The DOI matches its Crossref record.
Where did ‘weird’ Omicron come from?
Abstract
but WHO skipped the letters Nu and Xi, it said, “because Nu is too easily confounded with ‘new’ and Xi was not used because it is a common surname.”) One reason for concern about Omicron is that sequenced samples indicate it has rapidly replaced other variants in South Africa. But that picture might be skewed. For one, sequencing might have been focused on possible cases of the new variant in recent days, which could make it appear more frequent than it is. PCR data provide broader coverage and a less biased view, but there, too, samples with the S gene failure indicate a rapid rise of Omicron. The rising frequency could still be due in part to chance. In San Diego, a series of superspreading events at a university resulted in an explosion of one particular strain of SARS-CoV-2 earlier this year, Andersen says: “It was thousands of cases and they were all the same virus.” But the virus wasn’t notably more infectious. South Africa has seen relatively few cases recently, so a series of superspreading events could have led to the rapid increase of Omicron. “I suspect that a lot of that signal is explained by that and I desperately hope so,” Andersen says. Based on a comparison of different Omicron genomes, Andersen estimates the virus emerged sometime around late September or early October, which suggests it might be spreading more slowly than it appears to have. The other reason to be concerned is Omicron’s confusing genome. Its spike protein, which latches on to receptors on h…
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“While there are different hypotheses addressing the evolutionary origins of Omicron BA.1's emergence and this variant's unusual number of mutations 25 , the rising level of SARS-CoV-2 exposure in South Africa in 2020-2021 would be expected to promote the fitness advantage of immune escape variants over earlier variants.”
From Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa (2023) · cites this paper as [25]
Citations
Cited by
Sorted by citations
Items 101–154 of 154
Viro-immunological evaluation in an immunocompromised patient with long-lasting SARS-CoV-2 infection
Mancon, A., Rizzo, A., Mileto, D., Grosso, S., Foschi, A., Cutrera, M., Capetti, A. F., Faggion, I., Anselmo, A., Monte, A., et al. (2022) · Emerging Microbes & Infections · doi:10.1080/22221751.2022.2045877 · Cited by 4
Chua, J. X., Durrant, L. G., Chok, Y. L., & Lai, O. M. (2022) · iScience · doi:10.1016/j.isci.2022.105379 · Cited by 4
“…Omicron variant has been reported to exhibit unusually high mutations that are different from other known SARS-CoV-2 variants, which could be attributed to extensive and independent evolution in isolated human populations, immunocompromised patients or unknown animal species (Kupferschmidt, 2021).”
Origin and Reversion of Omicron Core Mutations in the Evolution of SARS-CoV-2 Genomes
Zhao, X., Qin, L., Ding, X. L., Zhang, Y., Niu, X., Gao, F., Jiang, T., & Chen, L. (2022) · Viruses · doi:10.3390/v15010030 · Cited by 4
Analysis of the immune response in COVID-19
Hromić‐Jahjefendić, A., & Aljabali, A. A. A. (2025) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2024.10.004 · Cited by 4
Piedra-Mora, C., Robinson, S. R., Tostanoski, L. H., Dayao, D., Chandrashekar, A., Bauer, K., Wrijil, L. M., Ducat, S., Hayes, T., Yu, J., et al. (2022) · Veterinary Pathology · doi:10.1177/03009858221095794 · Cited by 4
Ending the COVID‐19 pandemic: We still have a long way to go
Zeng, G., & Xia, W. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27980 · Cited by 5
Takke, A., Zarekar, M., Muthuraman, V., Ashar, A., Patil, K., Badhavkar, A., Trivedi, J., Khargekar, N. C., Madkaikar, M. R., & Banerjee, A. (2022) · Journal of Family Medicine and Primary Care · doi:10.4103/jfmpc.jfmpc_430_22 · Cited by 4
Miao, Y., Ren, Y., & Ren, T. (2023) · International Journal of General Medicine · doi:10.2147/ijgm.s409478 · Cited by 4
COVID-19 vaccine: what are we doing and what should we do?
Candelli, M. (2022) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(22)00003-2 · Cited by 4
Gerardi, V., Rohaim, M. A., Naggar, R. F. E., Atasoy, M. O., & Munir, M. (2023) · Vaccines · doi:10.3390/vaccines11030668 · Cited by 4
SARS-CoV-2 omicron variant: the black swan of microbiology
Cheng, Z. J., Xue, M., Chen, Y., Zhang, Y., & Sun, B. (2022) · Archives of Microbiology · doi:10.1007/s00203-022-03196-y · Cited by 3
“A leading theory is that Omicron results from accumulating evolutionary mutations in a patient with AIDS (Kupferschmidt 2021b).”
