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We describe the circulation of VOCs in South Africa and the potential role of low-frequency lineages on the emergence of future lineages. Whole genome sequencing was performed on SARS-CoV-2 samples from South Africa. Sequences were analysed with Nextstrain pangolin tools and Stanford University Coronavirus Antiviral &amp; Resistance Database. In 2020, 24 lineages were detected, with B.1 (3%; 8\/278), B.1.1 (16%; 45\/278), B.1.1.348 (3%; 8\/278), B.1.1.52 (5%; 13\/278), C.1 (13%; 37\/278) and C.2 (2%; 6\/278) circulating during the first wave. Beta emerged late in 2020, dominating the second wave of infection. B.1 and B.1.1 continued to circulate at low frequencies in 2021 and B.1.1 re-emerged in 2022. Beta was outcompeted by Delta in 2021, which was thereafter outcompeted by Omicron sub-lineages during the 4th and 5th waves in 2022. Several significant mutations identified in VOCs were also detected in low-frequency lineages, including S68F (E protein); I82T (M protein); P13L, R203K and G204R\/K (N protein); R126S (ORF3a); P323L (RdRp); and N501Y, E484K, D614G, H655Y and N679K (S protein). Low-frequency variants, together with VOCs circulating, may lead to convergence and the emergence of future lineages that may increase transmissibility, infectivity and escape vaccine-induced or natural host immunity.<\/jats:p>","DOI":"10.3390\/v15051194","type":"journal-article","created":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T07:35:50Z","timestamp":1684395350000},"page":"1194","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6037-9890","authenticated-orcid":false,"given":"Kathleen","family":"Subramoney","sequence":"first","affiliation":[{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa"},{"name":"Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa"},{"name":"Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg 2131, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nkhensani","family":"Mtileni","sequence":"additional","affiliation":[{"name":"Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2944-4583","authenticated-orcid":false,"given":"Jennifer","family":"Giandhari","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeshnee","family":"Naidoo","sequence":"additional","affiliation":[{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yajna","family":"Ramphal","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9288-7996","authenticated-orcid":false,"given":"Sureshnee","family":"Pillay","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2441-3868","authenticated-orcid":false,"given":"Upasana","family":"Ramphal","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akhil","family":"Maharaj","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5221-2126","authenticated-orcid":false,"given":"Derek","family":"Tshiabuila","sequence":"additional","affiliation":[{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7102-8540","authenticated-orcid":false,"given":"Houriiyah","family":"Tegally","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2503-9441","authenticated-orcid":false,"given":"Eduan","family":"Wilkinson","sequence":"additional","affiliation":[{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tulio","family":"de Oliveira","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research 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(2023). SARS-CoV-2 variant biology: Immune escape, transmission and fitness. Nat. Rev. Microbiol.","DOI":"10.1038\/s41579-022-00841-7"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1038\/s41586-021-03402-9","article-title":"Detection of a SARS-CoV-2 variant of concern in South Africa","volume":"592","author":"Tegally","year":"2021","journal-title":"Nature"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1126\/science.abj4336","article-title":"A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa","volume":"431","author":"Wilkinson","year":"2021","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1126\/science.abj9932","article-title":"Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India","volume":"374","author":"Dhar","year":"2021","journal-title":"Science"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1038\/s41591-022-01911-2","article-title":"Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa","volume":"28","author":"Tegally","year":"2022","journal-title":"Nat. Med."},{"key":"ref_6","unstructured":"Department of Health Republic of South Africa (2023, May 10). COVID-19 Policies, Available online: https:\/\/www.health.gov.za\/covid19\/downloads.html?type=policies%0D%0A."},{"key":"ref_7","unstructured":"(2023, May 10). SAPHRA (South African Health Products Regulatory Authority). Available online: https:\/\/www.sahpra.org.za\/news-and-updates\/sahpra-authorises-covishield-an-adenovirus-vectored-vaccine-for-the-prevention-of-covid-19\/."},{"key":"ref_8","unstructured":"(2023, May 10). World Health Organisation. Available online: https:\/\/covid19.who.int\/."},{"key":"ref_9","unstructured":"(2023, May 10). GISAID. Available online: https:\/\/www.epicov.org\/epi3\/frontend#30823%0D%0A."