2,501
Views
7
CrossRef citations to date
0
Altmetric
Review

Phylodynamic analysis in the understanding of the current COVID-19 pandemic and its utility in vaccine and antiviral design and assessment

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Pages 2437-2444 | Received 10 May 2020, Accepted 20 Jan 2021, Published online: 19 Feb 2021

References

  • Rife BD, Mavian C, Chen X, Ciccozzi M, Salemi M, Min J, Prosperi MC. Phylodynamic applications in 21(st) century global infectious disease research. Glob Health Res Policy. 2017;2:13. doi:10.1186/s41256-017-0034-y.
  • Holmes EC. Evolutionary history and phylogeography of human viruses. Annu Rev Microbiol. 2008;62:307–28. doi:10.1146/annurev.micro.62.081307.162912.
  • Ojosnegros S, Beerenwinkel N. Models of RNA virus evolution and their roles in vaccine design. Immunome Res. 2010;6(Suppl 2):S5. doi:10.1186/1745-7580-6-S2-S5.
  • Templeton AR. Genetic drift in large populations and coalescence. Populat Gen Microevolution Theory. 2006;118–67.
  • Biswas NK, Majumder PP. Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. Indian J Med Res. 2020;151:450–58. doi:10.4103/ijmr.IJMR_1125_20.
  • Nie Q, Li X, Chen W, Liu D, Chen Y, Li H, Li D, Tian M, Tan W, Zai J, et al. Phylogenetic and phylodynamic analyses of SARS-CoV-2. Virus Res. 2020;287:198098. doi:10.1016/j.virusres.2020.198098.
  • Sironi M, Hasnain SE, Rosenthal B, Phan T, Luciani F, Shaw MA, Sallum MA, Mirhashemi ME, Morand S, González-Candelas F, et al. SARS-CoV-2 and COVID-19: a genetic, epidemiological, and evolutionary perspective. Infect Genet Evol. 2020;84:104384. doi:10.1016/j.meegid.2020.104384.
  • Volz EM, Koelle K, Bedford T. Viral phylodynamics. PLoS Comput Biol. 2013;9:e1002947. doi:10.1371/journal.pcbi.1002947.
  • Benvenuto D, Giovanetti M, Salemi M, Prosperi M, De Flora C, Junior Alcantara LC, Angeletti S, Ciccozzi M. The global spread of 2019-nCoV: a molecular evolutionary analysis. Pathog Glob Health. 2020;114:64–67. doi:10.1080/20477724.2020.1725339.
  • Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, Holmes EC. Unifying the epidemiological and evolutionary dynamics of pathogens. Sci. 2004;303:327–32. doi:10.1126/science.1090727.
  • Lei N, Wang HB, Zhang YS, Zhao JH, Zhong Y, Wang YJ, Huang L-Y, Ma J-X, Sun Q, Yang L, et al. Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. Sci Rep. 2019;9:2432. doi:10.1038/s41598-018-38105-1.
  • Bush RM, Bender CA, Subbarao K, Cox NJ, Fitch WM. Predicting the evolution of human influenza A. Science. 1999;286:1921–25. doi:10.1126/science.286.5446.1921.
  • GISAID. Genomic epidemiology of novel coronavirus; 2020. [accessed 2020 Nov 05]. https://nextstrain.org/ncov
  • Shu Y, McCauley J. GISAID: global initiative on sharing all influenza data - from vision to reality. Euro Surveill. 2017;22(13):30494.
  • Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall. 2017;1:33–46. doi:10.1002/gch2.1018.
  • Rodriguez-Morales AJ, Balbin-Ramon GJ, Rabaan AA, Sah R, Dhama K, Paniz-Mondolfi A, Pagliano P, Esposito S. Genomic epidemiology and its importance in the study of the COVID-19 pandemic. Infez Med. 2020;28:139–42.
  • Evans AS. Viral infections of humans: epidemiology and control. Springer Sci Business Media. 2013.
  • Azuma K, Yanagi U, Kagi N, Kim H, Ogata M, Hayashi M. Environmental factors involved in SARS-CoV-2 transmission: effect and role of indoor environmental quality in the strategy for COVID-19 infection control. Environ Health Prev Med. 2020;25:66. doi:10.1186/s12199-020-00904-2.
  • Kuhnert D, Stadler T, Vaughan TG, Drummond AJ. Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model. J R Soc Interface. 2014;11:20131106. doi:10.1098/rsif.2013.1106.
  • Volz EM, Siveroni I. Bayesian phylodynamic inference with complex models. PLoS Comput Biol. 2018;14:e1006546. doi:10.1371/journal.pcbi.1006546.
