Supplementary File 1: Synthesized documents metadata.,,,,,,,,,,,,,,
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SN,Ref,Title,Source,Abstract,Study type,Review Type,Study Design,Access,Year,Month,Number of citations,Keywords,doi/link,...18
1,"Morens, D. M., Breman, J. G., Calisher, C. H., Doherty, P. C., Hahn, B. H., Keusch, G. T., ... & Taubenberger, J. K. (2020). The origin of COVID-19 and why it matters. The American journal of tropical medicine and hygiene, 103(3), 955.",The origin of COVID-19 and why it matters,Google schorlar,"The COVID-19 pandemic is among the deadliest infectious diseases to have emerged in recent history. As

 withall pastpandemics,thespecificmechanismofitsemergenceinhumansremainsunknown.Nevertheless,alargebody

 of virologic, epidemiologic, veterinary, and ecologic data establishes that the new virus, SARS-CoV-2, evolved directly or

 indirectly from a β-coronavirus in the sarbecovirus (SARS-like virus) group that naturally infect bats and pangolins in Asia

 andSoutheast Asia. Scientists have warned for decades that such sarbecoviruses are poised to emerge again and again,

 identified risk factors, and argued for enhanced pandemic prevention and control efforts. Unfortunately, few such pre

ventive actions were taken resulting in the latest coronavirus emergence detected in late 2019 which quickly spread

 pandemically. The risk of similar coronavirus outbreaks in the future remains high. In addition to controlling the COVID-19

 pandemic, we must undertake vigorous scientific, public health, and societal actions, including significantly increased

 funding for basic and applied research addressing disease emergence, to prevent this tragic history from repeating itself.",Perspective Piece,Peer reviewed,Expert commentary (non-empirical),open,2020,NA,172,NA,https://doi.org/10.4269/ajtmh.20-0849,PP
2,"Guo, Y. R., Cao, Q. D., Hong, Z. S., Tan, Y. Y., Chen, S. D., Jin, H. J., ... & Yan, Y. (2020). The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak–an update on the status. Military medical research, 7, 1-10.","The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak–an update on the status",Google schorlar,"An acute respiratory disease, caused by a novel coronavirus (SARS-CoV-2, previously known as 2019-nCoV), the coronavirus disease 2019 (COVID-19) has spread throughout China and received worldwide attention. On 30 January 2020, World Health Organization (WHO) officially declared the COVID-19 epidemic as a public health emergency of international concern. The emergence of SARS-CoV-2, since the severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, marked the third introduction of a highly pathogenic and large-scale epidemic coronavirus into the human population in the twenty-first century. As of 1 March 2020, a total of 87,137 confirmed cases globally, 79,968 confirmed in China and 7169 outside of China, with 2977 deaths (3.4%) had been reported by WHO. Meanwhile, several independent research groups have identified that SARS-CoV-2 belongs to β-coronavirus, with highly identical genome to bat coronavirus, pointing to bat as the natural host. The novel coronavirus uses the same receptor, angiotensin-converting enzyme 2 (ACE2) as that for SARS-CoV, and mainly spreads through the respiratory tract. Importantly, increasingly evidence showed sustained human-to-human transmission, along with many exported cases across the globe. The clinical symptoms of COVID-19 patients include fever, cough, fatigue and a small population of patients appeared gastrointestinal infection symptoms. The elderly and people with underlying diseases are susceptible to infection and prone to serious outcomes, which may be associated with acute respiratory distress syndrome (ARDS) and cytokine storm. Currently, there are few specific antiviral strategies, but several potent candidates of antivirals and repurposed drugs are under urgent investigation. In this review, we summarized the latest research progress of the epidemiology, pathogenesis, and clinical characteristics of COVID-19, and discussed the current treatment and scientific advancements to combat the epidemic novel coronavirus.",Review,Peer reviewed,Narrative literature review,open,2020,NA,0,"Clinical characteristics, Coronavirus disease 2019 (COVID-19), Origin, SARS-CoV-2, Therapy, Transmission",https://link.springer.com/article/10.1186/s40779-020-00240-0,PP
3,"Hao, Y. J., Wang, Y. L., Wang, M. Y., Zhou, L., Shi, J. Y., Cao, J. M., & Wang, D. P. (2022). The origins of COVID‐19 pandemic: A brief overview. Transboundary and emerging diseases, 69(6), 3181-3197.",The origins of COVID‐19 pandemic: A brief overview,Google schorlar,"The novel coronavirus disease (COVID-19) outbreak that emerged at the end of 2019 has now swept the world for more than 2 years, causing immeasurable damage to the lives and economies of the world. It has drawn so much attention to discovering how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated and entered the human body. The current argument revolves around two contradictory theories: a scenario of laboratory spillover events and human contact with zoonotic diseases. Here, we reviewed the transmission, pathogenesis, possible hosts, as well as the genome and protein structure of SARS-CoV-2, which play key roles in the COVID-19 pandemic. We believe the coronavirus was originally transmitted to human by animals rather than by a laboratory leak. However, there still needs more investigations to determine the source of the pandemic. Understanding how COVID-19 emerged is vital to developing global strategies for mitigating future outbreaks.",Review,Peer reviewed,Narrative literature review,open,2022,NA,30,NA,https://onlinelibrary.wiley.com/doi/abs/10.1111/tbed.14732,PP
4,"Bloom, J. D., Chan, Y. A., Baric, R. S., Bjorkman, P. J., Cobey, S., Deverman, B. E., ... & Relman, D. A. (2021). Investigate the origins of COVID-19. Science, 372(6543), 694-694.",Investigate the origins of COVID-19. Science,Google schorlar,NA,Opinion / Perspective,NA,Expert commentary (non-empirical),open,2021,45791,NA,NA,NA,PP
5,"Law, P. K. (2020). COVID-19 pandemic: its origin, implications and treatments. Open Journal of Regenerative Medicine, 9(2), 43-64.","COVID-19 pandemic: its origin, implications and treatments",Google schorlar,"This is a succinct and current review of pertinent literature to guide develop

ing serum therapy as an emergent treatment to save human lives at times of 

natural or genetically engineered viral/bacterial pandemics. The origin of 

2019-nCoV and implications of COVID-19 are discussed using direct quotes 

of published scientific literature to avoid misinterpretation on this very im

portant event that has caused great loss of human lives and international so

cial economy. It is the goal of this review to warn against and to correct inter

national misunderstanding created by deliberate falsification of scientific do

cumentations and events. This misunderstanding may lead to further destruc

tion of life, economy, and political relations. People should not be blind-sighted 

when making life decisions.",Research article,Peer reviewed,NA,open,2020,NA,NA,"2019-nCoV, COVID-19, Serum Therapy, Pandemics, Epidemics, Convalescent 

