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

