The coronavirus helicase synergizes with the viral polymerase to enable rapid RNA synthesis through duplex RNA

The genome of most positive-sense (+)RNA viruses encodes a helicase, such as the coronavirus (CoV) nsp13-helicase, but little is known about their actual function, despite being absolutely essential for CoV replication. The CoV polymerase associates with two nsp13-helicases, which translocates in the opposite direction, raising questions about nsp13-helicase role during viral RNA synthesis. Using magnetic tweezers, we show that nsp13-helicase specifically associates with the CoV polymerase and tranlocates on the strand opposite to the template, increasing the overall RNA synthesis rate on a double-stranded (ds) RNA template by ten-fold. Nsp13-helicase utilizes both ATP hydrolysis and allostery to assist the CoV polymerase through the dsRNA fork. Our kinetic modelling provides the energy landscape of the two nsp13-helicases association with the polymerase and describes the nucleotide addition mechanochemistry of the resulting complex. Our study demonstrates a new function for (+)RNA virus helicase and deepens the understanding of CoV replication and transcription.