Scientific papers on the origins of SARS-CoV-2

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Here is a list of scientific papers on the origins of SARS-CoV-2, the virus that causes COVID-19. This list is a work in progress. If you have suggestions for other readings that should be on this page, please send them to us via email at hana@usrighttoknow.wpenginepowered.com.

Huanan market hypothesis
Origins debated: Market and laboratory scenarios
Surprisingly well-adapted to infect humans
Earliest cases
Lab origin scenarios
Lab engineering scenarios
Bat coronavirus RaTG13 and the Mojiang mine
The Furin Cleavage Site and Bat coronavirus RmYN02
Pangolins: The Missing Intermediate(s)

Huanan Market: Epicenter or Superspreader Event?

bioRxiv. Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market. Jesse Bloom. April 26, 2023.

Nature. Surveillance of SARS-CoV-2 at the Huanan Seafood Market. William Liu et al. April 5, 2022.

Nature Portfolio. Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market. George Gao et al. February 25, 2022.

Science. The Huanan market was the epicenter of SARS-CoV-2 emergence . Michael Worobey et al. February 26, 2022.

Zenodo. SARS-CoV-2 emergence very likely resulted from at least two zoonotic events. Jonathan Pekar et al. February 26, 2022. DOI: 10.5281/zenodo.6299600

Origins Debated: Market and Laboratory Scenarios

Science. The animal origin of SARS-CoV-2. Spyros Lytras, Wei Xia, Joseph Hughes, Xiaowei Jiang and David L. Robertson. August 17, 2021.

Cell. The Origins of SARS-CoV-2: A Critical Review (pre-proof). Edward C. Holmes et al. August 20, 2021.

Medium. A response to “The Origins of SARS-CoV-2: A Critical Review. ” Alina Chan. July 12, 2021.

mBio. Can Science Help Resolve the Controversy on the Origins of the SARS-CoV-2 Pandemic? Arturo Casadevall, Susan R. Weiss and Michael Imperiale. August 2, 2021.

Infectious Diseases & Immunity. Origins of SARS-CoV-2: Focusing on Science. Zhengli Shi. April 2021 – Volume 1, Issue 1, p.3-4 doi: 10.1097/ID9.0000000000000008

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

Environmental Chemistry Letters. Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review. Erwan Sallard, José Halloy, Didier Casane, Etienne Decroly and Jacques van Helden. February 4, 2021. doi: https://doi.org/10.1007/s10311-020-01151-1

Surprisingly well-adapted to infect humans

Nature Scientific Reports. In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin. Sakshi Piplani, Puneet Kumar Singh, David A. Winkler, Nikolai Petrovsky. June 24, 2021. doi: https://doi.org/10.1038/s41598-021-92388-5

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

Earliest cases

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.

bioRxiv. Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic. Jesse Bloom. June 22, 2021. doi: https://doi.org/10.1101/2021.06.18.449051

Lab Origin Scenarios

bioRxiv. Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2. By Valentin Bruttel et al. October 20, 2022.

In Vivo. On the Origin of SARS-CoV-2: Did Cell Culture Experiments Lead to Increased Virulence of the Progenitor Virus for Humans? Bernd Kaina. May 2021, 35 (3) 1313-1326; DOI: https://doi.org/10.21873/invivo.12384

Environmental Chemistry Letters. Should we discount the laboratory origin of COVID-19? Rossana Segreto, Yuri Deigin, Kevin McCairn, Alejandro Sousa, Dan Sirotkin, Karl Sirotkin, Jonathan J. Couey, Adrian Jones & Daoyu Zhang. March 25, 2021.

ResearchGate. An investigation into the WIV databases that were taken offline. Billy Bostickson et al. February 2021.

ResearchGate. Wuhan Institute of Biological Products Co. Rodolphe de Maistre, Gilles Demaneuf and Billy Bostickson. March 2021.

Zenodo. 1. Proposed Forensic Investigation of Wuhan Laboratories. Billy Bostickson and Yvette Ghannam. March 2021. DOI: 10.5281/zenodo.4640383

ResearchGate. 2. Investigation of RaTG13 and the 7896 Clade. Billy Bostickson and Yvette Ghannam. March 2021. DOI: 10.13140/RG.2.2.22382.33607

ResearchGate. 3. Wuhan Laboratories, Bat Research and Biosafety. Billy Bostickson and Yvette Ghannam. April 2021. DOI: 10.13140/RG.2.2.32006.29761

Zenodo. A Bayesian analysis concludes beyond a reasonable doubt that SARS-CoV-2 is not a natural zoonosis but instead is laboratory derived. Dr. Steven Quay. January 29, 2021.

