This is an outdated version published on 2021-04-06. Read the most recent version.
Genetic Diversity and Comprehensive Phylodynamic Analysis of Whole Corona Viruses Genomes
Keywords:
COVID-19, Phylogeny, SARS-CoV, MERS-CoV, Coding Sequence(CDS)Abstract
Covid-19 is a rapidly emerging viral respiratory disease. The infection of corona virus disease (COVID-19) is initiated by the strains of severe acute respiratory syndrome. Corona virus 2 (SARS-CoV-2), is a highly transmittable viral infection that was first emerged in the of Wuhan, a city of China and ultimately extent in whole world. The World health organization (WHO) affirmed this infection as a global public health disaster. Genomic analysis showing that this novel SARSCoV-2 is hereditarily linked with severe acute respiratory syndrome-like (SARS-like) bat viruses indicating that bats might be the primary source of this epidemic infection. In this review we have summarized a comprehensive phylodynamic analysis of whole corona virus genome sequences in order to analyze the pathogenicity and emergence of novel COVID-19 infection and previous human coronaviruses. Our main objective is to describe the genetic relationships of the 2019-nCoV with other genera of coronavirus and to find out supposed recombination contained by sarbecovirus subgenus. Keywords: COVID-19, Phylogeny, SARS-CoV, MERS-CoV, Coding Sequence (CDS).
Downloads
Download data is not yet available.
References
1. Chan HL, Tsui SK, Sung JJ. Coronavirus in severe acute respiratory syndrome (SARS). Trends Mol Med 2003;
9:323-5. doi:10.1016/s1471-4914(03)00135-7.
2. Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 2019; 17:181-92.
doi:10.1038/s41579-018-0118-9.
3. 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; 395:497-506. doi:10.1016/S0140-6736(20)30183-5.
4. Wang X, Zhou Q, He Y, Liu L, Ma X, Wei X, et al. Nos-ocomial outbreak of COVID-19 pneumonia in Wuhan,
C h i n a . E u r R e spi r J 2 0 2 0 ; 5 5 : 2 0 0 0 5 4 4 . doi:10.1183/13993003.00544-2020.
5. 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; 382:727-33. doi:10.1056/NEJMoa2001017.
6. Yang Y, Xiao Z, Ye K, He X, Sun B, Qin Z, et al. SARS-CoV-2: characteristics and current advances in research.
Virol J 2020 29; 17:117. doi:10.1186/s12985-020-01369-z.
7. Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia of the Chinese Preventive Medicine Association. An update on the epidemiological characteristics of novel coronavirus pneumonia (COVID-19). Zhonghua Liu Xing Bing Xue Za Zhi 2020; 41:139-44. doi:10.3760/cma.j.issn.0254-6450.2020.02.002.
8. Song Z, Xu Y, Bao L, Zhang L, Yu P, Qu Y, et al. From SARS to MERS, Thrusting Coronaviruses into the Spotlight.
Viruses 2019; 11:59. doi:10.3390/v11010059.
9. Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, et al. Isolation and characterization of viruses related
to the SARS coronavirus from animals in southern China. Science 2003; 302:276-8. doi:10.1126/science.1087139.
10. Drosten C, Kellam P, Memish ZA. Evidence for camel-to-human transmission of MERS coronavirus. N Engl J
Med 2014; 371:1359-60. doi:10.1056/NEJMc1409847.
11. Li F. Structure, Function, and Evolution of Coronavirus Spike Proteins. Annu Rev Virol 2016; 3:237-61.
doi:10.1146/annurev-virology-110615-042301.
12. Tang Q, Song Y, Shi M, Cheng Y, Zhang W, Xia XQ. Inferring the hosts of coronavirus using dual statistical
models based on nucleotide composition. Sci Rep 2015; 5:17155. doi:10.1038/srep17155.
13. Ceraolo C, Giorgi FM. Genomic variance of the 2019-nC-oV coronavirus. J Med Virol 2020; 92:522-8.
doi:10.1002/jmv.25700.
14. Jiang S, Shi ZL. The First Disease X is Caused by a Highly Transmi s s ible Acute Respiratory Syndrome
C o r o n a v i r u s . V i r o l S i n 2 0 2 0 ; 3 5 : 2 6 3 - 5 . doi:10.1007/s12250-020-00206-5
15. Lai CC, Shih TP, Ko WC, Tang HJ, Hsueh PR. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and
corona virus disease-2019 (COVID-19): the epidemic and the challenges. Int J Antimicrob Agents 2020; 55:924.
doi.org/10.1016/j.ijantimicag.2020.105924
16. Li C, Yang Y, Ren L. Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species.
Infect Genet Evol 2020; 82:104285. doi:10.1016/j.meegid.2020.104285.
