Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Virus-immune dynamics determined by prey-predator interaction network
  and epistasis in viral fitness landscape   Population dynamics and evolutionary genetics underly the structure of
ecosystems, changing on the same timescale for interacting species with rapid
turnover, such as virus (e.g. HIV) and immune response. Thus, an important
problem in mathematical modeling is to connect ecology, evolution and genetics,
which often have been treated separately. Here, extending analysis of multiple
virus and immune response populations in a resource - prey (consumer) -
predator model from Browne and Smith \cite{browne2018dynamics}, we show that
long term dynamics of viral mutants evolving resistance at distinct epitopes
(viral proteins targeted by immune responses) are governed by epistasis in the
virus fitness landscape. In particular, the stability of persistent equilibrium
virus-immune (prey-predator) network structures, such as nested and one-to-one,
and bifurcations are determined by a collection of circuits defined by
combinations of viral fitnesses that are minimally additive within a hypercube
of binary sequences representing all possible viral epitope sequences ordered
according to immunodominance hierarchy. Numerical solutions of our ordinary
differential equation system, along with an extended stochastic version
including random mutation, demonstrate how pairwise or multiplicative epistatic
interactions shape viral evolution against concurrent immune responses and
convergence to the multi-variant steady state predicted by theoretical results.
Furthermore, simulations illustrate how periodic infusions of subdominant
immune responses can induce a bifurcation in the persistent viral strains,
offering superior host outcome over an alternative strategy of immunotherapy
with strongest immune response.

14
The categories of this paper are: math-ph
4
The categories of this paper are: cond-mat
1
The categories of this paper are: cs
35
The categories of this paper are: mtrl-th
11
The categories of this paper are: hep-lat
25
The categories of this paper are: patt-sol
29
The categories of this paper are: funct-an
2
The categories of this paper are: math
32
The categories of this paper are: atom-ph
27
The categories of this paper are: comp-gas
5
The categories of this paper are: gr-qc
3
The categories of this paper are: physics
31
The categories of this paper are: ao-sci
33
The categories of this paper are: plasm-ph
30
The categories of this paper are: q-alg
19
The categories of this paper are: eess