Skip to main content
SpringerLink
Log in

Evolution and Epidemiology of SARS-CoV-2 Virus

  • Protocol
  • First Online:
SARS-CoV-2

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2452))

Abstract

A novel coronavirus (CoV) that emerged in Wuhan, Hubei province in China, in December 2019, has rapidly spread worldwide. Named as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), this virus has been responsible for infecting about 153 million people and causing 3 million deaths by May 2021. There is obvious interest in gaining novel insights into the epidemiologic evolution of this virus; however, inappropriate application and interpretation of genomic and phylogenetic analyses has led to dangerous outcomes and misunderstandings. This chapter focuses on not only introducing this virus, its genomic characteristics and molecular mechanisms but also describing the application and interpretation of phylogenetic tree analyses, in order to provide useful information to better understand the evolution and epidemiology of this virus. In addition, recombinant region and genetic ancestry of SARS-CoV-2 remain unknown. It is urgently required to collect samples and obtain related viral genetic data from animal sources for identifying the intermediate host of SARS-CoV-2 that is responsible for its cross-species transmission.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W, China Novel Coronavirus Investigating and Research Team (2020) A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 382(8):727–733. https://doi.org/10.1056/NEJMoa2001017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Coronaviridae Study Group of the International Committee on Taxonomy of Viruses (2020) The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 5(4):536–544. https://doi.org/10.1038/s41564-020-0695-z

    Article  CAS  Google Scholar 

  3. Dong E, Du H, Gardner L (2020) An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis 20(5):533–534. https://doi.org/10.1016/S1473-3099(20)30120-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Shu Y, McCauley J (2017) GISAID: global initiative on sharing all influenza data - from vision to reality. Euro Surveill 22(13):30494. https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494

    Article  PubMed  PubMed Central  Google Scholar 

  5. Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG, Smith DB (2018) Virus taxonomy: the database of the international committee on taxonomy of viruses (ICTV). Nucleic Acids Res 46(D1):D708–D717. https://doi.org/10.1093/nar/gkx932

    Article  CAS  PubMed  Google Scholar 

  6. Drosten C, Gunther S, Preiser W, van der Werf S, Brodt HR, Becker S, Rabenau H, Panning M, Kolesnikova L, Fouchier RA, Berger A, Burguiere AM, Cinatl J, Eickmann M, Escriou N, Grywna K, Kramme S, Manuguerra JC, Muller S, Rickerts V, Sturmer M, Vieth S, Klenk HD, Osterhaus AD, Schmitz H, Doerr HW (2003) Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348(20):1967–1976. https://doi.org/10.1056/NEJMoa030747

    Article  CAS  PubMed  Google Scholar 

  7. van der Hoek L, Pyrc K, Jebbink MF, Vermeulen-Oost W, Berkhout RJ, Wolthers KC, Wertheim-van Dillen PM, Kaandorp J, Spaargaren J, Berkhout B (2004) Identification of a new human coronavirus. Nat Med 10(4):368–373. https://doi.org/10.1038/nm1024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Woo PC, Lau SK, Chu CM, Chan KH, Tsoi HW, Huang Y, Wong BH, Poon RW, Cai JJ, Luk WK, Poon LL, Wong SS, Guan Y, Peiris JS, Yuen KY (2005) Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol 79(2):884–895. https://doi.org/10.1128/JVI.79.2.884-895.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. de Groot RJ, Baker SC, Baric RS, Brown CS, Drosten C, Enjuanes L, Fouchier RA, Galiano M, Gorbalenya AE, Memish ZA, Perlman S, Poon LL, Snijder EJ, Stephens GM, Woo PC, Zaki AM, Zambon M, Ziebuhr J (2013) Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the coronavirus study group. J Virol 87(14):7790–7792. https://doi.org/10.1128/JVI.01244-13

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Seattle Flu Study I, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Muller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin JS, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR (2020) Cryptic transmission of SARS-CoV-2 in Washington state. Science 370(6516):571–575. https://doi.org/10.1126/science.abc0523

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ (2020) A new coronavirus associated with human respiratory disease in China. Nature 579(7798):265–269. https://doi.org/10.1038/s41586-020-2008-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Boursnell ME, Brown TD, Foulds IJ, Green PF, Tomley FM, Binns MM (1987) Completion of the sequence of the genome of the coronavirus avian infectious bronchitis virus. J Gen Virol 68(Pt 1):57–77. https://doi.org/10.1099/0022-1317-68-1-57