Plasma, Coronavirus, Vaccine, Bacteria, Mutation, Biologic Warfare Weapons",NA,PP
6,"Platto, S., Wang, Y., Zhou, J., & Carafoli, E. (2021). History of the COVID-19 pandemic: Origin, explosion, worldwide spreading. Biochemical and biophysical research communications, 538, 14-23.","History of the COVID-19 pandemic: Origin, explosion, worldwide spreading",Google schorlar,NA,Research article,Peer reviewed,Observational,open,2021,NA,NA,NA,NA,PP
7,"Rothan, H. A., & Byrareddy, S. N. (2020). The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. Journal of autoimmunity, 109, 102433.",The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak,Google schorlar,"Coronavirus disease (COVID-19) is caused by SARS-COV2 and represents the causative agent of a potentially fatal disease that is of great global public health concern. Based on the large number of infected people that were exposed to the wet animal market in Wuhan City, China, it is suggested that this is likely the zoonotic origin of COVID-19. Person-to-person transmission of COVID-19 infection led to the isolation of patients that were subsequently administered a variety of treatments. Extensive measures to reduce person-to-person transmission of COVID-19 have been implemented to control the current outbreak. Special attention and efforts to protect or reduce transmission should be applied in susceptible populations including children, health care providers, and elderly people. In this review, we highlights the symptoms, epidemiology, transmission, pathogenesis, phylogenetic analysis and future directions to control the spread of this fatal disease.",Research article,Peer reviewed,scoping review,open,2020,NA,3660,CoronavirusCOVID-19Wuhan cityPneumoniaPathogenesis,https://www.sciencedirect.com/science/article/pii/S0896841120300469,PP
8,"Alanagreh, L. A., Alzoughool, F., & Atoum, M. (2020). The human coronavirus disease COVID-19: its origin, characteristics, and insights into potential drugs and its mechanisms. Pathogens, 9(5), 331.","The human coronavirus disease COVID-19: its origin, characteristics, and insights into potential drugs and its mechanisms",Google schorlar,"The emerging coronavirus disease (COVID-19) swept across the world, affecting more than 200 countries and territories. Genomic analysis suggests that the COVID-19 virus originated in bats and transmitted to humans through unknown intermediate hosts in the Wuhan seafood market, China, in December of 2019. This virus belongs to the Betacoronavirus group, the same group of the 2003 severe acute respiratory syndrome coronavirus (SARS-CoV), and for the similarity, it was named SARS-CoV-2. Given the lack of registered clinical therapies or vaccines, many physicians and scientists are investigating previously used clinical drugs for COVID-19 treatment. In this review, we aim to provide an overview of the CoVs origin, pathogenicity, and genomic structure, with a focus on SARS-CoV-2. Besides, we summarize the recently investigated drugs that constitute an option for COVID-19 treatment.",Research article,Peer reviewed,NA,open,2020,NA,245,COVID-19; SARS-CoV-2; antiviral therapies,https://www.mdpi.com/2076-0817/9/5/331,PP
9,"Liu, Y. C., Kuo, R. L., & Shih, S. R. (2020). COVID-19: The first documented coronavirus pandemic in history. Biomedical journal, 43(4), 328-333.",COVID-19: The first documented coronavirus pandemic in history,Google schorlar,"The novel human coronavirus disease COVID-19 has become the fifth documented pandemic since the 1918 flu pandemic. COVID-19 was first reported in Wuhan, China, and subsequently spread worldwide. The coronavirus was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses based on phylogenetic analysis. SARS-CoV-2 is believed to be a spillover of an animal coronavirus and later adapted the ability of human-to-human transmission. Because the virus is highly contagious, it rapidly spreads and continuously evolves in the human population. In this review article, we discuss the basic properties, potential origin, and evolution of the novel human coronavirus. These factors may be critical for studies of pathogenicity, antiviral designs, and vaccine development against the virus.",Research article,NA,NA,open,2020,NA,610,COVID-19; SARS-COV-2; Coronavirus; Pandemic,https://doi.org/10.1016/j.bj.2020.04.007,PP
10,"Yesudhas, D., Srivastava, A., & Gromiha, M. M. (2021). COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics. Infection, 49, 199-213.","COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics",Google schorlar,"The coronavirus outbreak emerged as a severe pandemic, claiming more than 0.8 million lives across the world and raised a major global health concern. We survey the history and mechanism of coronaviruses, and the structural characteristics of the spike protein and its key residues responsible for human transmissions.



Methods

We have carried out a systematic review to summarize the origin, transmission and etiology of COVID-19. The structural analysis of the spike protein and its disordered residues explains the mechanism of the viral transmission. A meta-data analysis of the therapeutic compounds targeting the SARS-CoV-2 is also included.



Results

Coronaviruses can cross the species barrier and infect humans with unexpected consequences for public health. The transmission rate of SARS-CoV-2 infection is higher compared to that of the closely related SARS-CoV infections. In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. The key residues of the spike protein have stronger binding affinity with ACE2. These can be probable reasons for the higher transmission rate of SARS-CoV-2. In addition, we have also discussed the therapeutic compounds and the vaccines to target SARS-CoV-2, which can help researchers to develop effective drugs/vaccines for COVID-19.



Summary

The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs.",Research article,NA,NA,open,2021,NA,168,NA,https://link.springer.com/article/10.1007/s15010-020-01516-2,PP
11,"Ochani, R., Asad, A., Yasmin, F., Shaikh, S., Khalid, H., Batra, S., ... & Surani, S. (2021). COVID-19 pandemic: from origins to outcomes. A comprehensive review of viral pathogenesis, clinical manifestations, diagnostic evaluation, and management. Infez Med, 29(1), 20-36.","COVID-19 pandemic: from origins to outcomes. A comprehensive review of viral pathogenesis, clinical manifestations, diagnostic evaluation, and management",Google schorlar,"Severe Acute Respiratory Syndrome Coronavirus-2

(SARS-CoV-2), the causative pathogen for the COVID-19, first emerged in Wuhan, China, in December

2019 and by March 2020, it was declared a pandemic.

COVID-19 pandemic has overburdened healthcare systems in most countries and has led to massive economic losses. SARS-CoV-2 transmission typically occurs by

respiratory droplets. The average incubation period is

6.4 days and presenting symptoms typically include

fever, cough, dyspnea, myalgia or fatigue. While the

SUMMARY

majority of patients tend to have a mild illness, a minority of patients develop severe hypoxia requiring hospitalization and mechanical ventilation. Management is

mostly supportive. However, several direct anti-viral

agents, and immunomodulatory therapy with steroids

and various cytokine blockers seem promising in early

results. However, an effective vaccine has been established, which will help curb the pandemic.",Research article,NA,scoping review,open,2021,NA,NA,NA,NA,PP
12,"Hassanin, A., Grandcolas, P., & Veron, G. (2021). Covid-19: natural or anthropic origin?. Mammalia, 85(1), 1-7.",Covid-19: natural or anthropic origin?,Google schorlar,"Viruses similar to the Severe Acute Respiratory

 Syndrome Coronavirus 2 (SARS-CoV-2) have been discov

ered in bats of the genus Rhinolophus and in the Sunda

 pangolin, Manis javanica Desmarest, 1822, suggesting that

 these animals have played a key role in the emergence of

 the Covid-19 outbreak in the city of Wuhan, China. In this

 paper, we review the available data for sarbecoviruses

 (viruses related to SARS-CoV [2002–2003 outbreak] and

 SARS-CoV-2) to propose all possible hypotheses on the

 origin of Covid-19, i. e., involving direct transmission from

 horseshoe bats to humans, indirect transmission via the

 pangolin or another animal, with interspecies contamina

tion between either wild animals or animals kept in cage.