},{"key":"ref_10","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_11","doi-asserted-by":"crossref","first-page":"1976","DOI":"10.1038\/s41467-022-29579-9","article-title":"Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage","volume":"13","author":"Scheepers","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Brandt, C., Spott, R., H\u00f6lzer, M., K\u00fchnert, D., Fuchs, S., Lohde, M., Marquet, M., Viehweger, A., Rimek, D., and Pletz, M.W. (2021). Molecular epidemiology of SARS-CoV-2\u2014A regional to global perspective. medRxiv, 1\u20139.","DOI":"10.1101\/2021.01.25.21250447"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Quick, J. (2022, November 02). nCoV-2019 Sequencing Protocol v3 (LoCost) V.3. Available online: https:\/\/www.protocols.io\/view\/ncov-2019-sequencing-protocol-v3-locost-bh42j8yeJosh.","DOI":"10.17504\/protocols.io.bp2l6n26rgqe\/v3"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Reiling, S.J., Loranger, K., Roy, A.-M., Chen, S.-H., and Ragoussis, I. (2022, November 02). nCoV-2019 McGill Artic PCR Protocol, V4.1 at 63C V.2. McGill Genome Centre. Available online: https:\/\/www.protocols.io\/view\/ncov-2019-mcgill-artic-pcr-protocol-v4-1-at-63c-ewov18e4ygr2\/v2.","DOI":"10.17504\/protocols.io.ewov18e4ygr2\/v2"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41586-022-04411-y","article-title":"Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa","volume":"603","author":"Viana","year":"2022","journal-title":"Nature"},{"key":"ref_16","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":"11","author":"Cleemput","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_17","unstructured":"(2022, February 02). Exatype: Automated SARS-CoV-2 Variant Typing Directly from NGS Sequence Data Exatype. Hyrax BioSciences. Available online: https:\/\/ngs.exatype.com\/dashboard?product=SARSCoV2."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/s41586-020-2918-0","article-title":"Age-specific mortality and immunity patterns of SARS-CoV-2","volume":"590","author":"Wang","year":"2021","journal-title":"Nature"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1093\/infdis\/jiaa691","article-title":"On the effect of age on the transmission of SARS-CoV-2 in households, schools and the community","volume":"223","author":"Goldstein","year":"2021","journal-title":"J. Infect. Dis."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"6895","DOI":"10.1038\/s41467-021-27163-1","article-title":"SARS-CoV-2 transmission across age groups in France and implications for control","volume":"12","author":"Bosetti","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.7196\/SAMJ.2021.v111i11.15812","article-title":"Understanding the differential impacts of COVID-19 among hospitalised patients in South Africa for equitable response","volume":"111","author":"Shisana","year":"2021","journal-title":"S. Afr. Med. J."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"eabe8372","DOI":"10.1126\/science.abe8372","article-title":"Age groups that sustain resurging COVID-19 epidemics in the United States","volume":"371","author":"Monod","year":"2021","journal-title":"Science"},{"key":"ref_23","unstructured":"National Institute for Communicable Diseases (2023, February 02). SARS-CoV-2 Genomic Surveillance Update June 2021. Available online: https:\/\/www.nicd.ac.za\/wp-content\/uploads\/2021\/07\/Sequencing-update-1July-2021_V14.pdf."},{"key":"ref_24","unstructured":"Network for Genomic Surveillance in South Africa (NGS-SA) (2023, February 02). SARS-CoV-2 Sequencing Update 7 July 2021. Available online: https:\/\/www.nicd.ac.za\/wp-content\/uploads\/2021\/12\/Update-of-SA-sequencing-data-from-GISAID-1-Dec-Final.pdf."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/s41592-023-01769-3","article-title":"Outbreak.info genomic reports: Scalable and dynamic surveillance of SARS-CoV-2 variants 2 and mutations","volume":"20","author":"Gangavarapu","year":"2023","journal-title":"Nat. Methods"},{"key":"ref_26","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_27","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41467-020-20688-x","article-title":"Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy","volume":"12","author":"Alteri","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1080\/22221751.2021.2011617","article-title":"A year living with SARS-CoV-2: An epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain)","volume":"11","author":"Esperalba","year":"2022","journal-title":"Emerg. Microbes Infect."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Silva, C.L.J., Rivero, R., Douglas, J., Bouckaert, R., Arenas, C.J.V., Atkins, K., Gastelbondo, B., Calderon, A., Guzman, C., and Echeverri-De la Hoz, D. (2022). Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia. medRxiv, 1\u201324.","DOI":"10.21203\/rs.3.rs-1786224\/v1"},{"key":"ref_30","first-page":"4","article-title":"Evidence of natural selection and dominance of SARS-CoV-2 variant Lambda (C.37) over variants of concern in Cusco, Peru","volume":"168","author":"Sierra","year":"2023","journal-title":"Arch. Virol."