    Article  CAS  PubMed  Google Scholar 

  13. Brierley I, Boursnell ME, Binns MM, Bilimoria B, Blok VC, Brown TD, Inglis SC (1987) An efficient ribosomal frame-shifting signal in the polymerase-encoding region of the coronavirus IBV. EMBO J 6(12):3779–3785

    Article  CAS  Google Scholar 

  14. Brierley I, Digard P, Inglis SC (1989) Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot. Cell 57(4):537–547. https://doi.org/10.1016/0092-8674(89)90124-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Chan JF, Kok KH, Zhu Z, Chu H, To KK, Yuan S, Yuen KY (2020) Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect 9(1):221–236. https://doi.org/10.1080/22221751.2020.1719902

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Harcourt BH, Jukneliene D, Kanjanahaluethai A, Bechill J, Severson KM, Smith CM, Rota PA, Baker SC (2004) Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity. J Virol 78(24):13600–13612. https://doi.org/10.1128/JVI.78.24.13600-13612.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. V'Kovski P, Kratzel A, Steiner S, Stalder H, Thiel V (2021) Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 19(3):155–170. https://doi.org/10.1038/s41579-020-00468-6

    Article  CAS  PubMed  Google Scholar 

  18. Littler DR, Gully BS, Colson RN, Rossjohn J (2020) Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9. iScience 23(7):101258. https://doi.org/10.1016/j.isci.2020.101258

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Yin W, Mao C, Luan X, Shen DD, Shen Q, Su H, Wang X, Zhou F, Zhao W, Gao M, Chang S, Xie YC, Tian G, Jiang HW, Tao SC, Shen J, Jiang Y, Jiang H, Xu Y, Zhang S, Zhang Y, Xu HE (2020) Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science 368(6498):1499–1504. https://doi.org/10.1126/science.abc1560

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Hillen HS, Kokic G, Farnung L, Dienemann C, Tegunov D, Cramer P (2020) Structure of replicating SARS-CoV-2 polymerase. Nature 584(7819):154–156. https://doi.org/10.1038/s41586-020-2368-8

    Article  CAS  PubMed  Google Scholar 

  21. Tvarogova J, Madhugiri R, Bylapudi G, Ferguson LJ, Karl N, Ziebuhr J (2019) Identification and characterization of a human coronavirus 229E nonstructural protein 8-associated RNA 3′-terminal adenylyltransferase activity. J Virol 93(12):e00291-19. https://doi.org/10.1128/JVI.00291-19

    Article  PubMed  PubMed Central  Google Scholar 

  22. Chen J, Malone B, Llewellyn E, Grasso M, Shelton PMM, Olinares PDB, Maruthi K, Eng ET, Vatandaslar H, Chait BT, Kapoor TM, Darst SA, Campbell EA (2020) Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex. Cell 182(6):1560–1573.e13. https://doi.org/10.1016/j.cell.2020.07.033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Robson F, Khan KS, Le TK, Paris C, Demirbag S, Barfuss P, Rocchi P, Ng WL (2020) Coronavirus RNA proofreading: molecular basis and therapeutic targeting. Mol Cell 79(5):710–727. https://doi.org/10.1016/j.molcel.2020.07.027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Krafcikova P, Silhan J, Nencka R, Boura E (2020) Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. Nat Commun 11(1):3717. https://doi.org/10.1038/s41467-020-17495-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Ma Y, Wu L, Shaw N, Gao Y, Wang J, Sun Y, Lou Z, Yan L, Zhang R, Rao Z (2015) Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex. Proc Natl Acad Sci U S A 112(30):9436–9441. https://doi.org/10.1073/pnas.1508686112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Sola I, Almazan F, Zuniga S, Enjuanes L (2015) Continuous and discontinuous RNA synthesis in coronaviruses. Annu Rev Virol 2(1):265–288. https://doi.org/10.1146/annurev-virology-100114-055218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Lei X, Dong X, Ma R, Wang W, Xiao X, Tian Z, Wang C, Wang Y, Li L, Ren L, Guo F, Zhao Z, Zhou Z, Xiang Z, Wang J (2020) Activation and evasion of type I interferon responses by SARS-CoV-2. Nat Commun 11(1):3810. https://doi.org/10.1038/s41467-020-17665-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Miorin L, Kehrer T, Sanchez-Aparicio MT, Zhang K, Cohen P, Patel RS, Cupic A, Makio T, Mei M, Moreno E, Danziger O, White KM, Rathnasinghe R, Uccellini M, Gao S, Aydillo T, Mena I, Yin X, Martin-Sancho L, Krogan NJ, Chanda SK, Schotsaert M, Wozniak RW, Ren Y, Rosenberg BR, Fontoura BMA, Garcia-Sastre A (2020) SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. Proc Natl Acad Sci U S A 117(45):28344–28354. https://doi.org/10.1073/pnas.2016650117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Jiang HW, Zhang HN, Meng QF, Xie J, Li Y, Chen H, Zheng YX, Wang XN, Qi H, Zhang J, Wang PH, Han ZG, Tao SC (2020) SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. Cell Mol Immunol 17(9):998–1000. https://doi.org/10.1038/s41423-020-0514-8

