Coronavirus host divergence and novel coronavirus (SARS-CoV-2) outbreak

Year 2020, Volume: 2 Issue: 1, 6 - 14, 23.04.2020

Kadir Yeşilbağ , Gizem Aytoğu

Abstract

SARS-CoV-2 (novel coronavirus, nCoV-2019) outbreak started in November 2019 in China has created a public health concern all around the world. Since infected patients transported out of China, the outbreak status was quickly changed into pandemic. Comparison of available genome sequences of the virus strains enlightened most questions as the cell receptors (ACE2) responsible for the virus tropism which determines possible organs and tissues to be affected by the virus as well as possible involvement of the age groups and host diversity. SARS-Cov-2, new member of Coronaviridae shares some clinical and epidemiological aspects similar to previous high pathogenic human coronavirus, SARS-CoV, existed in 2002. The most outstanding property of SARS-CoV-2 is high transmission rate (reproduction number, R0=˷3.58) between suspected and susceptible people. While bats are pointed as the original host and pangolins as an intermediate host, possibility of other species contribution is still unknown. According to recent data, reptiles i.e. snakes seem to be out of the group for possible intermediate hosts. Also there is no data supporting involvement of domestic animals even pets or food producing in the infection spectrum. This review summarizes the key findings of ongoing pandemia since the day disease existed. Molecular divergences now show that disease agent evolved into two types (S and L). Mutations and natural selections besides recombination will still continue to be the common feature of coronaviruses. Though implementation of common global measures and treatments other than rapid sharing the information will contribute prevention efforts and reducing the number of losses.

