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User:RandomCanadian/The origins of COVID-19: literature review

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A lot of speculation and unfounded hypotheses are circulating regarding the origins of SARS-Cov-2, the virus which causes COVID-19. This has unfortunately led to many different actors attempting to disrupt the coverage of this subject here on Wikipedia, by citing poor sources or basing their coverage on newspapers. I will here endeavour to make a thorough inquest through existing research papers on the matter, to have a readily accessible annotated list which will allow to see what scientists say on the matter and to guide further discussions on the topic.

Methodology

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Papers were keyword searched through the databases of PUBMED and some leading publishers. Papers in journals which are not MEDLINE-indexed were not further investigated. Relevant papers were selected after reading the abstract and looking at the depth of coverage on the issue. Preference was given to reviews and papers from virologists in relevant journals.

Search queries and statistics

Total: 877 matching queries, 187 total selected, 16 from other sources (before removing all duplicates)

Work in progress

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Criteria:

  • Checking whether a journal is MEDLINE or not is simple enough. Clicking on the journal name (in PubMed) should allow directly viewing the journal in the NLM catalog (ex. [1]), where the relevant information should be easily retrievable.
  • An article cited by 10 or less other articles is "relatively few" checkY; although some caution when interpreting this should be given in regards to more recent articles. High-impact articles (cited by a 100 or more others) should be given an approximate count (rounded down) to highlight these. For consistency, numbers should be retrieved from the same source (PubMed), but this shouldn't be much of a factor for articles with a high amount of citations.
  • Author credibility is usually verifiable from the affiliations listed in the author list of the article, but if in doubt, it is always better to verify at the page of the named institution(s).