    Article  CAS  PubMed  Google Scholar 

  30. Young BE, Fong SW, Chan YH, Mak TM, Ang LW, Anderson DE, Lee CY, Amrun SN, Lee B, Goh YS, Su YCF, Wei WE, Kalimuddin S, Chai LYA, Pada S, Tan SY, Sun L, Parthasarathy P, Chen YYC, Barkham T, Lin RTP, Maurer-Stroh S, Leo YS, Wang LF, Renia L, Lee VJ, Smith GJD, Lye DC, Ng LFP (2020) Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study. Lancet 396(10251):603–611. https://doi.org/10.1016/S0140-6736(20)31757-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Kim D, Lee JY, Yang JS, Kim JW, Kim VN, Chang H (2020) The architecture of SARS-CoV-2 transcriptome. Cell 181(4):914–921.e10. https://doi.org/10.1016/j.cell.2020.04.011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Finkel Y, Mizrahi O, Nachshon A, Weingarten-Gabbay S, Morgenstern D, Yahalom-Ronen Y, Tamir H, Achdout H, Stein D, Israeli O, Beth-Din A, Melamed S, Weiss S, Israely T, Paran N, Schwartz M, Stern-Ginossar N (2020) The coding capacity of SARS-CoV-2. Nature 589(7840):125–130. https://doi.org/10.1038/s41586-020-2739-1

    Article  CAS  PubMed  Google Scholar 

  33. Mandala VS, McKay MJ, Shcherbakov AA, Dregni AJ, Kolocouris A, Hong M (2020) Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers. Nat Struct Mol Biol 27(12):1202–1208. https://doi.org/10.1038/s41594-020-00536-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Siu KL, Chan CP, Kok KH, Chiu-Yat Woo P, Jin DY (2014) Suppression of innate antiviral response by severe acute respiratory syndrome coronavirus M protein is mediated through the first transmembrane domain. Cell Mol Immunol 11(2):141–149. https://doi.org/10.1038/cmi.2013.61

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Mu J, Fang Y, Yang Q, Shu T, Wang A, Huang M, Jin L, Deng F, Qiu Y, Zhou X (2020) SARS-CoV-2 N protein antagonizes type I interferon signaling by suppressing phosphorylation and nuclear translocation of STAT1 and STAT2. Cell Discov 6:65. https://doi.org/10.1038/s41421-020-00208-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Wang Q, Zhang Y, Wu L, Niu S, Song C, Zhang Z, Lu G, Qiao C, Hu Y, Yuen KY, Wang Q, Zhou H, Yan J, Qi J (2020) Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell 181(4):894–904.e9. https://doi.org/10.1016/j.cell.2020.03.045

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Lan J, Ge J, Yu J, Shan S, Zhou H, Fan S, Zhang Q, Shi X, Wang Q, Zhang L, Wang X (2020) Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581(7807):215–220. https://doi.org/10.1038/s41586-020-2180-5

    Article  CAS  PubMed  Google Scholar 

  38. Benton DJ, Wrobel AG, Xu P, Roustan C, Martin SR, Rosenthal PB, Skehel JJ, Gamblin SJ (2020) Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion. Nature 588(7837):327–330. https://doi.org/10.1038/s41586-020-2772-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Shang J, Wan Y, Luo C, Ye G, Geng Q, Auerbach A, Li F (2020) Cell entry mechanisms of SARS-CoV-2. Proc Natl Acad Sci U S A 117(21):11727–11734. https://doi.org/10.1073/pnas.2003138117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Alouane T, Laamarti M, Essabbar A, Hakmi M, Bouricha EM, Chemao-Elfihri MW, Kartti S, Boumajdi N, Bendani H, Laamarti R, Ghrifi F, Allam L, Aanniz T, Ouadghiri M, El Hafidi N, El Jaoudi R, Benrahma H, Attar JE, Mentag R, Sbabou L, Nejjari C, Amzazi S, Belyamani L, Ibrahimi A (2020) Genomic diversity and hotspot mutations in 30,983 SARS-CoV-2 genomes: moving toward a universal vaccine for the “confined virus”? Pathogens 9(10):829. https://doi.org/10.3390/pathogens9100829

