Phylogeny and evolution of SARS-CoV-2 during Delta and Omicron variant waves in India

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Arshia, A. H., Shadravan, S., Solhjoo, A., Sakhteman, A., & Sami, A. (2021). De novo design of novel protease inhibitor candidates in the treatment of SARS-CoV-2 using deep learning, docking, and molecular dynamic simulations. Computers in Biology and Medicine, 139, 104967. https://doi.org/10.1016/j.compbiomed.2021.104967
   PubMed Web of Science ®Google Scholar
• Bai, C., Wang, J., Chen, G., Zhang, H., An, K., Xu, P., Du, Y., Ye, R. D., Saha, A., Zhang, A., & Warshel, A. (2021). Predicting mutational effects on receptor binding of the spike protein of SARS-CoV-2 variants. Journal of the American Chemical Society, 143(42), 17646–17654. https://doi.org/10.1021/jacs.1c07965
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., van der Spoel, D., & van Drunen, R. (1995). GROMACS, A message-passing parallel molecular dynamics implementation. Computer Physics Communications. 91(1-3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
   Web of Science ®Google Scholar
• Cao, Y., Yisimayi, A., Jian, F., Song, W., Xiao, T., Wang, L., Du, S., Wang, J., Li, Q., Chen, X., Yu, Y., Wang, P., Zhang, Z., Liu, P., An, R., Hao, X., Wang, Y., Wang, J., Feng, R., … Xie, X. S. (2022). BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature, 608(7923), 593–602. https://doi.org/10.1038/s41586-022-04980-y
   PubMed Web of Science ®Google Scholar
• Chen, S. L. (2019). Implementation of a Stirling number estimator enables direct calculation of population genetics tests for large sequence datasets. Bioinformatics (Oxford, England), 35(15), 2668–2670. https://doi.org/10.1093/bioinformatics/bty1012
   PubMed Web of Science ®Google Scholar
• Cheng, T. M., Blundell, T. L., & Fernandez-Recio, J. (2007). pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins, 68(2), 503–515. PMID: 17444519. https://doi.org/10.1002/prot.21419
   PubMed Web of Science ®Google Scholar
• Chen, J., Wang, R., Gilby, N. B., & Wei, G.-W. (2022). Omicron variant (B.1.1.529): Infectivity, vaccine breakthrough, and antibody resistance. Journal of Chemical Information and Modeling, 62(2), 412–422. https://doi.org/10.1021/acs.jcim.1c01451
   PubMed Web of Science ®Google Scholar
• Chen, J., & Wei, G. W. (2022). Omicron ba. 2 (b. 1.1. 529.2): High potential for becoming the next dominant variant. The Journal of Physical Chemistry Letters, 13(17), 3840–3849. https://doi.org/10.1021/acs.jpclett.2c00469
   PubMed Web of Science ®Google Scholar
• Cui, Z., Liu, P., Wang, N., Wang, L., Fan, K., Zhu, Q., Wang, K., Chen, R., Feng, R., Jia, Z., Yang, M., Xu, G., Zhu, B., Fu, W., Chu, T., Feng, L., Wang, Y., Pei, X., Yang, P., … Wang, X. (2022). Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell, 185(5), 860–871.e13. https://doi.org/10.1016/j.cell.2022.01.019
   PubMed Web of Science ®Google Scholar
• Daniloski, Z., Jordan, T. X., Ilmain, J. K., Guo, X., Bhabha, G., tenOever, B. R., & Sanjana, N. E. (2021). The spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. eLife, 10, e65365. https://doi.org/10.7554/eLife.65365
   PubMed Web of Science ®Google Scholar