BackgroundDiscovery of an ellipticine derivative as TLR3 inhibitor against influenza A virus and SARS-CoV-2
Pan, Y., Fu, Q., Li, Y., Yang, J. W., & Cheng, K. (2024) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2024.129672 · Cited by 3
The human microbiota is a beneficial reservoir for SARS-CoV-2 mutations
Cao, B., Wang, X.-X., Yin, W., Gao, Z., & Xia, B.-Q. (2024) · mBio · doi:10.1128/mbio.03187-23 · Cited by 3
Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources
Muñoz, M., Patiño, L. H., Ballesteros, N., Castañeda, S., Luna, N., Noguera, L. A. D., Hernández‐Pereira, C. E., Shaban, M. V., Muñoz, S. A., Paniz‐Mondolfi, A., et al. (2021) · One Health · doi:10.1016/j.onehlt.2021.100363 · Cited by 3
Ultrafast topological data analysis reveals pandemic-scale dynamics of convergent evolutionPreprint
Bleher, M., Hahn, L., Neumann, M., Ardern, Z., Patiño-Galindo, J. Á., Carrière, M., Bauer, U., Rabadán, R., & Ott, A. (2021) · medRxiv · doi:10.1101/2021.06.10.21258550 · Cited by 3
The rise and fall of SARS-CoV-2 variants and the mutational profile of OmicronPreprint
Wiegand, T., McVey, A., Nemudraia, A., Nemudryi, A. A., & Wiedenheft, B. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.16.473096 · Cited by 3
“…to the evolution of Omicron remain uncertain, some scientists suspect that Omicron arose in chronically infected immunocompromised patients where the immune response is too weak to clear the virus but is strong enough to select for mutations that increase viral fitness (Kupferschmidt, 2021).”
BackgroundKakeya, H., & Matsumoto, Y. (2022) · IPSJ Transactions on Bioinformatics · doi:10.2197/ipsjtbio.15.22 · Cited by 2
Yu, S., He, Y., Ji, W., Yang, R., Zhao, Y., Li, Y., Liu, Y., Ding, L., Ma, M., Wang, H., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231810644 · Cited by 2
Chernyaeva, E., Ayginin, A. A., Bulusheva, I. A., Vinogradov, K. S., Стеценко, И. Ф., Romanova, S. V., Tsypkina, A. V., Дмитриевна, М. А., Savochkina, Y. A., & Shipulin, G. A. (2022) · Pathogens · doi:10.3390/pathogens11121461 · Cited by 2
Mechanistic study of the transmission pattern of the SARS‐CoV ‐2 omicron variant
An, K., Yang, X., Luo, M., Yan, J., Xu, P., Zhang, H., Li, Y., Wu, S., Warshel, A., & Bai, C. (2024) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26663 · Cited by 2
“9,10 13 This variant showed fast spreading speed and resistance to many neutralizing antibodies 14 – 16 but exhibited lower risk of severe illness or fatality than other VOCs.”
BackgroundEmergence of the SARS-CoV-2 Omicron Variant: Current Treatments and Vaccines for COVID-19
Vidian, V., Dikson, Litanto, V., Christy, S. N. A., & Jo, J. (2022) · Exploratory Research and Hypothesis in Medicine · doi:10.14218/erhm.2022.00084 · Cited by 2
Wen, H., Shi, F., Liu, Y., Xie, C. H., Qin, G., Wang, F., Liu, X., Bai, J., Hong, Q., Ma, R., et al. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.914732 · Cited by 2
Mahmoud, Y., Hathout, A., Amen, R. A., Desouky, S., Shady, R. M., & Fahmy, H. M. (2023) · Reviews in Medical Microbiology · doi:10.1097/mrm.0000000000000386 · Cited by 1
Lugano, D. I., Mwangi, K. W., Mware, B., Kibet, G., Osiany, S., Kiritu, E., Dobi, P. O., Muli, C., Njeru, R., de Oliveira, T., et al. (2025) · Journal of Virology · doi:10.1128/jvi.00482-25 · Cited by 2
SARS-CoV-2 Omicron (B.1.1.529) Variant: No Time to Wait!
