Seasonal influenza circulation patterns and projections for September 2019 to September 2020

AbstractThis report details current seasonal influenza circulation patterns as of August 2019 and makes projections up to September 2020 to coincide with selection of the 2020 Southern Hemisphere vaccine strain. This is not meant as a comprehensive report, but is instead intended as particular observations that we’ve made that may be of relevance. Please also note that observed patterns reflect the GISAID database and may not be entirely representative of underlying dynamics. All analyses are based on the nextflu/nextstrain pipeline [1,2] with continual updates posted to nextstrain.org/flu. A/H3N2: A/H3N2 viruses continue to show substantial diversity in HA sequences with a deep split between 3c3.A and 3c2.A1b viruses. The most notable recent developments are the rapid rise of clade A1b/137F – a subclade of A1b/135K – in China and Bangladesh and clade A1b/197R – a subclade of A1b/131K – which dominates the ongoing season in Australia. Our models predict that A1b/137F and A1b/197R will be the dominant clades next year with A1b/197R accounting for most circulation. There is, however, large uncertainty in the true extent of A1b/137F circulation. A/H1N1pdm: The S183P substitution has risen to near fixation. The most successful subclade carrying this mutation is 183P-5 which has essentially replaced competing variants. A variant with substitutions 129D/185I is at 60% prevalence globally, while a second variant with substitution 130N is at 50% in North America and ~10% elsewhere. Substitutions at site 156 to D or K have arisen sporadically and result in loss of recognition by antisera raised against viruses with asparagine at position 156. Despite the large antigenic effect, viruses with mutations at site 156 don’t seem to spread. Beyond variants at site 156, little to no antigenic evolution is evident in assays with ferret antisera. B/Vic: Antigenically drifted deletion variants at HA1 sites 162, 163 and 164 are now dominating global circulation and have all but taken over. The double deletion variant V1A.1 had previously been circulating at high frequency in the Americas. However, over the course of 2009, the triple deletion variant V1A.3 has increased in frequency globally and is now dominating in all geographic regions. Importantly, V1A.1 and V1A.3 variants appear antigenically distinct by HI assays with 4-8 fold reductions in log2 titer in both directions. B/Yam: B/Yam has not circulated in large numbers since the Northern Hemisphere season 2017/2018 and displays relatively little amino acid variation in HA or antigenic diversity. Amino acid variants at sites 229 and 232 have begun to circulate and population is now split between 229D/232D, 229N/232D and 229D/232N variants. These variants show little sign of antigenic difference in HI assays.

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Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018

10.1101/191676 ◽

2017 ◽

Cited By ~ 1

Author(s):

Trevor Bedford ◽

Richard A. Neher

Keyword(s):

Genetic Diversity ◽

Amino Acid ◽

Seasonal Influenza ◽

Common Ancestor ◽

Amino Acid Deletion ◽

Circulation Patterns ◽

Antigenic Evolution ◽

The Common ◽

Amino Acid Mutations ◽

Selection Of

AbstractThis report details current seasonal influenza circulation patterns as of Sep 2017 and makes projections up to Sep 2018 to coincide with selection of the 2018 Southern Hemisphere vaccine strain. This is not meant as a comprehensive report, but is instead intended as particular observations that we’ve made that may be of relevance. Please also note that observed patterns reflect the GISAID database and may not be entirely representative of underlying dynamics. All analyses are based on the nextflu pipeline [1] with continual updates posted to nextflu.org.A/H3N2H3N2 continues to diversify with many coexisting clades, all of which carry several amino acid mutations at previously characterized epitope sites. The majority of viruses fall into the 3c2.a clade which has been dominating globally for >3 years, but 3c3.a viruses continue to persist. The common ancestor of circulating H3N2 viruses is now more than 5 years old, which is rare for H3N2. Despite extensive genetic diversity, serological assays suggest limited, but non-zero, antigenic evolution. We expect multiple competing clades within 3c2.a to persist into the future with no clear immediate winner.A/H1N1pdmA clade comprising mutations S74R and I295V has recently risen to >60% global frequency. Although it shows no antigenic distinction by ferret HI data, the rapidity of its rise suggests a selective origin.B/VicA clade with a two amino acid deletion 162-/163-has altered serological properties and is increasing in frequency, albeit slowly. Two other clades (carrying mutations K209N and V87A/I175V) have increased in frequency moderately.B/YamA clade comprising M251V within clade 3 viruses continues to dominate. The is little genetic differentiation within this clade and no evidence of antigenic evolution.

