{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:08:48Z","timestamp":1760144928775,"version":"build-2065373602"},"reference-count":45,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2024,6,3]],"date-time":"2024-06-03T00:00:00Z","timestamp":1717372800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Shanxi Provincial Key R&amp;D Project","award":["202003D31005\/GZ"],"award-info":[{"award-number":["202003D31005\/GZ"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA genome-containing virus which has infected millions of people all over the world. The virus has been mutating rapidly enough, resulting in the emergence of new variants and sub-variants which have reportedly been spread from Wuhan city in China, the epicenter of the virus, to the rest of China and all over the world. The occurrence of mutations in the viral genome, especially in the viral spike protein region, has resulted in the evolution of multiple variants and sub-variants which gives the virus the benefit of host immune evasion and thus renders modern-day vaccines and therapeutics ineffective. Therefore, there is a continuous need to study the genetic characteristics and evolutionary dynamics of the SARS-CoV-2 variants. Hence, in this study, a total of 832 complete genomes of SARS-CoV-2 variants from the cities of Taiyuan and Wuhan in China was genetically characterized and their phylogenetic and evolutionary dynamics studied using phylogenetics, genetic similarity, and phylogenetic network analyses. This study shows that the four most prevalent lineages in Taiyuan and Wuhan are as follows: the Omicron lineages EG.5.1.1, followed by HK.3, FY.3, and XBB.1.16 (Pangolin classification), and clades 23F (EG.5.1), followed by 23H (HK.3), 22F (XBB), and 23D (XBB.1.9) (Nextclade classification), and lineage B followed by the Omicron FY.3, lineage A, and Omicron FL.2.3 (Pangolin classification), and the clades 19A, followed by 22F (XBB), 23F (EG.5.1), and 23H (HK.3) (Nextclade classification), respectively. Furthermore, our genetic similarity analysis show that the SARS-CoV-2 clade 19A-B.4 from Wuhan (name starting with 412981) has the least genetic similarity of about 95.5% in the spike region of the genome as compared to the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234), followed by the Omicron FR.1.4 from Taiyuan (name starting with 18495199) with ~97.2% similarity and Omicron DY.3 (name starting with 17485740) with ~97.9% similarity. The rest of the variants showed \u226598% similarity with the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234). In addition, our recombination analysis results show that the SARS-CoV-2 variants have three statistically significant recombinant events which could have possibly resulted in the emergence of Omicron XBB.1.16 (recombination event 3), FY.3 (recombination event 5), and FL.2.4 (recombination event 7), suggesting some very important information regarding viral evolution. Also, our phylogenetic tree and network analyses show that there are a total of 14 clusters and more than 10,000 mutations which may have probably resulted in the emergence of cluster-I, followed by 47 mutations resulting in the emergence of cluster-II and so on. The clustering of the viral variants of both cities reveals significant information regarding the phylodynamics of the virus among them. The results of our temporal phylogenetic analysis suggest that the variants of Taiyuan have likely emerged as independent variants separate from the variants of Wuhan. This study, to the best of our knowledge, is the first ever genetic comparative study between Taiyuan and Wuhan cities in China. This study will help us better understand the virus and cope with the emergence and spread of new variants at a local as well as an international level, and keep the public health authorities informed for them to make better decisions in designing new viral vaccines and therapeutics. It will also help the outbreak investigators to better examine any future outbreak.<\/jats:p>","DOI":"10.3390\/v16060907","type":"journal-article","created":{"date-parts":[[2024,6,5]],"date-time":"2024-06-05T08:43:54Z","timestamp":1717577034000},"page":"907","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Evolutionary and Phylogenetic Dynamics of SARS-CoV-2 Variants: A Genetic Comparative Study of Taiyuan and Wuhan Cities of China"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7029-2940","authenticated-orcid":false,"given":"Behzad","family":"Hussain","sequence":"first","affiliation":[{"name":"Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China"},{"name":"Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Changxin","family":"Wu","sequence":"additional","affiliation":[{"name":"Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China"},{"name":"Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China"},{"name":"The Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China"},{"name":"Shanxi Provincial Key Laboratory for Major Infectious Disease Response, Taiyuan 030006, China"},{"name":"The Fourth People\u2019s Hospital of Taiyuan, Taiyuan 030006, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,6,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e48","DOI":"10.1016\/j.jinf.2020.06.059","article-title":"Viral dynamics of SARS-CoV-2 in saliva from infected patients","volume":"81","author":"Zhu","year":"2020","journal-title":"J. Infect."