{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T12:14:27Z","timestamp":1780575267890,"version":"3.54.1"},"reference-count":75,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2023,4,13]],"date-time":"2023-04-13T00:00:00Z","timestamp":1681344000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Universidad Iberoamericana","award":["MD007579"],"award-info":[{"award-number":["MD007579"]}]},{"name":"Research Vice-provost Office","award":["MD007579"],"award-info":[{"award-number":["MD007579"]}]},{"name":"National Health Service (SNS) of the Dominican Republic\u2019s Ministry of Health","award":["MD007579"],"award-info":[{"award-number":["MD007579"]}]},{"name":"Research Centers in Minority Institutions (RCMI) Center for Research Resources","award":["MD007579"],"award-info":[{"award-number":["MD007579"]}]},{"DOI":"10.13039\/100006545","name":"National Institute on Minority Health and Health Disparities","doi-asserted-by":"publisher","award":["MD007579"],"award-info":[{"award-number":["MD007579"]}],"id":[{"id":"10.13039\/100006545","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJERPH"],"abstract":"<jats:p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin\/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 \u00d7 10\u22123 (95% HPD: 1.2358 \u00d7 10\u22123, 1.8635 \u00d7 10\u22123) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.<\/jats:p>","DOI":"10.3390\/ijerph20085503","type":"journal-article","created":{"date-parts":[[2023,4,14]],"date-time":"2023-04-14T02:03:38Z","timestamp":1681437818000},"page":"5503","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage"],"prefix":"10.3390","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3676-0357","authenticated-orcid":false,"given":"Robert","family":"Paulino-Ram\u00edrez","sequence":"first","affiliation":[{"name":"Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"L\u00f3pez","sequence":"additional","affiliation":[{"name":"RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sayira","family":"Mueses","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paula","family":"Cuevas","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maridania","family":"Jabier","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic"},{"name":"Servicio Nacional de Salud (SNS), Ministry of Health, Santo Domingo 10201, Dominican Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4810-0871","authenticated-orcid":false,"given":"Vanessa","family":"Rivera-Amill","sequence":"additional","affiliation":[{"name":"RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA"},{"name":"Basic Sciences Department, School of Medicine, Ponce Health Sciences University, Ponce, PR 00716-2348, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,4,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1097\/CM9.0000000000000722","article-title":"Identification of a novel coronavirus causing severe pneumonia in human: A descriptive study","volume":"133","author":"Ren","year":"2020","journal-title":"Chin. Med. J."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.chom.2020.02.001","article-title":"Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China","volume":"27","author":"Wu","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41579-018-0118-9","article-title":"Origin and evolution of pathogenic coronaviruses","volume":"17","author":"Cui","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1038\/s41564-020-0770-5","article-title":"A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology","volume":"5","author":"Rambaut","year":"2020","journal-title":"Nat. Microbiol."},{"key":"ref_5","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_6","doi-asserted-by":"crossref","first-page":"3134","DOI":"10.1128\/JVI.01394-09","article-title":"Recombination, reservoirs, and the modular spike: Mechanisms of coronavirus cross-species transmission","volume":"84","author":"Graham","year":"2010","journal-title":"J. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"9241","DOI":"10.1073\/pnas.2004999117","article-title":"Phylogenetic network analysis of SARS-CoV-2 genomes","volume":"117","author":"Forster","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","first-page":"110","article-title":"Early appearance of two distinct genomic lineages of SARS-CoV-2 in different Wuhan wildlife markets suggests SARS-CoV-2 has a natural origin","volume":"900","author":"Garry","year":"2021","journal-title":"Virological"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1126\/science.abp8715","article-title":"The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic","volume":"377","author":"Worobey","year":"2022","journal-title":"Science"},{"key":"ref_10","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_11","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.1126\/science.abe8499","article-title":"SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo","volume":"370","author":"Hou","year":"2020","journal-title":"Science"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"eabf3671","DOI":"10.1126\/sciadv.abf3671","article-title":"The SARS-CoV-2 Spike variant D614G favors an open conformational state","volume":"7","author":"Mansbach","year":"2021","journal-title":"Sci. Adv."