},{"key":"ref_31","unstructured":"Or\u00f3stica, K.Y., Contreras, S., Mohr, S.B., Dehning, J., Ulloa, S., Castillo, A.E., Verdugo, R.A., and Fern\u00e1ndez, J. (2021). Mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants. arXiv."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"198936","DOI":"10.1016\/j.virusres.2022.198936","article-title":"Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina","volume":"323","author":"Culasso","year":"2023","journal-title":"Virus Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.ijid.2021.12.326","article-title":"Genomic characterization of SARS-CoV-2 and its association with clinical outcomes: A 1-year longitudinal study of the pandemic in Colombia","volume":"116","year":"2022","journal-title":"Int. J. Infect. Dis."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"935131","DOI":"10.3389\/fviro.2022.935131","article-title":"SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021","volume":"2","author":"Mwangi","year":"2022","journal-title":"Front. Virol."},{"key":"ref_35","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_36","doi-asserted-by":"crossref","first-page":"100675","DOI":"10.1016\/j.imu.2021.100675","article-title":"Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties","volume":"25","author":"Mou","year":"2020","journal-title":"Inform. Med. Unlocked"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"593548","DOI":"10.3389\/fmicb.2020.593548","article-title":"Genetic Spectrum and Distinct Evolution Patterns of SARS-CoV-2","volume":"11","author":"Liu","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1080\/22221751.2021.1922097","article-title":"Emerging variants of concern in SARS-CoV-2 membrane protein: A highly conserved target with potential pathological and therapeutic implications","volume":"10","author":"Shen","year":"2021","journal-title":"Emerg. Microbes Infect."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Marques-Pereira, C., Pires, M.N., Gouveia, R.P., Pereira, N.N., Caniceiro, A.B., Ros\u00e1rio-Ferreira, N., and Moreira, I.S. (2022). SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights. Int. J. Mol. Sci., 23.","DOI":"10.21203\/rs.3.rs-702792\/v2"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/s41392-022-01105-9","article-title":"Origin, virological features, immune evasion and intervention of SARS-CoV-2 Omicron sublineages","volume":"7","author":"Xia","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Alsuwairi, F.A., Alsaleh, A., Alsanea, M.S., and Al-qahtani, A.A. (2023). Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves. Microorganisms, 11.","DOI":"10.1101\/2023.02.26.23285573"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1080\/22221751.2021.1949948","article-title":"Emergence of the novel SARS-CoV-2 lineage VUI-NP13L and massive spread of P.2 in South Brazil","volume":"10","author":"Prichula","year":"2021","journal-title":"Emerg. Microbes Infect."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"199016","DOI":"10.1016\/j.virusres.2022.199016","article-title":"SARS-CoV-2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents","volume":"323","author":"Ghaleh","year":"2023","journal-title":"Virus Res."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Moen, L.V., Vollan, H.S., Br\u00e5te, J., Hungnes, O., and Bragstad, K. (2022). Molecular Epidemiology of the Norwegian SARS-CoV-2 Delta Lineage AY.63. Viruses, 14.","DOI":"10.3390\/v14122734"},{"key":"ref_45","first-page":"100933","article-title":"Variations in Orf3a protein of SARS-CoV-2 alter its structure and function","volume":"26","author":"Azad","year":"2021","journal-title":"Biochem. Biophys. Rep."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"e9587","DOI":"10.7717\/peerj.9587","article-title":"RdRp mutations are associated with SARS-CoV-2 genome evolution","volume":"8","author":"Eskier","year":"2020","journal-title":"PeerJ"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1186\/s12967-020-02344-6","article-title":"Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant","volume":"18","author":"Pachetti","year":"2020","journal-title":"J. Transl. Med."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"001584","DOI":"10.1099\/jgv.0.001584","article-title":"SARS-CoV-2 one year on: Evidence for ongoing viral adaptation","volume":"102","author":"Peacock","year":"2021","journal-title":"J. Gen. Virol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"109292","DOI":"10.1016\/j.celrep.2021.109292","article-title":"Recurrent emergence of SARS-CoV-2 spike deletion H69\/V70 and its role in the Alpha variant B.1.1.7","volume":"35","author":"Meng","year":"2021","journal-title":"Cell Rep."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2579","DOI":"10.2147\/IDR.S320658","article-title":"Detection of representative mutant strains and a case of prolonged infection by SARS-CoV-2 with spike 69\/70 deletion in Japan","volume":"14","author":"Takano","year":"2021","journal-title":"Infect. Drug Resist."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1016\/j.bj.2022.04.006","article-title":"SARS-CoV-2 variants\u2014Evolution, spike protein, and vaccines","volume":"45","author":"Chen","year":"2022","journal-title":"Biomed. J."