},{"key":"ref_3","unstructured":"Cucinotta, D., and Vanelli, M. (2020). WHO declares COVID-19 a pandemic. Acta Biomedica Atenei Parmensis, 91."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/S0140-6736(20)30251-8","article-title":"Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding","volume":"395","author":"Lu","year":"2020","journal-title":"Lancet"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"R849","DOI":"10.1016\/j.cub.2020.06.031","article-title":"On the evolutionary epidemiology of SARS-CoV-2","volume":"30","author":"Day","year":"2020","journal-title":"Curr. Biol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Tang, D., Comish, P., and Kang, R. (2020). The hallmarks of COVID-19 disease. PLoS Pathog., 16.","DOI":"10.1371\/journal.ppat.1008536"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Gribble, J., Stevens, L.J., Agostini, M.L., Anderson-Daniels, J., Chappell, J.D., Lu, X., Pruijssers, A.J., Routh, A.L., and Denison, M.R. (2021). The coronavirus proofreading exoribonuclease mediates extensive viral recombination. PLoS Pathog., 17.","DOI":"10.1371\/journal.ppat.1009226"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1016\/j.cell.2020.06.043","article-title":"Tracking changes in SARS-CoV-2 spike: Evidence that D614G increases infectivity of the COVID-19 virus","volume":"182","author":"Korber","year":"2020","journal-title":"Cell"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"veab064","DOI":"10.1093\/ve\/veab064","article-title":"Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool","volume":"7","author":"Scher","year":"2021","journal-title":"Virus Evol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1097\/JS9.0000000000000276","article-title":"SARS-CoV-2 variant omicron XBB. 1.5: Challenges and prospects\u2013correspondence","volume":"109","author":"Channabasappa","year":"2023","journal-title":"Int. J. Surg."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Haddad, D., John, S.E., Mohammad, A., Hammad, M.M., Hebbar, P., Channanath, A., Nizam, R., Al-Qabandi, S., Al Madhoun, A., and Alshukry, A. (2021). SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0251368"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41435-020-00120-6","article-title":"Evolutionary and structural analysis of SARS-CoV-2 specific evasion of host immunity","volume":"21","author":"Hussain","year":"2020","journal-title":"Genes Immun."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"veaa061","DOI":"10.1093\/ve\/veaa061","article-title":"Temporal signal and the phylodynamic threshold of SARS-CoV-2","volume":"6","author":"Duchene","year":"2020","journal-title":"Virus Evol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1038\/s41564-021-00908-w","article-title":"The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets","volume":"6","author":"Peacock","year":"2021","journal-title":"Nat. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"30494","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","article-title":"GISAID: Global initiative on sharing all influenza data\u2013from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Eurosurveillance"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1186\/s12985-023-02139-3","article-title":"Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations","volume":"20","author":"Bhattacharjee","year":"2023","journal-title":"Virol J."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"100682","DOI":"10.1016\/j.genrep.2020.100682","article-title":"Genomic characterization of a novel SARS-CoV-2","volume":"19","author":"Khailany","year":"2020","journal-title":"Gene Rep."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1038\/s41564-020-0771-4","article-title":"Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic","volume":"5","author":"Boni","year":"2020","journal-title":"Nat. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Rehman, S.U., Shafique, L., Ihsan, A., and Liu, Q. (2020). Evolutionary trajectory for the emergence of novel coronavirus SARS-CoV-2. Pathogens, 9.","DOI":"10.3390\/pathogens9030240"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1093\/bioinformatics\/bts091","article-title":"Unipro UGENE: A unified bioinformatics toolkit","volume":"28","author":"Okonechnikov","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization","volume":"20","author":"Katoh","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_22","first-page":"95","article-title":"BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95\/98\/NT","volume":"41","author":"Hall","year":"1999","journal-title":"Nucleic Acids Symp. Ser."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"W232","DOI":"10.1093\/nar\/gkw256","article-title":"W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis","volume":"44","author":"Trifinopoulos","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","article-title":"Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation","volume":"23","author":"Letunic","year":"2007","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","article-title":"Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination","volume":"73","author":"Lole","year":"1999","journal-title":"J. Virol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"veaa087","DOI":"10.1093\/ve\/veaa087","article-title":"RDP5: A computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets","volume":"7","author":"Martin","year":"2021","journal-title":"Virus Evol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1093\/bioinformatics\/bth500","article-title":"Recombination Analysis Tool (RAT): A program for the high-throughput detection of recombination","volume":"21","author":"Etherington","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"POPART: Full-feature software for haplotype network construction","volume":"6","author":"Leigh","year":"2015","journal-title":"Methods Ecol. Evol."