17. 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 22; 395:565-74.
doi:10.1016/S0140-6736(20)30251-8.
1 8 . P a r a s k e v i s D, Kos t a k i EG, Ma g ior k i n i s G, Panayiotakopoulos G, Sourvinos G, Tsiodras 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. doi:10.1016/j.meegid.2020.104212.
19. Zhu Z, Zhang Z, Chen W, Cai Z, Ge X, Zhu H, et al. Predicting the receptor-binding domain usage of the
coronavirus based on kmer frequency on spike protein. Infect Genet Evol 2018; 61:183-4.
doi:10.1016/j.meegid.2018.03.028.
20. Jeffers SA, Tusell SM, Gillim-Ross L, Hemmila EM, Achenbach JE, Babcock GJ, et al. CD209L (L-SIGN) is a
receptor for severe acute respiratory syndrome coronavirus. Proc Natl Acad Sci USA 2004; 101:15748-
53. doi:10.1073/pnas.0403812101.
21. Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, et al. Unique and conserved features of
genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol
Biol 2003; 331:991-1004. doi:10.1016/s0022-2836(03)00865-9.
22. Gorbalenya AE, Snijder EJ, Spaan WJ. Severe acute respiratory syndrome coronavirus phylogeny: toward
c o n s e n s u s . J V i r o l 2 0 0 4 ; 7 8 : 7 8 6 3 - 6 . doi:10.1128/JVI.78.15.7863-7866.2004.
23. Tang XC, Zhang JX, Zhang SY, Wang P, Fan XH, Li LF, et al. Prevalence and genetic diversity of coronaviruses in
bat s from China. J Virol 2006; 80:7481-90. doi:10.1128/JVI.00697-06.
24. Vijaykrishna D, Smith GJ, Zhang JX, Peiris JS, Chen H, Guan Y. Evolutionary insights into the ecology of
c o r o n a v ir u s e s . J V ir o l 2 0 0 7 ; 8 1: 4 0 1 2 - 2 0 . doi:10.1128/JVI.02605-06.
25. Liu Z, Xiao X, Wei X, Li J, Yang J, Tan H, et al. Composi- tion and divergence of coronavirus spike proteins and
host ACE2 receptors predict potential intermediate hosts of SARS-CoV-2. J Med Virol 2020; 92:595-601.
doi:10.1002/jmv.25726.
Ji W, Wang W, Zhao X, Zai J, Li X. Cross-species transmission of the newly identified coronavirus 2019- nCoV. J Med Virol 2020; 92:433-40. doi:10.1002/jmv.25682.
27. Li X, Zai J, Zhao Q, Nie Q, Li Y, Foley BT, et al. Evolutio-nary history, potential intermediate animal host, and
cross-species analyses of SARS-CoV-2. J Med Virol 2020; 92:602-11. doi:10.1002/jmv.25731.
28. Geller C, Varbanov M, Duval RE. Human coronaviruses: insights into environmental resistance and its
influence on the development of new antiseptic strategies. Viruses 2012; 4:3044-68. doi:10.3390/v4113044.
29. Chan KH, Peiris JS, Lam SY, Poon LL, Yuen KY, Seto WH. The Effects of Temperature and Relative Humidity on
the Viability of the SARS Coronavirus. Adv Virol 2011; 2011:734690. doi:10.1155/2011/734690.
30. Duan SM, Zhao XS, Wen RF, Huang JJ, Pi GH, Zhang SX, et al. Stability of SARS coronavirus in human
specimens and environment and its sensitivity to heating and UV irradiation. Biomed Environ Sci 2003;
16:246-55.
31. Darnell ME, Subbarao K, Feinstone SM, Taylor DR. Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV. J Virol Methods 2004; 121:85-91. doi:10.1016/j.jviromet.2004.06.006.
32. Lauring AS, Andino R. Quasispecies theory and the behavior of RNA viruses. PLoS Pathog 2010;
6:e1001005. doi:10.1371/journal.ppat.1001005.
33. Phan T. Genetic diversity and evolution of SARS-CoV-2. I n f e c t G e n e t E v o l 2 0 2 0 ; 8 1 : 1 0 4 2 6 0 .
doi:10.1016/j.meegid.2020.104260.
34. Alagaili AN, Briese T, Mishra N, Kapoor V, Sameroff SC, Burbelo PD, et al. Middle East respiratory syndrome
coronavirus infection in dromedary camels in Saudi A r a b i a . m B i o 2 0 1 4 ; 5 : e 0 0 8 8 4 - 1 4 .
doi:10.1128/mBio.00884-14.
35. Wu A, Peng Y, Huang B, Ding X, Wang X, Niu P, et al. Genome Composition and Divergence of the Novel
Coronavirus (2019-nCoV) Originating in China. Cell Host Microbe 2020; 27:325-8. doi:10.1016/j.chom.2020.02.001.