 Present evidence indicates that Rhinolophus bats are the

 natural reservoir of all sarbecoviruses, and that two

 divergent SARS-CoV-2-like viruses have circulated in

 southern China (at least in Guangxi and Guangdong

 provinces) between August2017andMarch2019incaptive

 pangolins destined for sale in wildlife markets. We per

formed a genetic analysis of seven seized pangolins found

 to be positive for SARS-CoV-2-like virus using mitochon

drial DNA sequences extracted from Sequence Reads

 Archive data. The results reveal that the sameSARS-CoV-2

like virus canbefoundinanimalswithdistincthaplotypes,

 whichmeansthattheywereprobablycapturedindifferent

 Southeast Asian regions. Our interpretation is that some

 pangolins were contaminated in captivity (by other pan

golins or by another species to be determined), suggesting that illegal trade of living wild mammals is at the origin

 of the Covid-19 outbreak. To definitely validate this hy

pothesis, it is however necessary to discover a virus almost

 identicaltoSARSCoV-2(atleast99%ofidentity)inanimals

 sold in wet markets. Although pangolins are good candi

dates, other mammals, such as small carnivores, should

 not be overlooked.",Research article,NA,NA,open,2021,NA,33,"bats; carnivores; covid-19; pangolins; SARS

CoV-2; wet market.",https://www.researchgate.net/publication/341425381_Covid-19_natural_or_anthropic_origin?enrichId=rgreq-625fba6101671f20d752a3ce88f7421a-XXX&enrichSource=Y292ZXJQYWdlOzM0MTQyNTM4MTtBUzo5MDA0MzkzMzE1Nzc4NTdAMTU5MTY5Mjg3NDI4OA%3D%3D&el=1_x_2&_esc=publicationCoverPdf,PP
13,"Congressional Research Service. (2021, June 11). Origins of the COVID-19 pandemic (CRS Report No. IF11822). https://sgp.fas.org/crs/misc/IF11822.pdf​",Origins of the COVID-19 pandemic (CRS Report No. IF11822),Google schorlar,NA,NA,NA,NA,open,2021,45819,NA,NA,NA,PP
14,"The Lancet Microbe. (2023, April). Searching for SARS-CoV-2 origins: confidence versus evidence. The Lancet Microbe, 4(4), e200. https://doi.org/10.1016/S2666-5247(23)00074-5",Searching for SARS-CoV-2 origins: confidence versus evidence,Google schorlar,NA,NA,NA,NA,open,2023,Apr,2,NA,NA,PP
15,"Pekar, J. E., Magee, A., Parker, E., Moshiri, N., Izhikevich, K., Havens, J. L., Gangavarapu, K., Malpica Serrano, L. M., Crits-Christoph, A., Matteson, N. L., Zeller, M., Levy, J. I., Wang, J. C., Hughes, S., Lee, J., Park, H., Park, M.-S., Yan, K. C. Z., Lin, R. T. P., Mat Isa, M. N., Noor, Y. M., Vasylyeva, T. I., Garry, R. F., Holmes, E. C., Rambaut, A., Suchard, M. A., Andersen, K. G., Worobey, M., & Wertheim, J. O. (2022). The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science, 377(6609), 960–966. https://doi.org/10.1126/science.abp8337",The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2,Google schorlar,NA,NA,NA,NA,open,2022,NA,145,NA,NA,PP
16,"Andersen, K.G., Rambaut, A., Lipkin, W.I. et al. The proximal origin of SARS-CoV-2. Nat Med 26, 450–452 (2020). https://doi.org/10.1038/s41591-020-0820-9", The proximal origin of SARS-CoV-2,Google schorlar,NA,NA,NA,NA,open,2020,NA,3232,NA,https://www.nature.com/articles/s41591-020-0820-9,PP
17,"Gostin, L. O., & Gronvall, G. K. (2023, June 7). The origins of Covid-19 — Why it matters (and why it doesn’t). The New England Journal of Medicine, 388(25), 2305–2308. https://doi.org/10.1056/NEJMp2305081",The origins of Covid-19 — Why it matters (and why it doesn’t),Google schorlar,NA,NA,NA,NA,open,2023,45815,39,NA,NA,PP
18,"Looi, M.-K. (2024, September 9). Will we ever know where COVID-19 came from? BMJ, 386, q1578. https://doi.org/10.1136/bmj.q1578",Will we ever know where COVID-19 came from,Google schorlar,NA,NA,NA,NA,open,2024,45909,1,NA,NA,PP
19,"Hadi, A. G., Kadhom, M., Hairunisa, N., Yousif, E., & Mohammed, S. A. (2020). A review on COVID-19: origin, spread, symptoms, treatment, and prevention. Biointerface Research in Applied Chemistry, 10(6), 7234-7242.","A review on COVID-19: origin, spread, symptoms, treatment, and prevention",Google schorlar,"A novel type of coronavirus, identified as 2019-nCoV or COVID-19, appeared in Wuhan,

China, in late 2019 and continued to spread in 2020. On January 24th, 2020, about 830 cases were

reported in nine countries, namely: China, Japan, Singapore, Thailand, South Korea, Nepal, Vietnam,

the United States, and Taiwan. Also, about 26 confirmed deaths have been recorded, especially for

patients with serious underlying diseases. On March 11th, 2020, the World Health Organization (WHO)

declared COVID-19 as a global pandemic. Until June 3rd, 2020, this outbreak virus caused over

6,500,000 detected infection cases in 210 countries and territories and around 383,000 confirmed death

cases. Although information about the appearance of the virus, i.e., its origin and capacity to spread

among people, is still unclear, there are growing numbers of cases that are occurring from the

communication of infected people with uninfected ones. 2019-nCoV is the third coronavirus which was

detected in humans in the past two decades, after SARS-CoV and Middle Eastern Respiratory

Coronavirus (MERS-CoV) that appeared in 2002 and 2012, respectively. In this review, we

summarized the up-to-date information regarding COVID-19’s origin, ways of spread, patients’

