Open science, COVID-19, and the news: Exploring controversies in the circulation of early SARS-CoV-2 genomic epidemiology research

References

• Adhanom, T. (2020). WHO director-general’s opening remarks at the media briefing on COVID-19—11 March 2020. World Health Organization. https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19—11-march-2020
   Google Scholar
• Ananny, M., & Finn, M. (2020). Anticipatory news infrastructures: Seeing journalism’s expectations of future publics in its sociotechnical systems. New Media & Society, 22(9), 1600–1618. https://doi.org/https://doi.org/10.1177/1461444820914873
   Web of Science ®Google Scholar
• Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020). The proximal origin of SARS-CoV-2. Nature Medicine, 26(4), 450–452. https://doi.org/https://doi.org/10.1038/s41591-020-0820-9
   PubMed Web of Science ®Google Scholar
• Armstrong, G. L., MacCannell, D. R., Taylor, J., Carleton, H. A., Neuhaus, E. B., Bradbury, R. S., Posey, J. E., & Gwinn, M. (2019). Pathogen genomics in public health. New England Journal of Medicine, 381(26), 2569–2580. https://doi.org/https://doi.org/10.1056/NEJMsr1813907
   PubMed Web of Science ®Google Scholar
• arXiv Trackbacks. (2013). Trackbacks for 1305.3913. ArXiv. https://arxiv.org/tb/1305.3913.
   Google Scholar
• BBC Staff. (2010, December 2). Arsenic-loving bacteria may help in hunt for alien life. BBC. https://www.bbc.com/news/science-environment-11886943#:~:text=The%20first%20organism%20able%20to,arsenic%20in%20place%20of%20phosphorus
   Google Scholar
• BBC Staff. (2012, July 9). Studies refute arsenic bug claim. https://www.bbc.com/news/science-environment-18770964.
   Google Scholar
• Bedford, T. (2020, March 2). Cryptic transmission of novel coronavirus revealed by genomic epidemiology. Bedford Lab Blog. https://bedford.io/blog/ncov-cryptic-transmission/.
   Google Scholar
• Bedford, T., Greninger, A. L., Roychoudhury, P., Starita, L. M., Famulare, M., Huang, M.-L., Nalla, A., Pepper, G., Reinhardt, A., Xie, H., Shrestha, L., Nguyen, T. N., Adler, A., Brandstetter, E., Cho, S., Giroux, D., Han, P. D., Fay, K., Frazar, C. D., … Jerome, K. R. (2020). Cryptic transmission of SARS-CoV-2 in Washington state. Science, 370, 571–575. https://doi.org/https://doi.org/10.1126/science.abc0523
   PubMed Web of Science ®Google Scholar
• Blanchard, S. (2020, March 4). TWO strains of the killer coronavirus are spreading around the world – And 70% of infected patients have caught the more aggressive and contagious type, study claims. Daily Mail. https://www.dailymail.co.uk/health/article-8073543/TWO-strains-killer-coronavirus-spreading-study-claims.html
   Google Scholar
• Blick, G., Kagan, R. M., Coakley, E., Petropoulos, C., Maroldo, L., Greiger-Zanlungo, P., Gretz, S., & Garton, T. (2007). The probable source of both the primary multidrug-resistant (MDR) HIV-1 strain found in a patient with rapid progression to AIDS and a second recombinant MDR strain found in a chronically HIV-1–infected patient. The Journal of Infectious Diseases, 195(9), 1250–1259. https://doi.org/https://doi.org/10.1086/512240
   PubMed Web of Science ®Google Scholar
• Braine, T. (2020, March 30). Coronavirus is mutating and now has eight strains: Doctors. New York Daily News. https://www.nydailynews.com/coronavirus/ny-coronavirus-8-strains-world-mutations-informative-20200330-foz5jltqyvbu7kd3wxv3zrbw7i-story.html
   Google Scholar
• Brufsky, A. (2020). Distinct viral clades of SARS-CoV-2: Implications for modeling of viral spread. Journal of Medical Virology, 92, 1386–1390. https://doi.org/https://doi.org/10.1002/jmv.25902
   PubMed Web of Science ®Google Scholar
• Callaway, E. (2020). Will the pandemic permanently alter scientific publishing? Nature, 582(7811), 167–168. https://doi.org/https://doi.org/10.1038/d41586-020-01520-4
   PubMed Web of Science ®Google Scholar
• Collins, H. (1985). Changing order: Replication and induction in scientific practice. Sage.
   Google Scholar
• Collins, H. (2014). Are we all scientific experts now? Polity.
