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are based on the nextflu pipeline [1] with continual updates posted to nextflu.org.A/H3N2: H3N2 diversity has largely been replaced by subclades A1b, A2 and A3 within 3c2.A. Subclades A1b and A2 predominate in the population and each shows increases in frequency, mutations at epitope sites and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 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 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 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 Epitope Peptide-Based Predication and Other Functional Regions of Antigenic F and HN Proteins of Waterfowl and Poultry Avian Avulavirus Serotype-1 Isolates From Uganda

2021 ◽  
Vol 8 ◽  
Author(s):  
John Bosco Omony ◽  
Agnes Wanyana ◽  
Kizito K. Mugimba ◽  
Halid Kirunda ◽  
Jessica L. Nakavuma ◽  
...  
Keyword(s):  
Amino Acid ◽  
B Cell ◽  
Vaccine Strain ◽  
Cleavage Site ◽  
Wild Type ◽  
B Cell Epitopes ◽  
Antigenic Diversity ◽  
F Gene ◽  
Evolutionary Forces ◽  
Serotype 1

Uganda is a Newcastle disease (ND) endemic country where the disease is controlled by vaccination using live LaSota (genotype II) and I2 (genotype I) vaccine strains. Resurgent outbreak episodes call for an urgent need to understand the antigenic diversity of circulating wild Avian Avulavirus serotype-1 (AAvV-1) strains. High mutation rates and the continuous emergence of genetic and antigenic variants that evade immunity make non-segmented RNA viruses difficult to control. Antigenic and functional analysis of the key viral surface proteins is a crucial step in understanding the antigen diversity between vaccine lineages and the endemic wild ND viruses in Uganda and designing ND peptide vaccines. In this study, we used computational analysis, phylogenetic characterization, and structural modeling to detect evolutionary forces affecting the predicted immune-dominant fusion (F) and hemagglutinin-neuraminidase (HN) proteins of AAvV-1 isolates from waterfowl and poultry in Uganda compared with that in LaSota vaccine strain. Our findings indicate that mutational amino acid variations at the F protein in LaSota strain, 25 poultry wild-type and 30 waterfowl wild-type isolates were distributed at regions including the functional domains of B-cell epitopes or N-glycosylation sites, cleavage site, fusion site that account for strain variations. Similarly, conserved regions of HN protein in 25 Ugandan domestic fowl isolates and the representative vaccine strain varied at the flanking regions and potential linear B-cell epitope. The fusion sites, signal peptides, cleavage sites, transmembrane domains, potential B-cell epitopes, and other specific regions of the two protein types in vaccine and wild viruses varied considerably at structure by effective online epitope prediction programs. Cleavage site of the waterfowl isolates had a typical avirulent motif of 111GGRQGR'L117 with the exception of one isolate which showed a virulent motif of 111GGRQKR'F117. All the poultry isolates showed the 111GRRQKR'F117 motif corresponding to virulent strains. Amino acid sequence variations in both HN and F proteins of AAvV-1 isolates from poultry, waterfowl, and vaccine strain were distributed over the length of the proteins with no detectable pattern, but using the experimentally derived 3D structure data revealed key-mapped mutations on the surfaces of the predicted conformational epitopes encompassing the experimental major neutralizing epitopes. The phylogenic tree constructed using the full F gene and partial F gene sequences of the isolates from poultry and waterfowl respectively, showed that Ugandan ND aquatic bird and poultry isolates share some functional amino acids in F sequences yet do remain unique at structure and the B-cell epitopes. Recombination analyses showed that the C-terminus and the rest of the F gene in poultry isolates originated from prevalent velogenic strains. Altogether, these could provide rationale for antigenic diversity in wild ND isolates of Uganda compared with the current ND vaccine strains.

Bioluminescent proteins prediction with voting strategy.

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.

scholarly journals Characterization of Resistance to the Nonnucleoside NS5B Inhibitor Filibuvir in Hepatitis C Virus-Infected Patients

2011 ◽  
Vol 56 (3) ◽  
pp. 1331-1341 ◽  
Author(s):  
Philip J. F. Troke ◽  
Marilyn Lewis ◽  
Paul Simpson ◽  
Katrina Gore ◽  
Jennifer Hammond ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid ◽  
Site Directed Mutagenesis ◽  
Phenotypic Resistance ◽  
Number Of Patients ◽  
Chronic Hcv ◽  
Selection Of

ABSTRACTFilibuvir (PF-00868554) is an investigational nonnucleoside inhibitor of the hepatitis C virus (HCV) nonstructural 5B (NS5B) RNA-dependent RNA polymerase currently in development for treating chronic HCV infection. The aim of this study was to characterize the selection of filibuvir-resistant variants in HCV-infected individuals receiving filibuvir as short (3- to 10-day) monotherapy. We identified amino acid M423 as the primary site of mutation arising upon filibuvir dosing. Through bulk cloning of clinical NS5B sequences into a transient-replicon system, and supported by site-directed mutagenesis of the Con1 replicon, we confirmed that mutations M423I/T/V mediate phenotypic resistance. Selection in patients of an NS5B mutation at M423 was associated with a reduced replicative capacityin vitrorelative to the pretherapy sequence; consistent with this, reversion to wild-type M423 was observed in the majority of patients following therapy cessation. Mutations at NS5B residues R422 and M426 were detected in a small number of patients at baseline or the end of therapy and also mediate reductions in filibuvir susceptibility, suggesting these are rare but clinically relevant alternative resistance pathways. Amino acid variants at position M423 in HCV NS5B polymerase are the preferred pathway for selection of viral resistance to filibuvirin vivo.

