscape of the viral proteins (i.e., knowledge of the viral fitness as a function of sequence). Here we present a computational method to infer the intrinsic mutational fitness landscape of influenza-like evolving antigens from yearly sequence data. We test inference performance with computer-generated sequence data that are based on stochastic simulations mimicking basic features of immune-driven viral evolution. Although the numerically simulated model does create a phylogeny based on the allowed mutations, the inference scheme does not use this information. This provides a contrast to other methods that rely on reconstruction of phylogenetic trees. Our method just needs a sufficient number of samples over multiple years. With our method we are able to infer single- as well as pairwise mutational fitness effects from the simulated sequence time series for short antigenic proteins. Our fitness inference approach may have potential future use for design of immunization protocols by identifying intrinsically vulnerable immune target combinations on antigens that evolve under immune-driven selection. This approach may in the future be applied to influenza and other novel viruses such as SARS-CoV-2, which evolves and, like influenza, might continue to escape the natural and vaccine-mediated immune pressures.

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Modelling and in vitro testing of the HIV-1 Nef fitness landscape

Virus Evolution ◽

10.1093/ve/vez029 ◽

2019 ◽

Vol 5 (2) ◽

Author(s):

John P Barton ◽

Erasha Rajkoomar ◽

Jaclyn K Mann ◽

Dariusz K Murakowski ◽

Mako Toyoda ◽

...

Keyword(s):

Clinical Data ◽

Fitness Landscape ◽

Effective Vaccine ◽

In Vitro Testing ◽

Multifunctional Protein ◽

Model Predictions ◽

The Cost ◽

Hiv 1

Abstract An effective vaccine is urgently required to curb the HIV-1 epidemic. We have previously described an approach to model the fitness landscape of several HIV-1 proteins, and have validated the results against experimental and clinical data. The fitness landscape may be used to identify mutation patterns harmful to virus viability, and consequently inform the design of immunogens that can target such regions for immunological control. Here we apply such an analysis and complementary experiments to HIV-1 Nef, a multifunctional protein which plays a key role in HIV-1 pathogenesis. We measured Nef-driven replication capacities as well as Nef-mediated CD4 and HLA-I down-modulation capacities of thirty-two different Nef mutants, and tested model predictions against these results. Furthermore, we evaluated the models using 448 patient-derived Nef sequences for which several Nef activities were previously measured. Model predictions correlated significantly with Nef-driven replication and CD4 down-modulation capacities, but not HLA-I down-modulation capacities, of the various Nef mutants. Similarly, in our analysis of patient-derived Nef sequences, CD4 down-modulation capacity correlated the most significantly with model predictions, suggesting that of the tested Nef functions, this is the most important in vivo. Overall, our results highlight how the fitness landscape inferred from patient-derived sequences captures, at least in part, the in vivo functional effects of mutations to Nef. However, the correlation between predictions of the fitness landscape and measured parameters of Nef function is not as accurate as the correlation observed in past studies for other proteins. This may be because of the additional complexity associated with inferring the cost of mutations on the diverse functions of Nef.

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Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

Science ◽

10.1126/science.abf6950 ◽

2021 ◽

Vol 371 (6534) ◽

pp. 1139-1142 ◽

Cited By ~ 34

Author(s):

Kevin R. McCarthy ◽

Linda J. Rennick ◽

Sham Nambulli ◽

Lindsey R. Robinson-McCarthy ◽

William G. Bain ◽

...

Keyword(s):

Amino Acids ◽

Neutralizing Antibodies ◽

Rna Viruses ◽

Human Populations ◽

Spike Glycoprotein ◽

Immune Pressure ◽

Global Concern ◽

Antigenic Evolution ◽

Antibody Epitopes ◽

Recurrent Deletion

Zoonotic pandemics, such as that caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can follow the spillover of animal viruses into highly susceptible human populations. The descendants of these viruses have adapted to the human host and evolved to evade immune pressure. Coronaviruses acquire substitutions more slowly than other RNA viruses. In the spike glycoprotein, we found that recurrent deletions overcome this slow substitution rate. Deletion variants arise in diverse genetic and geographic backgrounds, transmit efficiently, and are present in novel lineages, including those of current global concern. They frequently occupy recurrent deletion regions (RDRs), which map to defined antibody epitopes. Deletions in RDRs confer resistance to neutralizing antibodies. By altering stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution.

