Resources for Studying the 2019-nCoV Coronavirus (COVID-19): Databases and Tools

Resources for Studying the 2019-nCoV Coronavirus (COVID-19): Databases and Tools

  • “human coronaviruses such as …endemic human coronaviruses (HCoV) can persist on inanimate surfaces like metal, glass or plastic for up to 9 days…”

From Persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents (https://www.journalofhospitalinfection.com/article/S0195-6701(20)30046-3/fulltext)

Including the sequence data and the BLAST tool.

  • Coronavirus COVID-19 Global Cases by Johns Hopkins CSSE:

https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

Bioinformatics Analysis: Genes Identified in the 2019-nCoV Coronavirus (COVID-19)

  • E (envelope protein [Wuhan seafood market pneumonia virus])
  • M (membrane glycoprotein [Wuhan seafood market pneumonia virus])
  • N (nucleocapsid phosphoprotein [Wuhan seafood market pneumonia virus])
  • orf1ab (orf1a polyprotein;orf1ab polyprotein [Wuhan seafood market pneumonia virus])
  • ORF3a (ORF3a protein [Wuhan seafood market pneumonia virus])
  • ORF6 (ORF6 protein [Wuhan seafood market pneumonia virus])
  • ORF7a (ORF7a protein [Wuhan seafood market pneumonia virus])
  • ORF7b (ORF7b [Wuhan seafood market pneumonia virus])
  • ORF8 (ORF8 protein [Wuhan seafood market pneumonia virus])
  • ORF10 (ORF10 protein [Wuhan seafood market pneumonia virus])
  • S (surface glycoprotein [Wuhan seafood market pneumonia virus])

Publications about the 2019-nCoV Coronavirus (COVID-19)

Transmission and Epidemiology of 2019-nCoV (COVID-19)

  • Backer, J. A., Klinkenberg, D., & Wallinga, J. (2020). Incubation period of 2019 novel coronavirus (2019-nCoV) infections among travellers from Wuhan, China, 20-28 January 2020. Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 25(5). https://doi.org/10.2807/1560-7917.ES.2020.25.5.2000062
  • Giovanetti, M., Benvenuto, D., Angeletti, S., & Ciccozzi, M. (2020). The first two cases of 2019-nCoV in Italy: Where they come from? Journal of Medical Virology. https://doi.org/10.1002/jmv.25699
  • Habibzadeh, P., & Stoneman, E. K. (2020). The Novel Coronavirus: A Bird’s Eye View. The International Journal of Occupational and Environmental Medicine, 11(2), 65–71. https://doi.org/10.15171/ijoem.2020.1921
  • Holshue, M. L., DeBolt, C., Lindquist, S., Lofy, K. H., Wiesman, J., Bruce, H., Spitters, C., Ericson, K., Wilkerson, S., Tural, A., Diaz, G., Cohn, A., Fox, L., Patel, A., Gerber, S. I., Kim, L., Tong, S., Lu, X., Lindstrom, S., … Washington State 2019-nCoV Case Investigation Team. (2020). First Case of 2019 Novel Coronavirus in the United States. The New England Journal of Medicine. https://doi.org/10.1056/NEJMoa2001191
  • Nishiura, H., Jung, S.-M., Linton, N. M., Kinoshita, R., Yang, Y., Hayashi, K., Kobayashi, T., Yuan, B., & Akhmetzhanov, A. R. (2020). The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020. Journal of Clinical Medicine, 9(2). https://doi.org/10.3390/jcm9020330
  • Nishiura, H., Kobayashi, T., Yang, Y., Hayashi, K., Miyama, T., Kinoshita, R., Linton, N. M., Jung, S.-M., Yuan, B., Suzuki, A., & Akhmetzhanov, A. R. (2020). The Rate of Underascertainment of Novel Coronavirus (2019-nCoV) Infection: Estimation Using Japanese Passengers Data on Evacuation Flights. Journal of Clinical Medicine, 9(2). https://doi.org/10.3390/jcm9020419
  • Patel, A., Jernigan, D. B., & 2019-nCoV CDC Response Team. (2020). Initial Public Health Response and Interim Clinical Guidance for the 2019 Novel Coronavirus Outbreak—United States, December 31, 2019-February 4, 2020. MMWR. Morbidity and Mortality Weekly Report, 69(5), 140–146. https://doi.org/10.15585/mmwr.mm6905e1
  • Riou, J., & Althaus, C. L. (2020). Pattern of early human-to-human transmission of Wuhan 2019 novel coronavirus (2019-nCoV), December 2019 to January 2020. Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 25(4). https://doi.org/10.2807/1560-7917.ES.2020.25.4.2000058
  • Ryu, S., Chun, B. C., & Korean Society of Epidemiology 2019-nCoV Task Force Team. (2020). An interim review of the epidemiological characteristics of 2019 novel coronavirus. Epidemiology and Health, 42, e2020006. https://doi.org/10.4178/epih.e2020006
  • Wu, J. T., Leung, K., & Leung, G. M. (2020). Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: A modelling study. Lancet (London, England). https://doi.org/10.1016/S0140-6736(20)30260-9
  • Wu, P., Hao, X., Lau, E. H. Y., Wong, J. Y., Leung, K. S. M., Wu, J. T., Cowling, B. J., & Leung, G. M. (2020). Real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in Wuhan, China, as at 22 January 2020. Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 25(3). https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000044