symptoms, treatment, and prevention.",Research article,NA,scoping review,open,2020,NA,1,COVID-19; cough; SARS-CoV; RNA; 2019-nCoV; coronavirus,https://doi.org/10.33263/BRIAC106.72347242,PP
20,"Gaviria, A. Z., & Martin, R. B. (2023). c. Revista Clínica Española (English Edition), 223(4), 240-243.",What do we know about the origin of COVID-19 three years later?,Google schorlar,"More than three years have passed since the first case of a new coronavirus infection (SARS-CoV-2) in the city of Wuhan (Hubei, China). The Wuhan Institute of Virology was founded in that city in 1956 and the country’s first biosafety level 4 laboratory opened within that center in 2015. The coincidence that the first cases of infection emerged in the city where the virology institute’s headquarters is located, the failure to 100% identify the virus’ RNA in any of the coronaviruses isolated in bats, and the lack of evidence on a possible intermediate animal host in the contagion’s transmission make it so that at present, there are doubts about the real origin of SARS-CoV-2. This article will review two theories: SARS-CoV-2 as a virus of zoonotic origin or as a leak from the high-level biosafety laboratory in Wuhan.",Research article,NA,NA,open,2023,NA,0,SARS-CoV-2COVID-19COVID-19 originWuhan Institute of Virology,https://www.sciencedirect.com/science/article/pii/S2254887423000395,PP
21,"Nadeem, M. S., Zamzami, M. A., Choudhry, H., Murtaza, B. N., Kazmi, I., Ahmad, H., & Shakoori, A. R. (2020). Origin, potential therapeutic targets and treatment for coronavirus disease (COVID-19). Pathogens, 9(4), 307.","Origin, potential therapeutic targets and treatment for coronavirus disease (COVID-19)",Google schorlar,"The ongoing episode of coronavirus disease 19 (COVID-19) has imposed a serious threat to global health and the world economy. The disease has rapidly acquired a pandemic status affecting almost all populated areas of the planet. The causative agent of COVID-19 is a novel coronavirus known as SARS-CoV-2. The virus has an approximate 30 kb single-stranded positive-sense RNA genome, which is 74.5% to 99% identical to that of SARS-CoV, CoV-pangolin, and the coronavirus the from horseshoe bat. According to available information, SARS-CoV-2 is inferred to be a recombinant virus that originated from bats and was transmitted to humans, possibly using the pangolin as the intermediate host. The interaction of the SARS-CoV-2 spike protein with the human ACE2 (angiotensin-converting enzyme 2) receptor, and its subsequent cleavage by serine protease and fusion, are the main events in the pathophysiology. The serine protease inhibitors, spike protein-based vaccines, or ACE2 blockers may have therapeutic potential in the near future. At present, no vaccine is available against COVID-19. The disease is being treated with antiviral, antimalarial, anti-inflammatory, herbal medicines, and active plasma antibodies. In this context, the present review article provides a cumulative account of the recent information regarding the viral characteristics, potential therapeutic targets, treatment options, and prospective research questions.",Research article,NA,NA,open,2020,NA,72,COVID-19; SARS-CoV-2; origin; pathogenesis; therapeutics; challenges,https://www.mdpi.com/2076-0817/9/4/307,PP
22,"Bolsen, T., Palm, R., & Kingsland, J. T. (2020). Framing the Origins of COVID-19. Science Communication, 42(5), 562-585. https://doi.org/10.1177/1075547020953603 (Original work published 2020)",Framing the Origins of COVID-19,Sage,Conspiracy theories have flourished about the origins of a novel coronavirus (SARS-CoV-2) that causes an acute respiratory syndrome (coronavirus disease 2019 [COVID-19]) in humans. This article reports the results from a study that evaluates the impact of exposure to framed messages about the origins of COVID-19. We tested four hypotheses: two focusing on its origins as either zoonotic or human-engineered and two concerning the impacts of origin beliefs on the desire to penalize China or support increased funding for biomedical research. The results accentuate the importance of finding ways to combat the spread of misinformation and conspiracy theories related to this global pandemic.,Research article,NA,Survey,open,2021,NA,89,NA,NA,PP
23,"Wu, Y. C., Chen, C. S., & Chan, Y. J. (2020). The outbreak of COVID-19: An overview. Journal of the Chinese medical association, 83(3), 217-220.",The outbreak of COVID-19: An overview,Google schorlar,"In late December 2019, a previous unidentified coronavirus, currently named as the 2019 novel coronavirus#, emerged from Wuhan, China, and resulted in a formidable outbreak in many cities in China and expanded globally, including Thailand, Republic of Korea, Japan, United States, Philippines, Viet Nam, and our country (as of 2/6/2020 at least 25 countries). The disease is officially named as Coronavirus Disease-2019 (COVID-19, by WHO on February 11, 2020). It is also named as Severe Pneumonia with Novel Pathogens on January 15, 2019 by the Taiwan CDC, the Ministry of Health and is a notifiable communicable disease of the fifth category. COVID-19 is a potential zoonotic disease with low to moderate (estimated 2%–5%) mortality rate. Person-to-person transmission may occur through droplet or contact transmission and if there is a lack of stringent infection control or if no proper personal protective equipment available, it may jeopardize the first-line healthcare workers. Currently, there is no definite treatment for COVID-19 although some drugs are under investigation. To promptly identify patients and prevent further spreading, physicians should be aware of the travel or contact history of the patient with compatible symptoms.",Research article,NA,NA,open,2020,NA,1797,NA,https://journals.lww.com/jcma/fulltext/2020/03000/the_outbreak_of_covid_19_an_overview.3.aspx,PP
24,"Shereen, M. A., Khan, S., Kazmi, A., Bashir, N., & Siddique, R. (2020). COVID-19 infection: Emergence, transmission, and characteristics of human coronaviruses. Journal of advanced research, 24, 91-98","COVID-19 infection: Emergence, transmission, and characteristics of human coronaviruses",Google schorlar,"The coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused global pandemic that led to a dramatic loss of human life worldwide. Genomic analysis revealed that SARS-CoV-2 is phylogenetically related to severe acute respiratory syndrome-like (SARS-like) bat viruses, therefore bats could be the possible primary reservoir. The intermediate source of origin and transfer to humans is not known, however, the rapid human to human transfer has been confirmed widely. There is no clinically approved antiviral drug or vaccine available to be used against COVID-19. However, few broad-spectrum antiviral drugs have been evaluated against COVID-19 in clinical trials, resulted in clinical recovery. In the current review, we summarize and comparatively analyze the emergence and pathogenicity of COVID-19 infection and previous human coronaviruses including severe ascute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV). We also discuss the approaches for developing effective vaccines and therapeutic combinations to cope with this viral outbreak.",Research article,NA,NA,open,2020,NA,2593,Coronaviruses; COVID-19; Transmission; Outbreak; Spread,https://doi.org/10.1016/j.jare.2020.03.005,PP
25,"Heiat, M., Heiat, F., Halaji, M., Ranjbar, R., Marvasti, Z. T., Yaali-Jahromi, E., ... & Badri, T. (2021). Phobia and Fear of COVID-19: origins, complications and management, a narrative review. Annali Di Igiene Medicina Preventiva E Di Comunita, 33(4), 360-370.","Phobia and Fear of COVID-19: origins, complications and management, a narrative review",Google schorlar,"Introduction. The outbreak of Coronavirus Disease 2019 (COVID-19) have changed into a global crisis. Psychologically, this process of alteration can lead to feelings of fear, insecurity, and anxiety. This fear and anxiety can be caused by a variety of factors. However, due to the lack of extensive studies at this time, there are little data on these conditions related to COVID-19. Therefore, in this narrative review, we have tried to identify the most important possible causes of anxiety and fear due to this disease, based on logical shreds of evidence. Then we tried to discuss the consequences and ways to manage and prevent them. Methods. The current focus was on three major axes of corona-phobia, fear and anxiety. PubMed, Science Direct, Scopus, Google Scholar and authoritative news and information sources were considered as the data sources. Results. Findings from the analysis of the results revealed that, in addition to the real and the logical reasons which belong to the intrinsic properties of SARS-CoV-2, some misleadings and misconceptions induced by media, governmental policies, public awareness level, and non-scientific speculations and contradictory data expressed by experts, researchers and scientific societies, could provide the way for the development of corona-phobia, and fear. Conclusions. Each of these causal components, in its place, leads to some degrees of psychological disorders and subsequent consequences and complications. Finally, here we reviewed, summarized the previous research findings on how to prevent and manage this type of psychological disorder, and made comparisons.",Research article,NA,NA,open,2021,NA,83,"Corona phobia, Fear, Anxiety, Nosophobia, Social Panic

