HPV16 RNA patterns defined by novel high-throughput RT-qPCR as triage marker in HPV-based cervical cancer precursor screening

•To triage HPV16 DNA-positive women by transformation-specific viral RNA patterns we developed RT-qPCR for E6*I, E1^E4 and E1C.•85% of 58≤CIN1 samples were correctly identified as advanced lesion-negative and 90% of 59≥CIN3 samples as positive.•3 of 4 RNA patterns-positive initial≤CIN1 lesions 5-24 months later had progressed to≥CIN2.