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
Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift
Cameroni, E., Bowen, J. E., Rosen, L. E., Saliba, C., Zepeda, S. K., Culap, K., Pinto, D., VanBlargan, L. A., Marco, A. D., di Iulio, J., et al. (2021) · Nature · doi:10.1038/s41586-021-04386-2 · Cited by 1,070
Hoffmann, M., Krüger, N., Schulz, S., Cossmann, A., Rocha, C., Kempf, A., Nehlmeier, I., Graichen, L., Moldenhauer, A.-S., Winkler, M. S., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.032 · Cited by 889
“Analysis of the Omicron genomic sequence 105 revealed striking differences as compared to other known SARS-CoV-2 variants, suggesting 106 extensive, independent evolution, potentially in an isolated human population, 107 immunocompromised patients or an unknown animal species (Kupferschmidt, 2021).”
SARS-CoV-2 Omicron variant: recent progress and future perspectives
Fan, Y., Li, X., Zhang, L., Wan, S., Zhang, L., & Zhou, F. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00997-x · Cited by 599
SARS‐CoV‐2 Omicron variant: Characteristics and prevention
He, X., Hong, W., Pan, X., Lu, G., & Wei, X. (2021) · MedComm · doi:10.1002/mco2.110 · Cited by 513
Shrestha, L. B., Foster, C. S. P., Rawlinson, W. D., Tedla, N. T., & Bull, R. A. (2022) · Reviews in Medical Virology · doi:10.1002/rmv.2381 · Cited by 483
“Phylogenetic analysis of global SARS‐CoV‐2 sequences has not revealed any close intermediary sequences between Omicron and its closest relatives, therefore the pathway to the emergence of Omicron is unclear.30 The evolu- tionary analysis did not reveal any special mutational profile or frameshift event that could sugg…”
BackgroundInfluentialRen, S., Wang, W.-B., Gao, R.-D., & Zhou, A.-M. (2021) · World Journal of Clinical Cases · doi:10.12998/wjcc.v10.i1.1 · Cited by 349
Chatterjee, S., Bhattacharya, M., Nag, S., Dhama, K., & Chakraborty, C. (2023) · Viruses · doi:10.3390/v15010167 · Cited by 325
Khandia, R., Singhal, S., Alqahtani, T., Kamal, M. A., El-Shall, N. A., Nainu, F., Desingu, P. A., & Dhama, K. (2022) · Environmental Research · doi:10.1016/j.envres.2022.112816 · Cited by 308
“…with immune escape and the N501Y substitution associated with most VOC were reported, strengthening the hypothesis of intra-host evolution of VOCs (Kupferschmidt, 2021c). mRNA- and non-mRNA-based vaccines may have a role in generating Omicron variants in a chronically infected COVID-19 patient,…”
InfluentialSaxena, S. K., Kumar, S., Ansari, S. M., Pawęska, J., Maurya, V. K., Tripathi, A., & Abdel-Moneim, A. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27524 · Cited by 269
Evidence for a mouse origin of the SARS-CoV-2 Omicron variant
Wei, C., Shan, K.-J., Wang, W., Zhang, S., Huan, Q., & Qian, W. (2021) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2021.12.003 · Cited by 278
“The proximal origins of Omicron have quickly become a controversial topic of heated debate in the scientific and public health communities (Callaway, 2021; Kupferschmidt, 2021).”
Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift
Cameroni, E., Bowen, J. E., Rosen, L. E., Saliba, C., Zepeda, S. K., Culap, K., Pinto, D., VanBlargan, L. A., Marco, A. D., di Iulio, J., et al. (2021) · Nature · doi:10.1038/d41586-021-03825-4 · Cited by 251
Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies
Dhama, K., Nainu, F., Frediansyah, A., Yatoo, M. I., Mohapatra, R. K., Chakraborty, S., Zhou, H., Islam, M. R., Mamada, S. S., Kusuma, H. I., et al. (2022) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2022.11.024 · Cited by 247
“diverged at initial phases from other strains [75,76].”
BackgroundOMICRON (B.1.1.529): A new SARS‐CoV‐2 variant of concern mounting worldwide fear
Thakur, V., & Ratho, R. K. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27541 · Cited by 235
Omicron variant genome evolution and phylogenetics
Kandeel, M. K., Mohamed, M. E., El‐Lateef, H. M. A., Venugopala, K. N., & EL-BELTAGI, H. S. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27515 · Cited by 205
Origin, virological features, immune evasion and intervention of SARS-CoV-2 Omicron sublineages
Xia, S., Wang, L., Zhu, Y., Lu, L., & Jiang, S. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01105-9 · Cited by 167
Immune response in COVID-19: what is next?