Parole chiave: Fobia del Coronavirus, Paura, Ansia, Timore della malattia, Panico sociale",NA,PP
26,"Junejo, Y., Ozaslan, M., Safdar, M., Khailany, R. A., Rehman, S., Yousaf, W., & Khan, M. A. (2020). Novel SARS-CoV-2/COVID-19: Origin, pathogenesis, genes and genetic variations, immune responses and phylogenetic analysis. Gene reports, 20, 100752.","Novel SARS-CoV-2/COVID-19: Origin, pathogenesis, genes and genetic variations, immune responses and phylogenetic analysis",Google schorlar,"In this review, we focused on the origins of the novel coronavirus (SARS-CoV-2), origin, pathogenesis, immune responses, genes and genetic variations, phylogenetic analyses, and potential therapeutic strategies to summarize approaches for developing broadly effective preventions and vaccines to cope COVID-19. Towards the end of 2019, SARS-CoV-2 has emerged in association with the SARS, later was named COVID-19 caused an environment of chaos worldwide and infected a massive number of lives. Since these epidemics or pandemics had spread to 210 countries and territories around the world and 2 international conveyances with 6,467,229 confirmed cases, including, 382,766 deaths, as of June 03, 2020 (https://www.worldometers.info/coronavirus/), hence the World Health Organization declared it as a global Public Health Emergency. There are no clinically approved vaccines or antiviral drugs available for either of new or old corona infections; thus, the development of effective therapeutic and preventive strategies that can be readily available to cope with these strains.",Research article,NA,NA,open,2020,NA,39,SARS-CoV-2; Origin; Pathogenesis; Variations; Evolution; Phylogenetic analysis,https://doi.org/10.1016/j.genrep.2020.100752,PP
27,"World Health Organization. (2020, March 26). Recommendations to reduce risk of transmission of emerging pathogens from animals to humans in live animal markets or animal product markets (WHO/2019-nCoV/Human_animal_risk/2020.2). https://iris.who.int/bitstream/handle/10665/332217/WHO-2019-nCoV-Human_animal_risk-2020.2-eng.pdf",Recommendations to reduce risk of transmission of emerging pathogens from animals to humans in live animal markets or animal product markets,WHO,NA,NA,NA,NA,open,2020,NA,NA,NA,NA,PP
28,"World Health Organization. (2020, March 26). Origin of SARS-CoV-2 (WHO/2019-nCoV/FAQ/Virus_origin/2020.1). https://iris.who.int/bitstream/handle/10665/332197/WHO-2019-nCoV-FAQ-Virus_origin-2020.1-eng.pdf",Origin of SARS-CoV-2,WHO,NA,NA,NA,NA,open,2020,NA,NA,NA,NA,PP
29,"World Health Organization. (2020, February 28). Report of the WHO-China joint mission on coronavirus disease 2019 (COVID-19). https://www.who.int/publications/i/item/report-of-the-who-china-joint-mission-on-coronavirus-disease-2019-(covid-19)",Report of the WHO-China joint mission on coronavirus disease 2019,WHO,NA,NA,NA,NA,open,2020,NA,NA,NA,NA,PP
30,"Berekaa, M. M. (2020). Insights into the COVID-19 pandemic: Origin, pathogenesis, diagnosis, and therapeutic interventions. Frontiers in Bioscience-Elite, 13(1), 117-139.","Insights into the COVID-19 pandemic: Origin, pathogenesis, diagnosis, and therapeutic interventions",Google schorlar,"Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of the human coronavirus (HCoV) family that targets the lower part of the respiratory tract and causes severe acute respiratory syndrome (SARS). In a short span of time, this infection has led to a global pandemic and has become a significant threat to the existence of present human society. Currently, there are no treatments for this infection and the measures established across various countries such as social distancing, usage of mask to prevent entry of the virus into the respiratory tract, quarantine, and containment together have reduced the prevalence of this disease and mortality in highly susceptible individuals. Here, we examine the structure, replication cycle, phylogeny and genomic organization of this virus and discuss the role of spike (S) protein of the virus, an important structure that interacts with the host ACE2 receptor facilitating viral entry. Further, we explore the epidemiology, symptoms of the disease, describe the reverse transcriptase-polymerase chain reaction (RT-PCR) that establishes the diagnosis of the disease and also review its unique diagnostic features in the chest CT-Scan. Finally, we review the current approaches to develop therapies and vaccines as a measure for disease prevention and control.",Research article,NA,NA,open,2020,NA,28,"Coronaviruses