• Davis, J. J., & Olsen, G. J. (2010). Modal codon usage: Assessing the typical codon usage of a genome. Molecular Biology and Evolution, 27(4), 800–810. https://doi.org/10.1093/molbev/msp281
   PubMed Web of Science ®Google Scholar
• Delaune, D., Hul, V., Karlsson, E. A., Hassanin, A., Ou, T. P., Baidaliuk, A., Gámbaro, F., Prot, M., Tu, V. T., Chea, S., Keatts, L., Mazet, J., Johnson, C. K., Buchy, P., Dussart, P., Goldstein, T., Simon-Lorière, E., & Duong, V. (2021). A novel SARS-CoV-2 related coronavirus in bats from Cambodia. Nature Communications, 12(1), 1–7. https://doi.org/10.1038/s41467-021-26809-4
   PubMed Web of Science ®Google Scholar
• Desingu, P. A., & Nagarajan, K. (2022). Omicron variant losing its critical mutations in the receptor-binding domain. Journal of Medical Virology, 94(6), 2365–2368. https://doi.org/10.1002/jmv.27667
   PubMed Web of Science ®Google Scholar
• Devi, S. S., Kardam, V., Dubey, K. D., & Dwivedi, M. (2023). Deciphering the immunogenic T-cell epitopes from spike protein of SARS-CoV-2 concerning the diverse population of India. Journal of Biomolecular Structure and Dynamics, 41(7), 2713–2732. https://doi.org/10.1080/07391102.2022.2037462
   PubMed Web of Science ®Google Scholar
• Dhar, M. S., Marwal, R., Vs, R., Ponnusamy, K., Jolly, B., Bhoyar, R. C., Sardana, V., Naushin, S., Rophina, M., Mellan, T. A., Mishra, S., Whittaker, C., Fatihi, S., Datta, M., Singh, P., Sharma, U., Ujjainiya, R., Bhatheja, N., Divakar, M. K., … Cherian, S. S. (2021). Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science, 374(6570), 995–999. https://doi.org/10.1126/science.abj9932
   PubMed Web of Science ®Google Scholar
• Dorp, L., Richard, D., Tan, C. C., Shaw, L. P., Acman, M., & Balloux, F. (2020). No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. Nature Communications. 11(1), 1–8.
   PubMed Web of Science ®Google Scholar
• Ferenčak, I., Obrovac, M., Žmak, L., Kuzle, J., Petrović, G., Vilibić-Čavlek, T., Jurić, D., Jurić, A., Hruškar, Ž., Capak, K., Stevanović, V., Milanović, M., Govedarica, M., Vujošević, D., & Tabain, I. (2022). SARS-CoV-2 Omicron variant in croatia-rapid detection of the first case and cross-border spread. Pathogens, 11(5), 511. https://doi.org/10.3390/pathogens11050511
   PubMed Web of Science ®Google Scholar
• Fu, T., Li, F., Zhang, Y., Yin, J., Qiu, W., Li, X., Liu, X., Xin, W., Wang, C., Yu, L., Gao, J., Zheng, Q., Zeng, S., & Zhu, F. (2022). VARIDT 2.0: Structural variability of drug transporter. Nucleic Acids Research, 50(D1), D1417–D1431. https://doi.org/10.1093/nar/gkab1013
   PubMed Web of Science ®Google Scholar
• Fu, T-t., Tu, G., Ping, M., Zheng, G-x., Yang, F-y., Yang, J-y., Zhang, Y., Yao, X.-j., Xue, W.-w., & Zhu, F. (2021). Subtype-selective mechanisms of negative allosteric modulators binding to group I metabotropic glutamate receptors. Acta Pharmacologica Sinica, 42(8), 1354–1367.
   PubMed Web of Science ®Google Scholar
• Fu, T., Zheng, G., Tu, G., Yang, F., Chen, Y., & Yao, X. (2018). Exploring the binding mechanism of metabotropic glutamate receptor 5 negative allosteric modulators in clinical trials by molecular dynamics simulations. ACS Chemical Neuroscience, 9(6), 1492–1502.
