Abstract
Sudden emergence and a rapid outbreak of SARS-CoV-2 accompanied by a devastating impact on the economy and public health has driven extensive scientific mobilization to study and elucidate the various associated concerns about SARS-CoV-2. Bioinformatics plays a crucial role in addressing and providing solutions to questions about SARS-CoV-2. It helps shorten the duration for the vaccine development process and the discovery of potential clinical interventions through the simulation and information retrieval, and the development of well-ordered information hubs and resources, which are essential to derive data and meaningful findings from the current massive information about SARS-CoV-2. Advanced algorithms in this field also provide approaches that are essential to elucidate the relationship, origin, and evolutionary process of SARS-CoV-2. Here, we report essential bioinformatics entities, such as database and platform development, molecular evolution and phylogenetic analyses, and vaccine designs, that are useful to solve the SARS-CoV-2 conundrum.
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References
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389–3402. https://doi.org/10.1093/nar/25.17.3389
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
Babcock GJ, Esshaki DJ, Thomas WD, Ambrosino DM (2004) Amino acids 270 to 510 of the severe acute respiratory syndrome coronavirus spike protein are required for interaction with receptor. J. Virol. 78(9):4552–4560. https://doi.org/10.1128/jvi.78.9.4552-4560.2004
Balakrishnan VS (2020) Increasing accessibility in COVID-19 clinical trials. The Lancet Microbe 1(1):e13
Belouzard S, Millet JK, Licitra BN, Whittaker GR (2012) Mechanisms of coronavirus cell entry mediated by the viral spike protein. Viruses 4(6):1011–1033. https://doi.org/10.3390/v4061011
Boni MF, Lemey P, Jiang X, Lam TT-Y, Perry B, Castoe T, Rambaut A, Robertson DL (2020) Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. bioRxiv:2020.2003.2030.015008. https://doi.org/10.1101/2020.03.30.015008
Brainard J (2020) Scientists are drowning in COVID-19 papers. Can new tools keep them afloat? https://www.sciencemag.org/news/2020/05/scientists-are-drowning-covid-19-papers-can-new-tools-keep-them-afloat. Accessed 15 May 2020
Breitbart M, Rohwer F (2005) Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13(6):278–284. https://doi.org/10.1016/j.tim.2005.04.003
Brister JR, Ako-Adjei D, Bao Y, Blinkova O (2015) NCBI viral genomes resource. Nucleic Acids Res. 43(Database issue):D571–D577. https://doi.org/10.1093/nar/gku1207
Brown DWG (1997) Threat to humans from virus infections of non-human primates. Rev. Med. Virol. 7(4):239–246. https://doi.org/10.1002/(sici)1099-1654(199712)7:4<239::Aid-rmv210>3.0.Co;2-q
Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S (2017) Protein data Bank (PDB): the single global macromolecular structure archive. Methods Mol. Biol. 1607:627–641. https://doi.org/10.1007/978-1-4939-7000-1_26
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
Chang J (2015) Core services: reward bioinformaticians. Nature Nature 520(7546):151–152
Chen Q, Allot A, Lu Z (2020) Keep up with the latest coronavirus research. Nature 579(7798):193. https://doi.org/10.1038/d41586-020-00694-1
ClinicalTrials.gov (2000). ClinicalTrials.gov. https://clinicaltrials.gov/. Accessed 1 April 2020
COVID-evidence (2020) Find evidence on interventions for COVID-19. https://covid-evidence.org/. Accessed 1 May 2020
Delwart EL (2007) Viral metagenomics. Rev. Med. Virol. 17(2):115–131. https://doi.org/10.1002/rmv.532
Dhanda SK, Gupta S, Vir P, Raghava GPS (2013) Prediction of IL4 inducing peptides. Clin Dev Immunol 2013:263952
Dimitrov I, Garnev P, Flower DR, Doytchinova I (2010) EpiTOP—a proteochemometric tool for MHC class II binding prediction. Bioinformatics 26(16):2066–2068
Doytchinova IA, Flower DR (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 8(1):4. https://doi.org/10.1186/1471-2105-8-4
