Identification of Amino Acid Substitutions Supporting Antigenic Change of Influenza A(H1N1)pdm09 Viruses

ABSTRACTThe majority of currently circulating influenza A(H1N1) viruses are antigenically similar to the virus that caused the 2009 influenza pandemic. However, antigenic variants are expected to emerge as population immunity increases. Amino acid substitutions in the hemagglutinin protein can result in escape from neutralizing antibodies, affect viral fitness, and change receptor preference. In this study, we constructed mutants with substitutions in the hemagglutinin of A/Netherlands/602/09 in an attenuated backbone to explore amino acid changes that may contribute to emergence of antigenic variants in the human population. Our analysis revealed that single substitutions affecting the loop that consists of amino acid positions 151 to 159 located adjacent to the receptor binding site caused escape from ferret and human antibodies elicited after primary A(H1N1)pdm09 virus infection. The majority of these substitutions resulted in similar or increased replication efficiencyin vitrocompared to that of the virus carrying the wild-type hemagglutinin and did not result in a change of receptor preference. However, none of the substitutions was sufficient for escape from the antibodies in sera from individuals that experienced both seasonal and pandemic A(H1N1) virus infections. These results suggest that antibodies directed against epitopes on seasonal A(H1N1) viruses contribute to neutralization of A(H1N1)pdm09 antigenic variants, thereby limiting the number of possible substitutions that could lead to escape from population immunity.IMPORTANCEInfluenza A viruses can cause significant morbidity and mortality in humans. Amino acid substitutions in the hemagglutinin protein can result in escape from antibody-mediated neutralization. This allows the virus to reinfect individuals that have acquired immunity to previously circulating strains through infection or vaccination. To date, the vast majority of A(H1N1)pdm09 strains remain antigenically similar to the virus that caused the 2009 influenza pandemic. However, antigenic variants are expected to emerge as a result of increasing population immunity. We show that single amino acid substitutions near the receptor binding site were sufficient to escape from antibodies specific for A(H1N1)pdm09 viruses but not from antibodies elicited in response to infections with seasonal A(H1N1) and A(H1N1)pdm09 viruses. This study identified substitutions in A(H1N1)pdm09 viruses that support escape from population immunity but also suggested that the number of potential escape variants is limited by previous exposure to seasonal A(H1N1) viruses.

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Plasticity of Amino Acid Residue 145 Near the Receptor Binding Site of H3 Swine Influenza A Viruses and Its Impact on Receptor Binding and Antibody Recognition

Journal of Virology ◽

10.1128/jvi.01413-18 ◽

2018 ◽

Vol 93 (2) ◽

Author(s):

Jefferson J. S. Santos ◽

Eugenio J. Abente ◽

Adebimpe O. Obadan ◽

Andrew J. Thompson ◽

Lucas Ferreri ◽

...

Keyword(s):

