Human coronaviruses: Clinical features and phylogenetic analysis

Lai, 1990, Coronavirus: organization, replication and expression of genome, Ann Rev Microbiol, 44, 303, 10.1146/annurev.mi.44.100190.001511 Lai, 1990, Background paper. Transcription and replication of coronavirus RNA: a 1989 update, Adv Exp Med Biol, 276, 327, 10.1007/978-1-4684-5823-7_44 Gorbalenya, 1989, Coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis, Nucleic Acids Res, 17, 4847, 10.1093/nar/17.12.4847 Prentice, 2001, The cell biology of coronavirus infection, Adv Exp Med Biol, 494, 609, 10.1007/978-1-4615-1325-4_90 Loa, 2002, Purification of turkey coronavirus by Sephacryl size-exclusion chromatography, J Virol Methods, 104, 187, 10.1016/S0166-0934(02)00069-1 Wunschmann, 2002, Enteric coronavirus infection in a juvenile dromedary (Camelus dromedarius), J Vet Diagn Invest, 14, 441, 10.1177/104063870201400518 Theamboonlers, 2007, Human coronavirus infection among children with acute lower respiratory tract infection in Thailand, Intervirology, 50, 71, 10.1159/000097392 Pedersen, 2008, Pathogenesis of feline enteric coronavirus infection, J Feline Med Surg, 10, 529, 10.1016/j.jfms.2008.02.006 van der Hoek, 2010, Burden of disease due to human coronavirus NL63 infections and periodicity of infection, J Clin Virol, 48, 104, 10.1016/j.jcv.2010.02.023 Cavanagh, 2005, Coronaviruses in poultry and other birds, Avian Pathol, 34, 439, 10.1080/03079450500367682 Esper, 2006, Coronavirus HKU1 infection in the United States, Emerg Infect Dis, 12, 775, 10.3201/eid1205.051316 Vijgen, 2004, Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13), Int J Infect Dis, 8, 217, 10.1016/j.ijid.2004.03.004 van der Hoek, 2004, Identification of a new human coronavirus, Nat Med, 10, 368, 10.1038/nm1024 Hamre, 1966, A new virus isolated from the human respiratory tract, Proc Soc Exp Biol Med, 121, 190, 10.3181/00379727-121-30734 Sloots, 2006, Evidence of human coronavirus HKU1 and human bocavirus in Australian children, J Clin Virol, 35, 99, 10.1016/j.jcv.2005.09.008 Woo, 2005, Phylogenetic and recombination analysis of coronavirus HKU1, a novel coronavirus from patients with pneumonia, Arch Virol, 150, 2299, 10.1007/s00705-005-0573-2 2012 European Centre for Disease Prevention and Control, Rapid Risk Assessment: Severe respiratory disease associated with a novel coronavirus, ECDPC, September 24, 2012. Available at: http://ecdc.europa.eu/en/publications/Publications/RRA-Novel-coronavirus-final20120924.pdf [accessed 06.01.13]. Centers for Disease Control and Prevention (CDC). Severe respiratory illness associated with a novel coronavirus - Saudi Arabia and Qatar, 2012. MMWR Morb Mortal Wkly Rep 2012;61:820. Herold, 1993, Molecular analysis of the human coronavirus (strain 229E) genome, Arch Virol, 7, 63, 10.1007/978-3-7091-9300-6_6 Herold, 1993, Characterization of the human coronavirus 229E (HCV 229E) gene 1, Adv Exp Med Biol, 342, 75, 10.1007/978-1-4615-2996-5_12 Lai, 1994, Coronavirus: how a large RNA viral genome is replicated and transcribed, Infect Agents Dis, 3, 98 Haijema, 2003, Switching species tropism: an effective way to manipulate the feline coronavirus genome, J Virol, 77, 4528, 10.1128/JVI.77.8.4528-4538.2003 Thiel, 2003, Mechanisms and enzymes involved in SARS coronavirus genome expression, J Gen Virol, 84, 2305, 10.1099/vir.0.19424-0 Havlickova, 2005, [Newly identified representatives of the Coronaviridae family.], Klin Mikrobiol Infekc Lek, 11, 70 Gonzalez, 2003, A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae, Arch Virol, 148, 2207, 