},{"key":"ref_13","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_14","doi-asserted-by":"crossref","unstructured":"Sui, J., Aird, D.R., Tamin, A., Murakami, A., Yan, M., Yammanuru, A., Jing, H., Kan, B., Liu, X., and Zhu, Q. (2008). Broadening of neutralization activity to directly block a dominant antibody-driven SARS-coronavirus evolution pathway. PLoS Pathog., 4.","DOI":"10.1371\/journal.ppat.1000197"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e0095221","DOI":"10.1128\/MRA.00952-21","article-title":"Whole-Genome Sequences of SARS-CoV-2 Isolates from the Dominican Republic","volume":"10","author":"Riego","year":"2021","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Paulino-Ramirez, R., and Tapia, L. (2020). Learning from pandemics in the Americas: The Dominican Republic Programmatic response against a novel coronavirus (COVID-19). Inter. Am. J. Med. Health, 3.","DOI":"10.31005\/iajmh.v3i0.104"},{"key":"ref_17","unstructured":"Acosta, I. (2023, February 04). Response to COVID-19 in the Dominican Republic; WHO Country Report. Available online: https:\/\/apps.who.int\/gb\/COVID-19\/pdf_files\/24_09\/Dominican_Republic.pdf."},{"key":"ref_18","unstructured":"Andrickson, I. (2023, February 04). Measures Adopted by the Dominican Republic in Response to the COVID-19 Pandemic; 2020. Available online: http:\/\/phlaw.com\/imagen?file=articulos\/593\/measures-adopted-by-dominican-republic-in-response-to-covid-19-pandemic."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2343","DOI":"10.4269\/ajtmh.20-0907","article-title":"Seroprevalence of Specific Antibodies against SARS-CoV-2 from Hotspot Communities in the Dominican Republic","volume":"103","author":"Baez","year":"2020","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_20","unstructured":"(2023, February 04). Global Health Security Index 2019 Report. Available online: https:\/\/www.ghsindex.org\/wp-content\/uploads\/2019\/10\/2019-Global-Health-Security-Index.pdf."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"637187","DOI":"10.3389\/frma.2021.637187","article-title":"Decolonizing Science Diplomacy: A Case Study of the Dominican Republic\u2019s COVID-19 Response","volume":"6","author":"Jimenez","year":"2021","journal-title":"Front Res. Metr. Anal."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"104981","DOI":"10.1016\/j.compbiomed.2021.104981","article-title":"Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database","volume":"139","author":"Zelenova","year":"2021","journal-title":"Comput. Biol. Med."},{"key":"ref_23","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\u2014From vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Euro Surveill."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.46234\/ccdcw2021.255","article-title":"GISAID\u2019s Role in Pandemic Response","volume":"3","author":"Khare","year":"2021","journal-title":"China CDC Wkly."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3552","DOI":"10.1093\/bioinformatics\/btaa145","article-title":"Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes","volume":"36","author":"Cleemput","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"111599","DOI":"10.1016\/j.biopha.2021.111599","article-title":"Novel and emerging mutations of SARS-CoV-2: Biomedical implications","volume":"139","author":"Mohammadi","year":"2021","journal-title":"Biomed. Pharm."},{"key":"ref_27","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_28","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_29","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2\u2014A multiple sequence alignment editor and analysis workbench","volume":"25","author":"Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_30","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_31","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_32","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_33","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_34","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1093\/bioinformatics\/14.9.817","article-title":"Modeltest: Testing the model of DNA substitution","volume":"14","author":"Posada","year":"1998","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1038\/s41591-021-01255-3","article-title":"Sixteen novel lineages of SARS-CoV-2 in South Africa","volume":"27","author":"Tegally","year":"2021","journal-title":"Nat. Med."