Li, Q., Wang, Y., Sun, Q., Knopf, J., i, M. H., Lin, L., Jiang, J., Shao, C., Li, P., He, X., et al. (2022) · Cell Death and Differentiation · doi:10.1038/s41418-022-01015-x · Cited by 149
Grabowski, F., Kochańczyk, M., & Lipniacki, T. (2022) · Viruses · doi:10.3390/v14020294 · Cited by 121
Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection
Chaguza, C., Hahn, A. M., Petrone, M. E., Zhou, S., Ferguson, D. J. P., Breban, M. I., Pham, K., Peña-Hernández, M. A., Castaldi, C., Hill, V., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.100943 · Cited by 123
“chronic infections in immunocompromised individuals could be the most likely mechanism driving the unpredictable emergence of genetically diverse SARS-CoV-2 variants (Callaway, 2022; Kupferschmidt, 2021; Lemieux and Luban, 2022; Mallapaty, 2022).”
BackgroundArmando, F., Beythien, G., Kaiser, F. K., Allnoch, L., Heydemann, L., Rosiak, M., Becker, S., González-Hernández, M., Lamers, M. M., Haagmans, B. L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31200-y · Cited by 118
Cryo-EM structure of the SARS-CoV-2 Omicron spike
Cerutti, G., Guo, Y., Liu, L., Liu, L., Zhang, Z., Luo, Y., Huang, Y., Wang, H. H., Ho, D. D., Sheng, Z., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110428 · Cited by 107
“Some have proposed that it developed in a chronically infected individual with an impaired immune response, whereas others think it developed in parallel with other variants in a population not monitored by sequencing (Kupferschmidt, 2021).”
Omicron (B.1.1.529 variant of SARS‐CoV‐2); an emerging threat: Current global scenario
Mohapatra, R. K., Sarangi, A. K., Kandi, V., Azam, M., Tiwari, R., & Dhama, K. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27561 · Cited by 93
Omicron variant: Current insights and future directions
Rana, R., Kant, R., Huirem, R. S., Bohra, D., & Ganguly, N. K. (2022) · Microbiological Research · doi:10.1016/j.micres.2022.127204 · Cited by 83
“Mutations in Spike proteins are thought to have improved the Spike’s ability to bind to the ACE2 receptor on host cells (Kupferschmidt, 2021b).”
BackgroundInfluentialNext-Generation Sequencing for Confronting Virus Pandemics
Quer, J., Colomer‐Castell, S., de Campos, C. F., Andrés, C., Piñana, M., Cortese, M. F., Gónzalez‐Sánchez, A., García‐Cehic, D., Ibañez‐Lligoña, M., Pumarola, T., et al. (2022) · Viruses · doi:10.3390/v14030600 · Cited by 78
The mysterious origins of the Omicron variant of SARS-CoV-2
Du, P., Gao, G. F., & Wang, Q. (2022) · The Innovation · doi:10.1016/j.xinn.2022.100206 · Cited by 69
“Instead, they proposed that Omicron evolved from people living with HIV (PLHIV).(1) A recent study showed that depletion of CD4+ T cells leads to significantly slower clearance of SARSJo urn al Pr e-p roo f”
BackgroundGenomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant
Ma, W., Yang, J., Fu, H., Su, C., Yu, C., Wang, Q., de Vasconcelos, A. T. R., Bazykin, G. A., Bào, Y., & Li, M. (2022) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2022.01.001 · Cited by 59
“More discussion of the possible origin of the Omicron variant can be found in other studies [28].”
Gawish, R., Starkl, P. M., Pimenov, L., Hladik, A., Lakovits, K., Oberndorfer, F., Cronin, S. J., Ohradanova‐Repic, A., Wirnsberger, G., Agerer, B., et al. (2022) · eLife · doi:10.7554/elife.74623 · Cited by 61
“529 variant and maVie16, support the idea of Omicron being the result of reverse zoonosis and viral evolution in an animal reservoir (Kupferschmidt, 2021).”
