Related papers: Concepts and methods for predicting viral evolutio…
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…
Applying a ML approach to the temporal variability of the Spike protein sequence enables us to identify, classify and track emerging virus variants. Our analysis is unbiased, in the sense that it does not require any prior knowledge of the…
Viral zoonoses have emerged as the key drivers of recent pandemics. Human infection by zoonotic viruses are either spillover events -- isolated infections that fail to cause a widespread contagion -- or species jumps, where successful…
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…
Viruses like influenza have long coevolved with host immune systems, gradually shaping the evolutionary trajectory of these pathogens. Host immune systems develop immunity against circulating strains, which in turn avoid extinction by…
Seasonal influenza presents an ongoing challenge to public health. The rapid evolution of the flu virus necessitates annual vaccination campaigns, but the decision to get vaccinated or not in a given year is largely voluntary, at least in…
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…
Severe acute respiratory disease SARS-CoV-2 has had a found impact on public health systems and healthcare emergency response especially with respect to making decisions on the most effective measures to be taken at any given time. As…
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…
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…
Viral mutations pose significant threats to public health by increasing infectivity, strengthening vaccine resistance, and altering disease severity. To track these evolving patterns, agencies like the CDC annually evaluate thousands of…
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…
Accurate and reliable forecasting of emerging dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants enables policymakers and vaccine makers to get prepared for future waves of infections. The last three waves of…
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…
Recent outbreaks of infectious diseases have been monitored closely from an epidemiological and microbiological perspective. Extracting from this wealth of data the information that is relevant for the evolution of the pathogen and predict…
Influenza viruses mutate rapidly and can pose a threat to public health, especially to those in vulnerable groups. Throughout history, influenza A viruses have caused pandemics between different species. It is important to identify the…
The evolution of the hemagglutinin amino acids sequences of Influenza A virus is studied by a method based on an informational metrics, originally introduced by Rohlin for partitions in abstract probability spaces. This metrics does not…
More infectious virus variants can arise from rapid mutations in their proteins, creating new infection waves. These variants can evade one's immune system and infect vaccinated individuals, lowering vaccine efficacy. Hence, to improve…
Seasonal variation in environmental variables, and in rates of contact among individuals, are fundamental drivers of infectious disease dynamics. Unlike most periodically-forced physical systems, for which the precise pattern of forcing is…
The COVID-19 pandemic has given rise to numerous articles from different scientific fields (epidemiology, virology, immunology, airflow physics...) without any effort to link these different insights. In this review, we aim to establish…