10.1007/s00705-003-0162-1 Woo, 2005, Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia, J Virol, 79, 884, 10.1128/JVI.79.2.884-895.2005 Rota, 2003, Characterization of a novel coronavirus associated with severe acute respiratory syndrome, Science, 300, 1394, 10.1126/science.1085952 Ziebuh, 2004, Molecular biology of severe acute respiratory syndrome coronavirus, Curr Opin Microbiol, 7, 412, 10.1016/j.mib.2004.06.007 Zhang, 1992, The hemagglutinin/esterase gene of human coronavirus strain OC43: phylogenetic relationships to bovine and murine coronaviruses and influenza C virus, Virology, 186, 318, 10.1016/0042-6822(92)90089-8 Klausegger, 1999, Identification of a coronavirus hemagglutinin-esterase with a substrate specificity different from those of influenza C virus and bovine coronavirus, J Virol, 73, 3737, 10.1128/JVI.73.5.3737-3743.1999 Popova, 2002, The spike but not the hemagglutinin/esterase protein of bovine coronavirus is necessary and sufficient for viral infection, Virology, 294, 222, 10.1006/viro.2001.1307 Li, 2006, Insights from the association of SARS-CoV S-protein with its receptor, ACE2, Adv Exp Med Biol, 581, 209, 10.1007/978-0-387-33012-9_36 Li, 2006, Animal origins of the severe acute respiratory syndrome coronavirus: insight from ACE2-S-protein interactions, J Virol, 80, 4211, 10.1128/JVI.80.9.4211-4219.2006 Lin, 2011, Characterization of the spike protein of human coronavirus NL63 in receptor binding and pseudotype virus entry, Virus Res, 160, 283, 10.1016/j.virusres.2011.06.029 Ge, 2012, Metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in China, J Virol, 86, 4620, 10.1128/JVI.06671-11 van Boheemen, 2012, Genomic characterization of newly discovered coronavirus associated with acute respiratory distress syndrome in humans, mBio, 3, 10.1128/mBio.00473-12 Gholizadeh, 2012, Molecular phylogenetic analysis of Anopheles and Cellia subgenus Anophelines (Diptera: Culicidae) in temperate and tropical regions of Iran, Acta Tropica Guzmán, 2012, Waxy genes from spelt wheat: new alleles for modern wheat breeding and new phylogenetic inferences about the origin of this species, Ann Bot, 110, 1161, 10.1093/aob/mcs201 Booth, 2003, Clinical features and short-term outcomes of 144 patients with SARS in the greater Toronto area, JAMA, 289, 2801, 10.1001/jama.289.21.JOC30885 Peiris, 2003, Severe acute respiratory syndrome (SARS), J Clin Virol, 28, 245, 10.1016/j.jcv.2003.08.005 Peiris, 2003, Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study, Lancet, 361, 1767, 10.1016/S0140-6736(03)13412-5 Peiris, 2003, Coronavirus as a possible cause of severe acute respiratory syndrome, Lancet, 361, 1319, 10.1016/S0140-6736(03)13077-2 Rickerts, 2003, [Clinical presentation and management of the severe acute respiratory syndrome (SARS)], Dtsch Med Wochenschr, 128, 1109, 10.1055/s-2003-39253 2003 Li, 2012, Correlation between TGF-beta1 expression and proteomic profiling induced by severe acute respiratory syndrome coronavirus papain-like protease, Proteomics, 12, 3193, 10.1002/pmic.201200225 Lai, 2007, Proteomic analysis of up-regulated proteins in human promonocyte cells expressing severe acute respiratory syndrome coronavirus 3C-like protease, Proteomics, 7, 1446, 10.1002/pmic.200600459 Chan-Yeung, 2003, SARS: epidemiology, Respirology, 8, 5 Nicholls, 2003, Lung pathology of fatal severe acute respiratory syndrome, Lancet, 361, 1773, 10.1016/S0140-6736(03)13413-7 He, 2006, Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS, J Pathol, 210, 288, 10.1002/path.2067 Yan, 2004, SARS coronavirus induces apoptosis in Vero E6 