    Article  CAS  PubMed Central  Google Scholar 

  41. Grubaugh ND, Petrone ME, Holmes EC (2020) We shouldn’t worry when a virus mutates during disease outbreaks. Nat Microbiol 5(4):529–530. https://doi.org/10.1038/s41564-020-0690-4

    Article  CAS  PubMed  Google Scholar 

  42. Yurkovetskiy L, Wang X, Pascal KE, Tomkins-Tinch C, Nyalile TP, Wang Y, Baum A, Diehl WE, Dauphin A, Carbone C, Veinotte K, Egri SB, Schaffner SF, Lemieux JE, Munro JB, Rafique A, Barve A, Sabeti PC, Kyratsous CA, Dudkina NV, Shen K, Luban J (2020) Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant. Cell 183(3):739–751.e8. https://doi.org/10.1016/j.cell.2020.09.032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, Sheffield C-GG, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC (2020) Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell 182(4):812–827.e19. https://doi.org/10.1016/j.cell.2020.06.043

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Hou YJ, Chiba S, Halfmann P, Ehre C, Kuroda M, Dinnon KH 3rd, Leist SR, Schafer A, Nakajima N, Takahashi K, Lee RE, Mascenik TM, Graham R, Edwards CE, Tse LV, Okuda K, Markmann AJ, Bartelt L, de Silva A, Margolis DM, Boucher RC, Randell SH, Suzuki T, Gralinski LE, Kawaoka Y, Baric RS (2020) SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Science 370(6523):1464–1468. https://doi.org/10.1126/science.abe8499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, Zhang X, Muruato AE, Zou J, Fontes-Garfias CR, Mirchandani D, Scharton D, Bilello JP, Ku Z, An Z, Kalveram B, Freiberg AN, Menachery VD, Xie X, Plante KS, Weaver SC, Shi PY (2020) Spike mutation D614G alters SARS-CoV-2 fitness. Nature 592(7852):116–121. https://doi.org/10.1038/s41586-020-2895-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Su YCF, Anderson DE, Young BE, Linster M, Zhu F, Jayakumar J, Zhuang Y, Kalimuddin S, Low JGH, Tan CW, Chia WN, Mak TM, Octavia S, Chavatte JM, Lee RTC, Pada S, Tan SY, Sun L, Yan GZ, Maurer-Stroh S, Mendenhall IH, Leo YS, Lye DC, Wang LF, Smith GJD (2020) Discovery and genomic characterization of a 382-nucleotide deletion in ORF7b and ORF8 during the early evolution of SARS-CoV-2. mBio 11(4):e01610-20. https://doi.org/10.1128/mBio.01610-20

    Article  PubMed  PubMed Central  Google Scholar 

  47. Gong YN, Tsao KC, Hsiao MJ, Huang CG, Huang PN, Huang PW, Lee KM, Liu YC, Yang SL, Kuo RL, Chen KF, Liu YC, Huang SY, Huang HI, Liu MT, Yang JR, Chiu CH, Yang CT, Chen GW, Shih SR (2020) SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Emerg Microbes Infect 9(1):1457–1466. https://doi.org/10.1080/22221751.2020.1782271

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Liu Z, Zheng H, Lin H, Li M, Yuan R, Peng J, Xiong Q, Sun J, Li B, Wu J, Yi L, Peng X, Zhang H, Zhang W, Hulswit RJG, Loman N, Rambaut A, Ke C, Bowden TA, Pybus OG, Lu J (2020) Identification of common deletions in the spike protein of severe acute respiratory syndrome coronavirus 2. J Virol 94(17):e00790-20. https://doi.org/10.1128/JVI.00790-20

    Article  PubMed  PubMed Central  Google Scholar 

  49. Lau SY, Wang P, Mok BW, Zhang AJ, Chu H, Lee AC, Deng S, Chen P, Chan KH, Song W, Chen Z, To KK, Chan JF, Yuen KY, Chen H (2020) Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction. Emerg Microbes Infect 9(1):837–842. https://doi.org/10.1080/22221751.2020.1756700