BackgroundUpdate on SARS-CoV-2 Omicron Variant of Concern and Its Peculiar Mutational Profile
Alkhatib, M., Salpini, R., Carioti, L., Ambrosio, F. A., D’Anna, S., Duca, L., Costa, G., Bellocchi, M. C., Piermatteo, L., Artese, A., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02732-21 · Cited by 64
Rochman, N. D., Faure, G., Wolf, Y. I., Freddolino, L., Zhang, F., & Koonin, E. V. (2022) · mBio · doi:10.1128/mbio.00135-22 · Cited by 59
“mised individual(s) or an animal reservoir (31).”
SARS-CoV-2 Evolution: On the Sudden Appearance of the Omicron Variant
Berkhout, B., & Herrera-Carrillo, E. (2022) · Journal of Virology · doi:10.1128/jvi.00090-22 · Cited by 57
Nikolaidis, M., Papakyriakou, A., Chlichlia, K., Markoulatos, P., Oliver, S. G., & Amoutzias, G. D. (2022) · Viruses · doi:10.3390/v14040707 · Cited by 57
Tiecco, G., Storti, S., Antoni, M. D., Focà, E., Castelli, F., & Quirós-Roldán, E. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23041987 · Cited by 59
Li, L., Han, P., Huang, B., Xie, Y., Li, W., Zhang, D., Han, P., Xu, Z., Bai, B., Zhou, J., et al. (2022) · Cell Discovery · doi:10.1038/s41421-022-00431-0 · Cited by 49
Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa
Sun, K., Tempia, S., Kleynhans, J., von Gottberg, A., McMorrow, M. L., Wolter, N., Bhiman, J. N., Moyes, J., Carrim, M., Martinson, N. A., et al. (2023) · Nature Communications · doi:10.1038/s41467-022-35652-0 · Cited by 45
Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences
Hoteit, R., & Yassine, H. M. (2022) · Vaccines · doi:10.3390/vaccines10060919 · Cited by 47
“The Omicron variant is hypothesized to have evolved in a single immunocompromised human patient or a persistently infected COVID-19 patient over weeks or even months with little surveillance, or it may have developed in a non-human animal and recently spilled back into humans due to its rapid mutation rate [294].”
BackgroundEmergence of SARS-CoV-2 New Variants and Their Clinical Significance
Singh, H., Dahiya, N., Yadav, M., & Sehrawat, N. (2022) · The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · doi:10.1155/2022/7336309 · Cited by 37
“*ere are various theories postulated regarding the Omicron emergence: (1) circulation of infection in patients, (2) unreported new variants, (3) spike protein has improved its affinity for the ACE-2 receptor due to a mutation, (4) the reason behind a large number of mutations can be due to the involvement of unknown a…”
BackgroundCasadevall, A., & Focosi, D. (2023) · Journal of Clinical Investigation · doi:10.1172/jci168603 · Cited by 40
Strohl, W. R., Ku, Z., An, Z., Carroll, S. F., Keyt, B. A., & Strohl, L. M. (2022) · BioDrugs · doi:10.1007/s40259-022-00529-7 · Cited by 35
Quaglia, F., Salladini, E., Carraro, M., Minervini, G., Tosatto, S. C. E., & Mercier, P. L. (2022) · FEBS Journal · doi:10.1111/febs.16379 · Cited by 36
A comprehensive review on Covid-19 Omicron (B.1.1.529) variant
Manjunath, R., Gaonkar, S. L., Saleh, E. A. M., & Husain, K. (2022) · Saudi Journal of Biological Sciences · doi:10.1016/j.sjbs.2022.103372 · Cited by 42
“The examination of Severe acute respiratory syndrome-covid-2 variant sequences demonstrates that Omicron is well defined from the other SARS-CoV-2 types and that identifying its closest neighbor is problematic (Kupferschmidt, 2021b).”