Basic check completed

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  • Zhou, Hong; Ji, Jingkai; Chen, Xing; Bi, Yuhai; Li, Juan; Wang, Qihui; Hu, Tao; Song, Hao; Zhao, Runchu; Chen, Yanhua; Cui, Mingxue; Zhang, Yanyan; Hughes, Alice C.; Holmes, Edward C.; Shi, Weifeng (June 2021). "Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses". Cell (Cambridge). 184 (17): 4380–4391.e14. doi:10.1016/j.cell.2021.06.008. ISSN 0092-8674. PMC 8188299. PMID 34147139.
    • MEDLINE: checkY yes (NLM listing)
    • Cited by others: no, recent, cited in the news (ex. Guardian) checkY
    • Credible authors: Infectious diseases and public health experts from (mostly) China
  • Machado, Denis Jacob; Scott, Rachel; Guirales, Sayal; Janies, Daniel A. (2021). "Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses: SARS-CoV, MERS-CoV and SARS-CoV-2". Cladistics. 37 (5): 461–488. doi:10.1111/cla.12454. ISSN 1096-0031. PMC 8239696. PMID 34570933. {{cite journal}}: Unknown parameter |lay-url= ignored (help)
    • MEDLINE: only articles related to space life sciences Not sure [this might more be indicative of a topic restriction of MEDLINE than of the reliability of the other articles] - Journal is amongst the top journals in its field (Ecology, Evolutionary biology, ...) for impact factor, so appears credible nonetheless
    • Cited by others: no, recent ☒N
    • Credible authors: Bioinformatics Research Center (UNC Charlotte), first author is specialised in bioinformatics and phylogenetics.
    • Comment: Nota bene* Appears to be a primary study about an analysis of the title subject.
    • Quotes: "A recent literature review of the zoonotic origins of HCoVs (Ye et al., 2020) describes that the fundamental hosts of HCoVs can be Rodentia (for HCoV-OC43 and HCoV-HKU1) or Chiroptera (for HCoV-NL63, HCoV-229E, SARS-CoV, MERS-CoV and SARS-CoV-2). According to Ye et al. (2020), data on intermediate hosts of HCoV-NL63 and HCoV-HKU1 are absent. Furthermore, Ye et al. (2020) also point out that there is an open debate about the existence of intermediate hosts of HCoV-229E and SARS-CoV-2."; "Current public data indicate that the key epidemiological event in the history of SARS-CoV-2 was that a Chiroptera-hosted lineage of viruses infected an urban human population in Wuhan, China (Zhao et al., 2020) and this is perhaps linked to earlier infections in rural populations (Wang et al., 2018)."; "Other strategies, more speculative than those listed above, have been used to suggest that SARS-CoV-2 came from a laboratory accident at the Wuhan Institute of Virology (Rogin, 2020). The evidence indicates that SARS-CoV-2 was not purposefully manipulated (Andersen et al., 2020). Moreover, the notion that the SARS-CoV-2 pandemic resulted from a laboratory accident at the Wuhan Institute of Virology (Rogin, 2020) is not necessary to explain the pandemic."
    • Summary: Available literature shows multiple precedents for zoonotic transmission of HCoVs (human coronaviruses). Available evidence suggests that SARS-CoV-2 spread from Wuhan, although that might not be the actual origin. Speculation, such as claims of a lab leak, are not supported by evidence and are not needed to explain the emergence of the pandemic.
  • Attia, Y. A.; El-Saadony, M. T.; Swelum, A. A.; Qattan SYA; Al-Qurashi, A. D.; Asiry, K. A.; Shafi, M. E.; Elbestawy, A. R.; Gado, A. R.; Khafaga, A. F.; Hussein EOS; Ba-Awadh, H.; Tiwari, R.; Dhama, K.; Alhussaini, B.; Alyileili, S. R.; El-Tarabily, K. A.; Abd El-Hack, M. E. (2021). "COVID-19: Pathogenesis, advances in treatment and vaccine development and environmental impact-an updated review". Environmental Science and Pollution Research International. 28 (18): 22241–22264. doi:10.1007/s11356-021-13018-1. PMC 7969349. PMID 33733422.
    • MEDLINE: yes checkY
    • Cited by others: no, recent ☒N
    • Credible authors: broad experience including relevant fields, mostly agriculture and environment
    • Comment: Nota bene* "a few scientists believe that SARS-CoV-2 emerged through laboratory manipulations of SARS-CoV-like coronaviruses. The RBD of SARS-CoV-2 is optimized for binding ACE-2, which is distinct from other coronaviruses. However, the genetic data on SARS-CoV-2 does not show any evidence of a laboratory origin.... Most researchers agree that bats or pangolins are the primary reservoirs of coronaviruses, but the transmission route of SARS-CoV-2 to humans from this primary reservoir is still under study"
  • Mishra, S. K.; Tripathi, T. (2021). "One year update on the COVID-19 pandemic: Where are we now?". Acta Tropica. 214: 105778. doi:10.1016/j.actatropica.2020.105778. PMC 7695590. PMID 33253656.
    • MEDLINE: yes checkY
    • Cited by others: yes checkY
    • Credible authors: botany, biochemistry
    • Comment: Nota bene* Come across as highly confident in market zoonosis. "SARS-CoV-2 is thought to have originated in bats via genetic recombination of existing bat CoV strains and to have been transmitted from bats to humans either directly or through unknown intermediate hosts, similarly to the roles of civets and camels in SARS-CoV and MERS-CoV, respectively"
  • Guo, Yan-Rong; Cao, Qing-Dong; Hong, Zhong-Si; Tan, Yuan-Yang; Chen, Shou-Deng; Jin, Hong-Jun; Tan, Kai-Sen; Wang, De-Yun; Yan, Yan (2020-03-13). "The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak – an update on the status". Military Medical Research. 7 (1): 11. doi:10.1186/s40779-020-00240-0. ISSN 2095-7467. PMC 7068984. PMID 32169119.{{cite journal}}: CS1 maint: unflagged free DOI (link)
    • MEDLINE: yes checkY
    • Cited by others: yes (1100+) checkY
    • Credible authors: non-virologists, general medical expertise
    • Comment: Nota bene* dated source from Guangdong authors. Pretty typical origin explanation for early 2020. Based on virus genome sequencing results and evolutionary analysis, bat has been suspected as natural host of virus origin, and SARS-CoV-2 might be transmitted from bats via unknown intermediate hosts to infect humans. It is clear now that SARS-CoV-2 could use angiotensin-converting enzyme 2 (ACE2), the same receptor as SARS-CoV, to infect humans... Direct contact with intermediate host animals or consumption of wild animals was suspected to be the main route of SARS-CoV-2 transmission. However, the source(s) and transmission routine(s) of SARS-CoV-2 remain elusive.
