scholarly journals Seasonal influenza circulation patterns and projections for 2017-2018

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.

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

2017 ◽  
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.

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

2019 ◽  
Author(s):  
Trevor Bedford ◽  
John Huddleston ◽  
Barney Potter ◽  
Richard A. Neher
Keyword(s):  
Amino Acid ◽  
Seasonal Influenza ◽  
Deletion Variant ◽  
Global Circulation ◽  
Double Deletion ◽  
Large Numbers ◽  
Circulation Patterns ◽  
Recent Developments ◽  
Antigenic Evolution ◽  
Selection Of

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.

scholarly journals 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 ◽  
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.

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

2018 ◽  
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.

scholarly journals Genetic Variation and Evolution of the 2019 Novel Coronavirus

2021 ◽  
pp. 1-13
Author(s):  
Salvatore Dimonte ◽  
Muhammed Babakir-Mina ◽  
Taib Hama-Soor ◽  
Salar Ali
Keyword(s):  
Amino Acid ◽  
Receptor Binding ◽  
Rapid Evolution ◽  
Single Amino Acid ◽  
Angiotensin Converting Enzyme 2 ◽  
New Type ◽  
Amino Acid Mutations ◽  
Host Infection ◽  
Human Coronaviruses ◽  
Novel Coronavirus

<b><i>Introduction:</i></b> SARS-CoV-2 is a new type of coronavirus causing a pandemic severe acute respiratory syndrome (SARS-2). Coronaviruses are very diverting genetically and mutate so often periodically. The natural selection of viral mutations may cause host infection selectivity and infectivity. <b><i>Methods:</i></b> This study was aimed to indicate the diversity between human and animal coronaviruses through finding the rate of mutation in each of the spike, nucleocapsid, envelope, and membrane proteins. <b><i>Results:</i></b> The mutation rate is abundant in all 4 structural proteins. The most number of statistically significant amino acid mutations were found in spike receptor-binding domain (RBD) which may be because it is responsible for a corresponding receptor binding in a broad range of hosts and host selectivity to infect. Among 17 previously known amino acids which are important for binding of spike to angiotensin-converting enzyme 2 (ACE2) receptor, all of them are conservative among human coronaviruses, but only 3 of them significantly are mutated in animal coronaviruses. A single amino acid aspartate-454, that causes dissociation of the RBD of the spike and ACE2, and F486 which gives the strength of binding with ACE2 remain intact in all coronaviruses. <b><i>Discussion/Conclusion:</i></b> Observations of this study provided evidence of the genetic diversity and rapid evolution of SARS-CoV-2 as well as other human and animal coronaviruses.

scholarly journals Searching for signatures of positive selection in cytochrome b gene associated with subterranean lifestyle in fast-evolving arvicolines (Arvicolinae, Cricetidae, Rodentia)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Olga V. Bondareva ◽  
Nadezhda A. Potapova ◽  
Kirill A. Konovalov ◽  
Tatyana V. Petrova ◽  
Natalia I. Abramson
Keyword(s):  
Amino Acid ◽  
Oxidative Phosphorylation ◽  
Adaptive Evolution ◽  
Complex Structure ◽  
Subterranean Rodents ◽  
Amino Acid Sequence Variation ◽  
Tertiary Protein Structure ◽  
Metabolic Performance ◽  
The Impact ◽  
Subterranean Species

Abstract Background Mitochondrial genes encode proteins involved in oxidative phosphorylation. Variations in lifestyle and ecological niche can be directly reflected in metabolic performance. Subterranean rodents represent a good model for testing hypotheses on adaptive evolution driven by important ecological shifts. Voles and lemmings of the subfamily Arvicolinae (Rodentia: Cricetidae) provide a good example for studies of adaptive radiation. This is the youngest group within the order Rodentia showing the fastest rates of diversification, including the transition to the subterranean lifestyle in several phylogenetically independent lineages. Results We evaluated the signatures of selection in the mitochondrial cytochrome b (cytB) gene in 62 Arvicolinae species characterized by either subterranean or surface-dwelling lifestyle by assessing amino acid sequence variation, exploring the functional consequences of the observed variation in the tertiary protein structure, and estimating selection pressure. Our analysis revealed that: (1) three of the convergent amino acid substitutions were found among phylogenetically distant subterranean species and (2) these substitutions may have an influence on the protein complex structure, (3) cytB showed an increased ω and evidence of relaxed selection in subterranean lineages, relative to non-subterranean, and (4) eight protein domains possess increased nonsynonymous substitutions ratio in subterranean species. Conclusions Our study provides insights into the adaptive evolution of the cytochrome b gene in the Arvicolinae subfamily and its potential implications in the molecular mechanism of adaptation. We present a framework for future characterizations of the impact of specific mutations on the function, physiology, and interactions of the mtDNA-encoded proteins involved in oxidative phosphorylation.