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Holland LA, Kaelin EA, Maqsood R, Estifanos B, Wu LI, Varsani A, Halden RU, Hogue BG, Scotch M, Lim ES (2020) An 81-nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (January to March 2020). J Virol 94(14):e00711-20. https://doi.org/10.1128/JVI.00711-20

    Article  PubMed  PubMed Central  Google Scholar 

  51. Queromes G, Destras G, Bal A, Regue H, Burfin G, Brun S, Fanget R, Morfin F, Valette M, Trouillet-Assant S, Lina B, Frobert E, Josset L (2021) Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France. Emerg Microbes Infect 10(1):167–177. https://doi.org/10.1080/22221751.2021.1872351

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Benedetti F, Snyder GA, Giovanetti M, Angeletti S, Gallo RC, Ciccozzi M, Zella D (2020) Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1. J Transl Med 18(1):329. https://doi.org/10.1186/s12967-020-02507-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Islam MR, Hoque MN, Rahman MS, Alam A, Akther M, Puspo JA, Akter S, Sultana M, Crandall KA, Hossain MA (2020) Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity. Sci Rep 10(1):14004. https://doi.org/10.1038/s41598-020-70812-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. McNamara RP, Caro-Vegas C, Landis JT, Moorad R, Pluta LJ, Eason AB, Thompson C, Bailey A, Villamor FCS, Lange PT, Wong JP, Seltzer T, Seltzer J, Zhou Y, Vahrson W, Juarez A, Meyo JO, Calabre T, Broussard G, Rivera-Soto R, Chappell DL, Baric RS, Damania B, Miller MB, Dittmer DP (2020) High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States. Cell Rep 33(5):108352. https://doi.org/10.1016/j.celrep.2020.108352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579(7798):270–273. https://doi.org/10.1038/s41586-020-2012-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Lam TT, Jia N, Zhang YW, Shum MH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WY, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC (2020) Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 583(7815):282–285. https://doi.org/10.1038/s41586-020-2169-0

    Article  CAS  PubMed  Google Scholar 

  57. Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF (2020) The proximal origin of SARS-CoV-2. Nat Med 26(4):450–452. https://doi.org/10.1038/s41591-020-0820-9

    Article  CAS  PubMed  Google Scholar 

  58. Xiao K, Zhai J, Feng Y, Zhou N, Zhang X, Zou JJ, Li N, Guo Y, Li X, Shen X, Zhang Z, Shu F, Huang W, Li Y, Zhang Z, Chen RA, Wu YJ, Peng SM, Huang M, Xie WJ, Cai QH, Hou FH, Chen W, Xiao L, Shen Y (2020) Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature 583(7815):286–289. https://doi.org/10.1038/s41586-020-2313-x

    Article  CAS  PubMed  Google Scholar 

  59. Li X, Giorgi EE, Marichannegowda MH, Foley B, Xiao C, Kong XP, Chen Y, Gnanakaran S, Korber B, Gao F (2020) Emergence of SARS-CoV-2 through recombination and strong purifying selection. Sci Adv 6(27):eabb9153. https://doi.org/10.1126/sciadv.abb9153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Wan Y, Shang J, Graham R, Baric RS, Li F (2020) Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. J Virol 94(7):e00127-20. https://doi.org/10.1128/JVI.00127-20

    Article  PubMed  PubMed Central  Google Scholar 

  61. Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS (2020) Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367(6483):1260–1263. https://doi.org/10.1126/science.abb2507

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D (2020) Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 181:281–292.e6. https://doi.org/10.1016/j.cell.2020.02.058

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Jaimes JA, Millet JK, Whittaker GR (2020) Proteolytic cleavage of the SARS-CoV-2 spike protein and the role of the novel S1/S2 site. iScience 23(6):101212. https://doi.org/10.1016/j.isci.2020.101212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Zhang YZ, Holmes EC (2020) A genomic perspective on the origin and emergence of SARS-CoV-2. Cell 181(2):223–227. https://doi.org/10.1016/j.cell.2020.03.035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, Wang P, Liu D, Yang J, Holmes EC, Hughes AC, Bi Y, Shi W (2020) A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein. Curr Biol 30(11):2196–2203.e3. https://doi.org/10.1016/j.cub.2020.05.023

