Pandemic Influenza Strains Research Articles

1169. Unconjugated Multi-epitope Peptides Adjuvanted with ALFQ Induce Durable and Broadly Reactive Antibodies to Human and Avian Influenza Viruses

Abstract Background Traditional influenza vaccine production often leads to mismatch due to antigenic drift, thereby reducing protection. Alternate vaccine strategies that are peptide-based, nanoparticle-based or nucleic acid-based are being developed. Composite multi-epitope peptides provide a cost-effective and easily scalable strategy towards a universal influenza vaccine. In this study, we demonstrate that unconjugated, multi-epitope peptides formulated with the highly potent adjuvant Army Liposome Formulation with QS-21 (ALFQ) generate broadly reactive durable antibodies to human and avian influenza viruses when administered intramuscularly or intradermally. Methods ICR mice were immunized with an unconjugated composite influenza peptide vaccine comprising HA+NA (Flu Pep11) and Matrix (M1/M2/M2e)+T-cell epitope (Flu Pep5906) formulated with ALFQ. A low-dose (1 µg) and high-dose (20 µg) of vaccine was administered intramuscularly or intradermally. Isotype-specific IgG titers to composite peptides, individual epitopes, and multiple strains of influenza A (H1N1, H3N2, H5N1), and B (Yamagata, Victoria) were analyzed by ELISA. Neutralizing titers against Group 1 and Group 2 viruses were determined using microneutralization assay. Results A robust IgG1 and IgG2b antibody response was seen at day 21 post primary immunization and remained steady for all groups up to day 200 (duration of study). IgG2a and IgG3 titers were also generated. Antibodies recognized multiple strains each of human and avian influenza A and influenza B virus subtypes, 200 days post primary immunization, and were comparable between doses and routes. Strong neutralizing titers were shown against Group 1 and 2 influenza viruses. Conclusion An unconjugated peptide vaccine comprising multiple highly conserved epitopes of HA, NA and Matrix formulated with ALFQ adjuvant and administered intramuscularly or intradermally, generated broad and durable antibodies to human and avian influenza viruses. Induced antibodies neutralized seasonal and pandemic influenza strains. These composite peptides adjuvanted with ALFQ generate durable and broad immunity and provide a cost-effective and easily scalable strategy that moves us closer to a universal influenza vaccine. Disclosures All Authors: No reported disclosures

The rise and fall of excess winter mortality in New Zealand from 1876 to 2020

Excess winter mortality (EWM) has been used as a measure of how well populations and policy moderate the health effects of cold weather. We aimed to investigate long-term changes in the EWM of Aotearoa New Zealand (NZ), and potential drivers of change, and to test for structural breaks in trends. We calculated NZ EWM indices from 1876 (4,698 deaths) to 2020 (33,310 deaths), total and by age-group and sex, comparing deaths from June to September (the coldest months) to deaths from February to May and October to January. The mean age and sex-standardised EWM Index (EWMI) for the full study period, excluding 1918, was 1.22. However, mean EWMI increased from 1.20 for 1886 to 1917, to 1.34 for the 1920s, then reduced over time to 1.14 in the 2010s, with excess winter deaths averaging 4.5% of annual deaths (1,450 deaths per year) in the 2010s, compared to 7.9% in the 1920s. Children under 5 years transitioned from a summer to winter excess between 1886 and 1911. Otherwise, the EWMI age-distribution was J-shaped in all time periods. Structural break testing showed the 1918 influenza pandemic strain had a significant impact on trends in winter and non-winter mortality and winter excess for subsequent decades. It was not possible to attribute the post-1918 reduction in EWM to any single factor among improved living standards, reduced severe respiratory infections, or climate change.

Unconjugated Multi-Epitope Peptides Adjuvanted with ALFQ Induce Durable and Broadly Reactive Antibodies to Human and Avian Influenza Viruses.