   Google Scholar
• Coudert, F.-X. (2020). The rise of preprints in chemistry. Nature Chemistry, 12(6), 499–502. https://doi.org/https://doi.org/10.1038/s41557-020-0477-5
   PubMed Web of Science ®Google Scholar
• Davis, M., & Lohm, D. (2020). Pandemics, publics, and narrative. Oxford University Press.
   Google Scholar
• Davis, M., Whittaker, A., Lindgren, M., Djerf-Pierre, M., Manderson, L., & Flowers, P. (2018). Understanding media publics and the antimicrobial resistance crisis. Global Public Health, 13(9), 1158–1168. https://doi.org/https://doi.org/10.1080/17441692.2017.1336248
   PubMed Web of Science ®Google Scholar
• De Floriani, L. (2020). 2020: a journey of discovery, challenges, and opportunity. Computer, 53(9), 4–7. https://doi.org/https://doi.org/10.1109/MC.2020.3005646
   Web of Science ®Google Scholar
• Didier, E., & Guaspare-Cartron, C. (2018). The new watchdogs’ vision of science: A roundtable with Ivan Oransky (retraction watch) and Brandon Stell (PubPeer). Social Studies of Science, 48(1), 165–167. https://doi.org/https://doi.org/10.1177/0306312718756202
   PubMed Web of Science ®Google Scholar
• Diep, F. (2013, May 21). Cold fusion machine gets third-party verification, inventor says. Popular Science. https://www.popsci.com/science/article/2013-05/cold-fusion-machine-gets-third-party-verification-inventor-says/
   Google Scholar
• Epstein, S. (1996). Impure science: AIDS, activism, and the politics of knowledge. University of California Press.
   Google Scholar
• Fry, N. K., Marshall, H., & Mellins-Cohen, T. (2019). In praise of preprints: This article has been co-published in all Society journals. Microbial Genomics, 5(4). https://doi.org/https://doi.org/10.1099/mgen.0.000259
   Google Scholar
• Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T., & Neher, R. A. (2018). Nextstrain: Real-time tracking of pathogen evolution. Bioinformatics (Oxford, England), 34(23), 4121–4123. https://doi.org/https://doi.org/10.1093/bioinformatics/bty407
   PubMed Web of Science ®Google Scholar
• Hambling, D. (2013, May 24). Cold fusion gets red hot and aims for EU. WIRED UK. https://web.archive.org/web/20130526042432/https://www.wired.co.uk/news/archive/2013-05/24/cold-fusion-research
   Google Scholar
• Hastings, C. (2020). Writing for digital news: The Social Organization of news stories about HIV criminalization in an Age of convergence journalism [Doctoral dissertation, York University]. https://yorkspace.library.yorku.ca/xmlui/handle/10315/37731
   Google Scholar
• Koch, C., & Jones, A. (2016). Big science, team science, and open science for neuroscience. Neuron, 92(3), 612–616. https://doi.org/https://doi.org/10.1016/j.neuron.2016.10.019
   PubMed Web of Science ®Google Scholar
• Korber, B., Fischer, W., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Foley, B., Giorgi, E., Bhattacharya, T., Parker, M., Partridge, D., Evans, C., Freeman, T., de Silva, T., on behalf of the Sheffield COVID-19 Genomics Group, LaBranche, C., & Montefiori, D. (2020a). Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2. Evolutionary Biology. https://doi.org/https://doi.org/10.1101/2020.04.29.069054. [Preprint].