36. Dimonte S, Babakir-Mina M, Hama-Soor T, Ali S. Genetic Variation and Evolution of the 2019 Novel Coronavirus. P ubl i c H e a lt h G e n o m i c s 2 0 2 1; 2 4 : 5 4 - 6 6 doi:10.1159/000513530.
9:323-5. doi:10.1016/s1471-4914(03)00135-7.
2. Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 2019; 17:181-92.
doi:10.1038/s41579-018-0118-9.
3. 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; 395:497-506. doi:10.1016/S0140-6736(20)30183-5.
4. Wang X, Zhou Q, He Y, Liu L, Ma X, Wei X, et al. Nos-ocomial outbreak of COVID-19 pneumonia in Wuhan,
C h i n a . E u r R e spi r J 2 0 2 0 ; 5 5 : 2 0 0 0 5 4 4 . doi:10.1183/13993003.00544-2020.
5. 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; 382:727-33. doi:10.1056/NEJMoa2001017.
6. Yang Y, Xiao Z, Ye K, He X, Sun B, Qin Z, et al. SARS-CoV-2: characteristics and current advances in research.
Virol J 2020 29; 17:117. doi:10.1186/s12985-020-01369-z.
7. Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia of the Chinese Preventive Medicine Association. An update on the epidemiological characteristics of novel coronavirus pneumonia (COVID-19). Zhonghua Liu Xing Bing Xue Za Zhi 2020; 41:139-44. doi:10.3760/cma.j.issn.0254-6450.2020.02.002.
8. Song Z, Xu Y, Bao L, Zhang L, Yu P, Qu Y, et al. From SARS to MERS, Thrusting Coronaviruses into the Spotlight.
Viruses 2019; 11:59. doi:10.3390/v11010059.
9. Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, et al. Isolation and characterization of viruses related
to the SARS coronavirus from animals in southern China. Science 2003; 302:276-8. doi:10.1126/science.1087139.
10. Drosten C, Kellam P, Memish ZA. Evidence for camel-to-human transmission of MERS coronavirus. N Engl J
Med 2014; 371:1359-60. doi:10.1056/NEJMc1409847.
11. Li F. Structure, Function, and Evolution of Coronavirus Spike Proteins. Annu Rev Virol 2016; 3:237-61.
doi:10.1146/annurev-virology-110615-042301.
12. Tang Q, Song Y, Shi M, Cheng Y, Zhang W, Xia XQ. Inferring the hosts of coronavirus using dual statistical
models based on nucleotide composition. Sci Rep 2015; 5:17155. doi:10.1038/srep17155.
13. Ceraolo C, Giorgi FM. Genomic variance of the 2019-nC-oV coronavirus. J Med Virol 2020; 92:522-8.
doi:10.1002/jmv.25700.
14. Jiang S, Shi ZL. The First Disease X is Caused by a Highly Transmi s s ible Acute Respiratory Syndrome
C o r o n a v i r u s . V i r o l S i n 2 0 2 0 ; 3 5 : 2 6 3 - 5 . doi:10.1007/s12250-020-00206-5
15. Lai CC, Shih TP, Ko WC, Tang HJ, Hsueh PR. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and
corona virus disease-2019 (COVID-19): the epidemic and the challenges. Int J Antimicrob Agents 2020; 55:924.
doi.org/10.1016/j.ijantimicag.2020.105924
16. Li C, Yang Y, Ren L. Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species.
Infect Genet Evol 2020; 82:104285. doi:10.1016/j.meegid.2020.104285.
17. 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 22; 395:565-74.
doi:10.1016/S0140-6736(20)30251-8.
1 8 . P a r a s k e v i s D, Kos t a k i EG, Ma g ior k i n i s G, Panayiotakopoulos G, Sourvinos G, Tsiodras 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. doi:10.1016/j.meegid.2020.104212.
19. Zhu Z, Zhang Z, Chen W, Cai Z, Ge X, Zhu H, et al. Predicting the receptor-binding domain usage of the
coronavirus based on kmer frequency on spike protein. Infect Genet Evol 2018; 61:183-4.
doi:10.1016/j.meegid.2018.03.028.
20. Jeffers SA, Tusell SM, Gillim-Ross L, Hemmila EM, Achenbach JE, Babcock GJ, et al. CD209L (L-SIGN) is a
receptor for severe acute respiratory syndrome coronavirus. Proc Natl Acad Sci USA 2004; 101:15748-
53. doi:10.1073/pnas.0403812101.
21. Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, et al. Unique and conserved features of
genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol
Biol 2003; 331:991-1004. doi:10.1016/s0022-2836(03)00865-9.