Virus Evolution and Molecular Studies of 2019-nCoV (COVID-19)

  • Benvenuto, D., Giovanetti, M., Ciccozzi, A., Spoto, S., Angeletti, S., & Ciccozzi, M. (2020). The 2019-new coronavirus epidemic: Evidence for virus evolution. Journal of Medical Virology. https://doi.org/10.1002/jmv.25688
  • Benvenuto, D., Giovanetti, M., Salemi, M., Prosperi, M., De Flora, C., Junior Alcantara, L. C., Angeletti, S., & Ciccozzi, M. (2020). The global spread of 2019-nCoV: A molecular evolutionary analysis. Pathogens and Global Health, 1–4. https://doi.org/10.1080/20477724.2020.1725339
  • Ceraolo, C., & Giorgi, F. M. (2020). Genomic variance of the 2019-nCoV coronavirus. Journal of Medical Virology. https://doi.org/10.1002/jmv.25700

Detection and Diagnosis of 2019-nCoV (COVID-19)

  • Corman, V. M., Landt, O., Kaiser, M., Molenkamp, R., Meijer, A., Chu, D. K., Bleicker, T., Brünink, S., Schneider, J., Schmidt, M. L., Mulders, D. G., Haagmans, B. L., van der Veer, B., van den Brink, S., Wijsman, L., Goderski, G., Romette, J.-L., Ellis, J., Zambon, M., … Drosten, C. (2020). Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 25(3). https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045
  • Kampf, G., Todt, D., Pfaender, S., & Steinmann, E. (2020). Persistence of coronaviruses on inanimate surfaces and its inactivation with biocidal agents. The Journal of Hospital Infection. https://doi.org/10.1016/j.jhin.2020.01.022
  • Phan, T. (2020). Novel coronavirus: From discovery to clinical diagnostics. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 79, 104211. https://doi.org/10.1016/j.meegid.2020.104211
  • Quilty, B. J., Clifford, S., Cmmid nCoV Working Group, null, Flasche, S., & Eggo, R. M. (2020). Effectiveness of airport screening at detecting travellers infected with novel coronavirus (2019-nCoV). Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 25(5). https://doi.org/10.2807/1560-7917.ES.2020.25.5.2000080
  • To, K. K.-W., Tsang, O. T.-Y., Chik-Yan Yip, C., Chan, K.-H., Wu, T.-C., Chan, J. M. C., Leung, W.-S., Chik, T. S.-H., Choi, C. Y.-C., Kandamby, D. H., Lung, D. C., Tam, A. R., Poon, R. W.-S., Fung, A. Y.-F., Hung, I. F.-N., Cheng, V. C.-C., Chan, J. F.-W., & Yuen, K.-Y. (2020). Consistent detection of 2019 novel coronavirus in saliva. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America. https://doi.org/10.1093/cid/ciaa149
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