An unconjugated composite peptide vaccine targeting multiple conserved influenza epitopes from hemagglutinin, neuraminidase, and matrix protein and formulated with a safe and highly potent adjuvant, Army Liposome formulation (ALFQ), generated broad and durable immune responses in outbred mice. The antibodies recognized specific epitopes in influenza peptides and several human, avian, and swine influenza viruses. Comparable antibody responses to influenza viruses were observed with intramuscular and intradermal routes of vaccine administration. The peptide vaccine induced cross-reactive antibodies that recognized influenza virus subtypes A/H1N1, A/H3N2, A/H5N1, B/Victoria, and B/Yamagata. In addition, immune sera neutralized seasonal and pandemic influenza strains (Group 1 and Group 2). This composite multi-epitope peptide vaccine, formulated with ALFQ and administered via intramuscular and intradermal routes, provides a high-performance supra-seasonal vaccine that would be cost-effective and easily scalable, thus moving us closer to a viable strategy for a universal influenza vaccine and pandemic preparedness.

Highly Cross-Reactive and Protective Influenza A Virus H3N2 Hemagglutinin- and Neuraminidase-Specific Human Monoclonal Antibodies.

Due to antigenic drift and shift of influenza A viruses (IAV) and the tendency to elicit predominantly strain-specific antibodies, humanity remains susceptible to new strains of seasonal IAV and is at risk from viruses with pandemic potential for which limited or no immunity may exist. The genetic drift of H3N2 IAV is specifically pronounced, resulting in two distinct clades since 2014. Here, we demonstrate that immunization with a seasonal inactivated influenza vaccine (IIV) results in increased levels of H3N2 IAV-specific serum antibodies against hemagglutinin (HA) and neuraminidase (NA). Detailed analysis of the H3N2 B cell response indicated expansion of H3N2-specific peripheral blood plasmablasts 7 days after IIV immunization which expressed monoclonal antibodies (MAbs) with broad and potent antiviral activity against many H3N2 IAV strains as well as prophylactic and therapeutic activity in mice. These H3N2-specific B cell clonal lineages persisted in CD138+ long-lived bone marrow plasma cells. These results demonstrate that IIV-induced H3N2 human MAbs can protect and treat influenza virus infection in vivo and suggest that IIV can induce a subset of IAV H3N2-specific B cells with broad protective potential, a feature that warrants further study for universal influenza vaccine development. IMPORTANCE Influenza A virus (IAV) infections continue to cause substantial morbidity and mortality despite the availability of seasonal vaccines. The extensive genetic variability in seasonal and potentially pandemic influenza strains necessitates new vaccine strategies that can induce universal protection by focusing the immune response on generating protective antibodies against conserved targets within the influenza virus hemagglutinin and neuraminidase proteins. We have demonstrated that seasonal immunization with inactivated influenza vaccine (IIV) stimulates H3N2-specific monoclonal antibodies in humans that are broad and potent in their neutralization of virus in vitro. These antibodies also provide protection from H3N2 IAV in a mouse model of infection. Furthermore, they persist in the bone marrow, where they are expressed by long-lived antibody-producing plasma cells. This significantly demonstrates that seasonal IIV can induce a subset of H3N2-specific B cells with broad protective potential, a process that if further studied and enhanced could aid in the development of a universal influenza vaccine.

Pre-existing Fc profiles shape the evolution of neutralizing antibody breadth following influenza vaccination

Under the ever-present threat of a pandemic influenza strain, the evolution of a broadly reactive, neutralizing, functional, humoral immune response may hold the key to protection against both circulating and emerging influenza strains. We apply a systems approach to profile hemagglutinin- and neuraminidase-specific humoral signatures that track with the evolution of broad immunity in a cohort of vaccinated individuals and validate these findings in a second longitudinal cohort. Multivariate analysis reveals the presence of a unique pre-existing Fcγ-receptor-binding antibody profile in individuals that evolved broadly reactive hemagglutination inhibition activity (HAI), marked by the presence of elevated levels of pre-existing FCGR2B-binding antibodies. Moreover, vaccination with FCGR2B-binding antibody-opsonized influenza results in enhanced antibody titers and HAI activity in a murine model. Together, these data suggest that pre-existing FCGR2B binding antibodies are a key correlate of the evolution of broadly protective influenza-specific antibodies, providing insight for the design of next-generation influenza vaccines.