scholarly journals Potential Selection of LMP1 Variants in Nasopharyngeal Carcinoma

2004 ◽  
Vol 78 (2) ◽  
pp. 868-881 ◽  
Author(s):  
Rachel H. Edwards ◽  
Diane Sitki-Green ◽  
Dominic T. Moore ◽  
Nancy Raab-Traub
Keyword(s):  
Amino Acid ◽  
Cytotoxic T Lymphocyte ◽  
Amino Acid Sequences ◽  
Barr Virus ◽  
Distinct Sequence ◽  
Epstein Barr ◽  
Virus Latent Membrane Protein ◽  
Multiple Strains ◽  
Carboxy Terminal ◽  
Selection Of

ABSTRACT Seven distinct sequence variants of the Epstein-Barr virus latent membrane protein 1 (LMP1) have been identified by distinguishing amino acid changes in the carboxy-terminal domain. In this study the transmembrane domains are shown to segregate identically with the distinct carboxy-terminal amino acid sequences. Since strains of LMP1 have been shown to differ in abundance between blood and throat washes, nasopharyngeal carcinomas (NPCs) from areas of endemicity and nonendemicity with matching blood were analyzed by using a heteroduplex tracking assay to distinguish LMP1 variants. Striking differences were found between the compartments with the Ch1 strain prevalent in the NPCs from areas of endemicity and nonendemicity and the B958 strain prevalent in the blood of the endemic samples, whereas multiple strains of LMP1 were prevalent in the blood of the nonendemic samples. The possible selection against the B958 strain appearing in the tumor was highly significant (P < 0.0001). Sequence analysis of the full-length LMP1 variants revealed changes in many of the known and computer-predicted HLA-restricted epitopes with changes in key positions in multiple, potential epitopes for the specific HLA of the patients. These amino acid substitutions at key positions in the LMP1 epitopes may result in a reduced cytotoxic-T-lymphocyte response. These data indicate that strains with specific variants of LMP1 are more likely to be found in NPC. The predominance of specific LMP1 variants in NPC could reflect differences in the biologic or molecular properties of the distinct forms of LMP1 or possible immune selection.

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.

Six-fold increase in historical Northern Hemisphere concurrent large heatwaves driven by warming and changing atmospheric circulations

2021 ◽  
pp. 1-39
Author(s):  
Cassandra D.W. Rogers ◽  
Kai Kornhuber ◽  
Sarah E. Perkins-Kirkpatrick ◽  
Paul C. Loikith ◽  
Deepti Singh
Keyword(s):  
Northern Hemisphere ◽  
Large Scale ◽  
Warm Season ◽  
Fold Increase ◽  
Circulation Pattern ◽  
Positive Influence ◽  
Climate Risks ◽  
Circulation Patterns ◽  
Multiple Regions ◽  
Barents And Kara Seas

AbstractSimultaneous heatwaves affecting multiple regions (referred to as concurrent heatwaves), pose compounding threats to various natural and societal systems, including global food chains, emergency response systems, and reinsurance industries. While anthropogenic climate change is increasing heatwave risks across most regions, the interactions between warming and circulation changes that yield concurrent heatwaves remain understudied. Here, we quantify historical (1979-2019) trends in concurrent heatwaves during the warm-season (May-September, MJJAS) across the Northern Hemisphere mid- to high-latitudes. We find a significant increase of ~46% in the mean spatial extent of concurrent heatwaves, ~17% increase in their maximum intensity, and ~6-fold increase in their frequency. Using Self-Organising Maps, we identify large-scale circulation patterns (300 hPa) associated with specific concurrent heatwave configurations across Northern Hemisphere regions. We show that observed changes in the frequency of specific circulation patterns preferentially increase the risk of concurrent heatwaves across particular regions. Patterns linking concurrent heatwaves across eastern North America, eastern and northern Europe, parts of Asia, and the Barents and Kara Seas, show the largest increases in frequency (~5.9 additional days per decade). We also quantify the relative contributions of circulation pattern changes and warming to overall observed concurrent heatwave day frequency trends. While warming has a predominant and positive influence on increasing concurrent heatwaves, circulation pattern changes have a varying influence and account for up to 0.8 additional concurrent heatwave days per decade. Identifying regions with an elevated risk of concurrent heatwaves and understanding their drivers is indispensable for evaluating projected climate risks on interconnected societal systems and fostering regional preparedness in a changing climate.

Directed selection of amino acid changes in the influenza hemagglutinin and neuraminidase affecting protein antigenicity

Vaccine ◽  
2018 ◽  
Vol 36 (43) ◽  
pp. 6383-6392 ◽  
Author(s):  
Marta L. DeDiego ◽  
Kevin Chiem ◽  
David J. Topham
Keyword(s):  
Amino Acid ◽  
Influenza Hemagglutinin ◽  
Selection Of
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