5,728
Views
11
CrossRef citations to date
0
Altmetric
Research Paper

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

, , , , , , , , ORCID Icon, , , , , , , & show all
Pages 1209-1226 | Received 18 Nov 2020, Accepted 23 Mar 2021, Published online: 25 May 2021

References

  • Kunkel TA. Exonucleolytic proofreading. Cell. 1988;53(6):837–840.
  • Vaughan G, Goncalves Rossi LM, Forbi JC, et al. Hepatitis A virus: host interactions, molecular epidemiology and evolution. Infect Genet Evol. 2014;21:227–243.
  • Domingo E, Sheldon J, Perales C. Viral quasispecies evolution. Microbiol Mol Biol Rev. 2012;76:159–216.
  • Nowak MA. What is a quasispecies? Trends Ecol Evol. 1992;7(4):118–121.
  • Barik S, Das S, Vikalo H. QSdpR: viral quasispecies reconstruction via correlation clustering. Genomics. 2018;110(6):375–381.
  • Xu D, Zhang Z, Wang FS. SARS-associated coronavirus quasispecies in individual patients. N Engl J Med. 2004;350(13):1366–1367.
  • Park D, Huh HJ, Kim YJ, et al. Analysis of intrapatient heterogeneity uncovers the microevolution of middle east respiratory syndrome coronavirus. Cold Spring Harb Mol Case Stud. 2016;2(6):a001214.
  • Zhou P, Yang X, Wang X, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270–273.
  • Li X, Giorgi EE, Marichannegowda MH, et al. Emergence of SARS-CoV-2 through recombination and strong purifying selection. Sci Adv. 2020;6(27):eabb9153.
  • Forster P, Forster L, Renfrew C, et al. Phylogenetic network analysis of SARS-CoV-2 genomes. Proc Natl Acad Sci U S A. 2020;117(17):9241–9243.
  • Van Dorp L, Acman M, Richard D, et al. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infect Genet Evol. 2020;83:104351.
  • Rambaut A, Loman N, Pybus O, et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological org. 2020.
  • Domingo-Calap P, Schubert B, Joly M, et al. An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides. PLoS Pathog. 2018;14(10):e1007368.
  • Holmes EC, Dudas G, Rambaut A, et al. The evolution of Ebola virus: insights from the 2013–2016 epidemic. Nature. 2016;538(7624):193–200.
  • Gámbaro F, Behillil S, Baidaliuk A, et al. Introductions and early spread of SARS-CoV-2 in France. Euro Surveill. 2020;25(26):2001200.
  • Rambaut A, Holmes EC, Á O, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403–1407.
  • Kupferschmidt K. Fast-spreading U.K. virus variant raises alarms. Science. 2021;371(6524):9–10.
  • Santos JC, Passos GA. The high infectivity of SARS-CoV-2 B.1.1.7 is associated with increased interaction force between Spike-ACE2 caused by the viral N501Y mutation. bioRxiv. 2020. doi: 10.1101/2020.12.29.424708
  • Gaudieri S, Rauch A, Park LP, et al. Evidence of viral adaptation to HLA class I-restricted immune pressure in chronic hepatitis C virus infection. J Virol. 2006;80(22):11094–11104.
  • Cuypers L, Li G, Libin P, et al. Selective pressure in hepatitis C virus genotypes 1–6: significance for direct-acting antiviral treatment and drug resistance. Viruses. 2015;7(9):5018–5039.
  • Ghadimi-Moghadam A, Haghani M, Bevelacqua JJ, et al. COVID-19 tragic pandemic: concerns over unintentional “directed accelerated evolution” of novel coronavirus (SARS-CoV-2) and introducing a modified treatment method for ARDS. J Biomed Phys Eng. 2020;10(2):241–246.
  • Azkur AK, Akdis M, Azkur D, et al. Immune response to SARS-CoV-2 and mechanisms of immunopathological changes in COVID-19. Allergy. 2020;75(7):1564–1581.