COVID-19

ACE2

S spike protein

SARS-CoV-2

Pathogenesis

Genomic Organization

Transmission Diagnosis

Review",https://www.imrpress.com/journal/FBE/13/1/10.2741/874/htm,PP
31,"Shi, Y., Wang, G., Cai, X. P., Deng, J. W., Zheng, L., Zhu, H. H., ... & Chen, Z. (2020). cc. Journal of Zhejiang University. Science. B, 21(5), 343.",An overview of COVID-19,Google schorlar,"Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection emerged in Wuhan City, Hubei Province, China in December 2019. By Feb. 11, 2020, the World Health Organization (WHO) officially named the disease resulting from infection with SARS-CoV-2 as coronavirus disease 2019 (COVID-19). COVID-19 represents a spectrum of clinical manifestations that typically include fever, dry cough, and fatigue, often with pulmonary involvement. SARS-CoV-2 is highly contagious and most individuals within the population at large are susceptible to infection. Wild animal hosts and infected patients are currently the main sources of disease which is transmitted via respiratory droplets and direct contact. Since the outbreak, the Chinese government and scientific community have acted rapidly to identify the causative agent and promptly shared the viral gene sequence, and have carried out measures to contain the epidemic. Meanwhile, recent research has revealed critical aspects of SARS-CoV-2 biology and disease pathogenesis; other studies have focused on epidemiology, clinical features, diagnosis, management, as well as drug and vaccine development. This review aims to summarize the latest research findings and to provide expert consensus. We will also share ongoing efforts and experience in China, which may provide insight on how to contain the epidemic and improve our understanding of this emerging infectious disease, together with updated guidance for prevention, control, and critical management of this pandemic.",Research article,NA,NA,open,2020,NA,0,"Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Pathogenesis, Epidemiology, Prevention and management",https://pmc.ncbi.nlm.nih.gov/articles/PMC7205601/,PP
32,"Frutos, R., Gavotte, L., & Devaux, C. A. (2021). Understanding the origin of COVID-19 requires to change the paradigm on zoonotic emergence from the spillover to the circulation model. Infection, Genetics and Evolution, 95, 104812.",Understanding the origin of COVID-19 requires to change the paradigm on zoonotic emergence from the spillover to the circulation model,Google schorlar,"While the COVID-19 pandemic continues to spread with currently more than 117 million cumulated cases and 2.6 million deaths worldwide as per March 2021, its origin is still debated. Although several hypotheses have been proposed, there is still no clear explanation about how its causative agent, SARS-CoV-2, emerged in human populations. Today, scientifically-valid facts that deserve to be debated still coexist with unverified statements blurring thus the knowledge on the origin of COVID-19. Our retrospective analysis of scientific data supports the hypothesis that SARS-CoV-2 is indeed a naturally occurring virus. However, the spillover model considered today as the main explanation to zoonotic emergence does not match the virus dynamics and somehow misguided the way researches were conducted. We conclude this review by proposing a change of paradigm and model and introduce the circulation model for explaining the various aspects of the dynamic of SARS-CoV-2 emergence in humans.",Research article,NA,NA,open,2021,NA,45,COVID-19; SARS-CoV-2; Origin; Transmission; Zoonotic emergence; Spillover model; Circulation model,https://www.sciencedirect.com/science/article/pii/S156713482100109X,PP
33,Zarocostas J. WHO team begins COVID-19 origin investigation. Lancet. 2021 Feb 6;397(10273):459. doi: 10.1016/S0140-6736(21)00295-6. Erratum in: Lancet. 2021 Feb 27;397(10276):796. doi: 10.1016/S0140-6736(21)00385-8. PMID: 33549178; PMCID: PMC7906677.,WHO team begins COVID-19 origin investigation,PubMed,WHO team begins COVID-19 origin investigation,Article note,NA,NA,open,2021,NA,9,NA,NA,PP
34,"Zapatero Gaviria A, Barba Martin R. What do we know about the origin of COVID-19 three years later? Rev Clin Esp (Barc). 2023 Apr;223(4):240-243. doi: 10.1016/j.rceng.2023.02.010. Epub 2023 Mar 16. PMID: 36933695; PMCID: PMC10019034.",What do we know about the origin of COVID-19 three years later,PubMed,"More than three years have passed since the first case of a new coronavirus infection (SARS-CoV-2) in the city of Wuhan (Hubei, China). The Wuhan Institute of Virology was founded in that city in 1956 and the country’s first biosafety level 4 laboratory opened within that center in 2015. The coincidence that the first cases of infection emerged in the city where the virology institute’s headquarters is located, the failure to 100% identify the virus’ RNA in any of the coronaviruses isolated in bats, and the lack of evidence on a possible intermediate animal host in the contagion’s transmission make it so that at present, there are doubts about the real origin of SARS-CoV-2. This article will review two theories: SARS-CoV-2 as a virus of zoonotic origin or as a leak from the high-level biosafety laboratory in Wuhan.",Article note,NA,Summary,open,2023,Apr,0,"SARS-CoV-2, COVID-19, COVID-19 origin, Wuhan Institute of Virology",NA,PP
35,"Casadevall A, Weiss SR, Imperiale MJ. Can Science Help Resolve the Controversy on the Origins of the SARS-CoV-2 Pandemic? mBio. 2021 Aug 31;12(4):e0194821. doi: 10.1128/mBio.01948-21. Epub 2021 Aug 2. PMID: 34334001; PMCID: PMC8406229.",Can Science Help Resolve the Controversy on the Origins of the SARS-CoV-2 Pandemic?,PubMed,"The origins of the calamitous SARS-CoV-2 pandemic are now the subject of vigorous discussion and debate between two competing hypotheses for how it entered the human population: (i) direct infection from a feral source, likely a bat and possibly with an intermediate mammalian host, and (ii) a lab accident whereby bat isolates infected a researcher, who then passed it to others. Here, we ask whether the tools of science can help resolve the origins question and conclude that while such studies can provide important information, these are unlikely to provide a definitive answer. Currently available data combined with historical precedent from other outbreaks and viewed through the prism of Occam’s razor favor the feral source hypothesis, but science can provide only probabilities, not certainty.",Research article,NA,Summary,open,2021,45900,13,"COVID, SARS, SARS-CoV-2",NA,PP
36,Garry RF. The evidence remains clear: SARS-CoV-2 emerged via the wildlife trade. Proc Natl Acad Sci U S A. 2022 Nov 22;119(47):e2214427119. doi: 10.1073/pnas.2214427119. Epub 2022 Nov 10. PMID: 36355862; PMCID: PMC9704731.,The evidence remains clear: SARS-CoV-2 emerged via the wildlife trade,PubMed,NA,Opinion,NA,NA,open,2022,45983,20,NA,https://www.pnas.org/doi/10.1073/pnas.2214427119,PP
37,"Opriessnig T, Huang YW. SARS-CoV-2 does not infect pigs, but this has to be verified regularly. Xenotransplantation. 2022 Sep;29(5):e12772. doi: 10.1111/xen.12772. Epub 2022 Aug 30. PMID: 36039616; PMCID: PMC9538518.","SARS-CoV-2 does not infect pigs, but this has to be verified regularly",PubMed,"For successful xenotransplantation, freedom of the xenocraft donor from certain viral infections that may harm the organ recipient is important. A novel human coronavirus (CoV) with a respiratory tropism, designated as SARS‐CoV‐2, was first identified in January 2020 in China, but likely has been circulating unnoticed for some time before. Since then, this virus has reached most inhabited areas, resulting in a major global pandemic which is still ongoing. Due to a high number of subclinical infections, re‐infections, geographic differences in diagnostic tests used, and differences in result reporting programs, the percentage of the population infected with SARS‐CoV‐2 at least once has been challenging to estimate. With continuous ongoing infections in people and an overall high viral load, it makes sense to look into possible viral spillover events in pets and farm animals, who are often in close contact with humans. The pig is currently the main species considered for xenotransplantation and hence there is interest to know if pigs can become infected with SARS‐CoV‐2 and if so what the infection dynamics may look like. This review article summarizes the latest research findings on this topic. It would appear that pigs can currently be considered a low risk species, and hence do not pose an immediate risk to the human population or xenotransplantation recipients per se. Monitoring the ever‐changing SARS‐CoV‐2 variants appears important to recognize immediately should this change in the future.",Research article,NA,NA,open,2022,Sep,2,"COVID‐19, cross‐species transmission, pig models, SARS‐CoV‐2, therapeutics, xenotransplantation",NA,PP
38,"Nguyen TT, Abdelrazek M, Nguyen DT, Aryal S, Nguyen DT, Reddy S, Nguyen QVH, Khatami A, Nguyen TT, Hsu EB, Yang S. Origin of novel coronavirus causing COVID-19: A computational biology study using artificial intelligence. Mach Learn Appl. 2022 Sep 15;9:100328. doi: 10.1016/j.mlwa.2022.100328. Epub 2022 May 16. PMID: 35599960; PMCID: PMC9110011.",Origin of novel coronavirus causing COVID-19: A computational biology study using artificial intelligence,PubMed,"Origin of the COVID-19 virus (SARS-CoV-2) has been intensely debated in the scientific community since the first infected cases were detected in December 2019. The disease has caused a global pandemic, leading to deaths of thousands of people across the world and thus finding origin of this novel coronavirus is important in responding and controlling the pandemic. Recent research results suggest that bats or pangolins might be the hosts for SARS-CoV-2 based on comparative studies using its genomic sequences. This paper investigates the SARS-CoV-2 origin by using artificial intelligence (AI)-based unsupervised learning algorithms and raw genomic sequences of the virus. More than 300 genome sequences of COVID-19 infected cases collected from different countries are explored and analysed using unsupervised clustering methods. The results obtained from various AI-enabled experiments using clustering algorithms demonstrate that all examined SARS-CoV-2 genomes belong to a cluster that also contains bat and pangolin coronavirus genomes. This provides evidence strongly supporting scientific hypotheses that bats and pangolins are probable hosts for SARS-CoV-2. At the whole genome analysis level, our findings also indicate that bats are more likely the hosts for the COVID-19 virus than pangolins.",Research article,NA,NA,open,2022,45915,0," Artificial intelligence, AI, Machine learning, COVID-19, SARS-coV-2, Origin, Bat, Pangolin, Pandemic",https://pmc.ncbi.nlm.nih.gov/articles/PMC9110011/,PP
39,"Wambani J, Okoth P. SARS-CoV-2 origin, myths and diagnostic technology developments. Egypt J Med Hum Genet. 2022;23(1):42. doi: 10.1186/s43042-022-00255-3. Epub 2022 Mar 4. PMID: 37521834; PMCID: PMC8893981.","SARS-CoV-2 origin, myths and diagnostic technology developments",PubMed,"Background

After the first case of COVID-19 being announced in China in December 2019, various diagnostic technologies have been developed at unprecedented pace with the aim of providing a basis for accurate clinical intervention. However, some assays including CRISPR-based diagnostics and loop-mediated isothermal amplification (LAMP) have been less explored. As new COVID-19 technologies emerge, there is need for them to be assessed, validated and improved upon. Moreover, there is paucity of data on the essential factors governing the selection of an appropriate diagnostic approach within the correct timeframe. Myths and origin of SARS-CoV-2 remain to be controversial. Consequently, this review aims at exploring the current COVID-19 diagnostic technologies, performance evaluation, principles, suitability, specificity, sensitivity, successes and challenges of the technologies for laboratory and bedside testing.