   PubMed Web of Science ®Google Scholar
• Ghoshal, U., Garg, A., Vasanth, S., Arya, A. K., Pandey, A., Tejan, N., Patel, V., & Singh, V. P. (2021). Assessing a chip based rapid RTPCR test for SARS CoV-2 detection (TrueNat assay): A diagnostic accuracy study.Hasnain SE, editor. PLoS One, 16(10), e0257834. https://doi.org/10.1371/journal.pone.0257834
   PubMed Web of Science ®Google Scholar
• Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T., & Neher, R. A. (2018). Nextstrain: Real-time tracking of pathogen evolution. Bioinformatics (Oxford, England), 34(23), 4121–4123. https://doi.org/10.1093/bioinformatics/bty407
   PubMed Web of Science ®Google Scholar
• Hale, V. L., Dennis, P. M., McBride, D. S., Nolting, J. M., Madden, C., Huey, D., Ehrlich, M., Grieser, J., Winston, J., Lombardi, D., Gibson, S., Saif, L., Killian, M. L., Lantz, K., Tell, R. M., Torchetti, M., Robbe-Austerman, S., Nelson, M. I., Faith, S. A., & Bowman, A. S. (2022). SARS-CoV-2 infection in free-ranging white-tailed deer. Nature, 602(7897), 481–486. https://doi.org/10.1038/s41586-021-04353-x
   PubMed Web of Science ®Google Scholar
• Hossain, M. S., Roy, A. S., & Islam, M. S. (2020). In silico analysis predicting effects of deleterious SNPs of human RASSF5 gene on its structure and functions. Scientific Reports, 10(1), 14542. https://doi.org/10.1038/s41598-020-71457-1
   PubMed Web of Science ®Google Scholar
• Hui, K. P. Y., Ho, J. C. W., Cheung, M.-C., Ng, K.-C., Ching, R. H. H., Lai, K.-L., Kam, T. T., Gu, H., Sit, K.-Y., Hsin, M. K. Y., Au, T. W. K., Poon, L. L. M., Peiris, M., Nicholls, J. M., & Chan, M. C. W. (2022). SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo. Nature, 603(7902), 715–720. https://doi.org/10.1038/s41586-022-04479-6
   PubMed Web of Science ®Google Scholar
• Iketani, S., Liu, L., Guo, Y., Liu, L., Chan, J. F.-W., Huang, Y., Wang, M., Luo, Y., Yu, J., Chu, H., Chik, K. K.-H., Yuen, T. T.-T., Yin, M. T., Sobieszczyk, M. E., Huang, Y., Yuen, K.-Y., Wang, H. H., Sheng, Z., & Ho, D. D. (2022). Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Nature, 604(7906), 553–556. https://doi.org/10.1038/s41586-022-04594-4
   PubMed Web of Science ®Google Scholar
• INSACOG.INSACOG WEEKLY BULLETIN. (2022). https://dbtindia.gov.in/insacog_bulletin.
   Google Scholar
• Jangra, S., Ye, C., Rathnasinghe, R., Stadlbauer, D., Krammer, F., Simon, V., Martinez-Sobrido, L., García-Sastre, A., & Schotsaert, M. (2021). SARS-CoV-2 spike E484K mutation reduces antibody neutralisation. The Lancet. Microbe, 2(7), e283–e284. https://doi.org/10.1016/S2666-5247(21)00068-9
   PubMedGoogle Scholar
• Jankute, M., Nataraj, V., Lee, O. Y. C., Wu, H. H., Ridell, M., Garton, N. J., Barer, M. R., Minnikin, D. E., Bhatt, A., & Besra, G. S. (2017). The role of hydrophobicity in tuberculosis evolution and pathogenicity. Scientific reports, 7(1), 1315. https://doi.org/10.1038/s41598-017-01501-0
   PubMedGoogle Scholar
• Kannan, S. R., Spratt, A. N., Sharma, K., Goyal, R., Sönnerborg, A., Apparsundaram, S., Lorson, C. L., Byrareddy, S. N., & Singh, K. (2022). Complex mutation pattern of Omicron BA. 2: Evading antibodies without losing receptor interactions. International Journal of Molecular Sciences, 23(10), 5534. https://doi.org/10.3390/ijms23105534
   PubMed Web of Science ®Google Scholar
• 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 Research, 30(14), 3059–3066. https://doi.org/10.1093/nar/gkf436
   PubMed Web of Science ®Google Scholar
• Kousathanas, A., Pairo-Castineira, E., Rawlik, K., Stuckey, A., Odhams, C. A., Walker, S., Russell, C. D., Malinauskas, T., Wu, Y., Millar, J., Shen, X., Elliott, K. S., Griffiths, F., Oosthuyzen, W., Morrice, K., Keating, S., Wang, B., Rhodes, D., Klaric, L., … Baillie, J. K. (2022). Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature, 607(7917), 97–103. https://doi.org/10.1038/s41586-022-04576-6
   PubMed Web of Science ®Google Scholar
• Kumar, R., Murugan, N. A., & Srivastava, V. (2022). Improved binding affinity of Omicron’s spike protein for the human angiotensin-converting enzyme 2 receptor is the key behind its increased virulence. International Journal of Molecular Sciences, 23(6).