   Google Scholar
• Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., Hastie, K. M., Parker, M. D., Partridge, D. G., Evans, C. M., Freeman, T. M., de Silva, T. I., McDanal, C., Perez, L. G., Tang, H., … Wyles, M. D. (2020b). Tracking changes in SARS-CoV-2 spike: Evidence that D614G increases infectivity of the COVID-19 virus. Cell, 182(4), 812–827.e19. https://doi.org/https://doi.org/10.1016/j.cell.2020.06.043
   PubMed Web of Science ®Google Scholar
• Krieger, L. (2020, April 20). Feud over Stanford coronavirus study: ‘The authors owe us all an apology’. San Jose Mercury News. https://www.mercurynews.com/2020/04/20/feud-over-stanford-coronavirus-study-the-authors-owe-us-all-an-apology/
   Google Scholar
• LANL HIV Sequence Database. (n.d.). Los Alamos National Laboratory (LANL) HIV sequence database. https://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html
   Google Scholar
• Lauring, A. S., & Hodcroft, E. B. (2021). Genetic variants of SARS-CoV-2—What do they mean? JAMA, 325, 529. https://doi.org/https://doi.org/10.1001/jama.2020.27124
   PubMed Web of Science ®Google Scholar
• Leonelli, S., Spichtinger, D., & Prainsack, B. (2015). Sticks and carrots: Encouraging open science at its source. Geo: Geography and Environment, 2(1), 12–16. https://doi.org/https://doi.org/10.1002/geo2.2
   PubMedGoogle Scholar
• MacLean, O. A., Orton, R. J., Singer, J. B., & Robinson, D. L. (2020a). Response to “on the origin and continuing evolution of SARS-CoV-2.” Virological.Org. http://virological.org/t/response-to-on-the-origin-and-continuingevolution-of-sars-cov-2/418
   Google Scholar
• MacLean, O. A., Orton, R. J., Singer, J. B., & Robertson, D. L. (2020b). No evidence for distinct types in the evolution of SARS-CoV-2. Virus Evolution, 6(1), veaa034. https://doi.org/https://doi.org/10.1093/ve/veaa034
   PubMed Web of Science ®Google Scholar
• Majumder, M. S., & Mandl, K. D. (2020). Early in the epidemic: Impact of preprints on global discourse about COVID-19 transmissibility. The Lancet Global Health, 8(5), e627–e630. https://doi.org/https://doi.org/10.1016/S2214-109X(20)30113-3
   PubMed Web of Science ®Google Scholar
• Malički, M., & Marušić, A. (2014). Is there a solution to publication bias? Researchers call for changes in dissemination of clinical research results. Journal of Clinical Epidemiology, 67(10), 1103–1110. https://doi.org/https://doi.org/10.1016/j.jclinepi.2014.06.002
   PubMed Web of Science ®Google Scholar
• McKay, R. A. (2017). Patient zero and the making of the AIDS epidemic. The University of Chicago Press.
   Google Scholar
• Mendez, E., Lawrence, R., MacCallum, C. J., & Moar, E. (2020). Progress on open science: Towards a shared research knowledge system: Final report of the open science policy platform. Publications Office. https://data.europa.eu/doi/10.2777/00139
   Google Scholar
• Meredith, S. (2020, March 4). Chinese scientists identify two strains of the coronavirus, indicating it’s already mutated at least once. CNBC. https://www.cnbc.com/2020/03/04/coronavirus-chinese-scientists-identify-two-types-covid-19.html
   Google Scholar
• Mirowski, P. (2018). The future(s) of open science. Social Studies of Science, 48(2), 171–203. https://doi.org/https://doi.org/10.1177/0306312718772086
   PubMed Web of Science ®Google Scholar
• Molldrem, S., & Smith, A. K. J. (2020). Reassessing the ethics of molecular HIV surveillance in the era of cluster detection and response: Toward HIV data justice. The American Journal of Bioethics, 20(10), 10–23. https://doi.org/https://doi.org/10.1080/15265161.2020.1806373
   PubMed Web of Science ®Google Scholar
• Mountz, A., Bonds, A., Mansfield, B., Loyd, J., Hyndman, J., Walton-Roberts, M., Basu, R., Whitson, R., Hawkins, R., Hamilton, T., & Curran, W. (2015). For slow scholarship: A feminist politics of resistance through collective action in the neoliberal university. ACME: An International Journal for Critical Geographies, 14(4), 1235–1259.
   Web of Science ®Google Scholar
• National Science Review. (n.d.). National science review: About the journal. Oxford University Press. https://academic.oup.com/nsr
   Google Scholar
• Nerlich, B., & Koteyko, N. (2012). Crying wolf? Biosecurity and metacommunication in the context of the 2009 swine flu pandemic. Health & Place, 18(4), 710–717. https://doi.org/https://doi.org/10.1016/j.healthplace.2011.02.008
   PubMed Web of Science ®Google Scholar
• NextStrain.org. (n.d.). Nextstrain: Analysis and visualization of pathogen sequence data. https://nextstrain.org/help/general/about-nextstrain
   Google Scholar
• Piller, C. (2021). Many scientists citing two scandalous COVID-19 papers ignore their retractions. Science. https://doi.org/https://doi.org/10.1126/science.abg5806
   Google Scholar
• Publons. (2020, April 16). Help in the fight against COVID-19: Review and score preprints on Publons. https://web.archive.org/web/20200417013252/https://publons.com/announcement/
   Google Scholar
• Racaniello, V. (2020, May 7). There is one, and only one strain of SARS-CoV-2. Virology Blog: About Viruses and Viral Disease. https://www.virology.ws/2020/05/07/there-is-one-and-only-one-strain-of-sars-cov-2/
   Google Scholar
• Rambaut, A., Holmes, E. C., O’Toole, Á, Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403–1407. https://doi.org/https://doi.org/10.1038/s41564-020-0770-5
   PubMed Web of Science ®Google Scholar
• Reyes-Galindo, L. (2016). Automating the Horae: Boundary-work in the age of computers. Social Studies of Science, 46(4), 586–606. https://doi.org/https://doi.org/10.1177/0306312716642317
   PubMed Web of Science ®Google Scholar
• Roiter, N. (2010, July 9). Stress-testing your network. Network World.