  • Volz EM, Romero-Severson E, Leitner T. Phylodynamic Inference across Epidemic Scales. Mol Biol Evol. 2017;34:1276–88. doi:10.1093/molbev/msx077.
  • Volz E, Frost S. Scalable relaxed clock phylogenetic dating. Virus Evolution. 2017;3. doi:10.1093/ve/vex014.
  • Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2019;15(4):e1006650. doi:10.1371/journal.pcbi.1006650.
  • Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG. Measurably evolving populations. Trends Ecol Evol. 2003;18:481–88. doi:10.1016/S0169-5347(03)00216-7.
  • Magiorkinis G, Sypsa V, Magiorkinis E, Paraskevis D, Katsoulidou A, Belshaw R, Fraser C, Pybus OG, Hatzakis A, et al. Integrating phylodynamics and epidemiology to estimate transmission diversity in viral epidemics. PLoS Comput Biol. 2013;9:e1002876–e. doi:10.1371/journal.pcbi.1002876.
  • Rasmussen DA, Boni MF, Koelle K. Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam. Mol Biol Evol. 2014;31:258–71. doi:10.1093/molbev/mst203.
  • Volz E, Baguelin M, Bhatia S, Boonyasiri A, Cori A, Cucunubá Z, Cuomo-Dannenburg G, Donnelly CA, Dorigatti I, FitzJohn R. Report 5: Phylogenetic analysis of SARS-CoV-2.
  • Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y, Ren R, Leung KSM, Lau EHY, Wong JY, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. N Engl J Med. 2020;382:1199–207. doi:10.1056/NEJMoa2001316.
  • Park M, Cook AR, Lim JT, Sun Y, Dickens BL. A systematic review of COVID-19 epidemiology based on current evidence. J Clin Med. 2020;9(4):967.
  • Wu JT, Leung K, Leung GM. Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study. Lancet. 2020;395:689–97. doi:10.1016/S0140-6736(20)30260-9.
  • Rojas-Gallardo DM, Garzon-Castano SC, Millan N, Jimenez-Posada EV, Martinez-Gutierrez M, Ruiz-Saenz J, Cardona-Ospina JA. COVID-19 in Latin America: contrasting phylodynamic inference with epidemiological surveillance. (Molecular epidemiology of COVID-19 in Latin America). medRxiv 2020; 2020.05.23.20111443.
  • Seemann T, Lane CR, Sherry NL, Duchene S, Gonçalves da Silva A, Caly L, Sait M, Ballard SA, Horan K, Schultz MB, et al. Tracking the COVID-19 pandemic in Australia using genomics. Nat Commun. 2020;11:4376. doi:10.1038/s41467-020-18314-x.
  • Candido DS, Claro IM, de Jesus JG, Souza WM, Moreira FRR, Dellicour S, Mellan TA, du Plessis L, Pereira RHM, Sales FCS, et al. Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science. 2020; 369:1255–60.
  • Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, et al. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. bioRxiv. 2020.
  • Ciccozzi M, Lai A, Zehender G, Borsetti A, Cella E, Ciotti M, Sagnelli E, Sagnelli C, Angeletti S. The phylogenetic approach for viral infectious disease evolution and epidemiology: an updating review. J Med Virol. 2019;91:1707–24. doi:10.1002/jmv.25526.
  • Mandary MB, Masomian M, Poh CL. Impact of RNA virus evolution on Quasispecies formation and virulence. Int J Mol Sci. 2019;20. doi:10.3390/ijms20184657.
  • Zhao Z, Li H, Wu X, Zhong Y, Zhang K, Zhang Y-P, Boerwinkle E, Fu Y-X. Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol Biol. 2004;4:21. doi:10.1186/1471-2148-4-21.
  • Eckerle LD, Becker MM, Halpin RA, Li K, Venter E, Lu X, Scherbakova S, Graham RL, Baric RS, Stockwell TB, et al. Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing. PLoS Pathog. 2010;6(5):e1000896. doi:10.1371/journal.ppat.1000896.
  • Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet. 2008;9:267–76. doi:10.1038/nrg2323.
  • Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, et al. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. 2020;182(4):812–27.e19. doi:10.1016/j.cell.2020.06.043.
  • van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, Owen CJ, Pang J, Tan CCS, Boshier FAT, et al. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infect Genet Evol. 2020:104351. doi:10.1016/j.meegid.2020.104351.
  • Laha S, Chakraborty J, Das S, Manna SK, Biswas S, Chatterjee R. Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission. Infect Genet Evol. 2020;85:104445. doi:10.1016/j.meegid.2020.104445.
