Page 112 - MI-2-3
P. 112

Microbes & Immunity                                                SARS-CoV-2 complementary classification



               RNA viruses. J Biol Chem. 2022;298(5):101923.      J Virol. 2022;96(16):e0097122.
               doi: 10.1016/j.jbc.2022.101923                     doi: 10.1128/jvi.00971-22
            73.  Gupta S, Gupta D, Bhatnagar S. Analysis of SARS-CoV-2   84.  Kuiken C, Korber B, Shafer RW. HIV sequence databases.
               genome   evolutionary  patterns.  Microbiol  Spectr.   AIDS Rev. 2003;5(1):52-61.
               2024;12(2):e0265423.
                                                               85.  Kuiken C, Yusim K, Boykin L, Richardson R. The Los
               doi: 10.1128/spectrum.02654-23                     Alamos  hepatitis  C  sequence  database.  Bioinformatics.
                                                                  2005;21(3):379-384.
            74.  Fischer W, Giorgi EE, Chakraborty S,  et al. HIV-1 and
               SARS-CoV-2: Patterns in the evolution of two pandemic      doi: 10.1093/bioinformatics/bth485
               pathogens. Cell Host Microbe. 2021;29(7):1093-1110.
                                                               86.  Calhoun VC, Hatcher EL, Yankie L, Nawrocki EP. Influenza
               doi: 10.1016/j.chom.2021.05.012                    sequence validation and annotation using VADR. Database
                                                                  (Oxford). 2024;2024:baae091.
            75.  Wang X, Li J, Liu H, Hu X, Lin Z, Xiong N. SARS-CoV-2
               versus influenza A virus: Characteristics and co-treatments.      doi: 10.1093/database/baae091
               Microorganisms. 2023;11(3):580.
                                                               87.  Brister JR, Ako-Adjei D, Bao Y, Blinkova O. NCBI viral
               doi: 10.3390/microorganisms11030580                genomes resource.  Nucleic Acids Res. 2015;43(Database
                                                                  issue):D571-D577.
            76.  Tahir M. Coronavirus genomic nsp14-ExoN, structure, role,
               mechanism, and potential application as a drug target. J Med      doi: 10.1093/nar/gku1207
               Virol. 2021;93(7):4258-4264.
                                                               88.  Drummond AJ,  Ho  SY,  Phillips  MJ,  Rambaut  A.  Relaxed
               doi: 10.1002/jmv.27009                             phylogenetics and dating with confidence.  PLoS Biol.
                                                                  2006;4(5):e88.
            77.  Robson F, Khan KS, Le TK,  et  al. Coronavirus RNA
               proofreading: Molecular basis and therapeutic targeting.      doi: 10.1371/journal.pbio.0040088
               Mol Cell. 2020;79(5):710-727.
                                                               89.  Abecasis A, Vandamme AM. Origin and distribution of
               doi: 10.1016/j.molcel.2020.07.027                  HIV-1 subtypes. In: Hope TJ, Stevenson M, Richman D,
                                                                  editors. Encyclopedia of AIDS. Berlin: Springer New York;
            78.  Simmonds P. Rampant C→U hypermutation in the genomes
               of  SARS-CoV-2  and other  coronaviruses: Causes  and   2014. p. 1-16.
               consequences for their short- and long-term evolutionary   90.  Hemelaar J, Elangovan R, Yun J, et al. Global and regional
               trajectories. mSphere. 2020;5(3):e00408-20.        molecular epidemiology of HIV-1, 1990-2015: A systematic
                                                                  review, global survey, and trend analysis. Lancet Infect Dis.
               doi: 10.1128/mSphere.00408-20
                                                                  2019;19(2):143-155.
            79.  Neher  RA.  Contributions  of  adaptation  and
               purifying selection to SARS-CoV-2 evolution.  Virus      doi: 10.1016/s1473-3099(18)30647-9
               Evol. 2022;8(2):veac113.                        91.  Smith DB, Bukh J, Kuiken C, et al. Expanded classification of
                                                                  hepatitis C virus into 7 genotypes and 67 subtypes: Updated
               doi: 10.1093/ve/veac113
                                                                  criteria and genotype assignment web resource. Hepatology.
            80.  Liu J, Wu Y, Gao GF. A  structural voyage toward the   2014;59(1):318-327.
               landscape of humoral and cellular immune escapes of
               SARS-CoV-2. Immunol Rev. 2025;330(1):e70000.       doi: 10.1002/hep.26744
                                                               92.  Petrova VN, Russell CA. The evolution of seasonal influenza
               doi: 10.1111/imr.70000
                                                                  viruses. Nat Rev Microbiol. 2018;16(1):47-60.
            81.  Tong Y, Lavillette D, Li Q, Zhong J. Role of hepatitis C virus
               envelope glycoprotein E1 in virus entry and assembly. Front      doi: 10.1038/nrmicro.2017.118
               Immunol. 2018;9:1411.                           93.  Katoh K, Standley DM. MAFFT multiple sequence
                                                                  alignment software version 7: Improvements in performance
               doi: 10.3389/fimmu.2018.01411
                                                                  and usability. Mol Biol Evol. 2013;30(4):772-780.
            82.  Beretta M, Migraine J, Moreau A,  et  al. Common
               evolutionary features of the envelope glycoprotein of      doi: 10.1093/molbev/mst010
               HIV-1 in patients belonging to a transmission chain.  Sci   94.  Tamura K, Stecher G, Peterson D, Filipski A,
               Rep. 2020;10(1):16744.                             Kumar S. MEGA6: Molecular evolutionary genetics analysis
                                                                  version 6.0. Mol Biol Evol. 2013;30(12):2725-2729.
               doi: 10.1038/s41598-020-73975-4
                                                                  doi: 10.1093/molbev/mst197
            83.  Xu C, Zhang N, Yang Y,  et al. Immune escape adaptive
               mutations in hemagglutinin are responsible for the antigenic   95.  Tamura  K,  Nei  M,  Kumar  S.  Prospects  for  inferring  very
               drift of Eurasian avian-like H1N1 swine influenza viruses.   large phylogenies by using the neighbor-joining method.


            Volume 2 Issue 3 (2025)                        104                           doi: 10.36922/MI025190042
   107   108   109   110   111   112   113   114   115   116   117