Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method

• Main Authors: Dou, Dan, Hernández-Neuta, Iván, Wang, Hao, Östbye, Henrik, Qian, Xiaoyan, Thiele, Swantje, Resa-Infante, Patricia, Kouassi, Nancy Mounogou, Sender, Vicky, Hentrich, Karina, Mellroth, Peter, Henriques-Normark, Birgitta, Gabriel, Gülsah, Nilsson, Mats, Daniels, Robert
• Other Authors: Lee Kong Chian School of Medicine (LKCMedicine)
• Format: Article
• Language: English
• Published: 2018
• Subjects: IAV Cell Co-infections; IAV Entry
• Online Access: https://hdl.handle.net/10356/88620; http://hdl.handle.net/10220/44682
• Institution: Nanyang Technological University

Genome delivery to the proper cellular compartment for transcription and replication is a primary goal of viruses. However, methods for analyzing viral genome localization and differentiating genomes with high identity are lacking, making it difficult to investigate entry-related processes and co-examine heterogeneous RNA viral populations. Here, we present an RNA labeling approach for single-cell analysis of RNA viral replication and co-infection dynamics in situ, which uses the versatility of padlock probes. We applied this method to identify influenza A virus (IAV) infections in cells and lung tissue with single-nucleotide specificity and to classify entry and replication stages by gene segment localization. Extending the classification strategy to co-infections of IAVs with single-nucleotide variations, we found that the dependence on intracellular trafficking places a time restriction on secondary co-infections necessary for genome reassortment. Altogether, these data demonstrate how RNA viral genome labeling can help dissect entry and co-infections.