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Understanding how genetic changes allow emerging virus strains to escape the protection afforded by vaccination is vital for the maintenance of effective vaccines. In the current work, we use structural and phylogenetic differences between…

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 Influenza type A virus can be considered as one of the most severe viruses that can infect multiple species with often fatal consequences to the hosts. The Haemagglutinin (HA) gene of the virus has the potential to be a target for…

Transmission rates are key in understanding the spread of infectious diseases. Using the framework of compartmental models, we introduce a simple method that enables us to reconstruct time series of transmission rates directly from…

Consider a birth and death chain to model the number of types of a given virus. Each type gives birth to a new type at rate $\lambda$ and dies at rate 1. Each type is also assigned a fitness. When a death occurs either the least fit type…

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 Influenza virus can be considered as one of the most severe viruses that can infect multiple species with often fatal consequences to the hosts. The Hemagglutinin (HA) gene of the virus can be a target for antiviral drug development…

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…

Early estimates of the transmission potential of emerging and re-emerging infections are increasingly used to inform public health authorities on the level of risk posed by outbreaks. Existing methods to estimate the reproduction number…

We present a study of the worldwide spread of a pandemic influenza and its possible containment at a global level taking into account all available information on air travel. We studied a metapopulation stochastic epidemic model on a global…

Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between…

In contrast to the common assumption in epidemic models that the rate of infection between individuals is constant, in reality, an individual's viral load determines their infectiousness. We compare the average and individual reproductive…

On 11 June the World Health Organization officially raised the phase of pandemic alert (with regard to the new H1N1 influenza strain) to level 6. We use a global structured metapopulation model integrating mobility and transportation data…

We study the global spatio-temporal patterns of influenza dynamics. This is achieved by analysing and modelling weekly laboratory confirmed cases of influenza A and B from 138 countries between January 2006 and May 2014. The data were…

In this work we study the stability properties of the equilibrium points of deterministic epidemic models with nonconstant population size. Models with nonconstant population have been studied in the past only in particular cases, two of…

This study presents a family of stochastic models for the dynamics of influenza in a closed human population. We consider treatment for the disease in the form of vaccination, and incorporate the periods of effectiveness of the vaccine and…

Since its emergence in 1968, influenza A (H3N2) has evolved extensively in genotype and antigenic phenotype. Antigenic evolution occurs in the context of a two-dimensional 'antigenic map', while genetic evolution shows a characteristic…

Seasonal influenza kills hundreds of thousands every year, with multiple constantly-changing strains in circulation at any given time. A high mutation rate enables the influenza virus to evade recognition by the human immune system,…

Influenza virus contains two highly variable envelope glycoproteins, hemagglutinin (HA) and neuraminidase (NA). The structure and properties of HA, which is responsible for binding the virus to the cell that is being infected, change…

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…