Amino Acid ◽

Receptor Binding ◽

Influenza A ◽

Antigenic Drift ◽

Amino Acid Substitutions ◽

Receptor Binding Site ◽

Antibody Recognition ◽

Antigenic Characterization ◽

Antigenic Evolution

ABSTRACT The hemagglutinin (HA), a glycoprotein on the surface of influenza A virus (IAV), initiates the virus life cycle by binding to terminal sialic acid (SA) residues on host cells. The HA gradually accumulates amino acid substitutions that allow IAV to escape immunity through a mechanism known as antigenic drift. We recently confirmed that a small set of amino acid residues are largely responsible for driving antigenic drift in swine-origin H3 IAV. All identified residues are located adjacent to the HA receptor binding site (RBS), suggesting that substitutions associated with antigenic drift may also influence receptor binding. Among those substitutions, residue 145 was shown to be a major determinant of antigenic evolution. To determine whether there are functional constraints to substitutions near the RBS and their impact on receptor binding and antigenic properties, we carried out site-directed mutagenesis experiments at the single-amino-acid level. We generated a panel of viruses carrying substitutions at residue 145 representing all 20 amino acids. Despite limited amino acid usage in nature, most substitutions at residue 145 were well tolerated without having a major impact on virus replication in vitro. All substitution mutants retained receptor binding specificity, but the substitutions frequently led to decreased receptor binding. Glycan microarray analysis showed that substitutions at residue 145 modulate binding to a broad range of glycans. Furthermore, antigenic characterization identified specific substitutions at residue 145 that altered antibody recognition. This work provides a better understanding of the functional effects of amino acid substitutions near the RBS and the interplay between receptor binding and antigenic drift. IMPORTANCE The complex and continuous antigenic evolution of IAVs remains a major hurdle for vaccine selection and effective vaccination. On the hemagglutinin (HA) of the H3N2 IAVs, the amino acid substitution N 145 K causes significant antigenic changes. We show that amino acid 145 displays remarkable amino acid plasticity in vitro, tolerating multiple amino acid substitutions, many of which have not yet been observed in nature. Mutant viruses carrying substitutions at residue 145 showed no major impairment in virus replication in the presence of lower receptor binding avidity. However, their antigenic characterization confirmed the impact of the 145 K substitution in antibody immunodominance. We provide a better understanding of the functional effects of amino acid substitutions implicated in antigenic drift and its consequences for receptor binding and antigenicity. The mutation analyses presented in this report represent a significant data set to aid and test the ability of computational approaches to predict binding of glycans and in antigenic cartography analyses.

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The Molecular Basis for Antigenic Drift of Human A/H2N2 Influenza Viruses

Journal of Virology ◽

10.1128/jvi.01907-18 ◽

2019 ◽

Vol 93 (8) ◽

Cited By ~ 6

Author(s):

M. Linster ◽

E. J. A. Schrauwen ◽

S. van der Vliet ◽

D. F. Burke ◽

P. Lexmond ◽

...

Keyword(s):

Amino Acid ◽

Influenza A ◽

Influenza Pandemic ◽

Virus Evolution ◽

Influenza Viruses ◽

Antigenic Drift ◽

Amino Acid Substitutions ◽

Receptor Binding Site ◽

Antigenic Evolution ◽

H2n2 Virus

ABSTRACTInfluenza A/H2N2 viruses caused a pandemic in 1957 and continued to circulate in humans until 1968. The antigenic evolution of A/H2N2 viruses over time and the amino acid substitutions responsible for this antigenic evolution are not known. Here, the antigenic diversity of a representative set of human A/H2N2 viruses isolated between 1957 and 1968 was characterized. The antigenic change of influenza A/H2N2 viruses during the 12 years that this virus circulated was modest. Two amino acid substitutions, T128D and N139K, located in the head domain of the H2 hemagglutinin (HA) molecule, were identified as important determinants of antigenic change during A/H2N2 virus evolution. The rate of A/H2N2 virus antigenic evolution during the 12-year period after introduction in humans was half that of A/H3N2 viruses, despite similar rates of genetic change.IMPORTANCEWhile influenza A viruses of subtype H2N2 were at the origin of the Asian influenza pandemic, little is known about the antigenic changes that occurred during the twelve years of circulation in humans, the role of preexisting immunity, and the evolutionary rates of the virus. In this study, the antigenic map derived from hemagglutination inhibition (HI) titers of cell-cultured virus isolates and ferret postinfection sera displayed a directional evolution of viruses away from earlier isolates. Furthermore, individual mutations in close proximity to the receptor-binding site of the HA molecule determined the antigenic reactivity, confirming that individual amino acid substitutions in A/H2N2 viruses can confer major antigenic changes. This study adds to our understanding of virus evolution with respect to antigenic variability, rates of virus evolution, and potential escape mutants of A/H2N2.

