Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method
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-ex...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2018
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/88620 http://hdl.handle.net/10220/44682 |
| _version_ | 1811686139912781824 |
|---|---|
| author | 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 |
| author2 | Lee Kong Chian School of Medicine (LKCMedicine) |
| author_facet | Lee Kong Chian School of Medicine (LKCMedicine) 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 |
| author_sort | Dou, Dan |
| collection | NTU |
| description | 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. |
| first_indexed | 2024-10-01T04:55:41Z |
| format | Journal Article |
| id | ntu-10356/88620 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T04:55:41Z |
| publishDate | 2018 |
| record_format | dspace |
| spelling | ntu-10356/886202020-09-21T11:33:36Z Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method 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 Lee Kong Chian School of Medicine (LKCMedicine) Singapore Centre for Environmental Life Sciences Engineering IAV Cell Co-infections IAV Entry 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. Published version 2018-04-12T08:27:55Z 2019-12-06T17:07:26Z 2018-04-12T08:27:55Z 2019-12-06T17:07:26Z 2017 Journal Article Dou, D., Hernández-Neuta, I., Wang, H., Östbye, H., Qian, X., Thiele, S., et al. (2017). Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method. Cell Reports, 20(1), 251-263. 2211-1247 https://hdl.handle.net/10356/88620 http://hdl.handle.net/10220/44682 10.1016/j.celrep.2017.06.021 en Cell Reports © 2017 The Author(s). This paper was published in Cell Reports and is made available as an electronic reprint (preprint) with permission of The Author(s). The published version is available at: [http://dx.doi.org/10.1016/j.celrep.2017.06.021]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law. 13 p. application/pdf |
| spellingShingle | IAV Cell Co-infections IAV Entry 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 Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method |
| title | Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method |
| title_full | Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method |
| title_fullStr | Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method |
| title_full_unstemmed | Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method |
| title_short | Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method |
| title_sort | analysis of iav replication and co infection dynamics by a versatile rna viral genome labeling method |
| topic | IAV Cell Co-infections IAV Entry |
| url | https://hdl.handle.net/10356/88620 http://hdl.handle.net/10220/44682 |
| work_keys_str_mv | AT doudan analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT hernandezneutaivan analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT wanghao analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT ostbyehenrik analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT qianxiaoyan analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT thieleswantje analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT resainfantepatricia analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT kouassinancymounogou analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT sendervicky analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT hentrichkarina analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT mellrothpeter analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT henriquesnormarkbirgitta analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT gabrielgulsah analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT nilssonmats analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod AT danielsrobert analysisofiavreplicationandcoinfectiondynamicsbyaversatilernaviralgenomelabelingmethod |