  • Cui, Jie; Li, Fang; Shi, Zheng-Li (March 2019). "Origin and evolution of pathogenic coronaviruses". Nature Reviews. Microbiology. 17 (3): 181–192. doi:10.1038/s41579-018-0118-9. ISSN 1740-1534. PMC 7097006. PMID 30531947.
    • MEDLINE: yes (Nature Reviews) checkY checkY
    • Cited by others: yes (1200+), also Commentary in Front Immunol. 2020; 11: 811. checkY
    • Credible authors: virologists from the WIV + biomedicine (i.e. broadly relevant topic)
    • Comment: Nota bene* this isn't about SARS-Cov-2 (the commentary is). It could however be used (along with the commentary for the link to ) for information about the origin of other coronavirus outbreaks. It might be particularly interesting because it predates the current pandemic.
  • McAloose, Denise; Laverack, Melissa; Wang, Leyi; Killian, Mary Lea; Caserta, Leonardo C.; Yuan, Fangfeng; Mitchell, Patrick K.; Queen, Krista; Mauldin, Matthew R.; Cronk, Brittany D.; Bartlett, Susan L.; Sykes, John M.; Zec, Stephanie; Stokol, Tracy; Ingerman, Karen; Delaney, Martha A.; Fredrickson, Richard; Ivančić, Marina; Jenkins-Moore, Melinda; Mozingo, Katie; Franzen, Kerrie; Bergeson, Nichole Hines; Goodman, Laura; Wang, Haibin; Fang, Ying; Olmstead, Colleen; McCann, Colleen; Thomas, Patrick; Goodrich, Erin; Elvinger, François; Smith, David C.; Tong, Suxiang; Slavinski, Sally; Calle, Paul P.; Terio, Karen; Torchetti, Mia Kim; Diel, Diego G. (2020-10-27). "From People to Panthera : Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo". mBio. 11 (5). doi:10.1128/mBio.02220-20. PMC 7554670. PMID 33051368.
    • MEDLINE: yes checkY
    • Cited by others: yes checkY
    • Credible authors: Veterinary medicine, CDC, National Veterinary Services (credible expertise for what they're reporting about
    • Comment: Nota bene* This is a primary study regarding reverse zoonosis, although the background section (summarised below) is obviously not a primary study.
    • Summary: Despite multiple barriers to transmission, zoonoses are a major cause of the emergence of new human pathogens. The paper describes an example of reverse zoonosis, zoo animals being infected by SARS-CoV-2 from contact with humans. The paper describes the origin of the virus as a likely zoonotic event, since genome analysis has shown SARS-CoV-2 to be closely related to existing bat viruses, describing horseshoe bats as the likely reservoir where the virus might have circulated for decades without detection. While zoonotic origin is presented as a likely or "suspected" event, no alternative hypotheses are mentioned.
  • Islam, Md Saiful; Sarkar, Tonmoy; Khan, Sazzad Hossain; Mostofa Kamal, Abu-Hena; Hasan, S. M. Murshid; Kabir, Alamgir; Yeasmin, Dalia; Islam, Mohammad Ariful; Amin Chowdhury, Kamal Ibne; Anwar, Kazi Selim; Chughtai, Abrar Ahmad; Seale, Holly (October 2020). "COVID-19-Related Infodemic and Its Impact on Public Health: A Global Social Media Analysis". The American Journal of Tropical Medicine and Hygiene. 103 (4): 1621–1629. doi:10.4269/ajtmh.20-0812. ISSN 1476-1645. PMC 7543839. PMID 32783794.
    • MEDLINE: yes checkY
    • Cited by others: yes checkY
    • Credible authors: infectious diseases & microbiology, public health; one non-medical expert (engineering and technology - might be relevant for the misinformation bit)
    • Comment: Nota bene* this seems like a study about misinformation, so would be a primary source - but it's also not making claims about biomedicine, rather about misinformation.
  • Khan, Suliman; Siddique, Rabeea; Shereen, Muhammad Adnan; Ali, Ashaq; Liu, Jianbo; Bai, Qian; Bashir, Nadia; Xue, Mengzhou (2020-03-11). "Emergence of a Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2: Biology and Therapeutic Options". Journal of Clinical Microbiology. 58 (5): e00187–20, /jcm/58/5/JCM.00187–20.atom. doi:10.1128/JCM.00187-20. PMC 7180238. PMID 32161092.
    • MEDLINE: yes checkY
    • Cited by others: yes checkY
    • Credible authors: various, including virologists from the WIV
    • Comment: Nota bene* "This article has been corrected, see J Clin Microbiol. 2020 July 23; 58(8): e01297-20", but this appears to be minor (about one source being removed/changed).
    • Summary: (most relevant bits, quoted) "Although the zoonotic source of SARS-CoV-2 is not confirmed, its genome sequence exhibits close relatedness (88% identity) with two bat-derived SARS-like coronaviruses (bat-SL-CoVZC45 and bat-SL-CoVZXC21). [...] These observations suggest that bats are the source of origin, while an animal sold at the Wuhan seafood market might represent an intermediate host facilitating the emergence of the virus in humans"
  • Ye, Z. W.; Yuan, S.; Yuen, K. S.; Fung, S. Y.; Chan, C. P.; Jin, D. Y. (2020). "Zoonotic origins of human coronaviruses". International Journal of Biological Sciences. 16 (10): 1686–1697. doi:10.7150/ijbs.45472. PMC 7098031. PMID 32226286.
    • MEDLINE: yes checkY
    • Cited by others: yes (180+) checkY
    • Credible authors: Microbiologists from Hong Kong
    • Comment: Although early in the pandemic, it puts forwards reasonable doubts about some specifics, including the lack of evidence for the pangolin as an intermediary host. Concludes discussion about SARS-CoV-2 by stating that "the jury is still out on the immediate zoonotic origin of SARS-CoV-2.", but overall comes off as highly confident in a zoonotic origin being a matter of fact (not even under debate), with other hypotheses not even mentioned.

No check done yet (beyond screening through the title and the abstract)

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Nature: covid AND origin (limited to reviews: 109 results total, 7 retained before filtering for duplicates)

Reviews in Medical Virology:

Lancet [2] (196 results, 2 retained)

Covid and conspiracy theories

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covid AND conspiracy AND origin (not filtered for article type) (17 results, 4 retained)

"genetic%20engineering"&filter=pubt.review&filter=pubt.systematicreview&filter=journalcategory.medline&page=4 covid AND "genetic engineering" (39 results, 5 retained) [most of these do not seem to make much mention of genetic engineering, or it might be in an entirely different context than to the conspiracy theory]

Other (linked papers, similar content, ...)

See also

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Scholia has a profile for origin of COVID-19 (Q103224114).
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