cells, J Med Virol, 73, 323, 10.1002/jmv.20094 Wang, 2004, Detection of SARS-associated coronavirus in throat wash and saliva in early diagnosis, Emerg Infect Dis, 10, 1213, 10.3201/eid1007.031113 Huang, 2005, An interferon-gamma-related cytokine storm in SARS patients, J Med Virol, 75, 185, 10.1002/jmv.20255 Nicholls, 2003, SARS: clinical virology and pathogenesis, Respirology, 8, S6, 10.1046/j.1440-1843.2003.00517.x Lang, 2003, Pathological study on severe acute respiratory syndrome, Chin Med J (Engl), 116, 976 Wang, 2004, Anti-SARS virus antibody responses against human SARS-associated coronavirus and animal SARS-associated coronavirus-like virus, Chin Med J (Engl), 117, 1723 Cameron, 2007, Interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome, J Virol, 81, 8692, 10.1128/JVI.00527-07 Ding, 2004, Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways, J Pathol, 203, 622, 10.1002/path.1560 Drosten, 2003, Identification of a novel coronavirus in patients with severe acute respiratory syndrome, N Engl J Med, 348, 1967, 10.1056/NEJMoa030747 Gu, 2005, Multiple organ infection and the pathogenesis of SARS, J Exp Med, 202, 415, 10.1084/jem.20050828 Li, 2004, Significant changes of peripheral T lymphocyte subsets in patients with severe acute respiratory syndrome, J Infect Dis, 189, 648, 10.1086/381535 Perlman, 2005, Immunopathogenesis of coronavirus infections: implications for SARS, Nat Rev Immunol, 5, 917, 10.1038/nri1732 Pang, 2003, [Some problems about detecting the suspected cases of SARS according to the local skin temperatures on face], Space Med Med Eng (Beijing), 16, 231 Baas, 2006, SARS-CoV virus-host interactions and comparative etiologies of acute respiratory distress syndrome as determined by transcriptional and cytokine profiling of formalin-fixed paraffin-embedded tissues, J Interferon Cytokine Res, 26, 309, 10.1089/jir.2006.26.309 Wang, 2004, Temporal relationship of viral load, ribavirin, interleukin (IL)-6, IL-8, and clinical progression in patients with severe acute respiratory syndrome, Clin Infect Dis, 39, 1071, 10.1086/423808 Morgenstern, 2005, Ribavirin and interferon-beta synergistically inhibit SARS-associated coronavirus replication in animal and human cell lines, Biochem Biophys Res Commun, 326, 905, 10.1016/j.bbrc.2004.11.128 Hogan, 2004, Resolution of primary severe acute respiratory syndrome-associated coronavirus infection requires Stat1, J Virol, 78, 11416, 10.1128/JVI.78.20.11416-11421.2004 Sheahan, 2008, MyD88 is required for protection from lethal infection with a mouse-adapted SARS-CoV, PLoS Pathog, 4, e1000240, 10.1371/journal.ppat.1000240 Cheung, 2005, Cytokine responses in severe acute respiratory syndrome coronavirus-infected macrophages in vitro: possible relevance to pathogenesis, J Virol, 79, 7819, 10.1128/JVI.79.12.7819-7826.2005 Lin, 2007, Termination of TGF-beta superfamily signaling through SMAD dephosphorylation–a functional genomic view, JJ Genet Genomics, 34, 1, 10.1016/S1673-8527(07)60001-0 Ray, 2003, Transforming growth factor beta in hepatitis C virus infection: in vivo and in vitro findings, J Gastroenterol Hepatol, 18, 393, 10.1046/j.1440-1746.2003.02985.x Zhao, 2008, Severe acute respiratory syndrome-associated coronavirus nucleocapsid protein interacts with Smad3 and modulates transforming growth factor-beta signaling, J Biol Chem, 283, 3272, 10.1074/jbc.M708033200 Lu, 2011, SARS-CoV nucleocapsid protein antagonizes IFN-beta response by targeting initial step of IFN-beta induction pathway, and its C-terminal region is critical for the antagonism, Virus Genes, 