InfluentialThe Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron
Wiegand, T., Nemudryi, A. A., Nemudraia, A., McVey, A., Little, A., Taylor, D. N., Walk, S. T., & Wiedenheft, B. (2022) · Viruses · doi:10.3390/v14092009 · Cited by 36
Biological mechanisms underpinning the development of long COVID
Perumal, R., Shunmugam, L., Naidoo, K., Wilkins, D., Demo, A. G., Bréchot, C., Vahlne, A. G., & Nikolich‐Žugich, J. (2023) · iScience · doi:10.1016/j.isci.2023.106935 · Cited by 37
Cats and SARS-CoV-2: A Scoping Review
Doliff, R., & Martens, P. (2022) · Animals · doi:10.3390/ani12111413 · Cited by 34
SARS-CoV-2: tracing the origin, tracking the evolution
Voskarides, K. (2022) · BMC Medical Genomics · doi:10.1186/s12920-022-01208-w · Cited by 33
Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2
Nielsen, B. F., Saad-Roy, C. M., Li, Y., Sneppen, K., Simonsen, L., Viboud, C. G., Levin, S. A., & Grenfell, B. T. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010896 · Cited by 28
Sub‐lineages of the SARS‐CoV‐2 Omicron variants: Characteristics and prevention
Xu, A., Hong, B., Lou, F., Wang, S., Li, W., Shafqat, A., An, X., Zhao, Y., Song, L., Tong, Y., et al. (2022) · MedComm · doi:10.1002/mco2.172 · Cited by 30
HIV and COVID-19 Co-Infection: Epidemiology, Clinical Characteristics, and Treatment
Basoulis, D., Mastrogianni, E., Voutsinas, P.-M., & Psichοgiou, M. (2023) · Viruses · doi:10.3390/v15020577 · Cited by 29
Rajpal, V. R., Sharma, S., Kumar, A., Chand, S., Joshi, L., Chandra, A., Babbar, S., Goel, S., Raina, S. N., & Shiran, B. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27749 · Cited by 26
Boeger, W. A., Brooks, D. R., Trivellone, V., Agosta, S. J., & Hoberg, E. P. (2022) · Transboundary and Emerging Diseases · doi:10.1111/tbed.14557 · Cited by 27
“A recent op-ed piece (Kupferschmidt, 2021) presented three hypotheses posed by scientists from around the world.”
BackgroundLubin, J. H., Markosian, C., Balamurugan, D., Ma, M. T., Chen, C.-H., Liu, D., Pasqualini, R., Arap, W., Burley, S. K., & Khare, S. D. (2023) · JCI Insight · doi:10.1172/jci.insight.168296 · Cited by 26
Antigenic evolution of SARS-CoV-2 in immunocompromised hosts
Smith, C. A., & Ashby, B. (2022) · Evolution Medicine and Public Health · doi:10.1093/emph/eoac037 · Cited by 26
Human coronaviruses: The emergence of SARS-CoV-2 and management of COVID-19
Solomon, M., & Liang, C. (2022) · Virus Research · doi:10.1016/j.virusres.2022.198882 · Cited by 25
“Others have postulated that cross-species transmission of SARS-CoV-2 from humans to non-human hosts has enabled the virus to accumulate mutations and eventually spill back into the human population (Kupferschmidt, 2021).”
Omicron (B.1.1.529) variant: Development, dissemination, and dominance
Rahmani, S., & Rezaei, N. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27563 · Cited by 22
Coordinated evolution at amino acid sites of SARS-CoV-2 spike
Neverov, A. D., Fedonin, G. G., Popova, A. V., Bykova, D., & Bazykin, G. A. (2023) · eLife · doi:10.7554/elife.82516 · Cited by 23
Kung, Y.-A., Chuang, C.-H., Chen, Y.-C., Yang, H.-P., Li, H.-C., Chen, C., Janapatla, R. P., Chen, C.-J., Shih, S., & Chiu, C. (2024) · Journal of the Formosan Medical Association · doi:10.1016/j.jfma.2024.08.021 · Cited by 20
On the Origins of Omicron’s Unique Spike Gene Insertion
Venkatakrishnan, A., Anand, P., Lenehan, P. J., Suratekar, R., Raghunathan, B., Niesen, M. J. M., & Soundararajan, V. (2022) · Vaccines · doi:10.3390/vaccines10091509 · Cited by 75
Can the SARS-CoV-2 Omicron Variant Confer Natural Immunity against COVID-19?