BioEssays. The genetic structure of SARS‐CoV‐2 does not rule out a laboratory origin. Rossana Segreto and Yuri Deigin. November 17, 2020. https://doi.org/10.1002/bies.202000240

Zenodo. Where Did the 2019 Coronavirus Pandemic Begin and How Did it Spread? The People’s Liberation Army Hospital in Wuhan China and Line 2 of the Wuhan Metro System Are Compelling Answers . Steven Carl Quay. October 28, 2020. doi: 10.5281/zenodo.4119262

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

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

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

Preprint. The possible origins of 2019-nCoV coronavirus. Botao Xiao. February 2020. doi: 10.13140/RG.2.2.21799.29601

Lab Engineering Scenario

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

Johns Hopkins Center for Health Security. In Response: Yan et al Preprint Examinations of the Origin of SARS-CoV-2 . Kelsey Lane Warmbrod, Rachel M. West, Nancy D. Connell and Gigi Kwik Gronvall. September 21, 2020.

Bat coronavirus RaTG13 and the Mojiang Mine

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. February 3, 2020. 579(7798): 270-273. doi:10.1038/s41586-020-2012-7

Nature. Addendum: 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. November 17, 2020. https://doi.org/10.1038/s41586-020-2951-z

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

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

Zenodo. Proposed SARS-CoV-2 Spillover During 2019 Review of Samples from a Mineshaft in Mojiang, Yunnan Province, China. Anonymous. September 14, 2020. doi: 10.5281/zenodo.4029544

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 . Alex C. Speciale. July 13, 2021.

Independent Science News. Phylogeographic Mapping of Newly Discovered Coronaviruses Pinpoints the Direct Progenitor of SARS-CoV-2 as Originating from Mojiang, China . Jonathan Latham and Allison Wilson. August 2, 2021.

The Furin Cleavage Site and Bat coronavirus RmYN02

Antiviral Research. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Bruno Coutard et al. February 10, 2020. DOI: 10.1016/j.antiviral.2020.104742

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

aRxiv. The bat coronavirus RmYN02 is characterized by a 6-nucleotide deletion at the S1/S2 junction, and its claimed PAA insertion is highly doubtful. Yuri Deigin and Rossana Segreto. December 1, 2020.

Pangolins: The Missing Intermediate(s)

Scientific Reports. Animal sales from Wuhan wet markets immediately prior to the COVID-19 pandemic. Xiao Xiao et al. June 7, 2021. Sci Rep 11, 11898 (2021). https://doi.org/10.1038/s41598-021-91470-2

Nature. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins . Tommy Tsan-Yuk Lam, Na Jia, Ya-Wei Zhang, Marcus Ho-Hin Shum, Jia-Fu Jiang, Hua-Chen Zhu, Yi-Gang Tong, Yong-Xia Shi, Xue-Bing Ni, Yun-Shi Liao, Wen-Juan Li, Bao-Gui Jiang, Wei Wei, Ting-Ting Yuan, Kui Zheng, Xiao-Ming Cui, Jie Li, Guang-Qian Pei, Xin Qiang, William Yiu-Man Cheung, Lian-Feng Li, Fang-Fang Sun, Si Qin, Ji-Cheng Huang, Gabriel M. Leung, Edward C. Holmes, Yan-Ling Hu, Yi Guan & Wu-Chun Cao. March 26, 2020. doi: https://doi.org/10.1038/s41586-020-2169-0

PLoS Pathogens. Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? Ping Liu, Jing-Zhe Jiang, Xiu-Feng Wan, Yan Hua, Linmiao Li, Jiabin Zhou, Xiaohu Wang, Fanghui Hou, Jing Chen, Jiejian Zou, Jinping Chen. May 14, 2020. doi: https://doi.org/10.1371/journal.ppat.1008421

Nature. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins . Kangpeng Xiao, Junqiong Zhai, Yaoyu Feng, Niu Zhou, Xu Zhang, Jie-Jian Zou, Na Li, Yaqiong Guo, Xiaobing Li, Xuejuan Shen, Zhipeng Zhang, Fanfan Shu, Wanyi Huang, Yu Li, Ziding Zhang, Rui-Ai Chen, Ya-Jiang Wu, Shi-Ming Peng, Mian Huang, Wei-Jun Xie, Qin-Hui Cai, Fang-Hui Hou, Wu Chen, Lihua Xiao & Yongyi She. May 7, 2020. doi: https://doi.org/10.1038/s41586-020-2313-x

Current Biology. Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak . Tao Zhang, Qunfu Wu, Zhigang Zhang. March 19, 2020. doi: https://doi.org/10.1016/j.cub.2020.03.022

bioRxiv. Single source of pangolin CoVs with a near identical Spike RBD to SARS-CoV-2 . Yujia Alina Chan and Shing Hei Zhan. October 23, 2020. doi: https://doi.org/10.1101/2020.07.07.184374

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

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

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