TY - JOUR AU - Mahase, E. PY - 2020 DA - 2020// TI - Covid-19: WHO declares pandemic because of “alarming levels” of spread, severity, and inaction JO - BMJ VL - 368 UR - https://doi.org/10.1136/bmj.m1036 DO - 10.1136/bmj.m1036 ID - Mahase2020 ER - TY - STD TI - Chen Z, Hu J, Zhang Z, Jiang S, Wang T, Shi Z, et al. Caution: The clinical characteristics of COVID-19 patients at admission are changing. medRxiv preprint. https://doi.org/10.1101/2020.03.03.20030833. ID - ref2 ER - TY - STD TI - Jin X, Xu K, Jiang L, Hao S, Yao H, Jia H, et al. Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site. Emerg Microbes Infect. 2020; 1-74. https://doi.org/10.1080/22221751.2020.1781551. ID - ref3 ER - TY - JOUR AU - Xu, X. W. AU - Wu, X. X. AU - Jiang, X. G. AU - Xu, K. J. AU - Ying, L. J. AU - Ma, C. L. PY - 2020 DA - 2020// TI - Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective Case Series JO - BMJ VL - 368 UR - https://doi.org/10.1136/bmj.m606 DO - 10.1136/bmj.m606 ID - Xu2020 ER - TY - JOUR AU - Wu, Z. AU - McGoogan, J. M. PY - 2019 DA - 2019// TI - Characteristics of and important lessons from the coronavirus disease, (COVID-19) Outbreak in China: summary of a report of 72 314 cases from the Chinese Center for Disease Control and Prevention JO - JAMA UR - https://doi.org/10.1001/jama.2020.2648 DO - 10.1001/jama.2020.2648 ID - Wu2019 ER - TY - STD TI - Istituto Superiore di Sanità. https//www.epicentro.iss.it/en/coronavirus/sars-cob-2-integrated surveillance-data. UR - http://www.epicentro.iss.it/en/coronavirus/sars-cob-2-integrated ID - ref6 ER - TY - STD TI - Istituto Superiore di Sanità. Available from: https://www.epicentro.iss.it/coronavirus/bollettino/bollettino-sorveglianza-integrata-COVID-19_20-maggio-2020.pdf. UR - https://www.epicentro.iss.it/coronavirus/bollettino/bollettino-sorveglianza-integrata-COVID-19_20-maggio-2020.pdf ID - ref7 ER - TY - JOUR AU - Holmes, E. C. PY - 2010 DA - 2010// TI - The evolution and emergence of RNA viruses JO - Emerg Infect Dis VL - 16 UR - https://doi.org/10.3201/eid1605.100164 DO - 10.3201/eid1605.100164 ID - Holmes2010 ER - TY - JOUR AU - Guo, G. AU - Ye, L. AU - Pan, K. AU - Chen, Y. AU - Xing, D. AU - Yan, K. PY - 2020 DA - 2020// TI - New insights of emerging SARS-CoV-2: epidemiology, etiology, clinical features, clinical treatment, and prevention JO - Front Cell Dev Biol VL - 8 UR - https://doi.org/10.3389/fcell.2020.00410 DO - 10.3389/fcell.2020.00410 ID - Guo2020 ER - TY - JOUR AU - Tang, X. AU - Wu, C. AU - Li, X. AU - Song, Y. AU - Yao, X. AU - Wu, X. PY - 2020 DA - 2020// TI - On the origin and continuing evolution of SARS-CoV-2 JO - Natl Sci Rev UR - https://doi.org/10.1093/nsr/nwaa036 DO - 10.1093/nsr/nwaa036 ID - Tang2020 ER - TY - STD TI - Yao H, Lu X, Chen Q, Xu K, Chen Y, Cheng L, et al. Patient-derived mutations impact pathogenicity of SARS-CoV-2. MedRxiv preprint. https://doi.org/10.1101/2020.04.14.20060160. ID - ref11 ER - TY - JOUR AU - Lau, S. Y. AU - Wang, P. AU - Mok, B. W. Y. AU - Zhang, A. J. AU - Chu, H. AU - Lee, A. C. Y. PY - 2020 DA - 2020// TI - Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction JO - Emerg Micr Infect VL - 9 UR - https://doi.org/10.1080/22221751.2020.1756700 DO - 10.1080/22221751.2020.1756700 ID - Lau2020 ER - TY - JOUR AU - Wang, M. AU - Cao, R. AU - Zhang, L. AU - Yang, X. AU - Liu, J. AU - Xu, M. PY - 2020 DA - 2020// TI - Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro JO - Cell Res VL - 30 UR - https://doi.org/10.1038/s41422-020-0282-0 DO - 10.1038/s41422-020-0282-0 ID - Wang2020 ER - TY - JOUR AU - Kustin, T. AU - Ling, G. AU - Sharabi, S. AU - Ram, D. AU - Friedman, N. AU - Zuckerman, N. PY - 2019 DA - 2019// TI - A method to identify respiratory virus infections in clinical samples using next-generation sequencing JO - Sci Rep VL - 9 UR - https://doi.org/10.1038/s41598-018-37483-w DO - 10.1038/s41598-018-37483-w ID - Kustin2019 ER - TY - JOUR AU - Wood, D. E. AU - Lu, J. AU - Langmead, B. PY - 2019 DA - 2019// TI - Improved metagenomic analysis with Kraken 2 JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1891-0 DO - 10.1186/s13059-019-1891-0 ID - Wood2019 ER - TY - JOUR AU - Bolger, A. M. AU - Lohse, M. AU - Usadel, B. PY - 2014 DA - 2014// TI - Trimmomatic: a flexible trimmer for Illumina sequence data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu170 DO - 10.1093/bioinformatics/btu170 ID - Bolger2014 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, L. S. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Katoh, K. AU - Rozewicki, J. AU - Yamada, K. D. PY - 2019 DA - 2019// TI - MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization JO - Brief Bioinform VL - 20 UR - https://doi.org/10.1093/bib/bbx108 DO - 10.1093/bib/bbx108 ID - Katoh2019 ER - TY - JOUR AU - Laarson, A. PY - 2014 DA - 2014// TI - AliView: a fast and lightweight alignment viewer and editor for large data sets JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu531 DO - 10.1093/bioinformatics/btu531 ID - Laarson2014 ER - TY - JOUR AU - Nguyen, L. T. AU - Schmidt, H. A. AU - Haeseler, A. AU - Minh, B. Q. PY - 2015 DA - 2015// TI - IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies JO - Mol Biol Evol VL - 32 UR - https://doi.org/10.1093/molbev/msu300 DO - 10.1093/molbev/msu300 ID - Nguyen2015 ER - TY - STD TI - O’Toole Á, McCrone JT. Phylogenetic Assignment of Named Global Outbreak LINeages. 2020. https://github.com/hCoV-2019/pangolin. UR - https://github.com/hCoV-2019/pangolin ID - ref21 ER - TY - JOUR AU - Clementi, N. AU - Ferrarese, R. AU - Tonelli, M. AU - Amato, V. AU - Racca, S. AU - Locatelli, M. PY - 2020 DA - 2020// TI - Lower nasopharyngeal viral load during the latest phase of COVID-19 pandemic in a Northen Italy University Hospital JO - Clin Chem Med. UR - https://doi.org/10.1515/cclm-2020-0815 DO - 10.1515/cclm-2020-0815 ID - Clementi2020 ER - TY - STD TI - Rambaut A, Holmes EC, Hill V, O’Toole Á, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology. bioRxiv. 