Abas, A. H., Marfuah, S., Idroes, R., Kusumawaty, D., Fatimawali, F., Park, M. N., Siyadatpanah, A., Alhumaydhi, F. A., Mahmud, S., Tallei, T. E., et al. (2022) · Molecules · doi:10.3390/molecules27072221 · Cited by 18
Omicron: The rising fear for another wave in Malaysia
Law, L. N.-S., Loo, K.-Y., Goh, J. X. H., & Pusparajah, P. (2021) · Progress In Microbes & Molecular Biology · doi:10.36877/pmmb.a0000261 · Cited by 17
There is nothing exempt from the peril of mutation – The Omicron spike
Behl, T., Kaur, I., Sehgal, A., Singh, S., Sharma, N., Anwer, M. K., Makeen, H. A., Albratty, M., Alhazmi, H. A., Bhatia, S., et al. (2022) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2022.112756 · Cited by 16
Hamdy, M. E., El‐Deeb, A. H., Hagag, N. M., Shahein, M. A., Alaidi, O., & Hussein, H. A. (2023) · International Journal of Veterinary Science and Medicine · doi:10.1080/23144599.2023.2222981 · Cited by 17
HIV and covid-19 in South Africa
Freer, J., & Mudaly, V. (2022) · BMJ · doi:10.1136/bmj-2021-069807 · Cited by 17
Ding, K., Jiang, W., Xiong, C., & Lei, M. (2022) · Immunity Inflammation and Disease · doi:10.1002/iid3.606 · Cited by 14
Giron, C. C., Laaksonen, A., & da Silva, F. L. B. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2095305 · Cited by 18
“…is being caused by the new variant Omicron (B.1.1.529), a highly divergent variant with a high number of mutations and designated VOC by WHO first identified in South Africa at the end of November 2021 and responsible now by daily records of new cases on a global scale (Kupferschmidt, 2021b).”
BackgroundInfluentialPage, B. M., Martin, T. A., Wright, C. L., Fenton, L. A., Villar, M. T., Tang, Q., Artigues, A., Lamb, A. L., Fenton, A. W., & Swint‐Kruse, L. (2022) · Protein Science · doi:10.1002/pro.4336 · Cited by 13
“Exploring these possibilities is urgent, as illustrated by another compelling example: when it was first identified, the spike protein in the SARS-CoV2 omicron variant was the sole representative of its phylogenetic branch.(59) For the orphan sequences themselves, which lack other homologs with which to make meaningfu…”
BackgroundRole of Omicron variant of SARS-CoV-2 in children in Germany
Bittmann, S. (2022) · World Journal of Pediatrics · doi:10.1007/s12519-021-00511-3 · Cited by 14
Goes, L. R., Siqueira, J. D., Garrido, M. M., Alves, B. M., Cicala, C., Arthos, J. A., Viola, J. P. B., & Soares, M. A. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.946549 · Cited by 12
“Indeed, it has been suggested that VOC carrying many novel mutations appearing at once, as were the cases of Alpha and Omicron, were generated within chronically infected subjects with immune responses impaired by other underlying illnesses (Kupferschimidt, 2021).”
BackgroundRole of the Pangolin in Origin of SARS-CoV-2: An Evolutionary Perspective
Gupta, S. K., Minocha, R., Thapa, P. J., Srivastava, M., & Dandekar, T. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23169115 · Cited by 13
Artificial Intelligence: A Next-Level Approach in Confronting the COVID-19 Pandemic
Mahalakshmi, V. J., Balobaid, A. S., Kanisha, B., Sasirekha, R., & Raja, M. R. (2023) · Healthcare · doi:10.3390/healthcare11060854 · Cited by 12
Paz, M., Aldunate, F., Arce, R., Ferreiro, I., & Cristina, J. (2022) · Virus Research · doi:10.1016/j.virusres.2022.198753 · Cited by 11
de Campos, C. F., Colomer‐Castell, S., García‐Cehic, D., Gregori, J., Andrés, C., Piñana, M., Gónzalez‐Sánchez, A., Borràs-Bermejo, B., Parés‐Badell, O., Adombi, C. M., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-24918-8 · Cited by 11
Ren, Z., Shen, C., & Peng, J. (2023) · Viruses · doi:10.3390/v15061297 · Cited by 12
Risk assessment of SARS-CoV-2 replicating and evolving in animals
Zhao, J., Kang, M., Wu, H., Sun, B., Baele, G., He, W., Lu, M., Suchard, M. A., Ji, X., He, N., et al. (2023) · Trends in Microbiology · doi:10.1016/j.tim.2023.07.002 · Cited by 12