Dunbar J, Krawczyk K, Leem J, Marks C, Nowak J, Regep C, Georges G, Kelm S, Popovic B, Deane CM (2016) SAbPred: a structure-based antibody prediction server. Nucleic Acids Res 44(W1):W474–8
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792–1797. https://doi.org/10.1093/nar/gkh340
Elbe S, Buckland-Merrett G (2017) Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall 1(1):33–46. https://doi.org/10.1002/gch2.1018
EL-Manzalawy Y, Dobbs D, Honavar V (2008) Predicting linear B-cell epitopes using string kernels. J Mol Recognit 21(4):243–255
Fahmi M, Kubota Y, Ito M (2020) Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV. Infect. Genet. Evol. 81:104272. https://doi.org/10.1016/j.meegid.2020.104272
Fehr AR, Perlman S (2015) Coronaviruses: an overview of their replication and pathogenesis. Methods Mol. Biol. 1282:1–23. https://doi.org/10.1007/978-1-4939-2438-7_1
Flint SJ, Racaniello VR, Rall GF, Skalka AM, Enquist LW (2015) Principles of virology, vol 1, 4th edn. ASM Press, Washington, DC
Forni D, Cagliani R, Clerici M, Sironi M (2017) Molecular evolution of human coronavirus genomes. Trends Microbiol. 25(1):35–48. https://doi.org/10.1016/j.tim.2016.09.001
Friedman LM, Furberg C, DeMets DL, Reboussin DM, Granger CB (2010) Fundamentals of clinical trials, vol 4. Springer International Publishing, Cham. https://doi.org/10.1007/978-3-319-18539-2
Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM, Michael SF, Cummins LB, Arthur LO, Peeters M, Shaw GM, Sharp PM, Hahn BH (1999) Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 397(6718):436–441. https://doi.org/10.1038/17130
Gibbs MJ, Weiller GF (1999) Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. Proc. Natl. Acad. Sci. 96(14):8022–8027. https://doi.org/10.1073/pnas.96.14.8022
Guan P, Doytchinova IA, Zygouri C, Flower DR (2003) MHCPred: a server for quantitative prediction of peptide–MHC binding. Nucleic Acids Res 31:3621–3624
Holder M, Lewis PO (2003) Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4(4):275–284. https://doi.org/10.1038/nrg1044
Hon C-C, Lam T-Y, Shi Z-L, Drummond AJ, Yip C-W, Zeng F, Lam P-Y, Leung FC-C (2008) Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus. J. Virol. 82(4):1819–1826. https://doi.org/10.1128/jvi.01926-07
Horbach SPJM (2020) Pandemic publishing: medical journals drastically speed up their publication process for Covid-19. bioRxiv:2020.2004.2018.045963. https://doi.org/10.1101/2020.04.18.045963
Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q, Wang J, Cao B (2020) Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 395(10223):497–506. https://doi.org/10.1016/s0140-6736(20)30183-5
Hulo C, de Castro E, Masson P, Bougueleret L, Bairoch A, Xenarios I, Le Mercier P (2011) ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res. 39(Database issue):D576–D582. https://doi.org/10.1093/nar/gkq901
Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M (2018) Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology 154(3):394–406
Jespersen MC, Peters B, Nielsen M, Marcatili P (2017) BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 45(W1):W24–w29. https://doi.org/10.1093/nar/gkx346
Johns Hopkins Bloomberg School of Public Health (2020) 2019 novel coronavirus research compendium (NCRC). https://ncrc.jhsph.edu Accessed 8 May 2020
Johnson LS, Eddy SR, Portugaly E (2010) Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 11:431. https://doi.org/10.1186/1471-2105-11-431
Karosiene E, Rasmussen M, Blicher T, Lund O, Buus S, Nielsen M (2013) NetMHCIIpan-3. 0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ. Immunogenetics 65(10):711–724
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30(14):3059–3066. https://doi.org/10.1093/nar/gkf436
Kharisma V, Ansori A (2020) Construction of epitope-based peptide vaccine against SARS-CoV-2: Immunoinformatics study. J Pure Appl Microbiol 14(suppl 1):999–1005
