Reading list: What are the origins of SARS-CoV-2? What are the risks of gain-of-function research?

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Here is a reading list about what is known and not known about the origins of SARS-CoV-2, accidents and leaks at biosafety and biowarfare laboratories, and the health risks of gain-of-function (GOF) research, which aims to increase the host range, transmissibility, infectivity or pathogenicity of potential pandemic pathogens.

This reading list is a work in progress. We will update it. Please send readings we may have missed to Sainath Suryanarayanan at sainath@usrtk.org.

What are the origins of SARS-CoV-2?
Accidents, leaks, transparency failures in biosafety facilities
Networks of biodefense and biowarfare
Debates on gain-of-function research
Scientific papers on the origins of SARS-CoV-2

What are the origins of SARS-CoV-2?

Bulletin of the Atomic Scientists. Did the SARS-CoV-2 virus arise from a bat coronavirus research program in a Chinese laboratory? Very possibly. Milton Leitenberg. June 4, 2020.

The Washington Post. State Department cables warned of safety issues at Wuhan lab studying bat coronaviruses. Josh Rogin. April 14, 2020.

Houston Chronicle. UTMB scientist acknowledges safety risks at Chinese lab doing coronavirus research. Nick Powell. April 23, 2020. 

The Wall Street Journal. NIH presses U.S. nonprofit for information on Wuhan virology lab. Betsy McKay. August 19, 2020.  

The Wall Street Journal. So where did the virus come from? Matt Ridley. May 29, 2020. 

Boston Magazine. Could COVID-19 have escaped from a lab? Rowan Jacobsen. September 9, 2020. 

Newsweek. The controversial experiments and Wuhan lab suspected of starting the coronavirus pandemic. Fred Guterl, Naveed Jamali and Tom O’Connor. April 27, 2020.

The Washington Post. State Department releases cable that launched claims that coronavirus escaped from Chinese lab. John Hudson and Nate Jones. July 17, 2020. 

The Telegraph. Scientists to examine possibility Covid leaked from lab as part of investigation into virus origins. Paul Nuki. September 15, 2020.  

The Wall Street Journal. On the ground in Wuhan, signs of China stalling probe of coronavirus origins. Jeremy Page and Natasha Khan. May 12, 2020. 

NBC News. Report says cellphone data suggests October shutdown at Wuhan lab, but experts are skeptical. Ken Dilanian, Ruaridh Arrow, Courtney Kube, Carol E. Lee, Louise Jones and Lorand Bodo. May 9, 2020. 

Washington Post. How did covid-19 begin? Its initial origin story is shaky. David Ignatius. April 2, 2020.

The Times. Revealed: Seven year coronavirus trail from mine deaths to a Wuhan lab. George Arbuthnott, Jonathan Calvert, and Philip Sherwell. July 4, 2020.

BBC. Wuhan: City of silence; Looking for answers in the place where coronavirus started. John Sudworth. July 2020.

The New York Times, 8 questions from a disease detective on the pandemic’s origins. William J. Broad. July 8, 2020.

Independent. Coronavirus: Former MI6 head claims pandemic ‘started as accident’ in Chinese laboratory. Andy Gregory. June 4, 2020.

The Wall Street Journal. In rare move, U.S. intelligence agencies confirm investigating if coronavirus emerged from lab accident. Warren P. Strobel and Dustin Volz. April 30, 2020.

The Wall Street Journal. China bat expert says her Wuhan lab wasn’t source of new coronavirus. James T. Areddy. April 21, 2020.

ABC News. Sorry, conspiracy theorists. Study concludes COVID-19 ‘is not a laboratory construct’. Kate Holland. March 27, 2020. 

The Economist. The pieces of the puzzle of Covid-19’s origin are coming to light. May 2, 2020. 

The Wall Street Journal. The Wuhan lab theory. The Editorial Board. May 6, 2020. 

The Guardian. Ignore the conspiracy theories: Scientists know Covid-19 wasn’t created in a lab. Peter Daszak. June 9, 2020. 

Science. Trump ‘owes us an apology.’ Chinese scientist at the center of COVID-19 origin theories speaks out. Jon Cohen. July 24, 2020.

Science. Reply to Science Magazine: Shi Zhengli Q&A. Shi Zhengli. July 15, 2020.

Minerva. Contradicting statements cast doubts on Chinese raw data. Aksel Fridstrøm. September 10, 2020. 

