相关论文: Punctuated evolution of influenza virus neuraminid…

H5N1 highly pathogenic avian influenza (HPAI) has been recently circulating in previously unseen patterns. As the underlying causes are uncertain, we need a better understanding of the drivers of virus circulation, as they underpin the…

We introduce and discuss a minimal individual-based model for influenza dynamics. The model takes into account the effects of specific immunization against viral strains, but also infectivity randomness and the presence of a short-lived…

The impact of climate conditions on influenza epidemiology has mostly been studied by addressing a singular aspect of transmission and a climate variable correlating to it. As climate change unfolds at an unprecedented rate, we urgently…

The aftermath of influenza infection is determined by a complex set of host-pathogen interactions, where genomic variability on both viral and host sides influences the final outcome. Although there exists large body of literature…

Non structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism…

Influenza A is a serious disease that causes significant morbidity and mortality, and vaccines against the seasonal influenza disease are of variable effectiveness. In this paper, we discuss use of the $p_{\rm epitope}$ method to predict…

Influenza B viruses make a considerable contribution to morbidity attributed to seasonal influenza. Currently circulating influenza B isolates are known to belong to two antigenically distinct lineages referred to as B/Victoria and…

High order structures (cavities and cliques) of the gene network of influenza A virus reveal tight associations among viruses during evolution and are key signals that indicate viral cross-species infection and cause pandemics. As…

Laboratory models are often used to understand the interaction of related pathogens via host immunity. For example, recent experiments where ferrets were exposed to two influenza strains within a short period of time have shown how the…

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…

This paper analyzes a simplified model of viral infection and evolution using the 'grand canonical ensemble' and formalisms from statistical mechanics and thermodynamics to enumerate all possible viruses and to derive thermodynamic…

Knowledge of the severity of an influenza outbreak is crucial for informing and monitoring appropriate public health responses, both during and after an epidemic. However, case-fatality, case-intensive care admission and…

Within the human respiratory tract (HRT), viruses diffuse through the periciliary fluid (PCF) bathing the epithelium, and travel upwards via advection towards the nose and mouth, as the mucus escalator entrains the PCF. While many…

The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…

Background: Influenza A/H3N2 has been circulating in humans since 1968, causing considerable morbidity and mortality. Although H3N2 incidence is highly seasonal, how such seasonality contributes to global phylogeographic migration dynamics…

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…

Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show…

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.…

Spike proteins, 1200 amino acids, are divided into two nearly equal parts, S1 and S2. We review here phase transition theory, implemented quantitatively by thermodynamic scaling. The theory explains the evolution of Coronavirus extremely…

We review the development of thermodynamic protein hydropathic scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Darwinian evolution has organized each protein family…