Predictive modeling of influenza shows the promise of applied evolutionary biology
Seasonal influenza is controlled through vaccination campaigns. Evolution of influenza virus
antigens means that vaccines must be updated to match novel strains, and vaccine …
antigens means that vaccines must be updated to match novel strains, and vaccine …
Within-host evolution of human influenza virus
The rapid global evolution of influenza virus begins with mutations that arise de novo in
individual infections, but little is known about how evolution occurs within hosts. We review …
individual infections, but little is known about how evolution occurs within hosts. We review …
Stochastic processes constrain the within and between host evolution of influenza virus
The evolutionary dynamics of influenza virus ultimately derive from processes that take
place within and between infected individuals. Here we define influenza virus dynamics in …
place within and between infected individuals. Here we define influenza virus dynamics in …
Two-step fitness selection for intra-host variations in SARS-CoV-2
J Li, P Du, L Yang, J Zhang, C Song, D Chen, Y Song… - Cell reports, 2022 - cell.com
Spontaneous mutations introduce uncertainty into coronavirus disease 2019 (COVID-19)
control procedures and vaccine development. Here, we perform a spatiotemporal analysis …
control procedures and vaccine development. Here, we perform a spatiotemporal analysis …
Deep sequencing reveals potential antigenic variants at low frequencies in influenza A virus-infected humans
Influenza vaccines must be frequently reformulated to account for antigenic changes in the
viral envelope protein, hemagglutinin (HA). The rapid evolution of influenza virus under …
viral envelope protein, hemagglutinin (HA). The rapid evolution of influenza virus under …
Inferring epistasis from genetic time-series data
Epistasis refers to fitness or functional effects of mutations that depend on the sequence
background in which these mutations arise. Epistasis is prevalent in nature, including …
background in which these mutations arise. Epistasis is prevalent in nature, including …
MPL resolves genetic linkage in fitness inference from complex evolutionary histories
Genetic linkage causes the fate of new mutations in a population to be contingent on the
genetic background on which they appear. This makes it challenging to identify how …
genetic background on which they appear. This makes it challenging to identify how …
Fast and accurate estimation of selection coefficients and allele histories from ancient and modern DNA
We here present CLUES2, a full-likelihood method to infer natural selection from sequence
data that is an extension of the method CLUES. We make several substantial improvements …
data that is an extension of the method CLUES. We make several substantial improvements …
Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective
AS Malaspinas - Molecular Ecology, 2016 - Wiley Online Library
With hundreds of ancient genomes becoming available this year, ancient DNA research has
now entered the genomics era. Utilizing the temporal aspect of these new data, we can now …
now entered the genomics era. Utilizing the temporal aspect of these new data, we can now …
Improving pandemic influenza risk assessment
Assessing the pandemic risk posed by specific non-human influenza A viruses is an
important goal in public health research. As influenza virus genome sequencing becomes …
important goal in public health research. As influenza virus genome sequencing becomes …