2020. https://doi.org/10.1101/2020.04.17.046086. ID - ref23 ER - TY - JOUR AU - Darling, A. E. AU - Mau, B. AU - Perna, N. T. PY - 2010 DA - 2010// TI - ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement JO - PLoS ONE VL - 5 UR - https://doi.org/10.1371/journal.pone.0011147 DO - 10.1371/journal.pone.0011147 ID - Darling2010 ER - TY - JOUR AU - Pachetti, M. AU - Marini, B. AU - Benedetti, F. AU - Giudici, F. AU - Mauro, E. AU - Storici, P. PY - 2020 DA - 2020// TI - Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant JO - J Transl Med VL - 18 UR - https://doi.org/10.1186/s12967-020-02344-6 DO - 10.1186/s12967-020-02344-6 ID - Pachetti2020 ER - TY - JOUR AU - Sanjuán, R. AU - Domingo-Calap, P. PY - 2016 DA - 2016// TI - Mechanisms of viral mutation JO - Cell Mol Life Sci VL - 73 UR - https://doi.org/10.1007/s00018-016-2299-6 DO - 10.1007/s00018-016-2299-6 ID - Sanjuán2016 ER - TY - JOUR AU - Dorp, L. AU - Acman, M. AU - Richard, D. AU - Shaw, L. P. AU - Ford, C. E. AU - Ormond, L. PY - 2020 DA - 2020// TI - Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 JO - Infect Genet Evol VL - 83 UR - https://doi.org/10.1016/j.meegid.2020.104351 DO - 10.1016/j.meegid.2020.104351 ID - Dorp2020 ER - TY - JOUR AU - Holmes, E. C. AU - Dudas, G. AU - Rambaut, A. AU - Andersen, K. G. PY - 2016 DA - 2016// TI - The evolution of Ebola virus: insights from the 2013–2016 epidemic JO - Nature VL - 538 UR - https://doi.org/10.1038/nature19790 DO - 10.1038/nature19790 ID - Holmes2016 ER - TY - JOUR AU - Snijder, E. J. AU - Bredenbeek, P. J. AU - Dobbe, J. C. AU - Thiel, V. AU - Ziebuhr, J. AU - Poon, L. L. M. PY - 2003 DA - 2003// TI - Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage JO - J Mol Biol VL - 331 UR - https://doi.org/10.1016/s0022-2836(03)00865-9 DO - 10.1016/s0022-2836(03)00865-9 ID - Snijder2003 ER - TY - JOUR AU - Minskaia, E. AU - Hertzig, T. AU - Gorbalenya, A. E. AU - Campanacci, V. AU - Cambillau, C. AU - Canard, B. PY - 2006 DA - 2006// TI - Discovery of an RNA Virus 3′- > 5′ exoribonuclease that is critically involved in coronavirus RNA synthesis JO - Proc Natl Acad Sci U S A VL - 103 UR - https://doi.org/10.1073/pnas.0508200103 DO - 10.1073/pnas.0508200103 ID - Minskaia2006 ER - TY - STD TI - Shen Z, Xiao Y, Kang L, Ma W, Shi L, Zhang L, et al. Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients. Clin Infect Dis. 2020. https://doi.org/10.1093/cid/ciaa203. ID - ref31 ER - TY - JOUR AU - Danchin, A. AU - Timmis, K. PY - 2020 DA - 2020// TI - SARS-CoV-2 variants: Relevance for symptom granularity, epidemiology, immunity (herd, vaccines), virus origin and containment? JO - Environ Microbiol VL - 22 UR - https://doi.org/10.1111/1462-2920.15053 DO - 10.1111/1462-2920.15053 ID - Danchin2020 ER - TY - JOUR AU - Desmyter, J. AU - Melnick, J. L. AU - Rawls, W. E. PY - 1968 DA - 1968// TI - Defectiveness of interferon production and of rubella virus interference in a line of African green monkey kidney cells (Vero) JO - J Virol VL - 2 UR - https://doi.org/10.1128/JVI.2.10.955-961.1968 DO - 10.1128/JVI.2.10.955-961.1968 ID - Desmyter1968 ER - TY - STD TI - Mantlo E, Bukreyeva N, Maruyama J, Paessler S, Huang C. Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection. bioRxiv. 2020; https://doi.org/10.1101/2020.04.02.022764. ID - ref34 ER - TY - STD TI - Lokugamage KG, Hage A, Schindewolf C, Rajsbaum R, Menachery VD. SARS-CoV-2 is sensitive to type I interferon pretreatment. bioRxiv. 2020; https://doi.org/10.1101/2020.03.07.982264. ID - ref35 ER - TY - JOUR AU - Guo, R. AU - Shang, P. AU - Carrillo, C. A. AU - Sun, Z. AU - Lakshmanappa, Y. S. AU - Yan, X. PY - 2018 DA - 2018// TI - Double-stranded viral RNA persists in vitro and in vivo during prolonged infection of porcine reproductive and respiratory syndrome virus JO - Virology VL - 524 UR - https://doi.org/10.1016/j.virol.2018.08.006 DO - 10.1016/j.virol.2018.08.006 ID - Guo2018 ER - TY - JOUR AU - Frisk, G. PY - 2001 DA - 2001// TI - Mechanisms of chronic enteroviral persistence in tissue JO - Curr Opin Infect Dis VL - 14 UR - https://doi.org/10.1097/00001432-200106000-00002 DO - 10.1097/00001432-200106000-00002 ID - Frisk2001 ER - TY - JOUR AU - Alidjinou, E. K. AU - Engelmann, I. AU - Bossu, J. AU - Villenet, C. AU - Figeac, M. AU - Romond, M. B. PY - 2017 DA - 2017// TI - Persistence of Coxsackievirus B4 in pancreatic ductal-like cells results in cellular and viral changes JO - Virulence VL - 8 UR - https://doi.org/10.1080/21505594.2017.1284735 DO - 10.1080/21505594.2017.1284735 ID - Alidjinou2017 ER - TY - JOUR AU - Pacciarini, F. AU - Ghezzi, S. AU - Canducci, F. AU - Sims, A. AU - Sampaolo, M. AU - Ferioli, E. PY - 2008 DA - 2008// TI - Persistent replication of severe acute respiratory syndrome coronavirus in human tubular kidney cells selects for adaptive mutations in the membrane protein JO - J Virol VL - 82 UR - https://doi.org/10.1128/JVI.00096-08 DO - 10.1128/JVI.00096-08 ID - Pacciarini2008 ER - TY - JOUR AU - Roberts, A. AU - Deming, D. AU - Paddock, C. D. AU - Cheng, A. AU - Yount, B. AU - Vogel, L. PY - 2007 DA - 2007// TI - A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice JO - PLoS Pathog VL - 3 UR - https://doi.org/10.1371/journal.ppat.0030005 DO - 10.1371/journal.ppat.0030005 ID - Roberts2007 ER - TY - JOUR AU - Angeletti, S. AU - Benvenuto, D. AU - Bianchi, M. AU - Giovanetti, M. AU - Pascarella, S. AU - Ciccozzi, M. PY - 2020 DA - 2020// TI - COVID-2019: The Role of the nsp2 and nsp3 in Its Pathogenesis JO - J Med Virol VL - 92 UR - https://doi.org/10.1002/jmv.25719 DO - 10.1002/jmv.25719 ID - Angeletti2020 ER - TY - JOUR AU - Alhammad, Y. M. O. AU - Fehr, A. R. PY - 2020 DA - 2020// TI - The viral microdomain counters host antiviral ADP-Ribosylation JO - Viruses. VL - 12 UR - https://doi.org/10.3390/v12040384 DO - 10.3390/v12040384 ID - Alhammad2020 ER - TY - JOUR AU - Kusov, Y. AU - Tan, J. AU - Alvarez, E. AU - Enjuanes, L. AU - Hilgenfeld, R. PY - 2015 DA - 2015// TI - A G-quadruplex-binding macrodomain within the “SARS-unique domain” is