Minerva. The most logical explanation is that it comes from a laboratory. Aksel Fridstrøm and Nils August Andresen. July 2, 2020. 

Newsweek. Dr. Fauci backed controversial Wuhan lab with U.S. dollars for risky coronavirus research. Fred Guterl. April 28, 2020.

Independent Science News. The case is building that COVID-19 had a lab origin. Jonathan Latham and Allison Wilson. June 5, 2020.

Independent Science News. A proposed origin for SARS-CoV-2 and the COVID-19 pandemic. Jonathan Latham and Allison Wilson. July 15, 2020.

The Federalist. Virologist explains his quest to track down the origin of COVID-19. Julian Vigo. September 2, 2020. 

Sam Husseini Blog. Questioning the CDC: Is it a complete coincidence that China’s only BSL4 is in Wuhan? Audio and video. Sam Husseini. April 17, 2020.

GMWatch. Wuhan and US scientists used undetectable methods of genetic engineering on bat coronaviruses. Jonathan Matthews and Claire Robinson. May 20, 2020. 

Corporate Crime Reporter. Andrew Kimbrell on the origins of COVID-19. Russell Mokhiber. August 11, 2020.

GMWatch. Was the COVID-19 virus genetically engineered? Jonathan Matthews. April 22, 2020.

GMWatch. Why are the lab escape denialists telling such brazen lies? Jonathan Matthews. June 17, 2020. 

NBC News. Inside the Chinese lab central to the search for the coronavirus’ origin. Janis Mackey Frayer and Denise Chow. August 10, 2020.

Edizioni Cantagalli. Cina Covid 19. La chimera che ha cambiato il mondo (China COVID-19: The Chimera That Changed the World). Joseph Tritto. August 2020. 

Accidents, leaks, containment failures, transparency failures in biosafety facilities

The New Yorker. The risks of building too many bio labs. Elisabeth Eaves. March 18, 2020. 

Bulletin of the Atomic Scientists. Human error in high-biocontainment labs: a likely pandemic threat. Lynn Klotz. February 25, 2019. 

ProPublica. Here are six accidents UNC researchers had with lab-created coronaviruses. Alison Young and Jessica Blake. August 17, 2020. 

CBC. Canadian scientist sent deadly viruses to Wuhan lab months before RCMP asked to investigate. June 16, 2020.

The Frederick News-Post. CDC inspection findings reveal more about USAMRIID research suspension. Heather Mongilio. November 23, 2019. 

Centers for Disease Control and Prevention (CDC) and U.S. Department of Agriculture. U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID): description of inspection findings definitions. August 2019.

U.S. Government Accountability Office. High-containment laboratories: Comprehensive and up-to-date policies and stronger oversight mechanisms needed to improve safety. April 19, 2016. GAO-16-305. 

USA Today. 10 incidents discovered at the nation’s biolabs. Alison Young and Nick Penzenstadler. May 29, 2015. 

Bulletin of the Atomic Scientists. Threatened pandemics and laboratory escapes: self-fulfilling prophecies. Martin Furmanski. March 31, 2014.

Center for Arms Control and Nonproliferation. Laboratory Escapes and “Self-fulfilling prophecy” Epidemics. Martin Furmanski. February 17, 2014.

National Research Council. Biosecurity challenges of the global expansion of high-containment biological laboratories: summary of a workshop. 2012. Washington, DC: The National Academies Press. https://doi.org/10.17226/13315 

US House of Representatives. Committee on Energy and Commerce. Hearing on germs, viruses, and secrets: the silent proliferation of bio-laboratories in the United States, 110th Congress. October 4, 2007.

BMJ. Breaches of safety regulations are probable cause of recent SARS outbreak, WHO says. Jane Parry. May 22, 2004. doi: 10.1136/bmj.328.7450.1222-b

Independent Science News. The long history of accidental laboratory releases of potential pandemic pathogens is being ignored in the COVID-19 media coverage. Sam Husseini. May 5, 2020.

GMWatch. COVID-19: A wake-up call for biosafety. Jonathan Matthews. April 24, 2020. 

USA Today. CDC failed to disclose lab incidents with bioterror pathogens to Congress. Alison Young. June 24, 2016.

Global Times. Biosafety guideline issued to fix chronic management loopholes at virus labs. Liu Caiyu and Leng Shumei. February 16, 2020.