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MOLECULAR AND GENETIC CHARACTERISTICS OF SURFACE AND NONSTRUCTURE PROTEINS OF PANDEMIC INFLUENZA VIRUSES A(H1N1)PDM09 IN 2015-2016 EPIDEMIC SEASON

Bulletin of Taras Shevchenko National University of Kyiv Series Biology ◽

10.17721/1728_2748.2016.72.44-48 ◽

2016 ◽

Vol 72 (2) ◽

pp. 44-48

Author(s):

O. Smutko ◽

L. Radchenko ◽

A. Mironenko

Keyword(s):

Amino Acid ◽

Pandemic Influenza ◽

Influenza A ◽

Phylogenetic Trees ◽

Influenza Viruses ◽

Amino Acid Substitutions ◽

Ns1 Protein ◽

Genetic Characteristics ◽

Epidemic Season ◽

Influenza A H1n1

The aim of the present study was identifying of molecular and genetic changes in hemaglutinin (HA), neuraminidase (NA) and non-structure protein (NS1) genes of pandemic influenza A(H1N1)pdm09 strains, that circulated in Ukraine during 2015-2016 epidemic season. Samples (nasopharyngeal swabs from patients) were analyzed using real-time polymerase chain reaction (RTPCR). Phylogenetic trees were constructed using MEGA 7 software. 3D structures were constructed in Chimera 1.11.2rc software. Viruses were collected in 2015-2016 season fell into genetic group 6B and in two emerging subgroups, 6B.1 and 6B.2 by gene of HA and NA. Subgroups 6B.1 and 6B.2 are defined by the following amino acid substitutions. In the NS1 protein were identified new amino acid substitutions D2E, N48S, and E125D in 2015-2016 epidemic season. Specific changes were observed in HA protein antigenic sites, but viruses saved similarity to vaccine strain. NS1 protein acquired substitution associated with increased virulence of the influenza virus.

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Children under 10 years of age were more affected by the 2018/19 influenza A(H1N1)pdm09 epidemic in Canada: ‎possible cohort effect following the 2009 influenza pandemic

Eurosurveillance ◽

10.2807/1560-7917.es.2019.24.15.1900104 ◽

2019 ◽

Vol 24 (15) ◽

Cited By ~ 6

Author(s):

Danuta M Skowronski ◽

Siobhan Leir ◽

Gaston De Serres ◽

Michelle Murti ◽

James A Dickinson ◽

...

Keyword(s):

General Population ◽

Influenza A ◽

Influenza Pandemic ◽

Age Distribution ◽

Cohort Effect ◽

Surveillance Network ◽

Medical Visits ◽

Influenza A H1n1 ◽

2009 Influenza Pandemic ◽

Negative Controls

Introduction Findings from the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN) suggest children were more affected by the 2018/19 influenza A(H1N1)pdm09 epidemic. Aim To compare the age distribution of A(H1N1)pdm09 cases in 2018/19 to prior seasonal influenza epidemics in Canada. Methods The age distribution of unvaccinated influenza A(H1N1)pdm09 cases and test-negative controls were compared across A(H1N1)pdm09-dominant epidemics in 2018/19, 2015/16 and 2013/14 and with the general population of SPSN provinces. Similar comparisons were undertaken for influenza A(H3N2)-dominant epidemics. Results In 2018/19, more influenza A(H1N1)pdm09 cases were under 10 years old than controls (29% vs 16%; p < 0.001). In particular, children aged 5–9 years comprised 14% of cases, greater than their contribution to controls (4%) or the general population (5%) and at least twice their contribution in 2015/16 (7%; p < 0.001) or 2013/14 (5%; p < 0.001). Conversely, children aged 10–19 years (11% of the population) were under-represented among A(H1N1)pdm09 cases versus controls in 2018/19 (7% vs 12%; p < 0.001), 2015/16 (7% vs 13%; p < 0.001) and 2013/14 (9% vs 12%; p = 0.12). Conclusion Children under 10 years old contributed more to outpatient A(H1N1)pdm09 medical visits in 2018/19 than prior seasonal epidemics in Canada. In 2018/19, all children under 10 years old were born after the 2009 A(H1N1)pdm09 pandemic and therefore lacked pandemic-induced immunity. In addition, more than half those born after 2009 now attend school (i.e. 5–9-year-olds), a socio-behavioural context that may enhance transmission and did not apply during prior A(H1N1)pdm09 epidemics.