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Machine learning-guided acyl-ACP reductase engineering for improved in vivo fatty alcohol production

Nature Communications ◽

10.1038/s41467-021-25831-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jonathan C. Greenhalgh ◽

Sarah A. Fahlberg ◽

Brian F. Pfleger ◽

Philip A. Romero

Keyword(s):

Machine Learning ◽

Enzyme Activity ◽

Fitness Landscape ◽

Fatty Acyl ◽

Fatty Alcohols ◽

High Flux ◽

Net Charge ◽

Alcohol Production ◽

Catalytic Rate

AbstractAlcohol-forming fatty acyl reductases (FARs) catalyze the reduction of thioesters to alcohols and are key enzymes for microbial production of fatty alcohols. Many metabolic engineering strategies utilize FARs to produce fatty alcohols from intracellular acyl-CoA and acyl-ACP pools; however, enzyme activity, especially on acyl-ACPs, remains a significant bottleneck to high-flux production. Here, we engineer FARs with enhanced activity on acyl-ACP substrates by implementing a machine learning (ML)-driven approach to iteratively search the protein fitness landscape. Over the course of ten design-test-learn rounds, we engineer enzymes that produce over twofold more fatty alcohols than the starting natural sequences. We characterize the top sequence and show that it has an enhanced catalytic rate on palmitoyl-ACP. Finally, we analyze the sequence-function data to identify features, like the net charge near the substrate-binding site, that correlate with in vivo activity. This work demonstrates the power of ML to navigate the fitness landscape of traditionally difficult-to-engineer proteins.

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Antigenic evolution of SARS-CoV-2 in immunocompromised hosts

10.1101/2022.01.13.22269154 ◽

2022 ◽

Author(s):

Cameron A Smith ◽

Ben Ashby

Keyword(s):

Evolutionary Dynamics ◽

Immune Escape ◽

Middle Income ◽

Apparent Lack ◽

Middle Income Countries ◽

Persistent Infections ◽

Immune Pressure ◽

Qualitative Effect ◽

Antigenic Evolution ◽

Immunocompromised Hosts

The apparent lack of antigenic evolution by the Delta variant (B.1.617.2) of SARS-CoV-2 during the COVID-19 pandemic is puzzling. The combination of increasing immune pressure due to the rollout of vaccines and a relatively high number of infections following the relaxation of non-pharmaceutical interventions should have created perfect conditions for immune escape variants to evolve from the Delta lineage. Instead, the Omicron variant (B.1.1.529), which is hypothesised to have evolved in an immunocompromised individual, is the first major variant to exhibit significant immune escape following vaccination programmes and is set to become globally dominant in 2022. Here, we use a simple mathematical model to explore possible reasons why the Delta lineage did not exhibit antigenic evolution and to understand how and when immunocompromised individuals affect the emergence of immune escape variants. We show that when the pathogen does not have to cross a fitness valley for immune escape to occur, immunocompromised individuals have no qualitative effect on antigenic evolution (although they may accelerate immune escape if within-host evolutionary dynamics are faster in immunocompromised individuals). But if a fitness valley exists between immune escape variants at the between-host level, then persistent infections of immunocompromised individuals allow mutations to accumulate, therefore facilitating rather than simply speeding up antigenic evolution. Our results suggest that better global health equality, including improving access to vaccines and treatments for individuals who are immunocompromised (especially in lower- and middle-income countries), may be crucial to preventing the emergence of future immune escape variants of SARS-CoV-2.

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