CBS News. Investigation: U.S. company bungled Ebola response. The Associated Press. March 7, 2016. 

GMWatch. Journals censor lab origin theory for SARS-CoV-2. Claire Robinson. July 16, 2020. 

Networks of biodefense and biowarfare 

Salon. Did this virus come from a lab? Maybe not — but it exposes the threat of a biowarfare arms race. Sam Husseini. April 24, 2020.

Sam Husseini Blog. Averting our gaze from biowarfare: pandemics and self-fulfilling prophecies. Sam Husseini. May 2020. 

The Boston Globe. The lure of bio-weapons. Bernard Lown and Prasannan Parthasarathi. February 23, 2005. 

Monterey Institute of International Studies. Beijing on biohazards: Chinese experts on bioweapons nonproliferation issues. Amy E. Smithson, Editor. August 2007. The James Martin Center For Nonproliferation Studies.

Deadly Cultures: Biological Weapons since 1945. Mark Wheelis, Lajos Rózsa, and Malcolm Dando (Editors). Harvard University Press, 2006.

Biowarfare and Terrorism. Francis Boyle. 2005. Clarity Press, Inc.

Preventing a Biological Arms Race. Susan Wright (Editor). The MIT Press, 1990. 

Biohazard. Ken Alibek with Stephen Handelman. Random House: New York, 1999. 

Debates on gain-of-function research

The National Academies Press. Potential risks and benefits of gain-of-function research: summary of a workshop. 2015. 

Forbes. Should we allow scientists to create dangerous super-viruses? Steven Salzberg. October 20, 2014. 

The Cambridge Working Group. Cambridge Working Group consensus statement on the creation of potential pandemic pathogens (PPPs). July 14, 2014. 

mBio. Can limited scientific value of potential pandemic pathogen experiments justify the risks? Marc Lipsitch. October 14, 2014. doi: https://doi.org/10.1128/mBio.02008-14 

mBio. Falling down the rabbit hole: aTRIP toward lexiconic precision in the “gain-of-function” debate. W. Paul Duprex and Arturo Casadevall. vol. 5,6 e02421-14. 12 Dec. 2014, doi:10.1128/mBio.02421-14

PLoS Medicine. Ethical alternatives to experiments with novel potential pandemic pathogens. Marc Lipsitch and Alison Galvani. 2014. 11(5): e1001646. doi: 10.1371/journal.pmed.1001646  

Scientific papers on the origins of SARS-CoV-2

The Lancet. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Chaolin Huang et al. January 30, 2020. Volume 395: 497–506. 

Nature. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu,…and Zheng-Li Shi. 2020. 579(7798): 270-273. doi:10.1038/s41586-020-2012-7

Nature Medicine. The proximal origin of SARS-CoV-2. Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes, Robert F. Garry. April 2020. Volume 26, pages 450-455. 

Journal of Medical Virology. Questions concerning the proximal origin of SARS-CoV-2. Murat Seyran, Damiano Pizzol, Parise Adadi…and Adam M. Brufsky. September 3, 2020. doi: https://doi.org/10.1002/jmv.26478 

Frontiers in Public Health. Lethal pneumonia cases in Mojiang miners (2012) and the mineshaft could provide important clues to the origin of SARS-CoV-2. Monali Rahalkar and Rahul Bahulikar. September 17, 2020. doi: 10.3389/fpubh.2020.581569

Current Biology. A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein. Hong Zhou, Xing Chen, Tao Hu, Juan Li, Hao Song, Yanran Liu, Peihan Wang, Di Liu, Jing Yang, Edward C. Holmes, Alice C. Hughes, Yuhai Bi, and Weifeng Shi. June 8, 2020. 30: 2196-2203. doi: https://doi.org/10.1016/j.cub.2020.05.023 

BioEssays. Might SARS‐CoV‐2 have arisen via serial passage through an animal host or cell culture? Karl Sirotkin and Dan Sirotkin. August 12, 2020.  https://doi.org/10.1002/bies.202000091 

Archives of Virology. A palindromic RNA sequence as a common breakpoint contributor to copy-choice recombination in SARS-CoV-2. William R. Gallaher. July 31, 2020. 

Cell. A genomic perspective on the origin and emergence of SARS-CoV-2. Yong-Zhen Zhang, Edward C. Holmes. April 2020 181(2):223-227. doi: 10.1016/j.cell.2020.03.035.

