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We propose an approach based on a combination of physical, chemical, and mathematical methods to identify and characterize virulent influenza A viruses (IAVs) through the analysis of the hemagglutinin protein. These methods include the…
Influenza occurs every season and occasionally causes pandemics. Despite its low mortality rate, influenza is a major public health concern, as it can be complicated by severe diseases like pneumonia. A fast, accurate and low-cost method to…
A central challenge in every field of biology is to use existing measurements to predict the outcomes of future experiments. In this work, we consider the wealth of antibody inhibition data against variants of the influenza virus. Due to…
Until now, design of the annual influenza vaccine has relied on phylogenetic or whole-sequence comparisons of the viral coat proteins hemagglutinin and neuraminidase, with vaccine effectiveness assumed to correlate monotonically to the…
H1N1 influenza causes substantial seasonal illness and was the subtype of the 2009 influenza pandemic. Precise measures of antigenic distance between the vaccine and circulating virus strains help researchers design influenza vaccines with…
Influenza poses a significant threat to public health, particularly among the elderly, young children, and people with underlying dis-eases. The manifestation of severe conditions, such as pneumonia, highlights the importance of preventing…
Phylogenetic analyses based on small to moderately sized sets of sequential data lead to overestimating mutation rates in influenza hemagglutinin (HA) by at least an order of magnitude. Two major underlying reasons are: the incomplete…
The evolutionary dynamics of human Influenza A virus presents a challenging theoretical problem. An extremely high mutation rate allows the virus to escape, at each epidemic season, the host immune protection elicited by previous…
We predict vaccine efficacy with a measure of antigenic distance between influenza A(H3N2) and candidate vaccine viruses based on amino acid substitutions in the dominant epitopes. In 2016-2017, our model predicts 19% efficacy compared to…
This study focuses on the modeling, mathematical analysis, developing theories, and numerical simulation of Influenza virus transmission. We have proved the existence, uniqueness, positivity, and boundedness of the solutions. Also,…
The Influenza A virus belongs to the Orthomyxoviridae family. Influenza virus infection occurs yearly in all countries of the world. It usually kills between 250,000 and 500,000 people and causes severe illness in millions more. Over the…
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We…
The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune systems of infected populations get updated, chasing viruses…
Here we examine the evolution of beta-2 microglobulin in terms of its hydropathic shapes, a theoretical construct that has revealed important trends. The dynamics of many proteins are largely driven by interactions between the protein…
Analyses and visualizations by the ISSCOR method of influenza virus hemagglutinin genes of different A-subtypes revealed some rather striking temporal relationships between groups of individual gene subsets. Based on these findings we…
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with…
The cellular adaptive immune response plays a key role in resolving influenza infection. Experiments where individuals are successively infected with different strains within a short timeframe provide insight into the underlying viral…
Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how…
Most antigenically novel and evolutionarily successful strains of seasonal influenza A (H3N2) originate in East, South, and Southeast Asia. To understand this pattern, we simulated the ecological and evolutionary dynamics of influenza in a…
When analysing in vitro data, growth kinetics of influenza strains are often compared by computing their growth rates, which are sometimes used as proxies for fitness. However, analogous to mechanistic epidemic models, the growth rate can…