  • Xu X, Gao X. Immunological responses against SARS-coronavirus infection in humans. Cell Mol Immunol. 2004;1(2):119–122.
  • Hodgins B, Yam KK, Winter K, et al. A single intramuscular dose of a plant-made virus-like particle vaccine elicits a balanced humoral and cellular response and protects young and aged mice from influenza H1N1 virus challenge despite a modest/absent humoral response. Clin Vaccine Immunol. 2017;24(12):e00273–17.
  • Da Costa XJ, Brockman MA, Alicot E, et al. Humoral response to herpes simplex virus is complement-dependent. Proc Natl Acad Sci USA, 1999; 96(22):12708–12712.
  • Veron P, Leborgne C, Monteilhet V, et al. Humoral and cellular capsid-specific immune responses to adeno-associated virus type 1 in randomized healthy donors. J Immunol. 2012;188(12):6418–6424.
  • Rogers TF, Zhao F, Huang D, et al. Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. Science. 2020;369(6506):956–963.
  • Long QX, Liu BZ, Deng HJ, et al. Antibody responses to SARS-CoV-2 in patients with COVID-19. Nat Med. 2020;26(6):845–848.
  • Amanat F, Stadlbauer D, Strohmeier S, et al. A serological assay to detect SARS-CoV-2 seroconversion in humans. Nat Med. 2020;26(7):1033–1036.
  • Wu F, Wang A, Liu M, et al. Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications. medRxiv. 2020; doi: 10.1101/2020.03.30.20047365.
  • Ni L, Ye F, Cheng M-L, et al. Detection of SARS-CoV-2-Specific humoral and cellular immunity in COVID-19 convalescent individuals. Immunity. 2020;52(6):971–977.
  • Baruah V, Bose S. Immunoinformatics-aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019-nCoV. J Med Virol. 2020;92(5):495–500.
  • Draper JL, Hansen LM, Bernick DL, et al. Fallacy of the unique genome: sequence diversity within single helicobacter pylori strains. mBio. 2017;8(1):e02321–16.
  • Roedig JV, Rapp E, Höper D, et al. Impact of Host Cell Line Adaptation on Quasispecies Composition and Glycosylation of Influenza A Virus Hemagglutinin. Plos One. 2011;6(12):e27989.
  • Kissi B, Badrane H, Audry L, et al. Dynamics of rabies virus quasispecies during serial passages in heterologous hosts. J Gen Virol. 1999;80(8):2041–2050.
  • Ke R, Zitzmann C, Ribeiro RM, et al. Kinetics of SARS-CoV-2 infection in the human upper and lower respiratory tracts and their relationship with infectiousness. medRxiv. 2020. 2020.09.25.20201772. http://doi.org/10.1101/2020.09.25.20201772
  • Branchett WJ, Lloyd CM. Regulatory cytokine function in the respiratory tract. Mucosal Immunol. 2019;12(3):589–600.
  • Zuercher AW, Jiang H-Q, Thurnheer MC, et al. Distinct mechanisms for cross-protection of the upper versus lower respiratory tract through intestinal priming. J Immunol. 2002;169(7):3920–3925.
  • Kechin A, Boyarskikh U, Kel A, et al. cutPrimers: a new tool for accurate cutting of primers from reads of targeted next generation sequencing. J Comput Biol. 2017;24(11):1138–1143.
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25(14):1754–1760.
  • Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079.
  • McKenna A, Hanna M, Banks E, et al. The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–1303.
  • Tamura K, Peterson D, Peterson N, et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28(10):2731–2739.
  • Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–1650.
  • Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586–1591.
  • Yang Z, Nielsen R, Goldman N, et al. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 2000;155(1):431–449.
  • Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986;3(5):418–426.
  • Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25(11):1451–1452.
  • Kassambara A. ggplot2: guide to create beautiful graphics in R. Create Space Independent Publishing Platform; 2016; 1:236.
  • Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504.
  • Crawford KH, Eguia R, Dingens AS, et al. Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 spike protein for neutralization assays. Viruses. 2020;12(5):513.
