TY - JOUR AU - Wu, F. AU - Zhao, S. AU - Yu, B. AU - Chen, Y. -. M. AU - Wang, W. AU - Song, Z. -. G. PY - 2020 DA - 2020// TI - A new coronavirus associated with human respiratory disease in China JO - Nature. VL - 579 UR - https://doi.org/10.1038/s41586-020-2008-3 DO - 10.1038/s41586-020-2008-3 ID - Wu2020 ER - TY - JOUR AU - Plant, E. P. AU - Dinman, J. D. PY - 2008 DA - 2008// TI - The role of programmed-1 ribosomal frameshifting in coronavirus propagation JO - Front Biosci VL - 13 UR - https://doi.org/10.2741/3046 DO - 10.2741/3046 ID - Plant2008 ER - TY - JOUR AU - Narayanan, K. AU - Huang, C. AU - Makino, S. PY - 2008 DA - 2008// TI - SARS coronavirus accessory proteins JO - Virus Res VL - 133 UR - https://doi.org/10.1016/j.virusres.2007.10.009 DO - 10.1016/j.virusres.2007.10.009 ID - Narayanan2008 ER - TY - JOUR AU - Haan, C. A. AU - Masters, P. S. AU - Shen, X. AU - Weiss, S. AU - Rottier, P. J. PY - 2002 DA - 2002// TI - The group-specific murine coronavirus genes are not essential, but their deletion, by reverse genetics, is attenuating in the natural host JO - Virology. VL - 296 UR - https://doi.org/10.1006/viro.2002.1412 DO - 10.1006/viro.2002.1412 ID - Haan2002 ER - TY - JOUR AU - Yount, B. AU - Roberts, R. S. AU - Sims, A. C. AU - Deming, D. AU - Frieman, M. B. AU - Sparks, J. PY - 2005 DA - 2005// TI - Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice JO - J Virol VL - 79 UR - https://doi.org/10.1128/JVI.79.23.14909-14922.2005 DO - 10.1128/JVI.79.23.14909-14922.2005 ID - Yount2005 ER - TY - JOUR AU - Sawicki, S. G. AU - Sawicki, D. L. AU - Siddell, S. G. PY - 2007 DA - 2007// TI - A contemporary view of coronavirus transcription JO - J Virol VL - 81 UR - https://doi.org/10.1128/JVI.01358-06 DO - 10.1128/JVI.01358-06 ID - Sawicki2007 ER - TY - STD TI - Taiaroa G, Rawlinson D, Featherstone L, Pitt M, Caly L, Druce J, et al. Direct RNA sequencing and early evolution of SARS-CoV-2. bioRxiv. 2020:2020.03.05.976167. ID - ref7 ER - TY - STD TI - Kim D, Lee J-Y, Yang J-S, Kim JW, Kim VN, Chang H. The architecture of SARS-CoV-2 transcriptome. Cell. 2020:914–921.e10. ISSN 0092-8674. ID - ref8 ER - TY - STD TI - Davidson AD, Williamson MK, Lewis S. et al. Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein. Genome Med. 2020;12:68. https://doi.org/10.1186/s13073-020-00763-0. ID - ref9 ER - TY - STD TI - Finkel Y, Mizrahi O, Nachshon A. et al. The coding capacity of SARS-CoV-2. Nature. 2020. https://doi.org/10.1038/s41586-020-2739-1. ID - ref10 ER - TY - STD TI - Blanco-Melo D, Nilsson-Payant BE, Liu W-C, Uhl S, Hoagland D, Møller R, et al. Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell. 2020:1036–1045.e9. ID - ref11 ER - TY - STD TI - Suzuki T, Itoh Y, Sakai Y, Saito A, Okuzaki D, Motooka D, et al. Generation of human bronchial organoids for SARS-CoV-2 research. bioRxiv. 2020:2020.05.25.115600. ID - ref12 ER - TY - STD TI - Emanuel W, Kirstin M, Vedran F, Asija D, Theresa GL, Roberto A, et al. Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention. bioRxiv. 