A recent outbreak of human H1N2 infection: correspondence.

A recent outbreak of human H1N2 infection: correspondence.

Therapeutic Targeting of Inflammation and Virus Simultaneously Ameliorates Influenza Pneumonia and Protects from Morbidity and Mortality.

Influenza pneumonia is a severe complication caused by inflammation of the lungs following infection with seasonal and pandemic strains of influenza A virus (IAV), that can result in lung pathology, respiratory failure, and death. There is currently no treatment for severe disease and pneumonia caused by IAV. Antivirals are available but are only effective if treatment is initiated within 48 h of onset of symptoms. Influenza complications and mortality are often associated with high viral load and an excessive lung inflammatory cytokine response. Therefore, we simultaneously targeted the virus and inflammation. We used the antiviral oseltamivir and the anti-inflammatory drug etanercept to dampen TNF signaling after the onset of clinical signs to treat pneumonia in a mouse model of respiratory IAV infection. The combined treatment down-regulated the inflammatory cytokines TNF, IL-1β, IL-6, and IL-12p40, and the chemokines CCL2, CCL5, and CXCL10. Consequently, combined treatment with oseltamivir and a signal transducer and activator of transcription 3 (STAT3) inhibitor effectively reduced clinical disease and lung pathology. Combined treatment using etanercept or STAT3 inhibitor and oseltamivir dampened an overlapping set of cytokines. Thus, combined therapy targeting a specific cytokine or cytokine signaling pathway and an antiviral drug provide an effective treatment strategy for ameliorating IAV pneumonia. This approach might apply to treating pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Analysis of Regional Scenarios of New Epidemic Waves of SARS-CoV-2 Coronavirus Based on Equations with a Deviating Argument and Damping Functions

The methods we develop within the framework of transient technical process modeling are adaptable to the tasks of biophysics—both to the prediction of invasions of aggressive species and to the analysis of the dynamics of epidemics. The practical application of modeling results to predict the development of the modern pandemic in 2020 has shown the fundamental limitations of the basic methods of model building. Based on an analysis of the properties of the deterministic SIRS model, it has not been possible to present the variety of forms that the regional dynamics of coronavirus spread has taken. The characteristics of the epidemic process do not remain constant, as a variable pathogen evolves competitively. The phenomena since the outbreak of COVID-19 have proven to be much more complex than the naturally fading waves of pandemic influenza strains as immunity accumulates. The development of a scenario approach to the analysis of individual epidemic situations is promising, taking into account the logic of the evolution of the pathogen and adaptation to the peculiarities of its spread in local populations. We performed an analysis of the available data in terms of oscillation forms to get an idea of the real qualitative diversity of local wavelike dynamics of the epidemic of coronavirus strains and identify some special development scenarios described as a catastrophic cycle breakdown on the basis of the known phase-portrait transformations. Applying a bifurcation approach to the epidemic data, we were able to identify features of local forms of oscillatory epidemic processes. We classified the observed phenomena of outbreaks and attenuation of coronavirus infection waves by correlating the dynamics of epidemics with nonlinear effects. We derived scenarios for a number of epidemic situations (in Brazil, New York, and Japan) using lagged equations. It is shown on the basis of comparison of specific situations that the dynamics of epidemics evolve diversely and variably at the current stage according to the internal unpredictable logic of the confrontation process, which is determined by the rate of change in the joint evolution of the virus and population immunity, including the previously formed T-cell immunity. We were able to analyze variants of COVID-wave transformations in lagged equations using the idea of distinguishing bifurcation-inducing parameters. It is substantiated that all nonlinear effects and transformations of oscillatory modes, isolated by epidemic plots, cannot in principle be obtained within a single model. Comparative scenario analysis supports the hypothesis that epidemic processes are primarily influenced by population immunity and contact density. Vaccination has failed to complete the emergence of new waves of infections, but clearly affects the properties of local oscillatory regimes of disease incidence. Experience with new outbreaks of COVID-19 in 2023 in Sweden, New Zealand, Japan, and South India with fundamentally different coping strategies showed that sustained population immunity blocking coronavirus transmission could not be achieved over the long term. Our assumed scenario for the end of the pandemic is the formation of four stable strains whose sporadic circulation in the regions is controlled by CD8+ T-cell immunity.

