The Viral Growth Rate Calculation program is a bioinformatics tool for comparing and evaluating competitive viral fitness. Based on the assumption of exponential viral growth, the program will calculate with 95% confidence intervals the viral growth rate (g, a combined growth/decay parameter for viral production) of each virus in a competition as well as the growth rate difference (d) and ratio (r) of the two viruses.
Viral competition experimental data include fields of competid, day, replicate, Vf and Vm. Field competid is the unique ID for each unique pair of competing viruses; day is the day post infection when the sample is collected; replicate is the replicate ID for each replicate of a unique competition; Vf is the viral product of the founder or wild type virus and Vm is the viral product of the mutant virus.
Control experimental data are optional. If the founder/wild type and mutant viruses are in same viral background (e.g. NL4-3) but with different tags (e.g synonymous nucleotide differences introduced into a certain gene of the viral background), data from the competitions between founder/wild type viruses with different tags will be used as control to account for any growth differences caused by the differences in the tags and assay variations between different experiments.
Please cite the following paper if you use Viral Growth Rate Calculation:
Yi Liu, Sarah Holte, Ushnal Rao, Jan McClure, Philip Konopa, J. Victor Swain, Erinn Lanxon-Cookson, Moon Kim, Lennie Chen, and James I. Mullins. A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture. Journal of Virological Methods. 2013, 189:157-66.
For any questions, bugs and suggestions, please send email to mullspt+cfar@uw.edu and include a few sentences describing, briefly, the nature of your questions and include contact information.