2020:2020.05.05.079194. ID - ref13 ER - TY - JOUR AU - Viehweger, A. AU - Krautwurst, S. AU - Lamkiewicz, K. AU - Madhugiri, R. AU - Ziebuhr, J. AU - Hölzer, M. PY - 2019 DA - 2019// TI - Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis JO - Genome Res VL - 29 UR - https://doi.org/10.1101/gr.247064.118 DO - 10.1101/gr.247064.118 ID - Viehweger2019 ER - TY - JOUR AU - Li, H. PY - 2018 DA - 2018// TI - Minimap2: pairwise alignment for nucleotide sequences JO - Bioinformatics. VL - 34 UR - https://doi.org/10.1093/bioinformatics/bty191 DO - 10.1093/bioinformatics/bty191 ID - Li2018 ER - TY - JOUR AU - Dobin, A. AU - Davis, C. A. AU - Schlesinger, F. AU - Drenkow, J. AU - Zaleski, C. AU - Jha, S. PY - 2013 DA - 2013// TI - STAR: ultrafast universal RNA-seq aligner JO - Bioinformatics. VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts635 DO - 10.1093/bioinformatics/bts635 ID - Dobin2013 ER - TY - BOOK AU - Team, R. C. PY - 2013 DA - 2013// TI - R: a language and environment for statistical computing ID - Team2013 ER - TY - STD TI - Wickham H. ggplot2. Wiley Interdisciplinary Reviews: Computational Statistics 2011;3(2):180–185. ID - ref18 ER - TY - STD TI - Wilkins D. gggenes: draw gene arrow maps in ‘ggplot2’. R package version 0.4. 0. 2019. ID - ref19 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - Camacho, C. AU - Coulouris, G. AU - Avagyan, V. AU - Ma, N. AU - Papadopoulos, J. AU - Bealer, K. PY - 2009 DA - 2009// TI - BLAST+: architecture and applications JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-421 DO - 10.1186/1471-2105-10-421 ID - Camacho2009 ER - TY - JOUR AU - Hyatt, D. AU - Chen, G. -. L. AU - LoCascio, P. F. AU - Land, M. L. AU - Larimer, F. W. AU - Hauser, L. J. PY - 2010 DA - 2010// TI - Prodigal: prokaryotic gene recognition and translation initiation site identification JO - BMC Bioinformatics. VL - 11 UR - https://doi.org/10.1186/1471-2105-11-119 DO - 10.1186/1471-2105-11-119 ID - Hyatt2010 ER - TY - JOUR AU - Buchfink, B. AU - Xie, C. AU - Huson, D. H. PY - 2015 DA - 2015// TI - Fast and sensitive protein alignment using DIAMOND JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3176 DO - 10.1038/nmeth.3176 ID - Buchfink2015 ER - TY - JOUR AU - Genoyer, E. AU - López, C. B. PY - 2019 DA - 2019// TI - The impact of defective viruses on infection and immunity JO - Annual Review Virol VL - 6 UR - https://doi.org/10.1146/annurev-virology-092818-015652 DO - 10.1146/annurev-virology-092818-015652 ID - Genoyer2019 ER - TY - JOUR AU - Rang, F. J. AU - Kloosterman, W. P. AU - Ridder, J. PY - 2018 DA - 2018// TI - From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy JO - Genome Biol VL - 19 UR - https://doi.org/10.1186/s13059-018-1462-9 DO - 10.1186/s13059-018-1462-9 ID - Rang2018 ER - TY - JOUR AU - Workman, R. E. AU - Tang, A. D. AU - Tang, P. S. AU - Jain, M. AU - Tyson, J. R. AU - Razaghi, R. PY - 2019 DA - 2019// TI - Nanopore native RNA sequencing of a human poly (A) transcriptome JO - Nat Methods VL - 16 UR - https://doi.org/10.1038/s41592-019-0617-2 DO - 10.1038/s41592-019-0617-2 ID - Workman2019 ER - TY - JOUR AU - Bosch, B. J. AU - Martina, B. E. AU - Zee, R. AU - Lepault, J. AU - Haijema, B. J. AU - Versluis, C. PY - 2004 DA - 2004// TI - Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides JO - Proc Natl Acad Sci VL - 101 UR - https://doi.org/10.1073/pnas.0400576101 DO - 10.1073/pnas.0400576101 ID - Bosch2004 ER - TY - JOUR AU - Thompson, K. A. S. AU - Yin, J. PY - 2010 DA - 2010// TI - Population dynamics of an RNA virus and its defective interfering particles in passage cultures JO - Virol J VL - 7 UR - https://doi.org/10.1186/1743-422X-7-257 DO - 10.1186/1743-422X-7-257 ID - Thompson2010 ER - TY - JOUR AU - Brooke, C. B. PY - 2014 DA - 2014// TI - Biological activities of'noninfectious' influenza A virus particles JO - Futur Virol VL - 9 UR - https://doi.org/10.2217/fvl.13.118 DO - 10.2217/fvl.13.118 ID - Brooke2014 ER - TY - STD TI - Lan TCT, Allan MF, Malsick LE, Khandwala S, Nyeo SSY, Bathe M, et al. Structure of the full SARS-CoV-2 RNA genome in infected cells. bioRxiv. 2020:2020.06.29.178343. ID - ref30 ER - TY - STD TI - Gribble J, Pruijssers AJ, Agostini ML, Anderson-Daniels J, Chappell JD, Lu X, et al. The coronavirus proofreading exoribonuclease mediates extensive viral recombination. bioRxiv. 2020:2020.04.23.057786. ID - ref31 ER - TY - JOUR AU - Sun, Y. AU - Jain, D. AU - Koziol-White, C. J. AU - Genoyer, E. AU - Gilbert, M. AU - Tapia, K. PY - 2015 DA - 2015// TI - Immunostimulatory defective viral genomes from respiratory syncytial virus promote a strong innate antiviral response during infection in mice and humans JO - PLoS Pathog VL - 11 UR - https://doi.org/10.1371/journal.ppat.1005122 DO - 10.1371/journal.ppat.1005122 ID - Sun2015 ER - TY - JOUR AU - Strahle, L. AU - Garcin, D. AU - Kolakofsky, D. PY - 2006 DA - 2006// TI - Sendai virus defective-interfering genomes and the activation of interferon-beta JO - Virology. VL - 351 UR - https://doi.org/10.1016/j.virol.2006.03.022 DO - 10.1016/j.virol.2006.03.022 ID - Strahle2006 ER - TY - JOUR AU - Barbosa, C. AU - Peixeiro, I. AU - Romão, L. PY - 2013 DA - 2013// TI - Gene expression regulation by upstream open reading frames and human disease JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003529 DO - 10.1371/journal.pgen.1003529 ID - Barbosa2013 ER - TY - JOUR AU - Wrapp, D. AU - Wang, N. AU - Corbett, K. S. AU - Goldsmith, J. A. AU - Hsieh, C. -. L. AU - Abiona, O. PY - 2020 DA - 2020// TI - Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation JO - Science. VL - 367 UR - https://doi.org/10.1126/science.abb2507 DO - 10.1126/science.abb2507 ID - Wrapp2020 ER - TY - JOUR AU - Hussain, S. AU - Chen, Y. AU - Yang, Y. AU - Xu, J. AU - Peng, Y. AU - Wu, Y. PY - 2005 DA - 2005// TI - Identification of novel subgenomic RNAs and noncanonical transcription initiation signals of severe acute respiratory syndrome coronavirus JO - J Virol VL - 79 UR - https://doi.org/10.1128/JVI.79.9.5288-5295.2005 DO - 10.1128/JVI.79.9.5288-5295.2005 ID - Hussain2005 ER - TY - STD TI - Nomburg J, Meyerson M, DeCaprio JA. virORF_direct. GitHub. https://github.com/jnoms/virORF_direct. 2020. UR - https://github.com/jnoms/virORF_direct ID - ref37 ER - TY - STD TI - Nomburg J, Meyerson M, DeCaprio JA. virORF_direct - pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2 (version 1). Zenodo. https://doi.org/10.5281/zenodo.4253321. 2020. ID - ref38 ER -