22. Gorbalenya AE, Snijder EJ, Spaan WJ. Severe acute respiratory syndrome coronavirus phylogeny: toward
c o n s e n s u s . J V i r o l 2 0 0 4 ; 7 8 : 7 8 6 3 - 6 . doi:10.1128/JVI.78.15.7863-7866.2004.
23. Tang XC, Zhang JX, Zhang SY, Wang P, Fan XH, Li LF, et al. Prevalence and genetic diversity of coronaviruses in
bat s from China. J Virol 2006; 80:7481-90. doi:10.1128/JVI.00697-06.
24. Vijaykrishna D, Smith GJ, Zhang JX, Peiris JS, Chen H, Guan Y. Evolutionary insights into the ecology of
c o r o n a v ir u s e s . J V ir o l 2 0 0 7 ; 8 1: 4 0 1 2 - 2 0 . doi:10.1128/JVI.02605-06.
25. Liu Z, Xiao X, Wei X, Li J, Yang J, Tan H, et al. Composi- tion and divergence of coronavirus spike proteins and
host ACE2 receptors predict potential intermediate hosts of SARS-CoV-2. J Med Virol 2020; 92:595-601.
doi:10.1002/jmv.25726.
Ji W, Wang W, Zhao X, Zai J, Li X. Cross-species transmission of the newly identified coronavirus 2019- nCoV. J Med Virol 2020; 92:433-40. doi:10.1002/jmv.25682.
27. Li X, Zai J, Zhao Q, Nie Q, Li Y, Foley BT, et al. Evolutio-nary history, potential intermediate animal host, and
cross-species analyses of SARS-CoV-2. J Med Virol 2020; 92:602-11. doi:10.1002/jmv.25731.
28. Geller C, Varbanov M, Duval RE. Human coronaviruses: insights into environmental resistance and its
influence on the development of new antiseptic strategies. Viruses 2012; 4:3044-68. doi:10.3390/v4113044.
29. Chan KH, Peiris JS, Lam SY, Poon LL, Yuen KY, Seto WH. The Effects of Temperature and Relative Humidity on
the Viability of the SARS Coronavirus. Adv Virol 2011; 2011:734690. doi:10.1155/2011/734690.
30. Duan SM, Zhao XS, Wen RF, Huang JJ, Pi GH, Zhang SX, et al. Stability of SARS coronavirus in human
specimens and environment and its sensitivity to heating and UV irradiation. Biomed Environ Sci 2003;
16:246-55.
31. Darnell ME, Subbarao K, Feinstone SM, Taylor DR. Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV. J Virol Methods 2004; 121:85-91. doi:10.1016/j.jviromet.2004.06.006.
32. Lauring AS, Andino R. Quasispecies theory and the behavior of RNA viruses. PLoS Pathog 2010;
6:e1001005. doi:10.1371/journal.ppat.1001005.
33. Phan T. Genetic diversity and evolution of SARS-CoV-2. I n f e c t G e n e t E v o l 2 0 2 0 ; 8 1 : 1 0 4 2 6 0 .
doi:10.1016/j.meegid.2020.104260.
34. Alagaili AN, Briese T, Mishra N, Kapoor V, Sameroff SC, Burbelo PD, et al. Middle East respiratory syndrome
coronavirus infection in dromedary camels in Saudi A r a b i a . m B i o 2 0 1 4 ; 5 : e 0 0 8 8 4 - 1 4 .
doi:10.1128/mBio.00884-14.
35. Wu A, Peng Y, Huang B, Ding X, Wang X, Niu P, et al. Genome Composition and Divergence of the Novel
Coronavirus (2019-nCoV) Originating in China. Cell Host Microbe 2020; 27:325-8. doi:10.1016/j.chom.2020.02.001.
36. Dimonte S, Babakir-Mina M, Hama-Soor T, Ali S. Genetic Variation and Evolution of the 2019 Novel Coronavirus. P ubl i c H e a lt h G e n o m i c s 2 0 2 1; 2 4 : 5 4 - 6 6 doi:10.1159/000513530.
Downloads
Published
2021-04-06
Versions
- 2022-01-15 (2)
- 2021-04-06 (1)
How to Cite
Javaid, S., & Awais, H. (2021). Genetic Diversity and Comprehensive Phylodynamic Analysis of Whole Corona Viruses Genomes. Journal of the Dow University of Health Sciences (JDUHS), 15(1), 41–45. Retrieved from https://jduhs.com/index.php/jduhs/article/view/1112
Issue
Section
Commentary
License
Copyright (c) 2021 shehla Javaid
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Articles published in the Journal of Dow University of Health Sciences are distributed under the terms of the Creative Commons Attribution Non-Commercial License https://creativecommons.org/ licenses/by-nc/4.0/. This license permits use, distribution and reproduction in any medium; provided the original work is properly cited and initial publication in this journal. 