Keywords

SARS-CoVs, Coronavirus, Animal origin, Zoonosis, COVİD, COVİD19

References

• 1. Payne S. Family Coronaviridae. In: Payne S. eds. Viruses (1st ed). United Kingdom; Academic Press;2017:149-158.
• 2. Hulswit RJ, de Haan CA, Bosch BJ. Coronavirus Spike Protein and Tropism Changes. Adv Virus Res. 2016(96):29-57.
• 3. Chan JF, Lau SK, Woo PC. The emerging novel Middle East respiratory syndrome coronavirus: the "knowns" and "unknowns". J Formos Med Assoc. 2013;112:372-381.
• 4. Chan JF, To KK, Tse H, Jin DY, Yuen KY. Interspecies transmission and emergence of novel viruses: lessons from bats and birds. Trends Microbiol. 2013, 21(10):544-55.
• 5. National Institute of Allergy and Infectious Disease. New Images of Novel Coronavirus SARS-CoV-2 Now Available. 2020; https://www.niaid.nih.gov/news-events/novel-coronavirus-sarscov2-images
• 6. Viralzone. Coronaviridae. Aviable in 2020; https://viralzone.expasy.org/30?outline=all_by_species
• 7. Han Q, Lin Q, Jin S, You L. Recent insights into 2019-nCoV: a brief but comprehensive review. J Infect. 2020; S0163-4453(20)30087-6. doi: 10.1016/j.jinf.2020.02.010.
• 8. Li W, Wong SK, Li F, Kuhn JH, Huang IC, Choe H et al. Animal origins of the severe acute respiratory syndrome coronavirus: insight from ACE2-S-protein interactions. J Virol. 2006;80(9):4211–4219.
• 9. Lau SK, Woo PCY, Li KSM, Huang Y, Tsoi H, Wong BHLet al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. PNAS. 2005;102:14040-14045.
• 10. Cheng VCC, Lau SKP, Woo PCY, Yuen KY. Severe Acute Respiratory Syndrome Coronavirus as an Agent of Emerging and Reemerging Infection. Clin Microbiol Rev. 2007;20(4):660-694.
• 11. Chen TM, Rui J, Wang QP, Zhao ZY, Cui JA, Yin L. A mathematical model for simulating the phase-based transmissibility of a novel coronavirus. Infect Dis Poverty. 2020; https://doi.org/10.1186/s40249-020-00640-3
• 12. Woo PCY, Lau SKP, Li KSM, Tsang AKL Yuen K. Genetic relatedness of novel human group C betacoronavirus to Tylonyeteris bat coronavirus HKU4 and Pipistrellus bat coronavirus HKU5. Emerg Microbes Infec. 2012; 1e35. doi:10.1038/emi.2012.45
• 13. Liu Z, Xiao X, Wei X, Li J, Yang J, Tan H, et al. Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS-CoV-2. J Med Virol. 2020; doi: 10.1002/jmv.25726.
• 14. Vijgen L, Keyaerts E, Lemey P, Maes P, Van Reeth K, Nauwynck H, et al., Evolutionary history of the closely related group 2 coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus OC43. J Virol. 2006; 80 (14):7270–7274. http://dx.doi.org/10.1128/JVI.02675-05.
• 15. WHO Coronavirus disease 2019 (COVID-19), Situation Report – 52 https://www.who.int/docs/default-source/coronaviruse/20200312-sitrep-52-covid-19.pdf?sfvrsn=e2bfc9c0_2
• 16. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020;395(10224):565-574.
• 17. WHO Coronavirus disease 2019 (COVID-19), Situation Report – 63 https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200323-sitrep-63-covid-19.pdf?sfvrsn=2176eb7a_2
• 18. Lai CC, Shih TP, Ko WC, Tang HJ, Hsueh PR. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. Int J Antimicrob Agents. 2020;105924. doi: 10.1016/j.ijantimicag.2020.105924.
• 19. Xu J, Zhao S, Teng T, Abdalla AE, Zhu W, Xie L et al. Systematic comparison of two animal-to-human transmitted human coronaviruses: SARS-CoV-2 and SARS-CoV. Viruses. 2020;12(2). pii: E244. doi: 10.3390/v12020244.
• 20. Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y. Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia. N Engl J Med. 2020; 10.1056/NEJMoa2001316.
• 21. Biscayart C, Angeleri P, Lloveras S, Chaves TDSS, Schlagenhauf P, Rodríguez-Morales AJ. The next big threat to global health? 2019 novel coronavirus (2019-nCoV): What advice can we give to travellers? - Interim recommendations January 2020, from the Latin-American society for Travel Medicine (SLAMVI). Travel Med Infect Dis. 2020; 33:101567.
• 22. Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020; 395(10223):497-506.
• 23. Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020;395(10223):507-513.
• 24. van Doremalen N, Morris DH, Holbrook MG, Holbrook MG, Gamble A, Williamson BN et al. Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1. N Engl J Med. 2020; https://dx.doi.org/10.1056/NEJMc2004973
• 25. Kampf G, Todt D, Pfaender S, Steinmann E. Persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents J Hosp Infect. 2020;104: 246-251.
• 26. Li W, Moore MJ, Vasilieva N, Sui J, Wong SK, Berne MA et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature. 2003; 426(6965): 450-4.
• 27. Letko M, Marzi A, Munster V. Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses. Nat Microbiol. 2020; doi: 10.1038/s41564-020-0688-y.
• 28. Xu H, Zhong L, Deng J, Peng J, Dan H, Zeng X et al. High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa. Int J Oral Sci. 2020; 12(8): 1-5.
• 29. Fan C, Li K, Ding Y, Lu W, Wang J. ACE2 expression in kidney and testis may cause kidney and testis damage after 2019-nCoV infection. 2020; https://doi.org/10.1101/2020.02.12.20022418.