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1093\/molbev\/msi103","article-title":"Bayesian coalescent inference of past population dynamics from molecular sequences","volume":"22","author":"Drummond","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"ref_37","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_38","doi-asserted-by":"crossref","first-page":"veab087","DOI":"10.1093\/ve\/veab087","article-title":"Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil","volume":"7","author":"Moreira","year":"2021","journal-title":"Virus Evol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3238","DOI":"10.1002\/jmv.26678","article-title":"Coronapp: A web application to annotate and monitor SARS-CoV-2 mutations","volume":"93","author":"Mercatelli","year":"2021","journal-title":"J. Med. Virol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e11015","DOI":"10.7717\/peerj.11015","article-title":"Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon","volume":"9","author":"Feghali","year":"2021","journal-title":"PeerJ"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41579-021-00573-0","article-title":"SARS-CoV-2 variants, spike mutations and immune escape","volume":"19","author":"Harvey","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e0173621","DOI":"10.1128\/JCM.01736-21","article-title":"Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021","volume":"59","author":"Miqueleiz","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Doncarli, A., Araujo-Chaveron, L., Crenn-Hebert, C., Demiguel, V., Boudet-Berquier, J., Barry, Y., Gomes Do Espirito Santo, M.E., Guajardo-Villar, A., Menguy, C., and Tabai, A. (2021). Impact of the SARS-CoV-2 pandemic and first lockdown on pregnancy monitoring in France: The COVIMATER cross-sectional study. BMC Pregnancy Childbirth, 21.","DOI":"10.1186\/s12884-021-04256-9"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"267","DOI":"10.3201\/eid2701.202114","article-title":"Impact of a Nationwide Lockdown on SARS-CoV-2 Transmissibility, Italy","volume":"27","author":"Guzzetta","year":"2021","journal-title":"Emerg. Infect. Dis."},{"key":"ref_45","unstructured":"Tourism Doing Business Investing in Dominican Republic (2020). The World Tourism Organization a United Nations Specialized Agency (UNWTO), The World Tourism Organization."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/s12276-021-00604-z","article-title":"On the origin and evolution of SARS-CoV-2","volume":"53","author":"Singh","year":"2021","journal-title":"Exp. Mol. Med."},{"key":"ref_47","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_48","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1002\/jmv.25731","article-title":"Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2","volume":"92","author":"Li","year":"2020","journal-title":"J. Med. Virol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/s12929-020-00665-8","article-title":"The origin and underlying driving forces of the SARS-CoV-2 outbreak","volume":"27","author":"Chaw","year":"2020","journal-title":"J. BioMed. Sci."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"53","DOI":"10.14302\/issn.2689-4602.jes-21-3837","article-title":"Molecular Evolution of the Novel Coronavirus SARS-CoV-2","volume":"1","author":"Vook","year":"2021","journal-title":"J. Evol. Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"R918","DOI":"10.1016\/j.cub.2021.06.049","article-title":"The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic","volume":"31","author":"Otto","year":"2021","journal-title":"Curr. Biol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/j.chom.2021.03.002","article-title":"SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines","volume":"29","author":"Shen","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"6031","DOI":"10.3389\/fimmu.2021.830527","article-title":"Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies","volume":"12","author":"Shah","year":"2022","journal-title":"Front. Immunol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"751778","DOI":"10.3389\/fimmu.2021.751778","article-title":"The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape","volume":"12","author":"Tian","year":"2021","journal-title":"Front Immunol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1038\/s41586-021-03944-y","article-title":"SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion","volume":"599","author":"Mlcochova","year":"2021","journal-title":"Nature"},{"key":"ref_56","unstructured":"(2022, December 01). Available online: https:\/\/www.who.int\/news\/item\/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"864","DOI":"10.1126\/science.abn8652","article-title":"Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement","volume":"375","author":"McCallum","year":"2022","journal-title":"Science"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Venkatakrishnan, A.J., Anand, P., Lenehan, P.J., Suratekar, R., Raghunathan, B., Niesen, M.J.M., and Soundararajan, V. (2022). On the Origins of Omicron\u2019s Unique Spike Gene Insertion. Vaccines, 10.","DOI":"10.1101\/2022.06.03.22275976"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/s41392-022-00992-2","article-title":"Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events","volume":"7","author":"Ou","year":"2022","journal-title":"Signal Transduct. Target."