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Lam TT (2020) Tracking the genomic footprints of SARS-CoV-2 transmission. Trends Genet 36(8):544–546. https://doi.org/10.1016/j.tig.2020.05.009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria NR, Wang C, Yu G, Bushnell B, Pan CY, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, Miller S, Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Chu HY, Shendure J, Jerome KR, Anderson C, Gangavarapu K, Zeller M, Spencer E, Andersen KG, MacCannell D, Paden CR, Li Y, Zhang J, Tong S, Armstrong G, Morrow S, Willis M, Matyas BT, Mase S, Kasirye O, Park M, Masinde G, Chan C, Yu AT, Chai SJ, Villarino E, Bonin B, Wadford DA, Chiu CY (2020) Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science 369(6503):582–587. https://doi.org/10.1126/science.abb9263

    Article  CAS  PubMed  Google Scholar 

  68. Fauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J, Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott IM, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoudhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND (2020) Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States. Cell 181(5):990–996.e5. https://doi.org/10.1016/j.cell.2020.04.021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Oude Munnink BB, Nieuwenhuijse DF, Stein M, O'Toole A, Haverkate M, Mollers M, Kamga SK, Schapendonk C, Pronk M, Lexmond P, van der Linden A, Bestebroer T, Chestakova I, Overmars RJ, van Nieuwkoop S, Molenkamp R, van der Eijk AA, GeurtsvanKessel C, Vennema H, Meijer A, Rambaut A, van Dissel J, Sikkema RS, Timen A, Koopmans M, Dutch-Covid-19 response team (2020) Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat Med 26(9):1405–1410. https://doi.org/10.1038/s41591-020-0997-y

    Article  CAS  PubMed  Google Scholar 

  70. Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P (2020) The emergence of SARS-CoV-2 in Europe and North America. Science 370(6516):564–570. https://doi.org/10.1126/science.abc8169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Rambaut A, Holmes EC, O'Toole A, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG (2020) A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 5(11):1403–1407. https://doi.org/10.1038/s41564-020-0770-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Rambaut A, Holmes EC, O'Toole A, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG (2021) Addendum: a dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 6(3):415. https://doi.org/10.1038/s41564-021-00872-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA (2018) Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 34(23):4121–4123. https://doi.org/10.1093/bioinformatics/bty407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Eden JS, Rockett R, Carter I, Rahman H, de Ligt J, Hadfield J, Storey M, Ren X, Tulloch R, Basile K, Wells J, Byun R, Gilroy N, O'Sullivan MV, Sintchenko V, Chen SC, Maddocks S, Sorrell TC, Holmes EC, Dwyer DE, Kok J, 2019-nCoV Study Group (2020) An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evol 6(1):veaa027. https://doi.org/10.1093/ve/veaa027

    Article  PubMed  PubMed Central  Google Scholar 

  75. Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O'Toole A, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA (2020) Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nat Commun 11(1):5110. https://doi.org/10.1038/s41467-020-18877-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was financially supported by the Research Center for Emerging Viral Infections from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE) in Taiwan and the Ministry of Science and Technology (MOST), Taiwan (MOST 110-2222-E-182-004, 110-2634-F-182-001, 109-2320-B-182-045-MY2, and MOST 109-2327-B-182-002).

Author information

Authors and Affiliations

  1. Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan

    Yu-Nong Gong, Kuo-Ming Lee & Shin-Ru Shih

  2. Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan

    Yu-Nong Gong & Shin-Ru Shih

  3. Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan

    Kuo-Ming Lee

  4. Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan

    Shin-Ru Shih

  5. Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan

    Shin-Ru Shih

Authors
  1. Yu-Nong Gong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kuo-Ming Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shin-Ru Shih
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shin-Ru Shih .

Editor information

Editors and Affiliations

  1. Department of Microbiology and Immunology; Infectious Disease TRD; BSL3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore

    Justin Jang Hann Chu

  2. The University of British Columbia, Vancouver, BC, Canada

    Bintou Ahmadou Ahidjo

  3. BSL3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore

    Chee Keng Mok

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Gong, YN., Lee, KM., Shih, SR. (2022). Evolution and Epidemiology of SARS-CoV-2 Virus. In: Chu, J.J.H., Ahidjo, B.A., Mok, C.K. (eds) SARS-CoV-2. Methods in Molecular Biology, vol 2452. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2111-0_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2111-0_1

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2110-3

  • Online ISBN: 978-1-0716-2111-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation