SARS-CoV-2 transmission, persistence of immunity, and estimates of Omicron’s impact in South African population cohorts
Open accessPublished version of a preprint
Abstract
Understanding the build-up of immunity with successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and the epidemiological conditions that favor rapidly expanding epidemics will help facilitate future pandemic control. We analyzed high-resolution infection and serology data from two longitudinal household cohorts in South Africa to reveal high cumulative infection rates and durable cross-protective immunity conferred by prior infection in the pre-Omicron era. Building on the history of past exposures to different SARS-CoV-2 variants and vaccination in the cohort most representative of South Africa’s high urbanization rate, we used mathematical models to explore the fitness advantage of the Omicron variant and its epidemic trajectory. Modeling suggests that the Omicron wave likely infected a large fraction (44 to 81%) of the population, leaving a complex landscape of population immunity primed and boosted with antigenically distinct variants. We project that future SARS-CoV-2 resurgences are likely under a range of scenarios of viral characteristics, population contacts, and residual cross-protection.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
This observation is in line with the finding of a durable immune protection conferred by prior infection and vaccination in the pre-Omicron era.
“This observation is in line with the finding of a durable immune protection conferred by prior infection and vaccination in the pre-Omicron era 10 .”
From Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa (2023) · cites this paper as [10]
Infections predating the Omicron BA.1/2 wave were ascertained based on both variant-specific PCR tests and serology, covering the period through blood draw 8, or mid-September, 2021.
“We ascertained infections predating the Omicron BA.1/2 wave based on both variant-specific PCR tests and serology, as detailed in a prior study 10 , covering the period through blood draw 8, or mid-September, 2021.”
From Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa (2023) · cites this paper as [10]
Based on variant-typed respiratory specimens during the intense follow-up period, serologic testing, as well as information on vaccine administration, the study had the unusual opportunity to track each individual participant's SARS-CoV-2 antigen exposure history in chronological order.
“Based on variant-typed respiratory specimens during the intense follow-up period 9,10 , serologic testing, as well as information on vaccine administration, we had the unusual opportunity to track each individual participant's SARS-CoV-2 antigen exposure history in chronological order.”
From Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa (2023) · cites this paper as [10]
A unique feature of the cohort populations includes intense monitoring since the first SARS-CoV-2 epidemic wave, with nasal swab collection at a twice weekly frequency, combined with frequent serum specimen collection.
“A unique feature of our cohort populations includes intense monitoring since the first SARS-CoV-2 epidemic wave, with nasal swab collection at a twice weekly frequency, combined with frequent serum specimen collection 10 .”
From Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa (2023) · cites this paper as [10]
The infection ascertainment rate was estimated at 0.84% in the rural site district and 1.31% in the urban site district, considerably lower than the ascertainment rates of prior waves, indicating that the surveillance system captured only a very small fraction of all Omicron BA.1/2 infections.
“The infection ascertainment rate was estimated at 0.84% in the rural site district and 1.31% in the urban site district, considerably lower than the ascertainment rates of prior waves 10,11 , indicating that the surveillance system captured only a very small fraction of all Omicron BA.1/2 infections.”
From Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa (2023) · cites this paper as [10]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Fitting Linear Mixed-Effects Models Using <b>lme4</b>
Bates, D., Mächler, M., Bolker, B., & Walker, S. (2015) · Journal of Statistical Software · doi:10.18637/jss.v067.i01 · Cited by 86,835 · see citing works
Regression Models and Life-Tables
Cox, D. R. (1972) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1972.tb00899.x · Cited by 39,793 · see citing works
Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection.
Dan, J. M., Mateus, J., Kato, Y., Hastie, K. M., Yu, E. D., Faliti, C. E., Grifoni, A., Ramirez, S. I., Haupt, S., Frazier, A., et al. (2021) · Science · doi:10.1126/science.abf4063 · Cited by 2,656 · see citing works
Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510 · see citing works
Self-citationRapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana, R. P. E. S., Moyo, S. M., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., et al. (2022) · Nature · doi:10.1038/s41586-022-04411-y · Cited by 1,653 · see citing works
Self-citationProfiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19)
Guo, L., Ren, L., Yang, S., Xiao, M., Chang, D., Yang, F., Cruz, C. S. D., Wang, Y., Wu, C., Xiao, Y., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa310 · Cited by 1,585 · see citing works
Cele, S., Jackson, L., Khoury, D. S., Khan, K., Moyo-Gwete, T., Tegally, H., San, J. E., Cromer, D., Scheepers, C., Amoako, D., et al. (2021) · doi:10.1101/2021.12.08.21267417 · Cited by 1,333 · see citing works
Self-citationFactors that make an infectious disease outbreak controllable
Fraser, C., Riley, S., Anderson, R. M., & Ferguson, N. M. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307506101 · Cited by 1,144 · see citing works
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 1,043 · see citing works
Wolter, N., Jassat, W., Walaza, S., Welch, R., Moultrie, H., Groome, M., Amoako, D. G., Everatt, J., Bhiman, J. N., Scheepers, C., et al. (2022) · The Lancet · doi:10.1016/s0140-6736(22)00017-4 · Cited by 1,041 · see citing works
Self-citationIncreased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa
Pulliam, J. R. C., van Schalkwyk, C., Govender, N., Gottberg, A. V., Cohen, C., Groome, M. J., Dushoff, J., Mlisana, K., & Moultrie, H. (2021) · doi:10.1101/2021.11.11.21266068 · Cited by 1,037 · see citing works
Self-citationSARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses
Turner, J. S., O’Halloran, J. A., Kalaidina, E., Kim, W., Schmitz, A. J., Zhou, J. Q., Lei, T., Thapa, M., Chen, R. E., Case, J. B., et al. (2021) · Nature · doi:10.1038/s41586-021-03738-2 · Cited by 831 · see citing works
Estimating infectiousness throughout SARS-CoV-2 infection course
Jones, T. C., Biele, G., Mühlemann, B., Veith, T., Schneider, J. A., Beheim-Schwarzbach, J., Bleicker, T., Tesch, J., Schmidt, M. L., Sander, L. E., et al. (2021) · Science · doi:10.1126/science.abi5273 · Cited by 716 · see citing works
Britton, T., Ball, F., & Trapman, P. (2020) · Science · doi:10.1126/science.abc6810 · Cited by 645 · see citing works
Hansen, C. H., Michlmayr, D., Gubbels, S. M., Mølbak, K., & Ethelberg, S. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00575-4 · Cited by 586 · see citing works
Covariance Analysis of Censored Survival Data Using Log-Linear Analysis Techniques
Laird, N. M., & Olivier, D. (1981) · Journal of the American Statistical Association · doi:10.1080/01621459.1981.10477634 · Cited by 580 · see citing works
SARS-CoV-2 infection induces long-lived bone marrow plasma cells in humans
Turner, J. S., Kim, W., Kalaidina, E., Goss, C. W., Rauseo, A. M., Schmitz, A. J., Hansen, L., Haile, A., Klebert, M. K., Pusic, I., et al. (2021) · Nature · doi:10.1038/s41586-021-03647-4 · Cited by 515 · see citing works