Main Body

To date, there exist more publications on COVID-19 diagnostics as compared to the Zika virus. The SARS-CoV-2 virus genome profiles were readily available by 31st of December 2019. This was attributed to the fast-paced sharing of the epidemiological and diagnostics data of COVID-19. Timely profiling of the virus genome accelerated the development of diagnostic technologies. Furthermore, the rapid publication of studies that evaluated several diagnostic methods available provided baseline information on how the various technologies work and paved way for development of novel technologies.



Conclusion

Up to date, RT-PCR is the most preferred as compared to the other assays. This is despite the repeated false negatives reported in many of the study findings. Considering that COVID-19 has caused devastating effects on the economy, healthcare systems, agriculture and culture, timely and accurate detection of the virus is paramount in the provision of targeted therapy hence reducing chances of drug resistance, increased treatment costs and morbidity. However, information on the origin of SARS-CoV-2 still remains elusive. Furthermore, knowledge and perception of the patients toward management of SARS-CoV-2 are also paramount to proper diagnosis and management of the pandemic. Future implications of the misperceptions are that they may lead to increased non-compliance to SARS-CoV-2-related World Health Organization (WHO) policies and guidelines.",Research article,NA,NA,open,2022,NA,2,"COVID-19, SARS-CoV-2, ELISA, RT-PCR, LAMP, TMA, CRISPR",https://pmc.ncbi.nlm.nih.gov/articles/PMC8893981/,PP
40,"Tyshkovskiy A, Panchin AY. There is still no evidence of SARS-CoV-2 laboratory origin: Response to Segreto and Deigin (10.1002/bies.202100137). Bioessays. 2021 Dec;43(12):e2100194. doi: 10.1002/bies.202100194. Epub 2021 Oct 26. PMID: 34697827; PMCID: PMC8646886.",There is still no evidence of SARS-CoV-2 laboratory origin: Response to Segreto and Deigin,PubMed,"The causative agent of COVID‐19 SARS‐CoV‐2 has led to over 4 million deaths worldwide. Understanding the origin of this coronavirus is important for the prevention of future outbreaks. The dominant point of view that the virus transferred to humans either directly from bats or through an intermediate mammalian host has been challenged by Segreto and Deigin, who claim that the genome of SARS‐CoV‐2 has certain features suggestive of its artificial creation. Following their response to our commentary, here we continue the discussion of the proposed arguments for this hypothesis. We show that neither the existence of a furin cleavage site in SARS‐CoV‐2, nor the presence of specific sequences within the nucleotide insertion encoding that site are evidence for intelligent design. We also explain why existing genetic data, viral diversity and past human history suggest that a natural origin of the virus is the most likely scenario. Genetic evidence suggesting otherwise is yet to be presented.",Research article,NA,NA,open,2021,Dec,2,"comparative genomics, coronavirus, COVID‐19, evolution, furin cleavage site, SARS‐CoV‐2 laboratory origin, SARS‐CoV‐2",https://pmc.ncbi.nlm.nih.gov/articles/PMC8646886/,PP
41,"Li Z, Jiang J, Ruan X, Tong Y, Xu S, Han L, Xu J. The zoonotic and natural foci characteristics of SARS-CoV-2. J Biosaf Biosecur. 2021 Jun;3(1):51-55. doi: 10.1016/j.jobb.2021.06.002. Epub 2021 Jun 24. PMID: 34189426; PMCID: PMC8221912.",The zoonotic and natural foci characteristics of SARS-CoV-2,PubMed,"The origin of SARS-CoV-2 is still an unresolved mystery. In this study, we systematically reviewed the main research progress of wild animals carrying virus highly homologous to SARS-CoV-2 and analyzed the natural foci characteristics of SARS-CoV-2. The complexity of SARS-CoV-2 origin in wild animals and the possibility of SARS-CoV-2 long-term existence in human populations are also discussed. The joint investigation of corona virus carried by wildlife, as well as the ecology and patho-ecology of bats and other wildlife, are key measures to further clarify the characteristics of natural foci of SARS-CoV-2 and actively defend against future outbreaks of emerging zoonotic diseases.",Research article,NA,NA,open,2021,Jun,6," SARS-CoV-2, COVID-19, Natural foci disease, Zoonotic disease",https://pmc.ncbi.nlm.nih.gov/articles/PMC8221912/,PP
42,Shi ZL. Origins of SARS-CoV-2: Focusing on Science. Infect Dis Immun. 2021 Apr 20;1(1):3-4. doi: 10.1097/ID9.0000000000000008. PMID: 38630114; PMCID: PMC8057312.,Origins of SARS-CoV-2: Focusing on Science,PubMed,"The COVID-19 pandemic, caused by the severe acute respiratory syndrome virus 2 (SARS-CoV-2), has resulted in over 110 million confirmed cases and more than 2.4 million deaths globally as of February 23, 2021.[1] China succeeded in containing the nationwide spread of COVID-19 by implementing a lockdown in the city of Wuhan, where the first outbreak occurred. Following the containment of the first outbreak, China experienced more than a dozen small clusters of cases in other cities due to virus transmission by travelers and cold-chain transmission. However, widespread transmission of the virus was prevented by implementing strict quarantine policies and social distancing measures. Although great progress has been made in understanding the epidemiology, virology, immune response, and clinical outcomes of this disease 1 year after the start of the pandemic, the origin of the virus remains unresolved.",Scientific reports,NA,NA,open,2021,45767,14,NA,NA,PP
43,"Frutos R, Gavotte L, Devaux CA. Understanding the origin of COVID-19 requires to change the paradigm on zoonotic emergence from the spillover to the circulation model. Infect Genet Evol. 2021 Nov;95:104812. doi: 10.1016/j.meegid.2021.104812. Epub 2021 Mar 18. PMID: 33744401; PMCID: PMC7969828.",Understanding the origin of COVID-19 requires to change the paradigm on zoonotic emergence from the spillover to the circulation model,PubMed,"While the COVID-19 pandemic continues to spread with currently more than 117 million cumulated cases and 2.6 million deaths worldwide as per March 2021, its origin is still debated. Although several hypotheses have been proposed, there is still no clear explanation about how its causative agent, SARS-CoV-2, emerged in human populations. Today, scientifically-valid facts that deserve to be debated still coexist with unverified statements blurring thus the knowledge on the origin of COVID-19. Our retrospective analysis of scientific data supports the hypothesis that SARS-CoV-2 is indeed a naturally occurring virus. However, the spillover model considered today as the main explanation to zoonotic emergence does not match the virus dynamics and somehow misguided the way researches were conducted. We conclude this review by proposing a change of paradigm and model and introduce the circulation model for explaining the various aspects of the dynamic of SARS-CoV-2 emergence in humans.",Research article,NA,NA,open,2021,Nov,45,"COVID-19, SARS-CoV-2, Origin, Transmission, Zoonotic emergence, Spillover model, Circulation model",NA,PP