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"4958","DOI":"10.1038\/s41467-022-32665-7","article-title":"Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape","volume":"13","author":"Zhao","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Martin, D.P., Lytras, S., Lucaci, A.G., Maier, W., Gruning, B., Shank, S.D., Weaver, S., MacLean, O.A., Orton, R.J., and Lemey, P. (2022). Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function. bioRxiv.","DOI":"10.1101\/2022.01.14.476382"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1016\/j.jgg.2021.12.003","article-title":"Evidence for a mouse origin of the SARS-CoV-2 Omicron variant","volume":"48","author":"Wei","year":"2021","journal-title":"J. Genet. Genom."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s12981-020-00301-3","article-title":"Case report: One case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4+ T cell count","volume":"17","author":"Menghua","year":"2020","journal-title":"AIDS Res. Ther."},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Jary, A., Marot, S., Faycal, A., Leon, S., Sayon, S., Zafilaza, K., Ghidaoui, E., Quoc, S.N., Nemlaghi, S., and Choquet, S. (2022). Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. Viruses, 14.","DOI":"10.3390\/v14020226"},{"key":"ref_65","unstructured":"Agency, U.H.S. (2023, February 04). SARS-CoV-2 Variants of Concern and Variants under Investigation in England Technical Briefing: Update on Hospitalisation and Vaccine Effectiveness for Omicron VOC-21NOV-01 (B.1.1.529), Available online: https:\/\/assets.publishing.service.gov.uk\/government\/uploads\/system\/uploads\/attachment_data\/file\/1045619\/Technical-Briefing-31-Dec-2021-Omicron_severity_update.pdf."},{"key":"ref_66","first-page":"642","article-title":"Signals of significantly increased vaccine breakthrough, decreased hospitalization rates, and less severe disease in patients with COVID-19 caused by the Omicron variant of SARS-CoV-2 in Houston, Texas","volume":"192","author":"Christensen","year":"2022","journal-title":"medRxiv"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Ulloa, A.C., Buchan, S.A., Daneman, N., and Brown, K.A. (2022). Early estimates of SARS-CoV-2 Omicron variant severity based on a matched cohort study, Ontario, Canada. medRxiv.","DOI":"10.1101\/2021.12.24.21268382"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e28423","DOI":"10.1002\/jmv.28423","article-title":"Clinical severity of Omicron subvariants BA.1, BA.2, and BA.5 in a population-based cohort study in British Columbia, Canada","volume":"95","author":"Russell","year":"2023","journal-title":"J. Med. Virol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1486","DOI":"10.1016\/j.cmi.2022.05.020","article-title":"Differences in environmental stability among SARS-CoV-2 variants of concern: Both omicron BA.1 and BA.2 have higher stability","volume":"28","author":"Hirose","year":"2022","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Pagan, I., Gonzalez-Jara, P., Moreno-Letelier, A., Rodelo-Urrego, M., Fraile, A., Pinero, D., and Garcia-Arenal, F. (2012). Effect of biodiversity changes in disease risk: Exploring disease emergence in a plant-virus system. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1002796"},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Pagan, I., and Holguin, A. (2013). Reconstructing the timing and dispersion routes of HIV-1 subtype B epidemics in the Caribbean and Central America: A phylogenetic story. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0069218"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.15585\/mmwr.mm7030e2","article-title":"Guidance for Implementing COVID-19 Prevention Strategies in the Context of Varying Community Transmission Levels and Vaccination Coverage","volume":"70","author":"Christie","year":"2021","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s43162-021-00092-7","article-title":"Two years of SARS-CoV-2 infection (2019\u20132021): Structural biology, vaccination, and current global situation","volume":"34","author":"Ahmad","year":"2022","journal-title":"Egypt J. Intern. Med."},{"key":"ref_74","unstructured":"Srivastava, N., and Saxena, S.K. (2020). Coronavirus Disease 2019 (COVID-19)."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"evab087","DOI":"10.1093\/gbe\/evab087","article-title":"Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2","volume":"13","author":"Walker","year":"2021","journal-title":"Genome Biol. Evol."}],"container-title":["International Journal of Environmental Research and Public Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1660-4601\/20\/8\/5503\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:15:43Z","timestamp":1760123743000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1660-4601\/20\/8\/5503"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,13]]},"references-count":75,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2023,4]]}},"alternative-id":["ijerph20085503"],"URL":"https:\/\/doi.org\/10.3390\/ijerph20085503","relation":{},"ISSN":["1660-4601"],"issn-type":[{"value":"1660-4601","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,4,13]]}}}