Initial report of decreased SARS-CoV-2 viral load after inoculation with the BNT162b2 vaccine
Levine-Tiefenbrun, M., Yelin, I., Katz, R., Herzel, E., Golan, Z., Schreiber, L., Wolf, T., Nadler, V., Ben-Tov, A., Kuint, J., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01316-7 · Cited by 514 · see citing works
Decreased SARS-CoV-2 viral load following vaccination
Levine-Tiefenbrun, M., Yelin, I., Katz, R., Herzel, E., Golan, Z., Schreiber, L., Wolf, T., Nadler, V., Ben-Tov, A., Kuint, J., et al. (2021) · doi:10.1101/2021.02.06.21251283 · Cited by 514 · see citing works
Buss, L. F., Prete, C. A., Abrahim, C. M. M., Mendrone, A., Salomon, T., de Almeida-Neto, C., França, R. F. O., Belotti, M. C., Carvalho, M. P. S. S., Costa, A. G., et al. (2021) · Science · doi:10.1126/science.abe9728 · Cited by 488 · see citing works
Prevention and Attenuation of Covid-19 with the BNT162b2 and mRNA-1273 Vaccines
Thompson, M. G., Burgess, J. L., Naleway, A. L., Tyner, H. L., Yoon, S. K., Meece, J. K., Olsho, L. E. W., Caban-Martinez, A. J., Fowlkes, A. L., Lutrick, K., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2107058 · Cited by 469 · see citing works
SARS-CoV-2 Omicron Variant Neutralization in Serum from Vaccinated and Convalescent Persons
Rössler, A., Riepler, L., Bante, D., von Laer, D., & Kimpel, J. (2022) · New England Journal of Medicine · doi:10.1056/nejmc2119236 · Cited by 466 · see citing works
Activity of convalescent and vaccine serum against SARS-CoV-2 Omicron
Carreño, J. M., Alshammary, H., Tcheou, J., Singh, G., Raskin, A. J., Kawabata, H., Sominsky, L. A., Clark, J. J., Adelsberg, D. C., Bielak, D. A., et al. (2021) · Nature · doi:10.1038/s41586-022-04399-5 · Cited by 456 · see citing works
Protection against the Omicron Variant from Previous SARS-CoV-2 Infection
Altarawneh, H. N., Chemaitelly, H., Hasan, M. R., Ayoub, H. H., Qassim, S., AlMukdad, S., Coyle, P., Yassine, H. M., Al-Khatib, H. A., Benslimane, F. M., et al. (2022) · New England Journal of Medicine · doi:10.1056/nejmc2200133 · Cited by 445 · see citing works
Thompson, M. G., Natarajan, K., Irving, S. A., Rowley, E. A., Griggs, E. P., Gaglani, M., Klein, N. P., Grannis, S. J., DeSilva, M. B., Stenehjem, E., et al. (2022) · MMWR. Morbidity and Mortality Weekly Report · doi:10.15585/mmwr.mm7104e3 · Cited by 398 · see citing works
Lewnard, J. A., Hong, V. X., Patel, M. M., Kahn, R. J., Lipsitch, M., & Tartof, S. Y. (2022) · Nature Medicine · doi:10.1038/s41591-022-01887-z · Cited by 382 · see citing works
The Analysis of Rates and of Survivorship Using Log-Linear Models
Holford, T. R. (1980) · Biometrics · doi:10.2307/2529982 · Cited by 378 · see citing works
Sixteen novel lineages of SARS-CoV-2 in South Africa
Tegally, H., Wilkinson, E., Lessells, R. J., Giandhari, J., Pillay, S., Msomi, N., Mlisana, K., Bhiman, J. N., von Gottberg, A., Walaza, S., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01255-3 · Cited by 349 · see citing works
Self-citationInferring high-resolution human mixing patterns for disease modeling
Mistry, D., Litvinova, M., y Piontti, A. P., Chinazzi, M., Fumanelli, L., Gomes, M. F. D. C., Haque, S. A., Liu, Q.-H., Mu, K., Xiong, X., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20544-y · Cited by 281 · see citing works