Infection, Genetics and Evolution. COVID-19: Time to exonerate the pangolin from the transmission of SARS-CoV-2 to humans. Roger Frutos, Jordi Serra-Cobo, Tianmu Chen and Christian A. Devaux. Volume 84, October 2020, 104493. https://doi.org/10.1016/j.meegid.2020.104493 

Proceedings of the National Academy of Sciences. Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. Mary Hongying Cheng, She Zhang, Rebecca A. Porritt, Magali Noval Rivas, Lisa Paschold, Edith Willscher, Mascha Binder, Moshe Arditi, and Ivet Bahar. September 28, 2020. doi: https://doi.org/10.1073/pnas.2010722117 

bioRxiv. SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence? Shing Hei Zhan, Benjamin E. Deverman, Yujia Alina Chan. May 2, 2020. doi: https://doi.org/10.1101/2020.05.01.073262 

Medium. Lab-made? SARS-CoV-2 genealogy through the lens of gain-of-function research. Yuri Deigin. April 22, 2020. 

Minerva. The evidence which suggests that this is no naturally evolved Virus: a reconstructed historical aetiology of the SARS-CoV-2 spike. Birger Sørensen, Angus Dalgleish & Andres Susrud. July 1, 2020.

ResearchGate. Is considering a genetic-manipulation origin for SARS-CoV-2 a conspiracy theory that must be censored? Rossana Segreto and Yuri Deigin. April 2020. DOI: 10.13140/RG.2.2.31358.13129/1

Preprints. Major concerns on the identification of bat coronavirus strain RaTG13 and quality of related Nature paper. Xiaoxu Lin, Shizhong Chen. June 5, 2020. 2020060044. doi: 10.20944/preprints202006.0044.v1 

Preprints. The abnormal nature of the fecal swab sample used for NGS analysis of RaTG13 genome sequence imposes a question on the correctness of the RaTG13 sequence. Monali Rahalkar and Rahul Bahulikar. August 11, 2020. doi: 10.20944/preprints202008.0205.v1 

OSF Preprints. COVID-19, SARS and bats coronaviruses genomes unexpected exogeneous RNA sequences. Jean-Claude Perez and Luc Montagnier. April 25, 2020. doi:10.31219/osf.io/d9e5g 

Zenodo. HIV man-manipulated coronavirus genome evolution trends. Jean-Claude Perez and Luc Montagnier. August 2, 2020. 

Emerging Microbes & Infections. HIV-1 did not contribute to the 2019-nCoV genome. Xiao Chuan, Li Xiaojun, Liu Shuying, Sang Yongming, Gao Shou-Jiang and Gao Feng. 2020. 9(1): 378-381. doi: 10.1080/22221751.2020.1727299

arXiv. In silico comparison of spike protein-ACE2 binding affinities across species; significance for the possible origin of the SARS-CoV-2 virus. Sakshi Piplani, Puneet Kumar Singh, David A. Winkler, Nikolai Petrovsky. May 13, 2020. 

bioRxiv. No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia. Jimmy Lee, Tom Hughes, Mei-Ho Lee, Hume Field, Jeffrine Japning Rovie-Ryan, Frankie Thomas Sitam, Symphorosa Sipangkui, Senthilvel K.S.S. Nathan, Diana Ramirez, Subbiah Vijay Kumar, Helen Lasimbang, Jonathan H. Epstein, Peter Daszak. June 19, 2020. doi: https://doi.org/10.1101/2020.06.19.158717

bioRxiv. Furin cleavage site is key to SARS-CoV-2 pathogenesis. Bryan A. Johnson,…Kari Debbink, Pei Yong Shi, Alexander Freiberg and Vineet Menachery. August 26, 2020. doi: https://doi.org/10.1101/2020.08.26.268854 

bioRxiv. The furin cleavage site of SARS-CoV-2 spike protein is a key determinant for transmission due to enhanced replication in airway cells. Thomas Peacock, Daniel H. Goldhill, Jie Zhou,…and Wendy S. Barclay. September 30, 2020. doi. https://doi.org/10.1101/2020.09.30.318311 

Zenodo. Unusual features of the SARS-CoV-2 genome suggesting sophisticated laboratory modification rather than natural evolution and delineation of its probable synthetic route. Li-Meng Yan, Shu Kang, Jie Guan, and Shanchang Hu. September 14, 2020. doi: 10.5281/zenodo.4028829