   Web of Science ®Google Scholar
• Kumar, S., Thambiraja, T. S., Karuppanan, K., & Subramaniam, G. (2022). Omicron and Delta variant of SARS-CoV-2: A comparative computational study of spike protein. Journal of Medical Virology, 94(4), 1641–1649. https://doi.org/10.1002/jmv.27526
   PubMed Web of Science ®Google Scholar
• Lam, T. T.-Y., Jia, N., Zhang, Y.-W., Shum, M. H.-H., Jiang, J.-F., Zhu, H.-C., Tong, Y.-G., Shi, Y.-X., Ni, X.-B., Liao, Y.-S., Li, W.-J., Jiang, B.-G., Wei, W., Yuan, T.-T., Zheng, K., Cui, X.-M., Li, J., Pei, G.-Q., Qiang, X., … Cao, W.-C. (2020). Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature, 583(7815), 282–285. https://doi.org/10.1038/s41586-020-2169-0
   PubMed Web of Science ®Google Scholar
• Lauring, A. S., & Hodcroft, E. B. (2021). Genetic variants of SARS-CoV-2-what do they mean? JAMA, 325(6), 529–531. https://doi.org/10.1001/jama.2020.27124
   PubMed Web of Science ®Google Scholar
• Liu, L., Iketani, S., Guo, Y., Chan, J. F.-W., Wang, M., Liu, L., Luo, Y., Chu, H., Huang, Y., Nair, M. S., Yu, J., Chik, K. K.-H., Yuen, T. T.-T., Yoon, C., To, K. K.-W., Chen, H., Yin, M. T., Sobieszczyk, M. E., Huang, Y., … Ho, D. D. (2022). Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature, 602(7898), 676–681. https://doi.org/10.1038/s41586-021-04388-0
   PubMed Web of Science ®Google Scholar
• López, J. L., Lozano, M. J., Fabre, M. L., & Lagares, A. (2020). Codon usage optimization in the prokaryotic tree of life: How synonymous codons are differentially selected in sequence domains with different expression levels and degrees of conservation. MBio, 11(4), e00766-20. https://doi.org/10.1128/mBio.00766-20
   Web of Science ®Google Scholar
• Lyngse, F. P., Kirkeby, C. T., Denwood, M., Christiansen, L. E., Mølbak, K., Møller, C. H., Skov, R. L., Krause, T. G., Rasmussen, M., Sieber, R. N., & Johannesen, T. B. (2022). Transmission of SARS-CoV-2 Omicron VOC subvariants BA. 1 and BA. 2: evidence from Danish households. MedRxiv. 2022–2001.
   Google Scholar
• Ma, C., Chen, X., Mei, F., Xiong, Q., Liu, Q., Dong, L., Liu, C., Zou, W., Zhan, F., Hu, B., Liu, Y., Liu, F., Zhou, L., Xu, J., Jiang, Y., Xu, K., Cai, K., Chen, Y., Yan, H., & Lan, K. (2022). Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. Emerging Microbes & Infections, 11(1), 567–572. https://doi.org/10.1080/22221751.2022.2031311
   PubMed Web of Science ®Google Scholar
• Majumdar, S., & Sarkar, R. (2022). Mutational and phylogenetic analyses of the two lineages of the Omicron variant. Journal of Medical Virology, 94(5), 1777–1779. https://doi.org/10.1002/jmv.27558
   PubMed Web of Science ®Google Scholar
• Mandal, N., Padhi, A. K., & Rath, S. L. (2022). Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern. Journal of Molecular Graphics & Modelling, 114, 108194. https://doi.org/10.1016/j.jmgm.2022.108194
   PubMed Web of Science ®Google Scholar