Potential impact of seasonal forcing on a SARS-CoV-2 pandemic
Neher, R. A., Dyrdak, R., Druelle, V., Hodcroft, E. B., & Albert, J. (2020) · Swiss Medical Weekly · doi:10.4414/smw.2020.20224 · Cited by 279 · see citing works
Muecksch, F., Weisblum, Y., Barnes, C., Schmidt, F., Schaefer-Babajew, D. J., Wang, Z.-J., Lorenzi, J. C. C., Flyak, A., DeLaitsch, A. T., Huey-Tubman, K. E., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.07.008 · Cited by 256 · see citing works
Anti-SARS-CoV-2 receptor-binding domain antibody evolution after mRNA vaccination
Cho, A., Muecksch, F., Schaefer-Babajew, D. J., Wang, Z., Finkin, S., Gaebler, C., Ramos, V., Cipolla, M., Mendoza, P., Agudelo, M., et al. (2021) · Nature · doi:10.1038/s41586-021-04060-7 · Cited by 254 · see citing works
Kissler, S. M., Fauver, J. R., Mack, C. D., Olesen, S. W., Tai, C. G.-L., Shiue, K. Y., Kalinich, C. C., Jednak, S., Ott, I. M., Vogels, C. B. F., et al. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001333 · Cited by 251 · see citing works
Willett, B., Grove, J., MacLean, O., et al. (2022) · medRxiv · doi:10.1101/2022.01.03.21268111 · Cited by 182 · see citing works
SARS-CoV-2 Omicron VOC Transmission in Danish HouseholdsPreprint
Lyngse, F. P., Mortensen, L. H., Denwood, M. J., et al. (2021) · medRxiv · doi:10.1101/2021.12.27.21268278 · Cited by 157 · see citing works
Milder disease with Omicron: is it the virus or the pre-existing immunity?
Sigal, A. (2022) · Nature reviews. Immunology · doi:10.1038/s41577-022-00678-4 · Cited by 153 · see citing works
Cohen, C., Kleynhans, J., Gottberg, A. V., McMorrow, M. L., Wolter, N., Bhiman, J. N., Moyes, J., Plessis, M. D., Carrim, M., Buys, A., et al. (2021) · doi:10.1101/2021.07.20.21260855 · Cited by 153 · see citing works
Self-citationBacker, J. A., Eggink, D., Andeweg, S. P., Veldhuijzen, I. K., van Maarseveen, N. M., Vermaas, K., Vlaemynck, B., Schepers, R., van den Hof, S., Reusken, C. B. E. M., et al. (2022) · Eurosurveillance · doi:10.2807/1560-7917.es.2022.27.6.2200042 · Cited by 150 · see citing works
Potential impact of seasonal forcing on a SARS-CoV-2 pandemicPreprint
Neher, R. A., Dyrdak, R., Druelle, V., et al. (2020) · medRxiv · doi:10.1101/2020.02.13.20022806 · Cited by 148 · see citing works
Quantifying the relationship between SARS-CoV-2 viral load and infectiousness
Marc, A., Kerioui, M., Blanquart, F., Bertrand, J., Mitjà, J., Corbacho‐Monné, M., Marks, M., & Guedj, J. (2021) · eLife · doi:10.7554/elife.69302 · Cited by 146 · see citing works
Kang, M., Xin, H., Yuan, J., Ali, S. T., Liang, Z., Zhang, J., Hu, T., Lau, E. H. Y., Zhang, Y., Zhang, M., et al. (2022) · Eurosurveillance · doi:10.2807/1560-7917.es.2022.27.10.2100815 · Cited by 139 · see citing works
SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay
Peluso, M. J., Takahashi, S., Hakim, J., Kelly, J. D., Torres, L., Iyer, N. S., Turcios, K., Janson, O., Munter, S. E., Thanh, C., et al. (2021) · Science Advances · doi:10.1126/sciadv.abh3409 · Cited by 130 · see citing works
Cohen, C., Kleynhans, J., Moyes, J., McMorrow, M., Treurnicht, F. K., Hellferscee, O., Mathunjwa, A., von Gottberg, A., Wolter, N., Martinson, N. A., et al. (2021) · The Lancet Global Health · doi:10.1016/s2214-109x(21)00141-8 · Cited by 124 · see citing works