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Seasonal influenza circulation patterns and projections for 2017-2018

10.1101/113035 ◽

2017 ◽

Author(s):

Trevor Bedford ◽

Richard A. Neher

Keyword(s):

Amino Acid ◽

Seasonal Influenza ◽

Competitive Dynamics ◽

Amino Acid Sequence Variation ◽

Circulation Patterns ◽

Antigenic Evolution ◽

Amino Acid Mutations ◽

Serological Data ◽

Global Population ◽

Parallel Mutation

AbstractThis is not meant as a comprehensive report of recent influenza evolution, but is instead intended as particular observations that may be of relevance. Please also note that observed patterns reflect the GISAID database and may not be entirely representative of underlying dynamics. All analyses are based on the nextflu pipeline [1] with continual updates posted to nextflu.org. We arrive at the following results:H3N2In H3N2, clade 3c2.a has continued to diversify genetically with complicated and rapid dynamics of different subclades. This diversification is not reflected in serological data that shows only minor to moderate antigenic evolution. Nevertheless, the highly parallel mutation patterns and the rapid rise and fall of clades suggests competitive dynamics of phenotypically distinct viruses.H1N1pdmVery few H1N1pdm viruses have been observed in recent months. The dominant clade continues to be 6b.1 and there is little amino acid sequence variation within HA. The only notable subclade that has been growing recently is the clade bearing HA1:R205K/S183P. This clade is dominated by North American viruses and we see no evidence that this clade has a particular competitive advantage.B/VicClade 1A has continued to dominate and mutation 117V has all but taken over the global population. The rise of this mutation was fairly gradual and we have no evidence that it is associated with antigenic change or other benefit to the virus.B/YamClade 3 has continued to dominate. Within clade 3, a clade with mutation HA1:251V is globally at frequency of about 80% throughout 2016. Within this clade, mutation 211R is at 25% frequency. In addition, a clade without prominent amino acid mutations has been rising throughout 2016.

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Seasonal influenza circulation patterns and projections for Feb 2018 to Feb 2019

10.1101/271114 ◽

2018 ◽

Cited By ~ 8

Author(s):

Trevor Bedford ◽

Richard A. Neher

Keyword(s):

Amino Acid ◽

Northern Hemisphere ◽

Vaccine Strain ◽

Seasonal Influenza ◽

Rapid Rise ◽

Antigenic Diversity ◽

Amino Acid Variation ◽

Circulation Patterns ◽

Antigenic Phenotype ◽

Selection Of

AbstractThis report details current seasonal influenza circulation patterns as of Feb 2018 and makes projections up to Feb 2019 to coincide with selection of the 2018-2019 Northern Hemisphere vaccine strain. This is not meant as a comprehensive report, but is instead intended as particular observations that we’ve made that may be of relevance. Please also note that observed patterns reflect the GISAID database and may not be entirely representative of underlying dynamics. All analyses are based on the nextflu pipeline [1] with continual updates posted to nextflu.org.A/H3N2: H3N2 diversity has largely been replaced by subclades A1b, A2 and A3 within 3c2.A. Subclades A1b and A2 predominate in the population and each shows increases in frequency, mutations at epitope sites and evidence for minor changes to antigenic phenotype. Clade A1b may be marginally fitter than clade A2, but we expect both clades to persist into the future without a clear immediate winner.A/H1N1pdm: A clade comprising mutations S74R, S164T and I295V has recently swept to fixation. The rapidity of this sweep suggests a selective origin. However, there is no evidence of antigenic change.B/Vic: Very little B/Vic activity has been observed in recent months. A clade with a two codon deletion at sites HA1:162/163 has gradually risen in frequency. HI measurements suggest an 8 to 16-fold titer drop relative to the vaccine strain, but this antigenic change has not yet resulted in a rapid rise of this variant.B/Yam: Europe experienced a strong and early B/Yam season in absence of amino acid variation in HA or antigenic diversity. However, several mutations in NA have rapidly swept or risen to intermediate frequencies.

