Trifunctional enzyme that possesses a bifunctional polynucleotide kinase/phosphatase activity and an ATP-dependent RNA ligase activity. May therefore play a role to evade an RNA damage-based host response. a 5'-end dephospho-2'-deoxyribonucleoside-DNA + ATP = a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + ADP + H(+) ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate.