{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T18:44:12Z","timestamp":1782845052358,"version":"3.54.5"},"reference-count":72,"publisher":"JMIR Publications Inc.","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JMIR Bioinform Biotech"],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Emergence of the new SARS-CoV-2 variant B.1.1.529 worried health policy makers worldwide due to a large number of mutations in its genomic sequence, especially in the spike protein region. The World Health Organization (WHO) designated this variant as a global variant of concern (VOC), which was named \u201cOmicron.\u201d Following Omicron\u2019s emergence, a surge of new COVID-19 cases was reported globally, primarily in South Africa.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>The aim of this study was to understand whether Omicron had an epidemiological advantage over existing variants.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We performed an in silico analysis of the complete genomic sequences of Omicron available on the Global Initiative on Sharing Avian Influenza Data (GISAID) database to analyze the functional impact of the mutations present in this variant on virus-host interactions in terms of viral transmissibility, virulence\/lethality, and immune escape. In addition, we performed a correlation analysis of the relative proportion of the genomic sequences of specific SARS-CoV-2 variants (in the period from October 1 to November 29, 2021) with matched epidemiological data (new COVID-19 cases and deaths) from South Africa.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Compared with the current list of global VOCs\/variants of interest (VOIs), as per the WHO, Omicron bears more sequence variation, specifically in the spike protein and host receptor-binding motif (RBM). Omicron showed the closest nucleotide and protein sequence homology with the Alpha variant for the complete sequence and the RBM. The mutations were found to be primarily condensed in the spike region (n=28-48) of the virus. Further mutational analysis showed enrichment for the mutations decreasing binding affinity to angiotensin-converting enzyme 2 receptor and receptor-binding domain protein expression, and for increasing the propensity of immune escape. An inverse correlation of Omicron with the Delta variant was noted (r=\u20130.99, P&lt;.001; 95% CI \u20130.99 to \u20130.97) in the sequences reported from South Africa postemergence of the new variant, subsequently showing a decrease. There was a steep rise in new COVID-19 cases in parallel with the increase in the proportion of Omicron isolates since the report of the first case (74%-100%). By contrast, the incidence of new deaths did not increase (r=\u20130.04, P&gt;.05; 95% CI \u20130.52 to 0.58).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>In silico analysis of viral genomic sequences suggests that the Omicron variant has more remarkable immune-escape ability than existing VOCs\/VOIs, including Delta, but reduced virulence\/lethality than other reported variants. The higher power for immune escape for Omicron was a likely reason for the resurgence in COVID-19 cases and its rapid rise as the globally dominant strain. Being more infectious but less lethal than the existing variants, Omicron could have plausibly led to widespread unnoticed new, repeated, and vaccine breakthrough infections, raising the population-level immunity barrier against the emergence of new lethal variants. The Omicron variant could have thus paved the way for the end of the pandemic.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.2196\/42700","type":"journal-article","created":{"date-parts":[[2022,12,16]],"date-time":"2022-12-16T02:38:18Z","timestamp":1671158298000},"page":"e42700","source":"Crossref","is-referenced-by-count":4,"title":["SARS-CoV-2 Omicron Variant Genomic Sequences and Their Epidemiological Correlates Regarding the End of the Pandemic: In Silico Analysis"],"prefix":"10.2196","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1589-9568","authenticated-orcid":false,"given":"Ashutosh","family":"Kumar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1404-1298","authenticated-orcid":false,"given":"Adil","family":"Asghar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4111-5165","authenticated-orcid":false,"given":"Himanshu N","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1430-3139","authenticated-orcid":false,"given":"Muneeb A","family":"Faiq","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5427-8735","authenticated-orcid":false,"given":"Sujeet","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2510-6744","authenticated-orcid":false,"given":"Ravi K","family":"Narayan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3100-8908","authenticated-orcid":false,"given":"Gopichand","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8756-1676","authenticated-orcid":false,"given":"Prakhar","family":"Dwivedi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4301-4643","authenticated-orcid":false,"given":"Chetan","family":"Sahni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1292-5927","authenticated-orcid":false,"given":"Rakesh