Related papers: Integrating influenza antigenic dynamics with mole…
Influenza viruses enter a cell via endocytosis after binding to the surface. During the endosomal journey, acidification triggers a conformational change of the virus spike protein hemagglutinin (HA) that results in escape of the viral…
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…
We define a new parameter to quantify the antigenic distance between two H3N2 influenza strains: we use this parameter to measure antigenic distance between circulating H3N2 strains and the closest vaccine component of the influenza…
More virulent strains of influenza virus subtypes H1N1 appeared widely in 2007 and H3N2 in 2011, and especially 2013-4, when the effectiveness of the H3N2 vaccine decreased nearly to zero. The amino acid differences of neuraminidase from…
Influenza has been circulating in the human population and has caused three pandemics in the last century (1918 H1N1, 1957 H2N2, 1968 H3N2). The 2009 A(H1N1) was classified by the World Health Organization (WHO) as the fourth pandemic.…
One important feature of the mammalian immune system is the highly specific binding of antigens to antibodies. Antibodies generated in response to one infection may also provide some level of cross immunity to other infections. One model to…
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…
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The…
The ability to predict the evolution of a pathogen would significantly improve the ability to control, prevent, and treat disease. Despite significant progress in other problem spaces, deep learning has yet to contribute to the issue of…
More virulent strains of influenza virus subtypes H1N1 appeared in 2007 and H3N2 in 2011. The amino acid differences from prior less virulent strains appear to be small when tabulated through sequence alignments and counting site identities…
Antigenic escape constitutes the main mechanism allowing rapidly evolving viruses to achieve endemicity. Beyond granting immune escape, empirical evidence also suggests that mutations of viruses might increase their inter-host…
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…
We present a novel model that describes the within-host evolutionary dynamics of parasites undergoing antigenic variation. The approach uses a multi-type branching process with two types of entities defined according to their relationship…
Avian Influenza breakouts cause millions of dollars in damage each year globally, especially in Asian countries such as China and South Korea. The impact magnitude of a breakout directly correlates to time required to fully understand the…
Rapidly evolving pathogens like influenza viruses can persist by accumulating antigenic novelty fast enough to evade the adaptive immunity of the host population, yet without continuous accumulation of genetic diversity. This dynamical…
Influenza is a contagious respiratory illness that causes significant human morbidity and mortality, affecting 5-15% of the population in a typical epidemic season. Human influenza epidemics are caused by types A and B, with roughly 25% of…
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the…
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,…
For decades, the hemagglutination-inhibition (HI) assay has been used in epidemiological and basic biological studies of influenza viruses. The mechanistic basis of the assay results (called titers) is not well understood. The first part of…
This contribution is devoted to a new model of HIV multiplication motivated by the patent of one of the authors. We take into account the antigenic diversity through what we define "antigenicity", whether of the virus or of the adapted…