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.e910. https://doi.org/10.1016/j.cell.2020.04.011
Koonin EV, Galperin MY (2003) Sequence – evolution – function: computational approaches in comparative genomics. Springer US, Boston. https://doi.org/10.1007/978-1-4757-3783-7
Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S (2007) The ClusPro web server for protein-protein docking. Nat Protoc 12(2):255–278. https://doi.org/10.1038/nprot.2016.169
Kringelum JV, Lundegaard C, Lund O, Nielsen M (2012) Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Comput Biol 8(12):e1002829
Kühnert D, Wu CH, Drummond AJ (2011) Phylogenetic and epidemic modeling of rapidly evolving infectious diseases. Infect. Genet. Evol. 11(8):1825–1841. https://doi.org/10.1016/j.meegid.2011.08.005
Lai MM, Liao CL, Lin YJ, Zhang X (1994) Coronavirus: how a large RNA viral genome is replicated and transcribed. Infect. Agents Dis. 3(2–3):98–105
Lam HM, Ratmann O, Boni MF (2017) Improved algorithmic complexity for the 3SEQ recombination detection algorithm. Mol. Biol. Evol. 35(1):247–251. https://doi.org/10.1093/molbev/msx263
Lamiable A, Thévenet P, Rey J, Vavrusa M, Derreumaux P, Tufféry P (2016) PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Res. 44(W1):W449–W454. https://doi.org/10.1093/nar/gkw329
Lemey P, Salemi M, Vandamme A-M (2009) The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press
Li F (2008) Structural analysis of major species barriers between humans and palm civets for severe acute respiratory syndrome coronavirus infections. J. Virol. 82(14):6984–6991. https://doi.org/10.1128/jvi.00442-08
Li F (2015) Receptor recognition mechanisms of coronaviruses: a decade of structural studies. J. Virol. 89(4):1954–1964. https://doi.org/10.1128/jvi.02615-14
Li F, Li W, Farzan M, Harrison SC (2005a) Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science 309(5742):1864–1868. https://doi.org/10.1126/science.1116480
Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, Wang H, Crameri G, Hu Z, Zhang H, Zhang J, McEachern J, Field H, Daszak P, Eaton BT, Zhang S, Wang LF (2005b) Bats are natural reservoirs of SARS-like coronaviruses. Science 310(5748):676–679. https://doi.org/10.1126/science.1118391
Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y, Ren R, Leung KSM, Lau EHY, Wong JY, Xing X, Xiang N, Wu Y, Li C, Chen Q, Li D, Liu T, Zhao J, Liu M, Tu W, Chen C, Jin L, Yang R, Wang Q, Zhou S, Wang R, Liu H, Luo Y, Liu Y, Shao G, Li H, Tao Z, Yang Y, Deng Z, Liu B, Ma Z, Zhang Y, Shi G, Lam TTY, Wu JT, Gao GF, Cowling BJ, Yang B, Leung GM, Feng Z (2020a) Early transmission dynamics in Wuhan, China, of novel coronavirus infected pneumonia. N Engl J Med 382(13):1199–1207
Li X, Giorgi EE, Marichann MH, Foley B, Xiao C, Kong X-P, Chen Y, Korber B, Gao F (2020b) Emergence of SARS-CoV-2 through recombination and strong purifying selection. bioRxiv:2020.2003.2020.000885. doi:https://doi.org/10.1101/2020.03.20.000885
Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73(1):152–160. https://doi.org/10.1128/jvi.73.1.152-160.1999
Lorenc T, Khouja C, Raine G, Sutcliffe K, Wright K, Sowden A, Thomas J (2020) COVID-19: living map of the evidence. http://eppi.ioe.ac.uk/COVID19_MAP/covid_map_v11.html. Accessed 15 May 2020
Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W, Tan W (2020) Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 395(10224):565–574. https://doi.org/10.1016/s0140-6736(20)30251-8
Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M (2008) NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11. Nucleic Acids Res 1:W509–12
Markov PV, Pepin J, Frost E, Deslandes S, Labbé AC, Pybus OG (2009) Phylogeography and molecular epidemiology of hepatitis C virus genotype 2 in Africa. J. Gen. Virol. 90(Pt 9):2086–2096. https://doi.org/10.1099/vir.0.011569-0
Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, Khattra J, Asano JK, Barber SA, Chan SY, Cloutier A, Coughlin SM, Freeman D, Girn N, Griffith OL, Leach SR, Mayo M, McDonald H, Montgomery SB, Pandoh PK, Petrescu AS, Robertson AG, Schein JE, Siddiqui A, Smailus DE, Stott JM, Yang GS, Plummer F, Andonov A, Artsob H, Bastien N, Bernard K, Booth TF, Bowness D, Czub M, Drebot M, Fernando L, Flick R, Garbutt M, Gray M, Grolla A, Jones S, Feldmann H, Meyers A, Kabani A, Li Y, Normand S, Stroher U, Tipples GA, Tyler S, Vogrig R, Ward D, Watson B, Brunham RC, Krajden M, Petric M, Skowronski DM, Upton C, Roper RL (2003) The genome sequence of the SARS-associated coronavirus. Science 300(5624):1399–1404. https://doi.org/10.1126/science.1085953
Martin D, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16(6):562–563. https://doi.org/10.1093/bioinformatics/16.6.562
Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Töpfer A (2014) Challenges in RNA virus bioinformatics. Bioinformatics 30(13):1793–1799. https://doi.org/10.1093/bioinformatics/btu105
Mayrose I, Penn O, Erez E, Rubinstein ND, Shlomi T, Freund NT, Bublil EM, Ruppin E, Sharan R, Gershoni JM, Martz E, Pupko T (2007) Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics 23(23):3244–3246
Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF, Wright F (2008) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 25(1):126–127. https://doi.org/10.1093/bioinformatics/btn575
Nielsen M, Andreatta M (2016) NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med 8(1):1–9
Nielsen M, Lundegaard C, Lund O (2007) Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC bioinform 8(1):238
Nora T, Charpentier C, Tenaillon O, Hoede C, Clavel F, Hance AJ (2007) Contribution of recombination to the evolution of human immunodeficiency viruses expressing resistance to antiretroviral treatment. J. Virol. 81(14):7620–7628. https://doi.org/10.1128/jvi.00083-07
Paraskevis D, Kostaki EG, Magiorkinis G, Panayiotakopoulos G, Sourvinos G, Tsiodras S (2020) 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. 79:104212. https://doi.org/10.1016/j.meegid.2020.104212
Pearson WR (2013) An introduction to sequence similarity (“homology”) searching. Curr. Protoc. Bioinformatics. Chapter 3:Unit3.1. https://doi.org/10.1002/0471250953.bi0301s42
Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U. S. A. 85(8):2444–2448. https://doi.org/10.1073/pnas.85.8.2444
Ponomarenko J, Bui HH, Li W, Fusseder N, Bourne PE, Sette A, Peters B (2008) ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinform 9(1):514
Pybus OG, Barnes E, Taggart R, Lemey P, Markov PV, Rasachak B, Syhavong B, Phetsouvanah R, Sheridan I, Humphreys IS, Lu L, Newton PN, Klenerman P (2009) Genetic history of hepatitis C virus in East Asia. J. Virol. 83(2):1071–1082. https://doi.org/10.1128/jvi.01501-08
Reche PA, Reinherz EL (2005) PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands. Nucleic Acids Res 33(1):W138–42
Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Peñaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, Günther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ (2003) Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300(5624):1394–1399. https://doi.org/10.1126/science.1085952
Ruano J, Gómez-García F, Pieper D, Puljak L (2020) What evidence-based medicine researchers can do to help clinicians fighting COVID-19? J. Clin. Epidemiol. https://doi.org/10.1016/j.jclinepi.2020.04.015
Saha S, Raghava GPS (2006) Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network. Proteins 65(1):40–48
Santiago ML, Rodenburg CM, Kamenya S, Bibollet-Ruche F, Gao F, Bailes E, Meleth S, Soong SJ, Kilby JM, Moldoveanu Z, Fahey B, Muller MN, Ayouba A, Nerrienet E, McClure HM, Heeney JL, Pusey AE, Collins DA, Boesch C, Wrangham RW, Goodall J, Sharp PM, Shaw GM, Hahn BH (2002) SIVcpz in wild chimpanzees. Science 295(5554):465. https://doi.org/10.1126/science.295.5554.465
SciSight (2020) SciSight. https://scisight.apps.allenai.org/. Accessed 1 May 2020
Simon-Loriere E, Holmes EC (2011) Why do RNA viruses recombine? Nat. Rev. Microbiol. 9(8):617–626. https://doi.org/10.1038/nrmicro2614
