microorganisms Article Detection of Viral −RNA and +RNA Strands in Enterovirus-Infected Cells and Tissues Sami Salmikangas 1 , Jutta E. Laiho 2 , Kerttu Kalander 1, Mira Laajala 1 , Anni Honkimaa 2, Iryna Shanina 3, Sami Oikarinen 2, Marc S. Horwitz 3, Heikki Hyöty 2 and Varpu Marjomäki 1,* 1 Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Survontie 9C, FI-40500 Jyväskylä, Finland; sami.salmikangas@helsinki.fi (S.S.);
[email protected].fi (K.K.); mira.a.laajala@jyu.fi (M.L.) 2 Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; jutta.laiho@tuni.fi (J.E.L.); anni.honkimaa@tuni.fi (A.H.); sami.oikarinen@tuni.fi (S.O.); heikki.hyoty@tuni.fi (H.H.) 3 Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T1Z3, Canada;
[email protected] (I.S.);
[email protected] (M.S.H.) * Correspondence: Varpu.s.marjomaki@jyu.fi; Tel.: +358-405634422 Received: 30 October 2020; Accepted: 2 December 2020; Published: 4 December 2020 Abstract: The current methods to study the distribution and dynamics of viral RNA molecules inside infected cells are not ideal, as electron microscopy and immunohistochemistry can only detect mature virions, and quantitative real-time PCR does not reveal localized distribution of RNAs. We demonstrated here the branched DNA in situ hybridization (bDNA ISH) technology to study both the amount and location of the emerging RNA and +RNA during acute and persistent enterovirus − infections. According to our results, the replication of the viral RNA started 2–3 h after infection and the translation shortly after at 3–4 h post-infection.