Evolution and Introductions of Influenza A Virus H1N1 in a Farrow-to-Finish Farm in Guatemala.

Commercial swine farms provide unique systems for interspecies transmission of influenza A viruses (FLUAVs) at the animal-human interface. Bidirectional transmission of FLUAVs between pigs and humans plays a significant role in the generation of novel strains that become established in the new host population. Active FLUAV surveillance was conducted for 2 years on a commercial pig farm in Southern Guatemala with no history of FLUAV vaccination. Nasal swabs (n = 2,094) from fattening pigs (6 to 24 weeks old) with respiratory signs were collected weekly from May 2016 to February 2018. Swabs were screened for FLUAV by real-time reverse transcriptase PCR (RRT-PCR), and full virus genomes of FLUAV-positive swabs were sequenced by next-generation sequencing (NGS). FLUAV prevalence was 12.0% (95% confidence interval [CI], 10.6% to 13.4%) with two distinct periods of high infection. All samples were identified as FLUAVs of the H1N1 subtype within the H1 swine clade 1A.3.3.2 and whose ancestors are the human origin 2009 H1N1 influenza pandemic virus (H1N1 pdm09). Compared to the prototypic reference segment sequence, 10 amino acid signatures were observed on relevant antigenic sites on the hemagglutinin. The Guatemalan swine-origin FLUAVs show independent evolution from other H1N1 pdm09 FLUAVs circulating in Central America. The zoonotic risk of these viruses remains unknown but strongly calls for continued FLUAV surveillance in pigs in Guatemala. IMPORTANCE Despite increased surveillance efforts, the epidemiology of FLUAVs circulating in swine in Latin America remains understudied. For instance, the 2009 H1N1 influenza pandemic strain (H1N1 pdm09) emerged in Mexico, but its circulation remained undetected in pigs. In Central America, Guatemala is the country with the largest swine industry. We found a unique group of H1N1 pdm09 sequences that suggests independent evolution from similar viruses circulating in Central America. These viruses may represent the establishment of a novel genetic lineage with the potential to reassort with other cocirculating viruses and whose zoonotic risk remains to be determined.

Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis.

The respiratory epithelium constitutes the first line of defense against invading respiratory pathogens, such as the 2009 pandemic strain of influenza A virus (IAV, H1N1pdm09), and plays a crucial role in the host antiviral response to infection. Despite its importance, however, it remains unknown how individual cell types within the respiratory epithelium respond to IAV infection or how the latter may influence IAV disease progression and pathogenesis. Here, we used single cell RNA sequencing (scRNA-seq) to dissect the host response to IAV infection in its natural target cells. scRNA-seq was performed on human airway epithelial cell (hAEC) cultures infected with either wild-type pandemic IAV (WT) or with a mutant version of IAV (NS1R38A) that induced a robust innate immune response. We then characterized both the host and viral transcriptomes of more than 19,000 single cells across the 5 major cell types populating the human respiratory epithelium. For all cell types, we observed a wide spectrum of viral burden among single infected cells and a disparate host response between infected and bystander populations. Interestingly, we also identified multiple key differences in the host response to IAV among individual cell types, including high levels of pro-inflammatory cytokines and chemokines in secretory and basal cells and an important role for luminal cells in sensing and restricting incoming virus. Multiple infected cell types were shown to upregulate interferons (IFN), with type III IFNs clearly dominating the antiviral response. Transcriptional changes in genes related to cell differentiation, cell migration, and tissue repair were also identified. Strikingly, we also detected a shift in viral host cell tropism from non-ciliated cells to ciliated cells at later stages of infection and observed major changes in the cellular composition. Microscopic analysis of both WT and NS1R38A virus-infected hAECs at various stages of IAV infection revealed that the transcriptional changes we observed at 18 hpi were likely driving the downstream histopathological alterations in the airway epithelium. To our knowledge, this is the first study to provide a comprehensive analysis of the cell type-specific host antiviral response to influenza virus infection in its natural target cells – namely, the human respiratory epithelium.