  • Weisblum Y, Schmidt F, Zhang F, DaSilva J, Poston D, Lorenzi JC, Muecksch F, Rutkowska M, Hoffmann -H-H, Michailidis E, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife. 2020;9:e61312. doi:10.7554/eLife.61312.
  • Li Q, Wu J, Nie J, Zhang L, Hao H, Liu S, Zhao C, Zhang Q, Liu H, Nie L, et al. The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity. Cell. 2020;182(5):1284–94 e9. doi:10.1016/j.cell.2020.07.012.
  • Koyama T, Weeraratne D, Snowdon JL, Parida L. Emergence of drift variants that may affect COVID-19 vaccine development and antibody treatment. Pathogens. 2020;9:324. doi:10.3390/pathogens9050324.
  • Rosenberg NA, Nordborg M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet. 2002;3:380–90. doi:10.1038/nrg795.
  • Nayak MK, Banerjee A, Sarkar R, Mitra S, Dutta K, Ganguly N, Ghosh C, Girish Kumar CP, Niyogi P, Panda S, et al. Genetic characterization of group-A rotaviruses among children in eastern India during 2014–2016: phylodynamics of co-circulating genotypes. Vaccine. 2019;37(45):6842–56. doi:10.1016/j.vaccine.2019.06.062.
  • World Health Organization. Draft landscape of COVID-19 candidate vaccines. Geneva (Switzerland): World Health Organization; 2020.
  • Thanh Le T, Andreadakis Z, Kumar A, Gomez Roman R, Tollefsen S, Saville M, Mayhew S. The COVID-19 vaccine development landscape. Nat Rev Drug Discov. 2020;19(5):305–06. doi:10.1038/d41573-020-00073-5.
  • Ou X, Liu Y, Lei X, Li P, Mi D, Ren L, Guo L, Guo R, Chen T, Hu J, et al. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat Commun. 2020;11(1):1620. doi:10.1038/s41467-020-15562-9.
  • Yin C. Genotyping coronavirus SARS-CoV-2: methods and implications. Genomics. 2020;112:3588–96. doi:10.1016/j.ygeno.2020.04.016.
  • Rogers TF, Zhao F, Huang D, Beutler N, Burns A, He WT, Limbo O, Smith C, Song G, Woehl J, et al. Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. Science. 2020;369:956–63. doi:10.1126/science.abc7520.
  • Yuan Y, Wang N, Ou X. Caution should be exercised for the detection of SARS-CoV-2, especially in the elderly. J Med Virol. 2020;92(9):1641–48. doi:10.1002/jmv.25796.
  • Xiao AT, Tong YX, Zhang S. False-negative of RT-PCR and prolonged nucleic acid conversion in COVID-19: rather than recurrence. J Med Virol. 2020;92(10):1755–56. doi:10.1002/jmv.25855.
  • Xiang F, Wang X, He X, Peng Z, Yang B, Zhang J, Zhou Q, Ye H, Ma Y, Li H, et al. Antibody detection and dynamic characteristics in patients with COVID-19. Clin Infect Dis. 2020;71(8):1930–34. doi:10.1093/cid/ciaa461.
  • Peng J, Wang M, Zhang G, Lu E. Seven discharged patients turning positive again for SARS-CoV-2 on quantitative RT-PCR. Am J Infect Control. 2020;48(6):725–26. doi:10.1016/j.ajic.2020.03.017.
  • Okba NMA, Muller MA, Li W, Wang C, GeurtsvanKessel CH, Corman VM, Lamers MM, Sikkema RS, de Bruin E, Chandler FD, et al. Severe acute respiratory syndrome coronavirus 2-specific antibody responses in coronavirus disease 2019 patients. Emerg Infect Dis. 2020;26(7):1478–88.
  • Diaz-Quijano FA, Rodriguez-Morales AJ, Waldman EA. Translating transmissibility measures into recommendations for coronavirus prevention. Rev Saude Publica. 2020;54:43. doi:10.11606/s1518-8787.2020054002471.
  • Ke R, Li H, Wang S, Ding W, Ribeiro RM, EE G, Bhattacharya T, Barnard RJO, Hahn BH, Shaw GM, et al. Superinfection and cure of infected cells as mechanisms for hepatitis C virus adaptation and persistence. Proc Natl Acad Sci U S A. 2018;115:E7139. doi:10.1073/pnas.1805267115.
  • Capobianchi MR, Rueca M, Messina F, Giombini E, Carletti F, Colavita F, et al. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy. Clin Microbiol Infect. 2020;26(7):954–56.