Pezzotti, G., Ohgitani, E., Fujita, Y., Imamura, H., Pappone, F., Grillo, A., Nakashio, M., Shin‐Ya, M., Adachi, T., Yamamoto, T., et al. (2023) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.3c00312 · Cited by 11
Complexity of Viral Epitope Surfaces as Evasive Targets for Vaccines and Therapeutic Antibodies
Miller, N. L., Raman, R., Clark, T., & Sasisekharan, R. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.904609 · Cited by 12
Kumar, N., Kaushik, R., Singh, A., Uversky, V. N., Zhang, K. Y. J., Sahu, U., Bhatia, S., & Sanyal, A. (2022) · Viruses · doi:10.3390/v14122764 · Cited by 12
Veneziano, C., Marascio, N., Marco, C. D., Quaresima, B., Biamonte, F., Trecarichi, E. M., Santamaria, G., Quirino, A., Torella, D., Quattrone, A., et al. (2023) · Viruses · doi:10.3390/v15020408 · Cited by 10
Seasonal effects decouple SARS-CoV-2 haplotypes worldwide
Tomaszewski, T., Ali, M. A., Caetano-Anollés, K., & Caetano‐Anollés, G. (2023) · F1000Research · doi:10.12688/f1000research.131522.1 · Cited by 11
“Discussion VOC emergence There appears to be no ‘transparent’ path of transmission from viral ancestors to VOCs nor an explanation for themassive mutant constellation that characterizes the current VOC Omicron wave of the pandemic (Kupferschmidt, 2021; Mallapaty, 2022).”
BackgroundMapping Data to Deep Understanding: Making the Most of the Deluge of SARS-CoV-2 Genome Sequences
Sokhansanj, B. A., & ROSEN, G. L. (2022) · mSystems · doi:10.1128/msystems.00035-22 · Cited by 9
“The Omicron variant has such a long branch divergence, indicating that it may have emerged in an immunocompromised host or after incubating in a nonhuman host such as mice (41, 42).”
BackgroundChen, J., Wang, X., Li, L., Yi, L., Jiang, Y., Hao, P., Xu, Z., Zou, W., Li, P., Gao, Z., et al. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.967493 · Cited by 9
“A phylogenetic tree based on the mutations in the S1 subunit of viral Spike showed that the Omicron is far from other variants, indicating that Omicron evolved in parallel with other variants (Kupferschmidt, 2021).”
BackgroundIntrinsic Severity of the SARS-CoV-2 Omicron Variant
Bhattacharyya, R. P., & Hanage, W. P. (2022) · New England Journal of Medicine · doi:10.1056/nejmc2203679 · Cited by 9
Aw, Z. Q., Mok, C. K., Wong, Y. H., Chen, H., Mak, T. M., Lin, R. T. P., Lye, D. C., Tan, K. S., & Chu, J. J. H. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.950666 · Cited by 7
Gopcsa, L., Réti, M., Andrikovics, H., Bobek, I., Bekő, G., Bogyó, J., Ceglédi, A., Dobos, K., Giba-Kiss, L., Jankovics, I., et al. (2023) · GeroScience · doi:10.1007/s11357-023-00858-7 · Cited by 10
“In addition to life threatening outcomes, a persistent SARS-CoV-2 infection in immunocompromised hosts also carries the risk of giving rise to series of mutations in the viral genome [15–18].”
BackgroundOmicron variant receptor-binding domain phylogenetics and molecular dynamics
Kandeel, M. K., & El‐Deeb, W. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.105633 · Cited by 8
“Because of Africa’s low vaccination rate, the Omicron variant may have more readily circulated [25].”
SARS-CoV-2 Omicron variant (B.1.1.529): A concern with immune escape
Sanyaolu, A. O., Marinkovic, A., Prakash, S., Haider, N., Williams, M., Okorie, C., Badaru, O., & Smith, S. I. (2022) · World Journal of Virology · doi:10.5501/wjv.v11.i3.137 · Cited by 9
SARS-CoV-2 variants of concerns in animals: An unmonitored rising health threat
Saied, A. A., & Metwally, A. A. (2022) · VirusDisease · doi:10.1007/s13337-022-00794-8 · Cited by 8
Rochman, N. D., Faure, G., Wolf, Y. I., Freddolino, P. L., Zhang, F., & Koonin, E. V. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.30.458225 · Cited by 8
“425 At the time of writing, the origins of the Omicron variant are unclear and is suspected to 426 have evolved over an extended period of time within an immunocompromised 427 individual(s) or an animal reservoir(30).”