Self-citationDecreased infectivity following BNT162b2 vaccination: A prospective cohort study in Israel
Regev-Yochay, G., Amit, S., Bergwerk, M., Lipsitch, M., Leshem, E., Kahn, R., Lustig, Y., Cohen, C., Doolman, R., Ziv, A., et al. (2021) · The Lancet Regional Health - Europe · doi:10.1016/j.lanepe.2021.100150 · Cited by 111 · see citing works
Self-citationKleynhans, J., Tempia, S., Wolter, N., von Gottberg, A., Bhiman, J. N., Buys, A., Moyes, J., McMorrow, M. L., Kahn, K., Gómez-Olivé, F. X., et al. (2021) · Emerging Infectious Diseases · doi:10.3201/eid2712.211465 · Cited by 97 · see citing works
Self-citationTransmission dynamics and epidemiological characteristics of Delta variant infections in ChinaPreprint
Kang, M., Xin, H., Yuan, J., et al. (2021) · medRxiv · doi:10.1101/2021.08.12.21261991 · Cited by 84 · see citing works
Ulloa, A. C., Buchan, S. A., Daneman, N., et al. (2021) · medRxiv · doi:10.1101/2021.12.24.21268382 · Cited by 55 · see citing works
Omicron infection of vaccinated individuals enhances neutralizing immunity against the Delta variantPreprint
Khan, K., Karim, F., Cele, S., et al. (2021) · medRxiv · doi:10.1101/2021.12.27.21268439 · Cited by 48 · see citing works
Mapping the antigenic diversification of SARS-CoV-2Preprint
van der Straten, K., Guerra, D., van Gils, M. J., Bontjer, I., Caniels, T. G., van Willigen, H. D. G., Wynberg, E., Poniman, M., Burger, J. A., Bouhuijs, J. H., et al. (2022) · medRxiv · doi:10.1101/2022.01.03.21268582 · Cited by 46 · see citing works
Braeye, T., Cornelissen, L., Catteau, L., Haarhuis, F., Proesmans, K., Ridder, K. D., Djiena, A., Mahieu, R., Leeuw, F. D., Dreuw, A., et al. (2021) · Vaccine · doi:10.1016/j.vaccine.2021.08.060 · Cited by 45 · see citing works
Bounding the levels of transmissibility & immune evasion of the Omicron variant in South Africa
Pearson, C. A. B., Silal, S. P., Li, M. W. Z., Dushoff, J., Bolker, B. M., Abbott, S., van Schalkwyk, C., Davies, N. G., Barnard, R. C., Edmunds, W. J., et al. (2021) · doi:10.1101/2021.12.19.21268038 · Cited by 44 · see citing works
Self-citationPollett, S. D., Richard, S. A., Fries, A. C., Simons, M. P., Mende, K., Lalani, T., Lee, T., Chi, S., Mody, R. M., Madar, C., et al. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab543 · Cited by 37 · see citing works
Cohen, C., McMorrow, M., Martinson, N. A., Kahn, K., Treurnicht, F. K., Moyes, J., Mkhencele, T., Hellferscee, O., Lebina, L., Moroe, M., et al. (2021) · Influenza and Other Respiratory Viruses · doi:10.1111/irv.12881 · Cited by 31 · see citing works
Self-citationProtection afforded by prior infection against SARS-CoV-2 reinfection with the Omicron variantPreprint
Altarawneh, H., Chemaitelly, H., Tang, P., Hasan, M. R., Qassim, S., Ayoub, H., AlMukdad, S., Yassine, H., Benslimane, F., Khatib, H. A., et al. (2022) · medRxiv · doi:10.1101/2022.01.05.22268782 · Cited by 31 · see citing works
Hall, V. J., Foulkes, S., Insalata, F., et al. (2021) · medRxiv · doi:10.1101/2021.11.29.21267006 · Cited by 19 · see citing works
SARS-CoV-2 Seroprevalence before Delta Variant Surge, Chattogram, Bangladesh, March–June 2021
