Validation:
The performance of RV-Typer was validated using receiver operating characteristic (ROC) analysis.
The sequences in true positive (TP) and negative (TN) data sets were given as an input to RV-Typer. Based on the serotype predictions for
sequences in TP and TN data sets, the sensitivity and specificity values were calculated. They are as following,
Sensitivity: 100%
Specificity: 100%
The serotypes of all the sequences in TP data set were correctly predicted by RV-Typer.
No serotypes were predicted for sequences in TN data set.
Effect of recombination on RTD-based typing of Rhinoviruses
In order to assess the efficacy of RV-Typer in typing of recombinant VP1 gene sequences, the intra- and inter-type recombinant sequences of VP1 gene were simulated. The sequences were simulated at varying levels of proportions of major and minor parents such as 90-10, 80-20, 70-30, 60-40 and 50-50% of sequence regions from respective parent types. While compiling the simulated intra- and inter-typic recombinant data sets (100 sequences in each), we retained the equal proportion of sequences (~33%) from RV-A, B and C species.
These simulated sequences were given as an input to RV-Typer server. The results of serotype prediction for simulated recombinant sequences are available here. It can be observed from these tables that RV-Typer assigned the type of major parent to both intra- and inter-typic recombinant sequences having 90-10% and 80-20% of sequence contribution from respective parents. Whereas in case of recombinant sequences having 70-30%, 60-40% and 50-50% of sequence proportion from respective parents, RV-Typer did not assign any serotype to most of the sequences and in few cases it assigned serotype of minor parent. Only ~6% of recombinant sequences were assigned with the type other than parent types. Therefore, in case of inconsistent results between RV-Typer and BLAST report, we suggest users to carry out recombination detection analysis.
The simulated recombinant sequence data can be downloaded from here.