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The COVID-19 pandemic forced the rapid development of vaccines and the implementation of mass vaccination programs around the world. However, many hesitated to take the vaccine due to concerns about its effectiveness. By looking at an…
In early HIV infection, the virus population escapes from multiple CD8+ cell responses. The later an escape mutation emerges, the slower it outgrows its competition, i. e. the escape rate is lower. This pattern could indicate that the…
Multiple instances of Zika virus epidemic have been reported around the world in the last two decades, turning the related illness into an international concern. In this context the use of mathematical models for epidemics is of great…
RNA viruses are a widely used tool to study evolution experimentally. Many standard protocols of virus propagation and competition are done at nominally low multiplicity of infection (m.o.i.), but lead during one passage to two or more…
As the major target of many vaccines and neutralizing antibodies against SARS-CoV-2, the spike (S) protein is observed to mutate over time. In this paper, we present statistical approaches to tackle some challenges associated with the…
Protein phase transitions govern numerous diseases, including neurodegenerative disorders such as Parkinson's and Alzheimer's. In Parkinson's disease, distinct species of the protein alpha-synuclein undergo phase transitions from highly…
In this work, we analyze and model the cholera epidemics that affected South Sudan, the newest country in the world, during 2014 and 2015. South Sudan possibly represents one of the most difficult context in which adapt the deterministic…
In November 2015, El Salvador reported their first case of Zika virus (Zv) leading to an explosive outbreak that in just two months had over 6000 suspected cases. Many communities along with national agencies initiated the process to…
We investigated daily COVID-19 cases and deaths in the 337 lower tier local authority regions in England and Wales to better understand how the disease propagated over a 15-month period. Population density scaling models revealed residual…
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…
We compute the allele frequencies of the alpha (B.1.1.7), beta (B.1.351) and delta (B.167.2) variants of SARS-CoV-2 from almost two million genome sequences on the GISAID repository. We find that the frequencies of a majority of the…
The evolution of drug resistance in HIV occurs by the fixation of specific, well-known, drug-resistance mutations, but the underlying population genetic processes are not well understood. By analyzing within-patient longitudinal sequence…
The outbreak of mutant strains and vaccination behaviors have been the focus of recent epidemiological research, but most existing epidemic models failed to simultaneously capture viral mutation and consider the complexity and behavioral…
The fundamental models of epidemiology describe the progression of an infectious disease through a population using compartmentalized differential equations, but do not incorporate population-level heterogeneity in infection susceptibility.…
The rates of escape and reversion in response to selection pressure arising from the host immune system, notably the cytotoxic T-lymphocyte (CTL) response, are key factors determining the evolution of HIV. Existing methods for estimating…
Mobility restrictions - travel advisories, trade and travel bans, border closures and, in extreme cases, area quarantines or cordons sanitaires - are among the most widely used measures to control infectious diseases. Restrictions of this…
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation rates that allows viruses to thrive is…
In an increasingly interconnected world, a key scientific challenge is to examine mechanisms that lead to the widespread propagation of contagions, such as misinformation and pathogens, and identify risk factors that can trigger large-scale…
A possible explanation based on first principles for the appearance of the Omicron variant of the SARS-CoV-2 virus is proposed involving coinfection with HIV. The gist is that the resultant HIV-induced immunocompromise allows SARS-CoV-2…
The SARS CoV-2 virus emerged at the end of 2019 and rapidly developed several mutated variants, specifically the Delta and Omicron, which demonstrate higher infectivity and escalating infection cases worldwide. The dominant transmission…