  • Danchin A, Timmis K. SARS-CoV-2 variants: relevance for symptom granularity, epidemiology, immunity (herd, vaccines), virus origin and containment? Environ Microbiol. 2020;22(6):2001–2006.
  • Zhao WM, Song SH, Chen ML, et al. The 2019 novel coronavirus resource. Hereditas (Beijing). 2020;42:212–221.
  • Song S, Ma L, Zou D, et al. The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR. Genomics Proteom Bioinform. 2020 S1672-0229(20)30131-5.
  • Gong Z, Zhu JW, Li CP, et al. An online coronavirus analysis platform from the national genomics data center. Zool Res. 2020;41(6):705–708.
  • Ni M, Chen C, Qian J, et al. Intra-host dynamics of Ebola virus during 2014. Nat Microbiol. 2016;1(11):16151.
  • Zhang Y, Zhang J, Chen Y, et al. The ORF8 protein of SARS-CoV-2 mediates immune evasion through potently downregulating MHC-I. bioRxiv. 2020. doi: 10.1101/2020.05.24.111823.
  • Sapoval N, Mahmoud M, Jochum MD, et al. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res. 2021; 31(4):635-644
  • Robertson KD, Jones PA. DNA methylation: past, present and future directions. Carcinogenesis. 2000;21(3):461–467.
  • Tang X, Wu C, Li X, et al. On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev. 2020;7(6):1012–1023.
  • Wang Q, Zhang Y, Wu L, et al. Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell. 2020;181(4):894–904.e9.
  • Morse JS, Lalonde T, Xu S, et al. Learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by 2019-nCoV. Chembiochem. 2020;21(5):730–738.
  • Walls AC, Park YJ, Tortorici MA, et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. 2020;181(2):281–292.e6.
  • Cagliani R, Forni D, Clerici M, et al. Computational inference of selection underlying the evolution of the novel coronavirus, SARS-CoV-2. J Virol. 2020;94(12):e00411-20.
  • Baum A, Bo F, Wloga E, et al. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science. 2020;369(6506):1014–1018.
  • Paul S, Sidney J, Sette A, et al., TepiTool: A pipeline for computational prediction of T Cell Epitope Candidates. Curr Protoc Immunol. 2016; 114: 18.19.1-18.19.24.
  • Sun Y, Liu J, Yang M, et al. Identification and structural definition of H5-specific CTL epitopes restricted by HLA-A*0201 derived from the H5N1 subtype of influenza A viruses. J Gen Virol. 2010;91(4):919–30.
  • Yao H, Lu X, Chen Q, et al. Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo. Cell Discov. 2020;6(1):76.
  • Velazquez-Salinas L, Zarate S, Eberl S, et al. Positive selection of ORF1ab, ORF3a, and ORF8 genes drives the early evolutionary trends of SARS-CoV-2 during the 2020 COVID-19 pandemic. Front Microbiol. 2020;11:550674.
  • Su YCF, Anderson DE, Young BE, et al. Discovery and genomic characterization of a 382-nucleotide deletion in ORF7b and ORF8 during the early evolution of SARS-CoV-2. mBio. 2020;11(4):e01610–20.
  • Gong YN, Tsao KC, Hsiao MJ, et al. SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in middle east. Emerg Microbes Infect. 2020;25(1):1754–1760.
  • Wang X, Lam JY, Wong WM, et al. Accurate diagnosis of COVID-19 by a novel immunogenic secreted SARS-CoV-2 orf8 protein. mBio. 2020;11(5):e02431–20.
  • Kijak GH, Sanders-Buell E, Chenine AL, et al. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection. PLoS Pathog. 2017;13(7):e1006510.
  • Piantadosi A, Freije CA, Gosmann C, et al. Metagenomic sequencing of HIV-1 in the blood and female genital tract reveals little quasispecies diversity during acute infection. J Virol. 2019;93(2):93.
  • Subissi L, Posthuma CC, Collet A, et al. One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities. Proc Natl Acad Sci U S A. 2014;111(37):E3900–9.