},{"key":"ref_30","unstructured":"Centers for Disease Control and Prevention (2021). SARS-CoV-2 Variant Classifications and Definitions, Centers for Disease Control and Prevention."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1038\/s41586-021-04188-6","article-title":"The emergence, genomic diversity and global spread of SARS-CoV-2","volume":"600","author":"Li","year":"2021","journal-title":"Nature"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e30019","DOI":"10.1097\/MD.0000000000030019","article-title":"Epidemiologic characteristics of SARS-CoV-2 in Wuhan, other regions of China, and globally based on data gathered from January 2020 to February 2021","volume":"101","author":"Fengjiao","year":"2022","journal-title":"Medicine"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1981","DOI":"10.1007\/s11071-020-05770-9","article-title":"Transmission dynamics of COVID-19 in Wuhan, China: Effects of lockdown and medical resources","volume":"101","author":"Sun","year":"2020","journal-title":"Nonlinear Dyn."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1186\/s12879-021-06515-8","article-title":"Spatio-temporal distribution characteristics of COVID-19 in China: A city-level modeling study","volume":"21","author":"Ma","year":"2021","journal-title":"BMC Infect. Dis."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"891418","DOI":"10.3389\/fgene.2022.891418","article-title":"A bioinformatics approach to investigate structural and non-structural proteins in human coronaviruses","volume":"13","author":"Cicaloni","year":"2022","journal-title":"Front. Genet."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Ahmadi, E., Zabihi, M.R., Hosseinzadeh, R., Mohamed Khosroshahi, L., and Noorbakhsh, F. (2021). SARS-CoV-2 spike protein displays sequence similarities with paramyxovirus surface proteins; a bioinformatics study. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0260360"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Olivero, N.B., Gonzalez-Reiche, A.S., Re, V.E., Castro, G.M., Pisano, M.B., Sicilia, P., Barbas, M.G., Khan, Z., van de Guchte, A., and Dutta, J. (2022). Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina. BMC Genom., 23.","DOI":"10.1186\/s12864-022-08756-6"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"198098","DOI":"10.1016\/j.virusres.2020.198098","article-title":"Phylogenetic and phylodynamic analyses of SARS-CoV-2","volume":"287","author":"Nie","year":"2020","journal-title":"Virus Res."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Turkahia, Y., Thornlow, B., Hinrichs, A., McBroome, J., Ayala, N., Ye, C., De Maio, N., Haussler, D., Lanfear, R., and Corbett-Detig, R. (2021). Pandemic-scale phylogenomics reveals elevated recombination rates in the SARS-CoV-2 spike region. BioRxiv.","DOI":"10.1101\/2021.08.04.455157"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"5179","DOI":"10.1016\/j.cell.2021.08.014","article-title":"Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic","volume":"184","author":"Jackson","year":"2021","journal-title":"Cell"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1016\/j.medj.2022.10.002","article-title":"Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination","volume":"3","author":"Bolze","year":"2022","journal-title":"Med"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Focosi, D., and Maggi, F. (2022). Recombination in Coronaviruses, with a Focus on SARS-CoV-2. Viruses, 14.","DOI":"10.3390\/v14061239"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Al-Jawabreh, A., Ereqat, S., Dumaidi, K., Al-Jawabreh, H., and Nasereddin, A. (2021). Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. BMC Res. Notes, 14.","DOI":"10.1186\/s13104-021-05874-4"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2297","DOI":"10.1016\/j.scib.2021.02.012","article-title":"Evolutionary analysis and lineage designation of SARS-CoV-2 genomes","volume":"66","author":"Tang","year":"2021","journal-title":"Sci. Bull."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/j.ijid.2020.08.066","article-title":"Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes reveal its epidemic trends","volume":"100","author":"Bai","year":"2020","journal-title":"Int. J. Infect. Dis."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/6\/907\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:53:14Z","timestamp":1760107994000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/6\/907"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,3]]},"references-count":45,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2024,6]]}},"alternative-id":["v16060907"],"URL":"https:\/\/doi.org\/10.3390\/v16060907","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2024,6,3]]}}}