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Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018

Viruses ◽

10.3390/v12111304 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1304

Author(s):

Amélie Chastagner ◽

Séverine Hervé ◽

Stéphane Quéguiner ◽

Edouard Hirchaud ◽

Pierrick Lucas ◽

...

Keyword(s):

Amino Acid ◽

Influenza A ◽

Phylogenetic Analyses ◽

Swine Influenza ◽

Amino Acid Sequences ◽

Antigenic Drift ◽

Influenza A Viruses ◽

Double Deletion ◽

Antigenic Evolution ◽

Amino Acid Mutations

This study evaluated the genetic and antigenic evolution of swine influenza A viruses (swIAV) of the two main enzootic H1 lineages, i.e., HA-1C (H1av) and -1B (H1hu), circulating in France between 2000 and 2018. SwIAV RNAs extracted from 1220 swine nasal swabs were hemagglutinin/neuraminidase (HA/NA) subtyped by RT-qPCRs, and 293 virus isolates were sequenced. In addition, 146 H1avNy and 105 H1huNy strains were submitted to hemagglutination inhibition tests. H1avN1 (66.5%) and H1huN2 (25.4%) subtypes were predominant. Most H1 strains belonged to HA-1C.2.1 or -1B.1.2.3 clades, but HA-1C.2, -1C.2.2, -1C.2.3, -1B.1.1, and -1B.1.2.1 clades were also detected sporadically. Within HA-1B.1.2.3 clade, a group of strains named “Δ146-147” harbored several amino acid mutations and a double deletion in HA, that led to a marked antigenic drift. Phylogenetic analyses revealed that internal segments belonged mainly to the “Eurasian avian-like lineage”, with two distinct genogroups for the M segment. In total, 17 distinct genotypes were identified within the study period. Reassortments of H1av/H1hu strains with H1N1pdm virus were rarely evidenced until 2018. Analysis of amino acid sequences predicted a variability in length of PB1-F2 and PA-X proteins and identified the appearance of several mutations in PB1, PB1-F2, PA, NP and NS1 proteins that could be linked to virulence, while markers for antiviral resistance were identified in N1 and N2. Altogether, diversity and evolution of swIAV recall the importance of disrupting the spreading of swIAV within and between pig herds, as well as IAV inter-species transmissions.

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Global circulation patterns of seasonal influenza viruses vary with antigenic drift

Nature ◽

10.1038/nature14460 ◽

2015 ◽

Vol 523 (7559) ◽

pp. 217-220 ◽

Cited By ~ 263

Author(s):

Trevor Bedford ◽

Steven Riley ◽

Ian G. Barr ◽

Shobha Broor ◽

Mandeep Chadha ◽

...

Keyword(s):

Seasonal Influenza ◽

Influenza Viruses ◽

Antigenic Drift ◽

Global Circulation ◽

Circulation Patterns

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Exploring amino acid functions in a deep mutational landscape

10.1101/2020.05.26.116756 ◽

2020 ◽

Cited By ~ 2

Author(s):

Alistair Dunham ◽

Pedro Beltrao

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Clustering Analysis ◽

Chemical Properties ◽

Diverse Range ◽

Mutational Landscape ◽

Charged Amino Acids ◽

Large Numbers ◽

Recent Developments ◽

And Chemical Properties

AbstractAmino acids fulfil a diverse range of roles in proteins, each utilising its chemical properties in different ways in different contexts to create required functions. For example, cysteines form disulphide or hydrogen bonds in different circumstances and charged amino acids do not always make use of their charge. The repertoire of amino acid functions and the frequency at which they occur in proteins remains understudied. Measuring large numbers of mutational consequences, which can elucidate the role an amino acid plays, was prohibitively time consuming until recent developments in deep mutational scanning. In this study we gathered data from 28 deep mutational scanning studies, covering 6291 positions in 30 proteins, and used the consequences of mutation at each position to define a mutational landscape. We demonstrated rich relationships between this landscape and biophysical or evolutionary properties. Finally, we identified 100 functional amino acid subtypes with a data-driven clustering analysis and studied their features, including their frequencies and chemical properties such as tolerating polarity, hydrophobicity or being intolerant of charge or specific amino acids. The mutational landscape and amino acid subtypes provide a foundational catalogue of amino acid functional diversity, which will be refined as the number of studied protein positions increases.