Rahmani, S., & Rezaei, N. (2022) · Acta bio-medica dell'Ateneo parmense/Acta biomedica · doi:10.23750/abm.v93i2.12712 · Cited by 1
Limited permissibility of ENL-R and Mv-1-Lu mink cell lines to SARS-CoV-2
Bideau, M. L., de Souza, G. A. P., Boschi, C., Baudoin, J., Penant, G., Jardot, P., Fenollar, F., Colson, P., Lenk, M., & Scola, B. L. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1003824 · Cited by 1
“…variant, namely, (i) silent evolution in a population with little sequencing; (ii) longterm evolution in one or a few persons with chronic infection, or (iii) that this variant evolution occurred in another animal host, especially rodents (Kupferschmidt, 2021; Fan et al., 2022; Mallapaty, 2022).”
BackgroundNychyk, S. A., Mandygra, M., Bezymennyi, M., Hudz, N. V., Molozhanova, A. V., & Тарасов, О. А. (2024) · Agricultural science and practice · doi:10.15407/agrisp10.03.003 · Cited by 1
“…have proposed that the Omicron variant may have arisen from cross-species transmission, given its speci fi c combination of mutations, particularly in the spike protein responsible for host cell entry (Sun et al, 2022; Burki, 2022; Kupferschmidt, 2021; Doliff & Martens, 2022; Carabelli et al, 2023).”
BackgroundPERANCANGAN ANIMASI 2D EDUKASI MENGENAI VIRUS OMICRON DESAIN KOMUNIKASI VISUAL
Wicaksono, R. A. (2023) · KARTALA · doi:10.36080/kvs.v2i2.91 · Cited by 1
In vitro antibody-mediated SARS-CoV-2 infection suppression through human ACE2 receptor blockade
Redd, P. S., Merting, A. D., Klement, J. D., Poschel, D. B., Yang, D., & Liu, K. (2024) · Immunology Letters · doi:10.1016/j.imlet.2024.106887 · Cited by 1
Wouters, C., Sachithanandham, J., Akin, E., Pieterse, L., Fall, A., Truong, T., Bard, J. D., Yee, R., Sullivan, D. J., Mostafa, H. H., et al. (2024) · Viruses · doi:10.3390/v16091436 · Cited by 2
“Mutations in variants isolated over the course of persistent infections are reflected in global variants of concern, and Alpha and Omicron variants have been hypothesized to have evolved in immunocompromised persons [3,22–24].”
BackgroundPatil, R., Palkar, S. H., Mishra, A. C., & Arankalle, V. A. (2024) · Vaccines · doi:10.3390/vaccines12091039 · Cited by 1
“…study, we studied COVISHIELD vaccine-induced neutralizing antibodies at different time points up to 25–29 months, referred to as 2 years, and the effect of a booster dose. against a broad-range of SARS-CoV-2 variants including Omicron durability up to [16 (15–18)] months post-booster dose and two .”
BackgroundMethodAlameri, M. A., Gharaibeh, L. F., & ALRASHDAN, R. (2023) · The Open Public Health Journal · doi:10.2174/18749445-v16-e230505-2022-236 · Cited by 1
Chaudhary, S., El‐Shorbagi, A., Chaudhary, A., Agarwal, G., Tripathi, P. N., & Dumoga, S. (2022) · Biomedical & Pharmacology Journal · doi:10.13005/bpj/2456 · Cited by 1
The Truth about the Origin of OmicronPreprint
Dawood, A. A. (2022) · doi:10.32388/a06v74
Human microbiota is a reservoir of SARS-CoV-2 advantageous mutationsPreprint
Cao, B., Wang, X., Yin, W., Gao, Z., & Xia, B. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.16.567485 · Cited by 1
Omicron: a chimera of two early SARS-CoV-2 lineagesPreprint
Xiong, C., Liu, X., Xiong, J., Sun, Z., Hu, W. G., Hu, J., Wang, Y., Li, K., Thilakavathy, K., Chen, M., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1302993/v1
Omicron; past, current and future perspectives
Bareja, R., & Shinu, P. (2022) · IP International Journal of Medical Microbiology and Tropical Diseases · doi:10.18231/j.ijmmtd.2022.001
Chua, J. X., Durrant, L. G., Chok, Y. L., & Lai, O. M. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4062765
Wu, X., Shen, M. Y., Quan, H., Zhang, X., Xu, F., Li, J., He, M., Pan, D., Cao, L., Yue, C., et al. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.828819
SARS-CoV-2 Omicron (B.1.1.529) Varyantının Virolojik, Epidemiyolojik Özellikleri ve Korunma: Derleme
Kaya, G., & Altındiş, M. (2022) · Kocaeli Üniversitesi Sağlık Bilimleri Dergisi · doi:10.30934/kusbed.1060956
A Comprehensive Review on Covid-19 Variants
Asra, S., Anusha, C. V., Ahalya, M. T., Rehman, A., & Suman, P. (2022) · International Journal for Research in Applied Science and Engineering Technology · doi:10.22214/ijraset.2022.47073
Other forms of autonomic dysfunction
Appenzeller, O., Lamotte, G. J., & Coon, E. A. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-96011-3.00007-3
Epidemiological characteristics SAR-CoV-2 Omicron
Москалюк, В. Д., Syrota, B. V., Balaniuk, I. V., Chernetska, N. V., Меленко, С. Р., & Kolotylo, T. R. (2022) · Bukovinian Medical Herald · doi:10.24061/2413-0737.xxvi.2.102.2022.4
“Німецький вірусолог Крістіан Дростен вважає, що варіант не розвинувся в Південній Африці, тому що в Південній Африці проводиться велика кількість робіт із секвенування генів, варіант розвинувся в деяких країнах півдня Африки, де секвенування генів не проводилося [13].”