K","family":"Jha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6769-2596","authenticated-orcid":false,"given":"Maheswari","family":"Kulandhasamy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5035-3619","authenticated-orcid":false,"given":"Pranav","family":"Prasoon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6196-5565","authenticated-orcid":false,"given":"Kishore","family":"Sesham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8966-6268","authenticated-orcid":false,"given":"Kamla","family":"Kant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3201-2287","authenticated-orcid":false,"given":"Sada N","family":"Pandey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1010","published-online":{"date-parts":[[2023,1,10]]},"reference":[{"key":"ref1","unstructured":"Tracking of hCoV-19 variantsGISAID2021-07-20https:\/\/www.gisaid.org\/hcov19-variants\/"},{"key":"ref2","unstructured":"Update on OmicronWorld Health Organization202111282021-12-04https:\/\/www.who.int\/news\/item\/28-11-2021-update-on-omicron"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1038\/d41586-021-03552-w"},{"key":"ref4","unstructured":"Omicron variant reportoutbreak.info2022-11-26https:\/\/outbreak.info\/situation-reports\/omicron"},{"key":"ref5","unstructured":"One year since the emergence of COVID-19 virus variant OmicronWorld Health Organization202211252022-11-26https:\/\/www.who.int\/news-room\/feature-stories\/detail\/one-year-since-the-emergence-of-omicron"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(22)00056-3"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2119658"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMp2119682"},{"key":"ref9","unstructured":"StrasserZHadavandAMurphySStrasserZHadavandPAMurphySSARS-CoV-2 Omicron variant is as deadly as previous waves after adjusting for vaccinations, demographics, and comorbiditiesResearch Square Preprints202205022022-12-19https:\/\/assets.researchsquare.com\/files\/rs-1601788\/v1_covered.pdf?c=1651763984"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.27635"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(22)00100-3"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1136\/bmj-2021-068094"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1016\/j.tmaid.2022.102332"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.2196\/36860"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-12442-8"},{"key":"ref16","unstructured":"GISAID2022-11-26https:\/\/gisaid.org\/"},{"key":"ref17","unstructured":"Tracking SARS-CoV-2 variantsWorld Health Organization2021-06-17https:\/\/www.who.int\/en\/activities\/tracking-SARS-CoV-2-variants\/"},{"key":"ref18","unstructured":"SARS-CoV-2 data exploreroutbreak.info2022-11-26https:\/\/outbreak.info\/"},{"key":"ref19","unstructured":"ExpasySwiss Institute of Bioinformatics2022-12-19https:\/\/www.expasy.org\/"},{"key":"ref20","unstructured":"Basic Local Alignment Search ToolNational Library of Medicine2022-11-26https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.08.012"},{"key":"ref22","unstructured":"SARS-CoV-2 RBD DMSJBloom Lab202203032022-12-19https:\/\/jbloomlab.github.io\/SARS-CoV-2-RBD_DMS\/"},{"key":"ref23","unstructured":"South Africa COVID - Coronavirus StatisticsWorldometer2022-11-26https:\/\/www.worldometers.info\/coronavirus\/country\/south-africa"},{"key":"ref24","unstructured":"The statistics of similarity scoresNational Center for Biotechnology Information (NCBI)2022-11-26https:\/\/www.ncbi.nlm.nih.gov\/BLAST\/tutorial\/Altschul-1.html"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.07.012"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2021.1943540"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2020.11.007"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03398-2"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.687869"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2021.02.003"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M111.325803"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-021-01285-x"},{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.06.043"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1009373"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2020.06.020"},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1126\/science.abd0831"},{"key":"ref37","doi-asserted-by":"publisher","DOI":"10.1016\/j.genrep.2021.101420"},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.148855"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2021.103589"},{"key":"ref40","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00097-21"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2021.103353"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-04387-1"},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.10.049"},{"key":"ref44","unstructured":"KarimFMoosaMGosnellBCeleSGiandhariJPillaySPersistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infectionmedRxiv202106042022-12-19https:\/\/www.medrxiv.org\/content\/10.1101\/2021.06.03.21258228v1#:~:text=While%20most%20people%20effectively%20clear,HIV%20and%20antiretroviral%20treatment%20failure"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMc2031364"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veab078"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.27467"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.26615"},{"key":"ref49","unstructured":"S:P681H