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.bbrc.2020.11.026","article-title":"Functional importance of the D614G mutation in the SARS-CoV-2 spike protein","volume":"538","author":"Jackson","year":"2021","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1186\/s12985-022-01951-7","article-title":"Mutations in SARS-CoV-2 structural proteins: A global analysis","volume":"19","author":"Abavisani","year":"2022","journal-title":"Virol. J."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1007\/s42770-022-00743-z","article-title":"Spike protein of SARS-CoV-2 variants: A brief review and practical implications","volume":"53","author":"Candido","year":"2022","journal-title":"Braz. J. Microbiol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"201","DOI":"10.3390\/jmp3040018","article-title":"The Comparison of Mutational Progression in SARS-CoV-2: A Short Updated Overview","volume":"3","author":"Asif","year":"2022","journal-title":"J. Mol. Pathol."},{"key":"ref_56","unstructured":"Network for Genomic Surveillance in South Africa (NGS-SA) (2022, November 02). SARS-CoV-2 Seq Updat 3 December 2021. Available online: https:\/\/www.nicd.ac.za\/wp-content\/uploads\/2021\/12\/Update-of-SA-sequencing-data-from-GISAID-3-Dec-21-Final.pdf."},{"key":"ref_57","unstructured":"Network for Genomic Surveillance in South Africa (NGS-SA) (2022, November 02). SARS-CoV-2 Seq Update 14 January 2022. Glob Challenges. Available online: https:\/\/www.nicd.ac.za\/wp-content\/uploads\/2022\/01\/Update-of-SA-sequencing-data-from-GISAID-14-Jan-2022_dash_v2-Read-Only.pdf."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"3676","DOI":"10.1002\/jmv.27797","article-title":"Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021","volume":"94","author":"Subramoney","year":"2022","journal-title":"J. Med. Virol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Tegally, H., Wilkinson, E., Althaus, C.L., Giovanetti, M., San, J.E., Giandhari, J., Pillay, S., Naidoo, Y., Ramphal, U., and Msomi, N. (2021). Rapid replacement of the Beta variant by the Delta variant in South Africa. medRxiv, 1\u201326.","DOI":"10.1101\/2021.09.23.21264018"},{"key":"ref_60","unstructured":"Gangavarapu, K., Latif, A.A., Mullen, J.L., Alkuzweny, M., Hufbauer, E., Tsueng, G., Haag, E., Zeller, M., Aceves, C.M., and Zaiets, K. (2023, February 13). Lineage Comparison. Available online: https:\/\/outbreak.info\/compare-lineages?pango."},{"key":"ref_61","unstructured":"World Health Organization (2023, January 30). COVID-19 Weekly Epidemiological Update Edition 70. Edition 70, Published 14 December 2021. Available online: https:\/\/apps.who.int\/iris\/handle\/10665\/350646."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"2068883","DOI":"10.1080\/21645515.2022.2068883","article-title":"Delta variant (B.1.617.2) of SARS-CoV-2: Mutations, impact, challenges and possible solutions","volume":"18","author":"Dhawan","year":"2022","journal-title":"Hum. Vaccines Immunother."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"3506","DOI":"10.1002\/jmv.27780","article-title":"The recombinant variants of SARS-CoV-2: Concerns continues amid COVID-19 pandemic","volume":"94","author":"Mohapatra","year":"2022","journal-title":"J. Med. Virol."},{"key":"ref_64","unstructured":"World Health Organization (2023, January 30). COVID-19 Weekly Epidemiological Update Edition 115. Published 26 October 2022. Available online: https:\/\/apps.who.int\/iris\/handle\/10665\/363853."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1016\/S0140-6736(21)02758-6","article-title":"Omicron SARS-CoV-2 variant: A new chapter in the COVID-19 pandemic","volume":"398","author":"Karim","year":"2021","journal-title":"Lancet"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Focosi, D., Quiroga, R., McConnell, S., Johnson, M.C., and Casadevall, A. (2023). Convergent Evolution in SARS-CoV-2 Spike Creates a Variant Soup from Which New COVID-19 Waves Emerge. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24032264"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/S0140-6736(22)00017-4","article-title":"Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: A data linkage study","volume":"399","author":"Wolter","year":"2022","journal-title":"Lancet"}],"updated-by":[{"DOI":"10.3390\/v15071502","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T00:00:00Z","timestamp":1684368000000}}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/5\/1194\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,3]],"date-time":"2025-08-03T13:55:59Z","timestamp":1754229359000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/5\/1194"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,18]]},"references-count":67,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2023,5]]}},"alternative-id":["v15051194"],"URL":"https:\/\/doi.org\/10.3390\/v15051194","relation":{"correction":[{"id-type":"doi","id":"10.3390\/v15071502","asserted-by":"object"}]},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,5,18]]}}}