BackgroundLi, M., Zu, J., Zhang, Y., Ma, L., Shen, M., Li, Z., & Ji, F. (2022) · Virology Journal · doi:10.1186/s12985-022-01771-9 · Cited by 7
Structural basis and analysis of hamster ACE2 binding to different SARS-CoV-2 spike RBDs
Niu, S., Zhao, Z., Liu, Z., Rong, X., Chai, Y., Bai, B., Han, P., Shang, G., Ren, J., Wang, Y., et al. (2024) · Journal of Virology · doi:10.1128/jvi.01157-23 · Cited by 7
“As reported, omicron variants evolved independently of all other SARS-CoV-2 variants, and a possible animal origin was proposed to be related to rodents such as mice and rats (41).”
BackgroundNorwood, K., Deng, Z.-L., Reimering, S., Robertson, G., Foroughmand-Araabi, M.-H., Goliaei, S., Hölzer, M., Klawonn, F., & McHardy, A. C. (2025) · Nature Communications · doi:10.1038/s41467-025-60231-4 · Cited by 10
“• Line 273: Could statistical significance (e.g., Wilcoxon test) be tested for differences between designated and non-designated pVOIs?”
Viral syncytia evolve to resist interferon
Li, T., Kang, I., Ye, J., Hu, Z., Gibbs, J. S., Ye, C., Takeda, K., Košík, I., Shi, G., Hollý, J., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-74676-8 · Cited by 6
Geng, F., Chen, J., Tang, S., Azzam, E. I., Zhang, J., & Zhang, S. (2022) · Radiation Research · doi:10.1667/rade-22-00058.1 · Cited by 6
A SARS-CoV-2 vaccine based on conjugation of SARS-CoV-2 RBD with IC28 peptide and mannan
He, Y., Yu, W., Shen, L., Yan, W., Xiao, L., Qi, J., & Hu, T. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.09.180 · Cited by 6
Current status of mucosal vaccines against SARS-CoV2: a hope for protective immunity
García-Silva, I., Govea‐Alonso, D. O., & Rosales‐Mendoza, S. (2023) · Expert Opinion on Biological Therapy · doi:10.1080/14712598.2022.2156284 · Cited by 6
Urbina-Garcia, O., Fernández‐Gámiz, U., Zulueta, E., Ugarte-Anero, A., & Portal-Porras, K. (2024) · Buildings · doi:10.3390/buildings14041007 · Cited by 7
Goh, G. K., Dunker, A. K., Foster, J. A., & Uversky, V. N. (2022) · Biomolecules · doi:10.3390/biom12050631 · Cited by 6
Davies, E. R., Ryan, K. A., Bewley, K. R., Coombes, N. S., Salguero, F. J., Carnell, O. T., Biddlecombe, S. M., Charlton, M., Challis, A., Cross, E. S., et al. (2023) · Viruses · doi:10.3390/v15051133 · Cited by 5
Saini, S., Pareekh, S., & Kumar, Y. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2222174 · Cited by 5
“However, some studies suggest evolution of antigenic shifts in variants could be attributed to rigorous viral amplification in patients who are immunocompromised (Cameroni et al., 2022; Corey et al., 2021; Kupferschmidt, 2021).”
BackgroundWei, L., Song, L., Dunker, A. K., Foster, J. A., Uversky, V. N., & Goh, G. K. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25147537 · Cited by 5
“[ 23–25, 29 – Omicrons became available [26,34].”
BackgroundGoh, G. K., Dunker, A. K., Foster, J. A., & Uversky, V. N. (2022) · Biomolecules · doi:10.3390/biom12101353 · Cited by 5
Structural basis for antibody resistance to SARS-CoV-2 omicron variantPreprint
Cerutti, G., Guo, Y., Liu, L., Zhang, Z., Liu, L., Luo, Y., Huang, Y., Wang, H. H., Ho, D. D., Sheng, Z., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.21.473620 · Cited by 5
“Some have proposed that it developed in a chronically infected individual with an impaired immune response, whereas others think it developed in parallel with other variants in a population not monitored by sequencing (Kupferschmidt, 2021).”
BackgroundWhat Learned from Omicron Sub-Variants BQ.1 and BQ.1.1Preprint
Mustafa, M. I., & Makhawi, A. M. (2022) · Preprints.org · doi:10.20944/preprints202210.0361.v1 · Cited by 5
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