InfluentialIs Omicron Variant of COVID-19 Threatening Health Like Other Variants?
Ghelichi-Ghojogh, M., Ghasemloo, H., Hosseinpour, H., Valizadeh, R., & Sadighpour, T. (2022) · Journal of Cellular Immunology · doi:10.33696/immunology.4.154
Wallis, R. S., Srivastava, A. K., Wack, A., & Knirsch, C. A. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-87539-4.00003-8
A Systemic Review on Omicron Variant of SARS-CoV-2
Pappuswamy, M., Chaudhary, A., & Shitut, A. (2023) · Biomedical & Pharmacology Journal · doi:10.13005/bpj/2648
Source identification via contact tracing in the presence of asymptomatic patients
Ódor, G., Vuckovic, J., Ndoye, M.-A. S., & Thiran, P. (2023) · Applied Network Science · doi:10.1007/s41109-023-00566-3 · Cited by 1
Gaurav, K., Kumar, R., Chaudhary, R., & Dhariwal, R. (2023) · International Journal of Pharma Professional’s Research (IJPPR) · doi:10.48165/ijppronline.2023.14109
The Omicron variant of SARS-CoV-2
Zambrano, J. L., Jaspe, R. C., Loureiro, C. L., Rangel, H. R., Liprandi, F., & Pujol, F. H. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95646-8.00003-2
Arakawa, H. (2024) · SynBio · doi:10.3390/synbio2030017
“The SARS-CoV-2 Omicron variant (strain B.1.1.529) was first identified in Botswana [1] and reported to the World Health Organization (WHO) from South Africa on 24 November 2021 [2].”
BackgroundInfluentialDeterminants of susceptibility to SARS-CoV-2 infection in murine ACE2
Kondo, T., Suzuki, R., Yajima, H., Kawahara, S., Yamaya, K., Ichikawa, T., Tsujino, S., Suzuki, S., Tamura, T., Hashiguchi, T., et al. (2025) · Journal of Virology · doi:10.1128/jvi.00543-25 · Cited by 1
“One such hypothesis suggests that Omicron may have accumulated mutations in an animal host before spilling back into humans (15, 16).”
A Pilot Study of COVID-19 Outcomes in People Living with HIV in Tatarstan
Andreeva, N. I., Moiseeva, S., Garipova, A., Shakirova, V. G., Martynova, E. V., Salafutdinov, I. I., Khaiboullina, S. F., Davidyuk, Y. N., Khuzwayo, S. S., Gama, N., et al. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms27010288
“For example, the emergence of the Omicron variant in southern Africa was linked to HIV-associated immunosuppression [19].”
Clues to Long COVID Linked to Virulence and Infectivity Found in Shell Proteins
Goh, G. K., Foster, J. A., & Uversky, V. N. (2026) · Advances in respiratory medicine · doi:10.3390/arm94020018
“Furthermore, phylogenetic genetic algorithms tend to make mistakes when recombination has taken place [93].”
Metadata
- Authors
- Kupferschmidt, K.
- Corresponding author
- Kupferschmidt, Kai
- Venue
- Science
- Published
- 2021-12-03
- Volume
- 374
- Issue
- 6572
- Pages
- 1179-1179
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W3215456302
- Cited by
- 154
- References
- 0
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 14 · 2023: 30 · 2022: 86 · 2021: 17
- FWCI
- 11.63
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Keywords
- Omicron variant, SARS-CoV-2, viral evolution, COVID-19 pandemic
- MeSH terms
- Vaccination Coverage, COVID-19, SARS-CoV-2, COVID-19 Vaccines, Persistent Infection, Animals, Humans, Mutation, Genome, Viral, Immunocompromised Host, Evolution, Molecular
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
