vFitness: Calculation and Estimation in Competitive Virus Fitness


For the in vitro experiments of competitive virus fitness, the conventional relative fitness (1+s) and two new parameters (the pure relative fitness and the absolute fitness difference) are calculated based on the mathematical models. In the two-point calculation module, the parameters can be directly calculated from any combination of the pair of time points. On the other hand, the standard linear regression (least square method) and the measurement error models are used in the multi-point estimation module. Finally, the calculation tool deals with the competition experiment of the mutant virus (M) and the wild-type virus (W). It can also be used when the experiment involves two mutants (letting W represent the other mutant).

 

                                 Two-point Calculation                         Multi-point Estimation

 

The estimation/calculation for the competitive virus fitness is based on the following mathematical model,

where T, Tm, and Tw are number of uninfected target cells, number of cells infected by mutant virus, and number of cells infected by wild-type virus, respectively. The procduction rate ratio p is defined as the ratio of km/kw.

With the assumption of the target cells T being constant or large enough, the prue growth rate of mutant infected cells is defined as gm = kmT - δm, and the pure growth rate of wild-type cells as gw = kwT - δw. Then, the log fitness fitness r is deifned as the ratio of gm/gw, and the log relative fitness d defined as the difference of (gm - gw). The relative fitness (1+ s) is defined as exp(d).

 

See the following reference for more discussions about vFitness,

Ma J, Dykes C, Wu T, Huang Y, Demeter L, Wu H,  vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments. BMC Bioinformatics 2010 11:261.  [Abstract] [PDF]