mutation reportoutbreak.info2021-12-08https:\/\/outbreak.info\/situation-reports?muts=S%3AP681H"},{"key":"ref50","unstructured":"S:P681R mutation reportoutbreak.info2021-12-08https:\/\/outbreak.info\/situation-reports?muts=S%3AP681R"},{"key":"ref51","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiac411"},{"key":"ref52","doi-asserted-by":"publisher","DOI":"10.3389\/fepid.2022.891162"},{"key":"ref53","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbadis.2020.165878"},{"key":"ref54","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04479-6"},{"key":"ref55","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2022.104158"},{"key":"ref56","doi-asserted-by":"publisher","DOI":"10.1038\/s41423-021-00836-z"},{"key":"ref57","doi-asserted-by":"publisher","DOI":"10.1126\/science.abl6251"},{"key":"ref58","unstructured":"ReddANardinAKaredHBlochEAbelBPekoszALaeyendeckerOFehlingsMQuinnTCTobianAAMinimal cross-over between mutations associated with Omicron variant of SARS-CoV-2 and CD8+ T cell epitopes identified in COVID-19 convalescent individualsbioRxiv202112092022-12-19https:\/\/www.biorxiv.org\/content\/10.1101\/2021.12.06.471446v1"},{"key":"ref59","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2021.05.010"},{"key":"ref60","unstructured":"SARS-CoV-2 variants of concern and variants under investigation in England. Variant of concern: Omicron, VOC21NOV-01 (B.1.1.529). Technical briefing 30UK Health Security Agency202112032022-12-19https:\/\/assets.publishing.service.gov.uk\/government\/uploads\/system\/uploads\/attachment_data\/file\/1038404\/Technical_Briefing_30.pdf"},{"key":"ref61","unstructured":"TegallyHWilkinsonEAlthausCGiovanettiMSanJGiandhariJRapid replacement of the Beta variant by the Delta variant in South AfricamedRxiv202109272022-12-19https:\/\/www.medrxiv.org\/content\/10.1101\/2021.09.23.21264018v1"},{"key":"ref62","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-022-00720-5"},{"key":"ref63","doi-asserted-by":"publisher","DOI":"10.1136\/bmj-2022-070695"},{"key":"ref64","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(22)00462-7"},{"key":"ref65","unstructured":"PearsonCSilalSDushoffJAbbottSvan SchalkwykCBinghamJMeyer-RathGJamiesonLGlassAWolterNMoultrieHPulliamJon behalf of the South African COVID-19 Modelling ConsortiumGoogle Drive2021-12-04https:\/\/drive.google.com\/file\/d\/1hA6Mec2Gq3LGqTEOj35RqSeAb_SmXpbI\/view"},{"key":"ref66","unstructured":"SARS-CoV-2 variants of concern and variants under investigation in England. Technical briefing 31UK Health Security Agency202112102022-12-19https:\/\/assets.publishing.service.gov.uk\/government\/uploads\/system\/uploads\/attachment_data\/file\/1040076\/Technical_Briefing_31.pdf"},{"key":"ref67","doi-asserted-by":"publisher","DOI":"10.2196\/35763"},{"key":"ref68","doi-asserted-by":"publisher","DOI":"10.2196\/37377"},{"key":"ref69","unstructured":"Coronavirus (COVID-19) vaccinationsOur World in Data2021-12-06https:\/\/ourworldindata.org\/covid-vaccinations?country=~ZAF)"},{"key":"ref70","unstructured":"Threat Assessment Brief: Implications of the further emergence and spread of the SARS-CoV-2 B.1.1.529 variant of concern (Omicron) for the EU\/EEA - first updateEuropean Centre for Disease Prevention and Control202112022021-12-05https:\/\/www.ecdc.europa.eu\/en\/publications-data\/covid-19-threat-assessment-spread-omicron-first-update"},{"key":"ref71","unstructured":"Science Brief: Omicron (B.1.1.529) VariantCenters for Disease Control and Prevention202112022021-12-05https:\/\/www.cdc.gov\/coronavirus\/2019-ncov\/science\/science-briefs\/scientific-brief-omicron-variant.html#6"},{"key":"ref72","doi-asserted-by":"publisher","DOI":"10.1126\/science.abn4947"}],"container-title":["JMIR Bioinformatics and Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/bioinform.jmir.org\/2023\/1\/e42700","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T17:44:15Z","timestamp":1782841455000},"score":1,"resource":{"primary":{"URL":"https:\/\/bioinform.jmir.org\/2023\/1\/e42700"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,10]]},"references-count":72,"URL":"https:\/\/doi.org\/10.2196\/42700","relation":{},"ISSN":["2563-3570"],"issn-type":[{"value":"2563-3570","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,10]]}}}