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Faculty Opinions recommendation of The global circulation of seasonal influenza A (H3N2) viruses.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1108999.566163 ◽

2008 ◽

Author(s):

Oliver Pybus

Keyword(s):

Influenza A ◽

Seasonal Influenza ◽

Global Circulation

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Bioluminescent proteins prediction with voting strategy.

Current Bioinformatics ◽

10.2174/1574893615999200601122328 ◽

2020 ◽

Vol 15 ◽

Author(s):

Shulin Zhao ◽

Ying Ju ◽

Xiucai Ye ◽

Jun Zhang ◽

Shuguang Han

Keyword(s):

Amino Acid ◽

Model Building ◽

Prediction Method ◽

Pair Composition ◽

Proposed Model ◽

Counting Rules ◽

Significant Phenomenon ◽

Voting Strategy ◽

Improved Accuracy ◽

Selection Of

Background: Bioluminescence is a unique and significant phenomenon in nature. Bioluminescence is important for the lifecycle of some organisms and is valuable in biomedical research, including for gene expression analysis and bioluminescence imaging technology.In recent years, researchers have identified a number of methods for predicting bioluminescent proteins (BLPs), which have increased in accuracy, but could be further improved. Method: In this paper, we propose a new bioluminescent proteins prediction method based on a voting algorithm. We used four methods of feature extraction based on the amino acid sequence. We extracted 314 dimensional features in total from amino acid composition, physicochemical properties and k-spacer amino acid pair composition. In order to obtain the highest MCC value to establish the optimal prediction model, then used a voting algorithm to build the model.To create the best performing model, we discuss the selection of base classifiers and vote counting rules. Results: Our proposed model achieved 93.4% accuracy, 93.4% sensitivity and 91.7% specificity in the test set, which was better than any other method. We also improved a previous prediction of bioluminescent proteins in three lineages using our model building method, resulting in greatly improved accuracy.

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Oxford Studies in Metaethics Volume 15

10.1093/oso/9780198859512.001.0001 ◽

2020 ◽

Keyword(s):

Philosophy Of Mind ◽

Philosophy Of Language ◽

Moral Realism ◽

Ethical Theory ◽

Philosophical Work ◽

Moral Explanation ◽

Recent Developments ◽

Selection Of

This series is devoted to original philosophical work in the foundations of ethics. It provides an annual selection of much of the best new scholarship being done in the field. Its broad purview includes work being done at the intersection of ethical theory and metaphysics, epistemology, philosophy of language, and philosophy of mind. The chapters included in the series provide a basis for understanding recent developments in the field. Chapters in this volume explore topics including the nature of reasons, the tenability of moral realism, moral explanation and grounding, and a variety of epistemological challenges.

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Microbial Electrochemical Systems: Principles, Construction and Biosensing Applications

Sensors ◽

10.3390/s21041279 ◽

2021 ◽

Vol 21 (4) ◽

pp. 1279

Author(s):

Rabeay Y.A. Hassan ◽

Ferdinando Febbraio ◽

Silvana Andreescu

Keyword(s):

Electrode Materials ◽

Electrical Power ◽

Chemical Energy ◽

Practical Implementation ◽

Development Status ◽

Electrochemical Systems ◽

Recent Developments ◽

Energy Environment ◽

Microbial Electrochemical Systems ◽

Selection Of

Microbial electrochemical systems are a fast emerging technology that use microorganisms to harvest the chemical energy from bioorganic materials to produce electrical power. Due to their flexibility and the wide variety of materials that can be used as a source, these devices show promise for applications in many fields including energy, environment and sensing. Microbial electrochemical systems rely on the integration of microbial cells, bioelectrochemistry, material science and electrochemical technologies to achieve effective conversion of the chemical energy stored in organic materials into electrical power. Therefore, the interaction between microorganisms and electrodes and their operation at physiological important potentials are critical for their development. This article provides an overview of the principles and applications of microbial electrochemical systems, their development status and potential for implementation in the biosensing field. It also provides a discussion of the recent developments in the selection of electrode materials to improve electron transfer using nanomaterials along with challenges for achieving practical implementation, and examples of applications in the biosensing field.

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