Singh H, Raghava GPS (2001) ProPred: prediction of HLA-DR binding sites. Bioinformatics 17(12):1236–1237
Singh H, Ansari HR, Raghava GPS (2013) Improved method for linear B-cell epitope prediction using antigen’s primary sequence. PLOS ONE 8(5):e62216
Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J. Mol. Biol. 147(1):195–197. https://doi.org/10.1016/0022-2836(81)90087-5
SPIKE-COVID (2020) SPIKE-COVID: Extractive search over CORD 19. https://spike.covid-19.apps.allenai.org/search/covid19. Accessed 2 April 2020
Sun B, Zhang Y (2014) Overview of orchestration of CD4+ T cell subsets in immune responses. Adv. Exp. Med. Biol. 841:1–13. https://doi.org/10.1007/978-94-017-9487-9_1
Sussman JL, Lin D, Jiang J, Manning NO, Prilusky J, Ritter O, Abola EE (1998) Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr. D Biol. Crystallogr. 54(Pt 6 Pt 1):1078–1084. https://doi.org/10.1107/s0907444998009378
Suttle CA (2005) Viruses in the sea. Nature 437(7057):356–361. https://doi.org/10.1038/nature04160
Sweredoski MJ, Baldi P (2009) COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel 22(3):113–120
Tang X, Wu C, Li X, Song Y, Yao X, Wu X, Duan Y, Zhang H, Wang Y, Qian Z, Cui J, Lu J (2020) On the origin and continuing evolution of SARS-CoV-2. Natl. Sci. Rev. https://doi.org/10.1093/nsr/nwaa036
Thiel V, Ivanov KA, Putics Á, Hertzig T, Schelle B, Bayer S, Weißbrich B, Snijder EJ, Rabenau H, Doerr HW, Gorbalenya AE, Ziebuhr J (2003) Mechanisms and enzymes involved in SARS coronavirus genome expression. J. Gen. Virol. 84(Pt 9):2305–2315. https://doi.org/10.1099/vir.0.19424-0
Thorlund K, Dron L, Park J, Hsu G, Forrest JI, Mills EJ (2020) A real-time dashboard of clinical trials for COVID-19. Lancet Digit Health 2(6):e286–e287. https://doi.org/10.1016/s2589-7500(20)30086-8
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(2):281–292.e286. https://doi.org/10.1016/j.cell.2020.02.058
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–e00120. https://doi.org/10.1128/jvi.00127-20
Wang LL, Lo K, Chandrasekhar Y, Reas R, Yang J, Eide D, Funk K, Kinney R, Liu Z, Merrill W (2020) CORD-19: the Covid-19 open research dataset. arXiv preprint arXiv:200410706
World Health Organization (2005) The international clinical trials registry platform – ICTRP. https://www.who.int/ictrp/en/. Accessed 2 April 2020
World Health Organization (2020a) Coronavirus disease 2019 (COVID-19) situation report – 51, 11 March 2020. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports. Accessed 15 April 2020
World Health Organization (2020b) WHO coronavirus disease (COVID-19) dashboard. https://covid19.who.int/. Accessed 1 May 2020
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
Xiong J (2006) Essential bioinformatics. Cambridge University Press, New York
Yang Z, Rannala B (2012) Molecular phylogenetics: principles and practice. Nat. Rev. Genet. 13(5):303–314. https://doi.org/10.1038/nrg3186
Yao B, Zhang L, Liang S, Zhang C (2012) SVMTriP: a method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity. PLOS ONE 7(9):e45152
Zhang Y-Z, 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
Zhang T, Wu Q, Zhang Z (2020) Pangolin homology associated with 2019-nCoV. bioRxiv:2020.2002.2019.950253. doi:https://doi.org/10.1101/2020.02.19.950253
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
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 (2020) A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 382(8):727–733
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Fahmi, M., Kharisma, V.D., Ansori, A.N.M., Ito, M. (2021). Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. In: Rezaei, N. (eds) Coronavirus Disease - COVID-19. Advances in Experimental Medicine and Biology, vol 1318. Springer, Cham. https://doi.org/10.1007/978-3-030-63761-3_47
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DOI: https://doi.org/10.1007/978-3-030-63761-3_47
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