essential for the activity of the SARS-coronavirus replication–transcription complex JO - Virology VL - 484 UR - https://doi.org/10.1016/j.virol.2015.06.016 DO - 10.1016/j.virol.2015.06.016 ID - Kusov2015 ER - TY - STD TI - Fehr AR, Channappanavar R, Jankevicius G, Fett C, Zhao J, Athmer J, et al. The conserved coronavirus macrodomain promotes virulence and suppresses the innate immune response during severe acute respiratory syndrome coronavirus infection. mBio. 2016; 7(6):e01721-16. https://doi.org/10.1128/mbio.01721-16. ID - ref44 ER - TY - JOUR AU - Eriksson, K. K. AU - Cervantes-Barragán, L. AU - Ludewig, B. AU - Thiel, V. PY - 2008 DA - 2008// TI - Mouse hepatitis virus liver pathology is dependent on ADP-ribose-1″-phosphatase, a viral function conserved in the alpha-like supergroup JO - J Virol VL - 82 UR - https://doi.org/10.1128/JVI.02082-08 DO - 10.1128/JVI.02082-08 ID - Eriksson2008 ER - TY - JOUR AU - Fehr, A. R. AU - Athmer, J. AU - Channappanavar, R. AU - Phillips, J. M. AU - Meyerholz, D. K. AU - Perlman, S. PY - 2015 DA - 2015// TI - The nsp3 macrodomain promotes virulence in mice with coronavirus-induced encephalitis JO - J Virol VL - 89 UR - https://doi.org/10.1128/JVI.02596-14 DO - 10.1128/JVI.02596-14 ID - Fehr2015 ER - TY - JOUR AU - Ye, Q. AU - West, A. M. V. AU - Silletti, S. AU - Corbett, K. D. PY - 2020 DA - 2020// TI - Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein JO - Protein Sci UR - https://doi.org/10.1002/pro.3909.10.1002/pro.3909 DO - 10.1002/pro.3909.10.1002/pro.3909 ID - Ye2020 ER - TY - JOUR AU - Lai, A. AU - Bergna, A. AU - Caucci, S. AU - Clementi, N. AU - Vicenti, I. AU - Dragoni, F. PY - 2020 DA - 2020// TI - Molecular tracing of SARS-CoV-2 in Italy in the first three months of the epidemic JO - Viruses. VL - 12 UR - https://doi.org/10.3390/v12080798 DO - 10.3390/v12080798 ID - Lai2020 ER - TY - JOUR AU - Surjit, M. AU - Kumar, R. AU - Mishra, R. N. AU - Reddy, M. K. AU - Chow, V. T. K. AU - Lal, S. K. PY - 2005 DA - 2005// TI - The severe acute respiratory syndrome coronavirus nucleocapsid protein is phosphorylated and localizes in the cytoplasm by 14-3-3-mediated translocation JO - J Virol VL - 79 UR - https://doi.org/10.1128/JVI.79.17.11476-11486.2005 DO - 10.1128/JVI.79.17.11476-11486.2005 ID - Surjit2005 ER - TY - JOUR AU - Surjit, M. AU - Liu, B. AU - Chow, V. T. K. AU - Lal, S. K. PY - 2006 DA - 2006// TI - The nucleocapsid protein of severe acute respiratory syndrome-coronavirus inhibits the activity of cyclin-cyclin-dependent kinase complex and blocks S phase progression in mammalian cells JO - J Biol Chem VL - 281 UR - https://doi.org/10.1074/jbc.M509233200 DO - 10.1074/jbc.M509233200 ID - Surjit2006 ER - TY - JOUR AU - Xie, X. AU - Muruato, A. AU - Lokugamage, K. G. AU - Narayanan, K. AU - Zhang, X. AU - Zou, J. PY - 2020 DA - 2020// TI - An Infectious cDNA Clone of SARS-CoV-2 JO - Cell Host Microbe VL - 27 UR - https://doi.org/10.1016/j.chom.2020.04.004 DO - 10.1016/j.chom.2020.04.004 ID - Xie2020 ER -