The time is now: a call to contain H9N2 avian influenza viruses

In the past century, we have seen four pandemics caused by human influenza A: H1N1 Spanish influenza (1918–1920), H2N2 Asian influenza (1957–58), H3N2 Hong Kong influenza (1968–69), and H1N1 swine influenza (2009–10).1 Phylogenetic analyses have shown that reassortment of genetic segments from human, animal, or avian influenza viruses is linked to the origin of the four influenza pandemic strains.

TreeKnit: Inferring ancestral reassortment graphs of influenza viruses.

When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortment events from viral sequence data, little is known about their role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments.

Characterizing Receptor Flexibility to Predict Mutations That Lead to Human Adaptation of Influenza Hemagglutinin.

A key step in the emergence of human pandemic influenza strains has been a switch in binding preference of the viral glycoprotein hemagglutinin (HA) from avian to human sialic acid (SA) receptors. The conformation of the bound SA varies substantially with HA sequence, and crystallographic evidence suggests that the bound SA is flexible, making it difficult to predict which mutations are responsible for changing HA-binding preference. We performed molecular dynamics (MD) simulations of SA analogues binding to various HAs and observed a dynamic equilibrium among structurally diverse receptor conformations, including conformations that have not been experimentally observed. Using one such novel conformation, we predicted—and experimentally confirmed—a set of mutations that substantially increased an HA’s affinity for a human SA analogue. This prediction could not have been inferred from the existing crystal structures, suggesting that MD-generated HA–SA conformational ensembles could help researchers predict human-adaptive mutations, aiding surveillance of emerging pandemic threats.

Optimisation of Neuraminidase Expression for Use in Drug Discovery by Using HEK293-6E Cells.

Influenza virus is a highly contagious virus that causes significant human mortality and morbidity annually. The most effective drugs for treating influenza are the neuraminidase inhibitors, but resistance to these inhibitors has emerged, and additional drug discovery research on neuraminidase and other targets is needed. Traditional methods of neuraminidase production from embryonated eggs are cumbersome, while insect cell derived protein is less reflective of neuraminidase produced during human infection. Herein we describe a method for producing neuraminidase from a human cell line, HEK293-6E, and demonstrate the method by producing the neuraminidase from the 1918 H1N1 pandemic influenza strain. This method produced high levels of soluble neuraminidase expression (>3000 EU/mL), was enhanced by including a secretion signal from a viral chemokine binding protein, and does not require co-expression of additional proteins. The neuraminidase produced was of sufficient quantity and purity to support high resolution crystal structure determination. The structure solved using this protein conformed to the previously reported structure. Notably the glycosylation at three asparagine residues was superior in quality to that from insect cell derived neuraminidase. This method of production of neuraminidase should prove useful in further studies, such as the characterisation of inhibitor binding.

Understanding why superspreading drives the COVID-19 pandemic but not the H1N1 pandemic

Understanding why superspreading drives the COVID-19 pandemic but not the H1N1 pandemic

Gene Segment Interactions Can Drive the Emergence of Dominant Yet Suboptimal Gene Constellations During Influenza Virus Reassortment.