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Immune response of human volunteers and animals to vaccination with egg-grown influenza A (H1N1) virus is influenced by three amino acid substitutions in the haemagglutinin molecule

Vaccine ◽

10.1016/0264-410x(93)90279-7 ◽

1993 ◽

Vol 11 (4) ◽

pp. 400-406 ◽

Cited By ~ 21

Author(s):

R.W. Newman ◽

R. Jennings ◽

D.L. Major ◽

J.S. Robertson ◽

R. Jenkins ◽

...

Keyword(s):

Immune Response ◽

Amino Acid ◽

Influenza A ◽

H1n1 Virus ◽

Amino Acid Substitutions ◽

Human Volunteers ◽

Influenza A H1n1

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Amino Acid Substitutions Analysis of the Putative Epitopes of Neuraminidase Protein from Influenza A H1N1 Virus

Revista Unimontes Científica ◽

10.46551/ruc.v22n1a04 ◽

2021 ◽

Vol 22 (1) ◽

pp. 1-16

Author(s):

Ludmila Alves Dias Souto ◽

Alessandra Rejane Ericsson de Oliveira Xavier ◽

Mauro Aparecido de Sousa Xavier

Keyword(s):

Amino Acid ◽

Influenza A ◽

H1n1 Virus ◽

Epitope Prediction ◽

Viral Population ◽

Amino Acid Substitutions ◽

Specific Amino Acid ◽

Influenza A H1n1 ◽

Virus Sequence ◽

Clustal Omega

Objective: This study verified whether the neuraminidase protein of Influenza A H1N1 virus sequence has modified from 2009–2017 and its impact on the 2018 Brazilian vaccine. Method: The reference neuraminidase protein sequence from H1N1 Puerto Rico/1934 strain was subjected to three different methods of epitope prediction and the top five from each method were aligned using Clustal omega, resulting in eight putative epitopes. These epitopes were aligned to 7,438 neuraminidase sequences spanning from 2009–2017 and analyzed for specific amino acid substitutions and counted. The resultant neuraminidase protein was aligned against the 2015 and 2018 neuraminidase proteins, from Influenza A H1N1 virus subtypes, used for vaccine production. Result: Twenty-one main substitutions were detected, of which 16/21 (76.2%) substitutions points remained stable and 1/21 (4.8%) returned to the original amino acid residue in the viral population from 2009–2017. Additionally, 19% (4/21) substitutions occurred in Brazil and worldwide in this period, indicating that changes in the neuraminidase viral population profile is time-dependent rather than geographical. Conclusion: The neuraminidase protein containing these amino acid substitutions is more closely related to the neuraminidase protein from influenza A/Michigan/45/2015 than A/California/7/2009, supporting the replacement of this virus subtype in the Brazilian vaccine in 2018.

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Pandemic influenza A(H1N1) 2009 breakthrough infections and estimates of vaccine effectiveness in Germany 2009-2010

Eurosurveillance ◽

10.2807/ese.15.18.19561-en ◽

2010 ◽

Vol 15 (18) ◽

Author(s):

O Wichmann ◽

P Stöcker ◽

G Poggensee ◽

D Altmann ◽

D Walter ◽

...

Keyword(s):

Pandemic Influenza ◽

Influenza A ◽

Influenza Pandemic ◽

Rapid Assessment ◽

Screening Method ◽

Age Groups ◽

Vaccine Effectiveness ◽

Influenza A H1n1 ◽

Reported Data ◽

2009 Influenza Pandemic

During the 2009 influenza pandemic, a monovalent AS03-adjuvanted vaccine was almost exclusively used in Germany for immunisation against the 2009 pandemic influenza A(H1N1) virus. One-dose vaccination was recommended for all age groups. We applied the screening method for the rapid assessment of vaccine effectiveness (VE) based on reported data of vaccinated and unvaccinated pandemic influenza cases and vaccination coverage estimates. Preliminary results demonstrate excellent VE in persons aged 14-59 years (96.8%; 95% confidence interval (CI): 95.2-97.9) and moderately high VE in those 60 years or older (83.3%; 95% CI: 71.0-90.5).

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