  • Beerenwinkel N, Daumer M, Sing T, Rahnenfuhrer J, Lengauer T, Selbig J, Hoffmann D, Kaiser R. Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. J Infect Dis. 2005;191:1953–60. doi:10.1086/430005.
  • Beerenwinkel N, Lengauer T, Daumer M, Kaiser R, Walter H, Korn K, Hoffmann D, Selbig J. Methods for optimizing antiviral combination therapies. Bioinformatics. 2003;19(Suppl 1):i16–25. doi:10.1093/bioinformatics/btg1001.
  • Andreakos E, Tsiodras S. COVID-19: lambda interferon against viral load and hyperinflammation. EMBO Mol Med. 2020. doi:10.15252/emmm.202012465.
  • Diurno F, Numis FG, Porta G, Cirillo F, Maddaluno S, Ragozzino A, De Negri P, Di Gennaro C, Pagano A, Allegorico E, et al. Eculizumab treatment in patients with COVID-19: preliminary results from real life ASL Napoli 2 Nord experience. Eur Rev Med Pharmacol Sci. 2020;24:4040–47. doi:10.26355/eurrev_202004_20875.
  • Abena PM, Decloedt EH, Bottieau E, Suleman F, Adejumo P, Sam-Agudu NA, Muyembe TamFum -J-J, Seydi M, Eholie SP, Mills EJ, et al. Chloroquine and hydroxychloroquine for the prevention or treatment of novel coronavirus disease (COVID-19) in Africa: caution for inappropriate off-label use in healthcare settings. Am J Trop Med Hyg. 2020;102(6):1184–88. doi:10.4269/ajtmh.20-0290.
  • Borba MGS, Val FFA, Sampaio VS, Alexandre MAA, Melo GC, Brito M, Mourão MPG, Brito-Sousa JD, Baía-da-Silva D, Guerra MVF, et al. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial. JAMA Netw Open. 2020;3:e208857. doi:10.1001/jamanetworkopen.2020.8857.
  • Costanzo M, De Giglio MAR, Roviello GN. SARS-CoV-2: recent reports on antiviral therapies based on lopinavir/ ritonavir,darunavir/ umifenovir,hydroxychloroquine, remdesivir, favipiravir and other drugs for the treatment of the new coronavirus. Curr Med Chem. 2020. doi:10.2174/0929867327666200416131117.
  • Damle B, Vourvahis M, Wang E, Leaney J, Corrigan B. Clinical pharmacology perspectives on the antiviral activity of azithromycin and use in COVID-19. Clin Pharmacol Ther. 2020;108(2):201–11. doi:10.1002/cpt.1857.
  • Zhai P, Ding Y, Wu X, Long J, Zhong Y, Li Y. The epidemiology, diagnosis and treatment of COVID-19. Int J Antimicrob Agents. 2020;55(5):105955. doi:10.1016/j.ijantimicag.2020.105955.
  • Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, Shi Z, Hu Z, Zhong W, Xiao G, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020;30(3):269–71. doi:10.1038/s41422-020-0282-0.
  • Felsenstein S, Herbert JA, McNamara PS, Hedrich CM. COVID-19: immunology and treatment options. J Clin Immunol. 2020;215:108448. doi:10.1016/j.clim.2020.108448.
  • Frost SDW, Volz EM. Viral phylodynamics and the search for an ‘effective number of infections’. Philos Trans R Soc Lond B Biol Sci. 2010;365:1879–90. doi:10.1098/rstb.2010.0060.
  • Meriki HD, Tufon KA, Anong DN, Atanga PN, Anyangwe IA, Cho-Ngwa F, et al. Genetic diversity and antiretroviral resistance-associated mutation profile of treated and naive HIV-1 infected patients from the Northwest and Southwest regions of Cameroon. PLoS One. 2019;14:e0225575. doi:10.1371/journal.pone.0225575.
  • Perez-Losada M, Castel AD, Lewis B, Kharfen M, Cartwright CP, Huang B, et al. Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC. PLoS One. 2017;12:e0185644. doi:10.1371/journal.pone.0185644.
  • Rodriguez-Morales AJ, Rodriguez-Morales AG, Méndez CA, Hernández-Botero S. Tracing new clinical manifestations in patients with COVID-19 in Chile and its potential relationship with the SARS-CoV-2 divergence. Curr Trop Med Rep. 2020;18:1–4.
  • Sah R, Rodriguez-Morales AJ, Jha R, Chu DKW, Gu H, Peiris M, et al. Complete genome sequence of a 2019 novel coronavirus (SARS-CoV-2) strain isolated in Nepal. Microbiol Resour Announc. 2020:9. doi:10.1128/MRA.00169-20.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.