• Meng, B., Kemp, S. A., Papa, G., Datir, R., Ferreira, I. A. T. M., Marelli, S., Harvey, W. T., Lytras, S., Mohamed, A., Gallo, G., Thakur, N., Collier, D. A., Mlcochova, P., Duncan, L. M., Carabelli, A. M., Kenyon, J. C., Lever, A. M., De Marco, A., Saliba, C., … Gupta, R. K. (2021). Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Reports, 35(13), 109292. https://doi.org/10.1016/j.celrep.2021.109292
   PubMed Web of Science ®Google Scholar
• Moran, A., Beavis, K. G., Matushek, S. M., Ciaglia, C., Francois, N., Tesic, V., & Love, N. (2020). Detection of SARS-CoV-2 by use of the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 assays. Journal of Clinical Microbiology, 58(8), e00772-20. https://doi.org/10.1128/JCM.00772-20
   PubMed Web of Science ®Google Scholar
• Neuman, B. W., Brashear, W. A., Brun, M., Chaki, S. P., Fischer, R. S. B., Guidry, S. J., Hill, J. E., Hillhouse, A. E., Johnson, C. D., Kahl-McDonagh, M. M., Metz, R. P., Rice-Ficht, A. C., Shuford, J. A., Skaggs, T. A., Stull, M. A., Threadgill, D. W., Akpalu, Y., & Zuelke, K. (2021). Case Report: Paucisymptomatic college-age population as a reservoir for potentially neutralization-resistant severe acute respiratory syndrome coronavirus 2 variants. The American Journal of Tropical Medicine and Hygiene, 105(5), 1227–1229. https://doi.org/10.4269/ajtmh.21-0542
   PubMed Web of Science ®Google Scholar
• Ozono, S., Zhang, Y., Ode, H., Sano, K., Tan, T. S., Imai, K., Miyoshi, K., Kishigami, S., Ueno, T., Iwatani, Y., Suzuki, T., & Tokunaga, K. (2021). SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Nature Communications, 12(1), 848. https://doi.org/10.1038/s41467-021-21118-2
   PubMed Web of Science ®Google Scholar
• Pascarella, S., Ciccozzi, M., Zella, D., Bianchi, M., Benedetti, F., Benvenuto, D., Broccolo, F., Cauda, R., Caruso, A., Angeletti, S., Giovanetti, M., & Cassone, A. (2021). SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Journal of Medical Virology, 93(12), 6551–6556. https://doi.org/10.1002/jmv.27210
   PubMed Web of Science ®Google Scholar
• Pastorio, C., Zech, F., Noettger, S., Jung, C., Jacob, T., Sanderson, T., Sparrer, K. M. J., & Kirchhoff, F. (2022). Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA. 1 and BA. 2. Cell Host & Microbe, 30(9), 1255–1268.e5. https://doi.org/10.1016/j.chom.2022.07.006
   PubMed Web of Science ®Google Scholar
• Paz, M., Aldunate, F., Arce, R., Ferreiro, I., & Cristina, J. (2022). An evolutionary insight into Severe Acute Respiratory Syndrome Coronavirus 2 Omicron variant of concern. Virus Research, 314, 198753. https://doi.org/10.1016/j.virusres.2022.198753
   PubMed Web of Science ®Google Scholar
• Peden, J. F. (1999). Analysis of codon usage. Doctoral dissertation, University of Nottingham.
   Google Scholar
• Pfeifer, B., Wittelsbürger, U., Ramos-Onsins, S. E., & Lercher, M. J. (2014). PopGenome: An efficient Swiss army knife for population genomic analyses in R. Molecular Biology and Evolution, 31(7), 1929–1936. https://doi.org/10.1093/molbev/msu136
   PubMed Web of Science ®Google Scholar
• Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN). Package https://pangolin.cog-uk.io/.
   Google Scholar
• Plante, J. A., Liu, Y., Liu, J., Xia, H., Johnson, B. A., Lokugamage, K. G., Zhang, X., Muruato, A. E., Zou, J., Fontes-Garfias, C. R., Mirchandani, D., Scharton, D., Bilello, J. P., Ku, Z., An, Z., Kalveram, B., Freiberg, A. N., Menachery, V. D., Xie, X., … Shi, P.-Y. (2021). Spike mutation D614G alters SARS-CoV-2 fitness. Nature, 592(7852), 116–121. https://doi.org/10.1038/s41586-020-2895-3
   PubMed Web of Science ®Google Scholar
• Puigbò, P., Bravo, I. G., & Garcia-Vallve, S. (2008). CAIcal: A combined set of tools to assess codon usage adaptation. Biology Direct, 3, 38. https://doi.org/10.1186/1745-6150-3-38
   PubMed Web of Science ®Google Scholar
• Rambaut, A., Holmes, E. C., O'Toole, Á., Hill, V., McCrone, J. T., Ruis, C., Du Plessis, L., & Pybus, O. G. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403–1407. https://doi.org/10.1038/s41564-020-0770-5
   PubMed Web of Science ®Google Scholar
• Ramesh, S., Govindarajulu, M., Parise, R. S., Neel, L., Shankar, T., Patel, S., Lowery, P., Smith, F., Dhanasekaran, M., & Moore, T. (2021). Emerging SARS-CoV-2 variants: A review of its mutations, its implications and vaccine efficacy. Vaccines, 9(10), 1195. https://doi.org/10.3390/vaccines9101195
   Web of Science ®Google Scholar
• Rath, S. L., Padhi, A. K., & Mandal, N. (2022). Scanning the RBD-ACE2 molecular interactions in Omicron variant. Biochemical and Biophysical Research Communications, 592, 18–23. https://doi.org/10.1016/j.bbrc.2022.01.006
   PubMed Web of Science ®Google Scholar
• Saha, S., & Raghava, G. P. (2007). Predicting virulence factors of immunological interest. Methods in Molecular Biology. 409, 407–415.
   PubMedGoogle Scholar
• Saha, S., & Raghava, G. P. S. (2006). VICMpred: SVM-based method for the prediction of functional proteins of gram-negative bacteria using amino acid patterns and composition. Genomics, Proteomics & Bioinformatics, 4(1), 42–47. https://doi.org/10.1016/S1672-0229(06)60015-6
   PubMedGoogle Scholar
• Saville, J. W., Mannar, D., Zhu, X., Srivastava, S. S., Berezuk, A. M., Demers, J.-P., Zhou, S., Tuttle, K. S., Sekirov, I., Kim, A., Li, W., Dimitrov, D. S., & Subramaniam, S. (2022). Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Nature Communications, 13(1), 742. https://doi.org/10.1038/s41467-022-28324-6
   PubMed Web of Science ®Google Scholar
• Schwede, T., Kopp, J., Guex, N., & Peitsch, M. C. (2003). SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Research, 31(13), 3381–3385. https://doi.org/10.1093/nar/gkg520
   PubMed Web of Science ®Google Scholar
• Sharp, P. M., Tuohy, T. M., & Mosurski, K. R. (1986). Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Research, 14(13), 5125–5143. https://doi.org/10.1093/nar/14.13.5125
   PubMed Web of Science ®Google Scholar
• Silverj, A., & Rota-Stabelli, O. (2020). On the correct interpretation of similarity index in codon usage studies: Comparison with four other metrics and implications for Zika and West Nile virus. Virus Research, 286, 198097. https://doi.org/10.1016/j.virusres.2020.198097
   PubMed Web of Science ®Google Scholar
• Simmonds, P. (2020). Rampant C→U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses: Causes and consequences for their short- and long-term evolutionary trajectories. mSphere, 5(3), e00408-20. https://doi.org/10.1128/mSphere.00408-20
   PubMed Web of Science ®Google Scholar
• Sunita, Singhvi, N., Singh, Y., & Shukla, P. (2020). Computational approaches in epitope design using DNA binding proteins as vaccine candidate in Mycobacterium tuberculosis. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 83, 104357. https://doi.org/10.1016/j.meegid.2020.104357
   PubMed Web of Science ®Google Scholar
• Tragni, V., Preziusi, F., Laera, L., Onofrio, A., Mercurio, I., Todisco, S., Volpicella, M., De Grassi, A., & Pierri, C. L. (2022). Modeling SARS-CoV-2 spike/ACE2 protein–protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. The EPMA Journal, 13(1), 149–175. https://doi.org/10.1007/s13167-021-00267-w