• 30. Zhang X, Chen X, Chen L, Deng C, Zou X, Liu W et al. The infection evidence of SARS-COV-2 in ocular surface： a single-center cross-sectional study. 2020; doi: https://doi.org/10.1101/2020.02.26.2002793.
• 31. Wang R, Zhang X, Irwin DM, Shen Y. Emergence of SARS-like coronavirus poses new challenge in China. J Infect. 2020;80(3):350-371.
• 32. Paraskevisa D, Kostakia EG, Magiorkinisa G, Panayiotakopoulosb G, Sourvinosc G, Tsiodrasd S. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infect Genet Evol. 2020;79:104212.
• 33. Li R, Qiao S, Zhang G. Analysis of angiotensin-converting enzyme 2 (ACE2) from different species sheds some light on cross-species receptor usage of a novel coronavirus 2019-nCoV. J Infect. 2020; https://doi.org/10.1016/j.jinf.2020.02.013
• 34. Zhang C, Zheng W, Huang X, Bell EW, Zhou X, Zhang Y. Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1. 2020; doi: 10.1101/2020.02.04.933135.
• 35. Xiao K, Zhai J, Feng Y, Zhou N, Zhang X, Zou JJ et al. Isolation and characterization of 2019-nCoV-like coronavirus from Malayan pangolins. 2020; doi: https://doi.org/10.1101/2020.02.17.951335.
• 36. OIE Follow-up report No. 1; 07/03/2020, COVID-19-Honkong https://www.oie.int/wahis_2/public/wahid.php/Reviewreport/Review?page_refer=MapFullEventReport&reportid=33455 aviability;17.03.2020
• 37. Cao Y, Li L, Feng Z, Wan S, Huang P, Sun X, et al. Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations. Cell Discov. 2020;6:11.
• 38. Chen Y, Shan K, Qian W. Asians and other races express similar levels of and share the same genetic polymorphisms of the SARS-CoV-2 cell-entry receptor. 2020; doi:10.20944/preprints202002.0258.v1.
• 39. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; doi: 10.1038/s41586-020-2012-7.
• 40. Harcourt J, Tamin A, Lu X, Kamili S, Sakthivel SK, Murray J et al. Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with 2019 Novel Coronavirus Disease, United States. J Emerg Infect Dis. 2020; 26(6), https://doi.org/10.3201/eid2606.200516
• 41. Matsuyama S, Nao N, Shirato K, Kawase M, Saito S, Takayama et al. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. P Natl Acad Sci Usa. 2020; 202002589; doi: 10.1073/pnas.2002589117
• 42. Tang X, Wu C, Li X, Song Y, YaoX, Wu X et al. On the origin and continuing evolution of SARS-CoV-2, Natl Sci Rev. 2020; nwaa036, https://doi.org/10.1093/nsr/nwaa036
• 43. Chu DKW, Pan Y, Cheng SMS, Hui KPY, Krishnan P, Liu Y et al. Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia. Clin Chem. 2020; pii: hvaa029. doi: 10.1093/clinchem/hvaa029.
• 44. WHO- Coronavirus disease (COVID-19) technical guidance: Laboratory testing for 2019-nCoV in humans https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance
• 45. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020;382(8):727-733. doi: 10.1056/NEJMoa2001017.
• 46. To KK, Tsang OT, Chik-Yan Yip C, Chan KH, Wu TC, Chan JMC et al. Consistent detection of 2019 novel coronavirus in saliva. Clin Infect Dis. 2020; doi: 10.1093/cid/ciaa149.
• 47. Lin X, Gong Z, Xiao Z, Xiong J, Fan B, Liu J. Novel Coronavirus Pneumonia Outbreak in 2019: Computed Tomographic Findings in Two Cases. Korean J Radiol. 2020; 21(3):365-368.
• 48. Bastola A, Sah R, Rodriguez-Morales AJ, Lal BK, Jha R, Ojha et al. The first 2019 novel coronavirus case in Nepal. Lancet Infect Dis. 2020;20(3):279-280.
• 49. Pan Y, Zhang D, Yang P, Poon LLM, Wang Q. Viral load of SARS-CoV-2 in clinical samples. Lancet Infect Dis. 2020; doi: 10.1016/S1473-3099(20)30113-4.
• 50. Peng L, Liu J, Xu W, Luo Q, Deng K, Bingliang L et al. 2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples. 2020; https://doi.org/10.1101/2020.02.21.20026179.
• 51. Jianhua Xia MM, Jianping Tong MD, Mengyun Liu MM, Ye Shen MD. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection. 2020; https://doi.org/10.1002/jmv.25725.
• 52. Zhou Y, Zeng Y, Tong T, Chen C. Ophthalmologic evidence against the interpersonal transmission of 2019 novel coronavirus through conjunctiva. 2020, https://doi.org/10.1101/2020.02.11.20021956.
• 53. Deng W, Bao L, Gao H, Xiang Z, Qu Y, Son Z et al. Rhesus macaques can be effectively infected with SARS-CoV-2 via ocular conjunctival route. 2020; doi: https://doi.org/10.1101/2020.03.13.990036.
• 54. Sun CH, Wang Y, Liu G, Liu Z. Role of the Eye in Transmitting Human Coronavirus: What We Know and What We Do Not Know. 2020; doi: 10.20944/preprints202003.0271.v2 (Preprint).
• 55. Poland GA. Another coronavirus, another epidemic, another warning. Vaccine. 2020; 38(10):v-vi. doi: 10.1016/j.vaccine.2020.02.039.
• 56. Cai Q, Yang M, Liu D, Chen J, Shu D, Xia J. Experimental Treatment with Favipiravir for COVID-19: An Open-Label Control Study. 2020;https://doi.org/10.1016/j.eng.2020.03.007
• 57. Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M et al. Remdesivir and chloroquine effectively inhibit the recent emerged novel coronavirus (2019-nCoV) invitro. Cell Res. 2020;30(3):269-271.
• 58. Oliveiros B, Caramelo L, Ferreira NC, Caramelo F. Role of temperature and humidity in the modulation of the doubling time of COVID-19 cases. 2020; doi: https://doi.org/10.1101/2020.03.05.20031872.