Bhuiyan, T. R., Hulse, J. D., Hegde, S. T., et al. (2022) · Emerging infectious diseases · doi:10.3201/eid2802.211689 · Cited by 16 · see citing works
Huete‐Pérez, J. A., Ernst, K. C., Cabezas-Robelo, C., et al. (2021) · BMJ Open · doi:10.1136/bmjopen-2021-051836 · Cited by 7 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [35]35. J. A. Lewnard, V. X. Hong, M. M. Patel, R. Kahn, M. Lipsitch, S. Y. Tartof, Clinical outcomes among patients infected with Omicron (B.1.1.529) SARS-CoV-2 variant in southern California. bioRxiv (2022), doi:. 10.1101/2022.01.11.22269045 PMC10208005 35675841 · DOI
Cited by
Sorted by citations
Markov, P. V., Ghafari, M., Beer, M., Lythgoe, K., Simmonds, P., Stilianakis, N. I., & Katzourakis, A. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00878-2 · Cited by 1,179 · see citing works
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Tegally, H., Moir, M., Everatt, J., Giovanetti, M., Scheepers, C., Wilkinson, E., Subramoney, K., Makatini, Z., Moyo, S., Amoako, D. G., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01911-2 · Cited by 707 · see citing works
Self-citationRapidly 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 · see citing works
Self-citation
- Authors
- Sun, K., Tempia, S., Kleynhans, J., von Gottberg, A., McMorrow, M. L., Wolter, N., Bhiman, J. N., Moyes, J., du Plessis, M., Carrim, M., Buys, A., Martinson, N. A., Kahn, K., Tollman, S., Lebina, L., Wafawanaka, F., du Toit, J. D., Gómez-Olivé, F. X., Mkhencele, T., Viboud, C., & Cohen, C.
- Affiliations
- National Institutes of Health (US)
- National Health Laboratory Service (ZA)
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa.
- Centers for Disease Control and Prevention (US)
- Johns Hopkins University (US)
- University of the Witwatersrand (ZA)
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa.
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892-2220, USA.
- Corresponding author
- Sun, Kaiyuan
- Cohen, Cheryl
- ORCID
- Sun, Kaiyuan
- Tempia, Stefano
- Kleynhans, Jackie
- von Gottberg, Anne
- McMorrow, Meredith L.
- Wolter, Nicole
- Bhiman, Jinal N.
- Moyes, Jocelyn
- Carrim, Maimuna
- Buys, Amelia
- Martinson, Neil A.
- Kahn, Kathleen
- Tollman, Stephen
- Lebina, Limakatso
- Wafawanaka, Floidy
- du Toit, Jacques D.
- Gómez-Olivé, Francesc Xavier
- Mkhencele, Thulisa
- Viboud, Cécile
- Cohen, Cheryl
- Venue
- Science Translational Medicine
- Published
- 2022-08-24
- Volume
- 14
- Issue
- 659
- Pages
- eabo7081-eabo7081
- ISSN
- 1946-6234 (ISSN-L)
- 1946-6242
- PMC
- PMC9161370
- OpenAlex
- W4281663532
- Cited by
- 52
- References
- 58
- Citations by year
- 2026: 4 · 2025: 3 · 2024: 10 · 2023: 21 · 2022: 14
- FWCI
- 5.87
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Science Translational Medicine (publishedVersion, cc-by)
- medRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (221003/Z/20/Z)
- Centers for Disease Control and Prevention (U01IP001048)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Keywords
- SARS-CoV-2, Omicron variant, cross-protective immunity, prior infection, serology, epidemic trajectory, viral fitness, epidemic projection, SARS-CoV-2 variants, vaccination, South Africa, herd immunity
- MeSH terms
- COVID-19, SARS-CoV-2, Humans, South Africa, Pandemics
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