42, 37, 10.1007/s11262-010-0544-x Chang, 2004, Induction of IL-8 release in lung cells via activator protein-1 by recombinant baculovirus displaying severe acute respiratory syndrome-coronavirus spike proteins: identification of two functional regions, J Immunol, 173, 7602, 10.4049/jimmunol.173.12.7602 Dosch, 2009, SARS coronavirus spike protein-induced innate immune response occurs via activation of the NF-kappaB pathway in human monocyte macrophages in vitro, Virus Res, 142, 19, 10.1016/j.virusres.2009.01.005 Law, 2007, Role for nonstructural protein 1 of severe acute respiratory syndrome coronavirus in chemokine dysregulation, J Virol, 81, 416, 10.1128/JVI.02336-05 Lu, 2009, Humoral and cellular immune responses induced by 3a DNA vaccines against severe acute respiratory syndrome (SARS) or SARS-like coronavirus in mice, Clin Vaccine Immunol, 16, 73, 10.1128/CVI.00261-08 Sulea, 2005, Deubiquitination, a new function of the severe acute respiratory syndrome coronavirus papain-like protease?, J Virol, 79, 4550, 10.1128/JVI.79.7.4550-4551.2005 Spiegel, 2005, Inhibition of Beta interferon induction by severe acute respiratory syndrome coronavirus suggests a two-step model for activation of interferon regulatory factor 3, J Virol, 79, 2079, 10.1128/JVI.79.4.2079-2086.2005 Frieman, 2009, Severe acute respiratory syndrome coronavirus papain-like protease ubiquitin-like domain and catalytic domain regulate antagonism of IRF3 and NF-kappaB signaling, J Virol, 83, 6689, 10.1128/JVI.02220-08 Devaraj, 2007, Regulation of IRF-3-dependent innate immunity by the papain-like protease domain of the severe acute respiratory syndrome coronavirus, J Biol Chem, 282, 32208, 10.1074/jbc.M704870200 Li, 2011, Severe acute respiratory syndrome coronavirus papain-like protease suppressed alpha interferon-induced responses through downregulation of extracellular signal-regulated kinase 1-mediated signalling pathways, J Gen Virol, 92, 1127, 10.1099/vir.0.028936-0 Hofmann, 2005, Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entry, Proc Natl Acad Sci U S A, 102, 7988, 10.1073/pnas.0409465102 Han, 2007, Human Coronavirus-NL63 infections in Korean children, 2004-2006, J Clin Virol, 38, 27, 10.1016/j.jcv.2006.10.009 Vabret, 2005, Human coronavirus NL63, France, Emerg Infect Dis, 11, 1225, 10.3201/eid1108.050110 Woo, 2005, In silico analysis of ORF1ab in coronavirus HKU1 genome reveals a unique putative cleavage site of coronavirus HKU1 3C-like protease, Microbiol Immunol, 49, 899, 10.1111/j.1348-0421.2005.tb03681.x Pyrc, 2007, The novel human coronaviruses NL63 and HKU1, J Virol, 81, 3051, 10.1128/JVI.01466-06 Lau, 2006, Coronavirus HKU1 and other coronavirus infections in Hong Kong, J Clin Microbiol, 44, 2063, 10.1128/JCM.02614-05 Health Protection Agency, Novel Coronavirus 2012, HPA, 2012. Available at: http://www.hpa.org.uk/Topics/InfectiousDiseases/InfectionsAZ/NovelCoronavirus2012/ [accessed 06.01.13]. World Health Organization, 2012 Danielsson, 2012, Novel coronavirus associated with severe respiratory disease: case definition and public health measures, Euro Surveill, 17, 10.2807/ese.17.39.20282-en 2012 Corman, 2012, Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction, Euro Surveill, 17, 10.2807/ese.17.39.20285-en Balboni, 2012, A real-time PCR assay for bat SARS-like coronavirus detection and its application to Italian greater horseshoe bat faecal sample surveys, ScientificWorldJournal, 2012, 989514, 10.1100/2012/989514 Moës, 2005, A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium, BMC Infect Dis, 5, 6, 10.1186/1471-2334-5-6