   Google Scholar
• Sheldon, T. (2018). Preprints could promote confusion and distortion. Nature, 559(7715), 445–445. https://doi.org/https://doi.org/10.1038/d41586-018-05789-4
   PubMed Web of Science ®Google Scholar
• Steen, R. G. (2011). Retractions in the medical literature: How many patients are put at risk by flawed research? Journal of Medical Ethics, 37(11), 688–692. https://doi.org/https://doi.org/10.1136/jme.2011.043133
   PubMed Web of Science ®Google Scholar
• Sudhir, K. (2016). Editorial—The exploration-exploitation tradeoff and efficiency in knowledge production. Marketing Science, 35(1), 1–9. https://doi.org/https://doi.org/10.1287/mksc.2015.0974
   Web of Science ®Google Scholar
• Tang, X., Wu, C., Li, X., Song, Y., Yao, X., Wu, X., Duan, Y., Zhang, H., Wang, Y., Qian, Z., Cui, J., & Lu, J. (2020). On the origin and continuing evolution of SARS-CoV-2. National Science Review, 7, 1012–1023. https://doi.org/https://doi.org/10.1093/nsr/nwaa036
   PubMed Web of Science ®Google Scholar
• Thaczuk, D. (2007, April 10). New light on the “New York patient”: “Super-bug” fears were exaggerated by media. NAM AIDSMap. https://www.aidsmap.com/news/apr-2007/new-light-new-york-patient-super-bug-fears-were-exaggerated-media
   Google Scholar
• Vartabedian, R. (2020, May 5). Scientists say a now-dominant strain of the coronavirus could be more contagious than original. Los Angeles Times. https://www.latimes.com/california/story/2020-05-05/mutant-coronavirus-has-emerged-more-contagious-than-original
   Google Scholar
• Villasanta, A. (2020, March 5). Coronavirus mutation confirmed: Scientists found two types of COVID-19 infecting world. International Business Times. https://www.ibtimes.com/coronavirus-mutation-confirmed-scientists-found-two-types-covid-19-infecting-world-2934239
   Google Scholar
• Virological.org. (n.d.). About Virological. http://virological.org/about
   Google Scholar
• Vogel, G. (2020, April 21). Antibody surveys suggesting vast undercount of coronavirus infections may be unreliable. Science. https://www.sciencemag.org/news/2020/04/antibody-surveys-suggesting-vast-undercount-coronavirus-infections-may-be-unreliable#
   Google Scholar
• Watney, S. (1996). Policing desire: Pornography, AIDS, and the media (3rd ed.). University of Minnesota Press.
   Google Scholar
• Weise, E. (2020, March 27). 8 strains of the coronavirus are circling the globe. Here’s what clues they’re giving scientists. USA Today. https://www.usatoday.com/story/news/nation/2020/03/27/scientists-track-coronavirus-strains-mutation/5080571002/
   Google Scholar
• Willinsky, J. (2005). The unacknowledged convergence of open source, open access, and open science. First Monday, 10(8). https://doi.org/https://doi.org/10.5210/fm.v10i8.1265
   Google Scholar
• Wolfe-Simon, F., Blum, J. S., Kulp, T. R., Gordon, G. W., Hoeft, S. E., Pett-Ridge, J., Stolz, J. F., Webb, S. M., Weber, P. K., Davies, P. C. W., Anbar, A. D., & Oremland, R. S. (2011). Response to comments on “a bacterium that can grow using arsenic instead of phosphorus.” Science, 332(6034), 1149–1149. https://doi.org/https://doi.org/10.1126/science.1202098
   Web of Science ®Google Scholar
• World Health Organization. (2020). SARS-CoV-2 Variants. https://www.who.int/csr/don/31-december-2020-sars-cov2-variants/en/
   Google Scholar
• 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. The Lancet, 395(10225), 689–697. https://doi.org/https://doi.org/10.1016/S0140-6736(20)30260-9
   PubMed Web of Science ®Google Scholar