44,"Shahhosseini N, Wong G, Kobinger GP, Chinikar S. SARS-CoV-2 spillover transmission due to recombination event. Gene Rep. 2021 Jun;23:101045. doi: 10.1016/j.genrep.2021.101045. Epub 2021 Feb 16. PMID: 33615041; PMCID: PMC7884226.",SARS-CoV-2 spillover transmission due to recombination event,PubMed,"In late 2019, a novel Coronavirus emerged in China. Perceiving the modulating factors of cross-species virus transmission is critical to elucidate the nature of virus emergence. Using bioinformatics tools, we analyzed the mapping of the SARS-CoV-2 genome, modeling of protein structure, and analyze the evolutionary origin of SARS-CoV-2, as well as potential recombination events. Phylogenetic tree analysis shows that SARS-CoV-2 has the closest evolutionary relationship with Bat-SL-CoV-2 (RaTG13) at the scale of the complete virus genome, and less similarity to Pangolin-CoV. However, the Receptor Binding Domain (RBD) of SARS-CoV-2 is almost identical to Pangolin-CoV at the aa level, suggesting that spillover transmission probably occurred directly from pangolins, but not bats. Further recombination analysis revealed the pathway for spillover transmission from Bat-SL-CoV-2 and Pangolin-CoV. Here, we provide evidence for recombination event between Bat-SL-CoV-2 and Pangolin-CoV that resulted in the emergence of SARS-CoV-2. Nevertheless, the role of mutations should be noted as another influencing factor in the continuing evolution and resurgence of novel SARS-CoV-2 variants.",Research article,NA,NA,open,2021,Jun,14,"SARS-CoV-2, Virulence, Phylogenetics, Recombination, Mutation, Pandemic",https://pmc.ncbi.nlm.nih.gov/articles/PMC7884226/,PP
45,"Zappulli V, Ferro S, Bonsembiante F, Brocca G, Calore A, Cavicchioli L, Centelleghe C, Corazzola G, De Vreese S, Gelain ME, Mazzariol S, Moccia V, Rensi N, Sammarco A, Torrigiani F, Verin R, Castagnaro M. Pathology of Coronavirus Infections: A Review of Lesions in Animals in the One-Health Perspective. Animals (Basel). 2020 Dec 11;10(12):2377. doi: 10.3390/ani10122377. PMID: 33322366; PMCID: PMC7764021.",Pathology of Coronavirus Infections: A Review of Lesions in Animals in the One-Health Perspective,PubMed,"Coronaviruses (CoVs) are worldwide distributed RNA-viruses affecting several species, including humans, and causing a broad spectrum of diseases. Historically, they have not been considered a severe threat to public health until two outbreaks of COVs-related atypical human pneumonia derived from animal hosts appeared in 2002 and in 2012. The concern related to CoVs infection dramatically rose after the COVID-19 global outbreak, for which a spill-over from wild animals is also most likely. In light of this CoV zoonotic risk, and their ability to adapt to new species and dramatically spread, it appears pivotal to understand the pathophysiology and mechanisms of tissue injury of known CoVs within the “One-Health” concept. This review specifically describes all CoVs diseases in animals, schematically representing the tissue damage and summarizing the major lesions in an attempt to compare and put them in relation, also with human infections. Some information on pathogenesis and genetic diversity is also included. Investigating the lesions and distribution of CoVs can be crucial to understand and monitor the evolution of these viruses as well as of other pathogens and to further deepen the pathogenesis and transmission of this disease to help public health preventive measures and therapies.",Research article,NA,NA,open,2020,46002,35,"coronavirus, pathology, veterinary medicine, One Health",https://pmc.ncbi.nlm.nih.gov/articles/PMC7764021/,PP
46,"Lundstrom K, Seyran M, Pizzol D, Adadi P, Mohamed Abd El-Aziz T, Hassan SS, Soares A, Kandimalla R, Tambuwala MM, Aljabali AAA, Kumar Azad G, Pal Choudhury P, Uversky VN, Sherchan SP, Uhal BD, Rezaei N, Brufsky AM. Viewpoint: Origin of SARS-CoV-2. Viruses. 2020 Oct 22;12(11):1203. doi: 10.3390/v12111203. PMID: 33105685; PMCID: PMC7690418.",The Importance of Research on the Origin of SARS-CoV-2,PubMed,"The origin of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) virus causing the COVID-19 pandemic has not yet been fully determined. Despite the consensus about the SARS-CoV-2 origin from bat CoV RaTG13, discrepancy to host tropism to other human Coronaviruses exist. SARS-CoV-2 also possesses some differences in its S protein receptor-binding domain, glycan-binding N-terminal domain and the surface of the sialic acid-binding domain. Despite similarities based on cryo-EM and biochemical studies, the SARS-CoV-2 shows higher stability and binding affinity to the ACE2 receptor. The SARS-CoV-2 does not appear to present a mutational “hot spot” as only the D614G mutation has been identified from clinical isolates. As laboratory manipulation is highly unlikely for the origin of SARS-CoV-2, the current possibilities comprise either natural selection in animal host before zoonotic transfer or natural selection in humans following zoonotic transfer. In the former case, despite SARS-CoV-2 and bat RaTG13 showing 96% identity some pangolin Coronaviruses exhibit very high similarity to particularly the receptor-binding domain of SARS-CoV-2. In the latter case, it can be hypothesized that the SARS-CoV-2 genome has adapted during human-to-human transmission and based on available data, the isolated SARS-CoV-2 genomes derive from a common origin. Before the origin of SARS-CoV-2 can be confirmed additional research is required",Research article,NA,NA,open,2020,45952,35,"coronavirus, COVID-19 pandemic, origin of SARS-CoV-2, receptor binding domain, genome homology, natural selection, zoonotic transfer",https://pmc.ncbi.nlm.nih.gov/articles/PMC7690418/,PP
47,"The Lancet Microbe. (2024, August). COVID-19 origins: Plain speaking is overdue. The Lancet Microbe, 5(8), 100953. https://doi.org/10.1016/j.lanmicro.2024.100953",COVID-19 origins: plain speaking is overdue,Google schorlar,"SARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 97 million infections and 2 million deaths in 12 months. Understanding the origin of this virus is an important issue, and it is necessary to determine the mechanisms of viral dissemination in order to contain future epidemics. Based on phylogenetic inferences, sequence analysis and structure–function relationships of coronavirus proteins, informed by the knowledge currently available on the virus, we discuss the different scenarios on the origin—natural or synthetic—of the virus. The data currently available are not sufficient to firmly assert whether SARS-CoV2 results from a zoonotic emergence or from an accidental escape of a laboratory strain. This question needs to be solved because it has important consequences on the risk/benefit balance of our interactions with ecosystems, on intensive breeding of wild and domestic animals, on some laboratory practices and on scientific policy and biosafety regulations. Regardless of COVID-19 origin, studying the evolution of the molecular mechanisms involved in the emergence of pandemic viruses is essential to develop therapeutic and vaccine strategies and to prevent future zoonoses. This article is a translation and update of a French article published in Médecine/Sciences, August/September 2020 (https://doi.org/10.1051/medsci/2020123).",Research article,NA,NA,open,2024,NA,1,NA,https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(24)00206-4/fulltext,PP
48,"The White House. (2025, April). 2024.12.04 SSCP final report [PDF]. https://www.whitehouse.gov/wp-content/uploads/2025/04/2024.12.04-SSCP-FINAL-REPORT-ANS.pdf",2024.12.04 SSCP final report [PDF],whitehouse.gov,NA,report,NA,NA,open,2025,45759,NA,NA,https://www.whitehouse.gov/wp-content/uploads/2025/04/2024.12.04-SSCP-FINAL-REPORT-ANS.pdf,PP
49,"U.S. Senate Committee on Health, Education, Labor, and Pensions. (2023). An analysis of the origins of COVID-19: Interim report [Report]. https://www.documentcloud.org/documents/23782224-senate-covid-19-origins-report/",An analysis of the origins of COVID-19: Interim report [Report],senate-covid-19,NA,report,NA,NA,open,2023,NA,NA,NA,https://www.documentcloud.org/documents/23782224-senate-covid-19-origins-report/,PP