Detection of neutral amino acid mutations by immobilized pH gradients: The case of the Tγ variant in fetal hemoglobin Sardinia

1986 ◽  
Vol 7 (5) ◽  
pp. 213-216 ◽  
Author(s):  
Gianfranco Cossu ◽  
Mario Manca ◽  
Pier Giorgio Righetti ◽  
Elisabetta Gianazza ◽  
VÉRonique Baudin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Fetal Hemoglobin ◽  
Neutral Amino Acid ◽  
Ph Gradients ◽  
Amino Acid Mutations

Structural assessment of single amino acid mutations: application to TP53 function

2006 ◽  
Vol 27 (9) ◽  
pp. 926-937 ◽  
Author(s):  
Yum L. Yip ◽  
Vincent Zoete ◽  
Holger Scheib ◽  
Olivier Michielin
Keyword(s):  
Amino Acid ◽  
Single Amino Acid ◽  
Structural Assessment ◽  
Amino Acid Mutations

Glycosylation of prions and its effects on protein conformation relevant to amino acid mutations

2000 ◽  
Vol 18 (2) ◽  
pp. 126-134 ◽  
Author(s):  
Nicky K.C Wong ◽  
David V Renouf ◽  
Sylvain Lehmann ◽  
Elizabeth F Hounsell
Keyword(s):  
Amino Acid ◽  
Protein Conformation ◽  
Amino Acid Mutations

scholarly journals Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018–2019

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 977
Author(s):  
Kobporn Boonnak ◽  
Chayasin Mansanguan ◽  
Dennis Schuerch ◽  
Usa Boonyuen ◽  
Hatairat Lerdsamran ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Seasonal Influenza ◽  
Influenza Viruses ◽  
Surface Proteins ◽  
Antigenic Drift ◽  
Influenza B ◽  
Receptor Binding Site ◽  
Antigenic Sites ◽  
Ha Protein

Influenza viruses continue to be a major public health threat due to the possible emergence of more virulent influenza virus strains resulting from dynamic changes in virus adaptability, consequent of functional mutations and antigenic drift in surface proteins, especially hemagglutinin (HA) and neuraminidase (NA). In this study, we describe the genetic and evolutionary characteristics of H1N1, H3N2, and influenza B strains detected in severe cases of seasonal influenza in Thailand from 2018 to 2019. We genetically characterized seven A/H1N1 isolates, seven A/H3N2 isolates, and six influenza B isolates. Five of the seven A/H1N1 viruses were found to belong to clade 6B.1 and were antigenically similar to A/Switzerland/3330/2017 (H1N1), whereas two isolates belonged to clade 6B.1A1 and clustered with A/Brisbane/02/2018 (H1N1). Interestingly, we observed additional mutations at antigenic sites (S91R, S181T, T202I) as well as a unique mutation at a receptor binding site (S200P). Three-dimensional (3D) protein structure analysis of hemagglutinin protein reveals that this unique mutation may lead to the altered binding of the HA protein to a sialic acid receptor. A/H3N2 isolates were found to belong to clade 3C.2a2 and 3C.2a1b, clustering with A/Switzerland/8060/2017 (H3N2) and A/South Australia/34/2019 (H3N2), respectively. Amino acid sequence analysis revealed 10 mutations at antigenic sites including T144A/I, T151K, Q213R, S214P, T176K, D69N, Q277R, N137K, N187K, and E78K/G. All influenza B isolates in this study belong to the Victoria lineage. Five out of six isolates belong to clade 1A3-DEL, which relate closely to B/Washington/02/2009, with one isolate lacking the three amino acid deletion on the HA segment at position K162, N163, and D164. In comparison to the B/Colorado/06/2017, which is the representative of influenza B Victoria lineage vaccine strain, these substitutions include G129D, G133R, K136E, and V180R for HA protein. Importantly, the susceptibility to oseltamivir of influenza B isolates, but not A/H1N1 and A/H3N2 isolates, were reduced as assessed by the phenotypic assay. This study demonstrates the importance of monitoring genetic variation in influenza viruses regarding how acquired mutations could be associated with an improved adaptability for efficient transmission.

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