   PubMed Web of Science ®Google Scholar
• Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A., & Minh, B. Q. (2016). W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research, 44(W1), W232–5. https://doi.org/10.1093/nar/gkw256
   PubMed Web of Science ®Google Scholar
• Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., Olsson, I., Edlund, K., Lundberg, E., Navani, S., Szigyarto, C. A.-K., Odeberg, J., Djureinovic, D., Takanen, J. O., Hober, S., … Pontén, F. (2015). Proteomics. Tissue-based map of the human proteome. Science (New York, N.Y.), 347(6220), 1260419. https://doi.org/10.1126/science.1260419
   PubMed Web of Science ®Google Scholar
• Uraki, R., Kiso, M., Iida, S., Imai, M., Takashita, E., Kuroda, M., Halfmann, P. J., Loeber, S., Maemura, T., Yamayoshi, S., Fujisaki, S., Wang, Z., Ito, M., Ujie, M., Iwatsuki-Horimoto, K., Furusawa, Y., Wright, R., Chong, Z., Ozono, S., … Kawaoka, Y. (2022). Characterization and antiviral susceptibility of SARS-CoV-2 Omicron BA. 2. Nature, 607(7917), 119–127. https://doi.org/10.1038/s41586-022-04856-1
   PubMed Web of Science ®Google Scholar
• Wacharapluesadee, S., Tan, C. W., Maneeorn, P., Duengkae, P., Zhu, F., Joyjinda, Y., Kaewpom, T., Chia, W. N., Ampoot, W., Lim, B. L., Worachotsueptrakun, K., Chen, V. C.-W., Sirichan, N., Ruchisrisarod, C., Rodpan, A., Noradechanon, K., Phaichana, T., Jantarat, N., Thongnumchaima, B., … Wang, L. F. (2021). Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia. Nature Communications, 12(1), 1–9.
   PubMed Web of Science ®Google Scholar
• Weissman, D., Alameh, M.-G., de Silva, T., Collini, P., Hornsby, H., Brown, R., LaBranche, C. C., Edwards, R. J., Sutherland, L., Santra, S., Mansouri, K., Gobeil, S., McDanal, C., Pardi, N., Hengartner, N., Lin, P. J. C., Tam, Y., Shaw, P. A., Lewis, M. G., … Montefiori, D. C. (2021). D614G spike mutation increases SARS CoV-2 susceptibility to neutralization. Cell Host & Microbe, 29(1), 23–31.e4. https://doi.org/10.1016/j.chom.2020.11.012
   PubMed Web of Science ®Google Scholar
• WHO Statement on Omicron sublineage BA.2. (2022). https://www.who.int/news/item/22-02-2022-statement-on-omicron-sublineage-ba.2.
   Google Scholar
• Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., Yuan, M.-L., Zhang, Y.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E. C., & Zhang, Y.-Z. (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
   PubMed Web of Science ®Google Scholar
• Xu, Y., Wu, C., Cao, X., Gu, C., Liu, H., Jiang, M., Wang, X., Yuan, Q., Wu, K., Liu, J., Wang, D., He, X., Wang, X., Deng, S.-J., Xu, H. E., & Yin, W. (2022). Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins. Cell Research, 32(7), 609–620. https://doi.org/10.1038/s41422-022-00672-4
   PubMed Web of Science ®Google Scholar
• Yamasoba, D., Kimura, I., Nasser, H., Morioka, Y., Nao, N., Ito, J., Uriu, K., Tsuda, M., Zahradnik, J., Shirakawa, K., Suzuki, R., Kishimoto, M., Kosugi, Y., Kobiyama, K., Hara, T., Toyoda, M., Tanaka, Y. L., Butlertanaka, E. P., Shimizu, R., … Sato, K. (2022). Virological characteristics of the SARS-CoV-2 Omicron BA. 2 spike. Cell, 185(12), 2103–2115.e19. https://doi.org/10.1016/j.cell.2022.04.035
   PubMed Web of Science ®Google Scholar
• Yamasoba, D., Kimura, I., Nasser, H., Morioka, Y., Nao, N., Ito, J., Uriu, K., Tsuda, M., Zahradnik, J., Shirakawa, K., & Suzuki, R. (2022). Virological characteristics of SARS-CoV-2 BA. 2 variant. Biorxiv.
   Google Scholar
• Zhou, J-h., Zhang, J., Sun, D-j., Ma, Q., Chen, H-t., Ma, L-n., Ding, Y-z., & Liu, Y-s (2013). The distribution of synonymous codon choice in the translation initiation region of dengue virus. PLoS One, 8(10), e77239. https://doi.org/10.1371/journal.pone.0077239
   PubMed Web of Science ®Google Scholar