A segmented genome enables influenza virus to undergo reassortment when two viruses infect the same cell. Although reassortment is involved in the creation of pandemic influenza strains and is routinely used to produce influenza vaccines, our understanding of the factors that drive the emergence of dominant gene constellations during this process is incomplete. Recently, we defined a spectrum of interactions between the gene segments of the A/Udorn/307/72 (H3N2) (Udorn) strain that occur within virus particles, a major interaction being between the NA and PB1 gene segments. In addition, we showed that the Udorn PB1 is preferentially incorporated into reassortant viruses that express the Udorn NA. Here we use an influenza vaccine seed production model where eggs are coinfected with Udorn and the high yielding A/Puerto Rico/8/34 (H1N1) (PR8) virus and track viral genotypes through the reassortment process under antibody selective pressure to determine the impact of Udorn NA-PB1 co-selection. We discovered that 86% of the reassortants contained the PB1 from the Udorn parent after the initial co-infection and this bias towards Udorn PB1 was maintained after two further passages. Included in these were certain gene constellations containing Udorn HA, NA, and PB1 that confered low replicative fitness yet rapidly became dominant at the expense of more fit progeny, even when co-infection ratios of the two viruses favoured PR8. Fitness was not compromised, however, in the corresponding reassortants that also contained Udorn NP. Of particular note is the observation that relatively unfit reassortants could still fulfil the role of vaccine seed candidates as they provided high haemagglutinin (HA) antigen yields through co-production of non-infectious particles and/or by more HA molecules per virion. Our data illustrate the dynamics and complexity of reassortment and highlight how major gene segment interactions formed during packaging, in addition to antibody pressure, initially restrict the reassortant viruses that are formed.

Epidemic situation of the complex seasonality of imported influenza A and B virus transmission in Guangxi ports of China

Background/aimAnalysis of the characteristics of influenza virus in imported cases in Guangxi province of China.Materials and methodsThroat swabs of imported cases with influenza-like symptoms were detected by real-time PCR from July 2016 to December 2019.Results1292 laboratory detections of influenza were reported in 3974 influenza-like cases, of which 71.67% (926) were influenza A. The ratio of test positive was 32.82%. The proportion of detections of influenza B was 28.33% (366). A total of 70.51% of the cases mostly came from Vietnam (911). A total of 86.76% (1121) of the cases were imported from Dongxing Port, Nanning Airport, and Pingxiang Port. There was no statistical difference in all age groups. At the same time, 3 of the untyped A-type specimens were sequenced by next-generation sequencing. Among them, the sequences of 2 specimens from Vietnam had high homology with the influenza strain H3N2 in Hong Kong in 2017. The specimen sequence from Thailand is highly homologous to the influenza pandemic strain H1N1 in Brisbane, Australia in 2018.ConclusionImported influenza cases in Guangxi have occurred throughout the year, with higher numbers in winter and spring. The cases mostly came from Vietnam with influenza A. Relevant measures should be taken to control the further spread of the virus.

Conserved Influenza Hemagglutinin, Neuraminidase and Matrix Peptides Adjuvanted with ALFQ Induce Broadly Neutralizing Antibodies.

A universal influenza candidate vaccine that targets multiple conserved influenza virus epitopes from hemagglutinin (HA), neuraminidase (NA) and matrix (M2e) proteins was combined with the potent Army liposomal adjuvant (ALFQ) to promote induction of broad immunity to seasonal and pandemic influenza strains. The unconjugated and CRM-conjugated composite peptides formulated with ALFQ were highly immunogenic and induced both humoral and cellular immune responses in mice. Broadly reactive serum antibodies were induced across various IgG isotypes. Mice immunized with the unconjugated composite peptide developed antibody responses earlier than mice immunized with conjugated peptides, and the IgG antibodies were broadly reactive and neutralizing across Groups 1 and 2 influenza viruses. Multi-epitope unconjugated influenza composite peptides formulated with ALFQ provide a novel strategy for the development of a universal influenza vaccine. These synthetic peptide vaccines avoid the pitfalls of egg-produced influenza vaccines and production can be scaled up rapidly and economically.

Which influenza viruses will emerge following the SARS-CoV-2 pandemic?

The world has experienced five pandemics in just over one hundred years, four due to influenza and one due to coronavirus (SARS‐CoV‐2). In each case of pandemic influenza, the pandemic influenza strain has replaced the previous seasonal influenza virus. Notably, throughout the SARS‐CoV‐2 pandemic, there has been a 99% reduction in influenza isolation globally. It is anticipated that influenza will re‐emerge following the SARS‐CoV‐2 pandemic and circulate again. The potential for which influenza viruses will emerge is examined.

Obituary

Obituary