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M., Yu E. for each infection episode, aligned based on the estimated timing of trough test (A-B) and z-test (C). Abbreviations: HIV- (HIV-uninfected individuals), PLWH+ CD4 200 (Persons living with HIV, CD4+ T cell count under 200 cells/ml), PLWH+ CD4 =200 (Persons living with HIV, CD4+ T cell count equal or above 200 cells/ml). The population of the PHIRST-C cohort had a high prevalence of HIV, 13% in the rural site and 16% in the urban site, reflecting the burden of HIV infections in South Africa (Table 1). However, in this cohort, most (93.8%) persons living with HIV (PLWH) had CD4+ T cell counts 200 cells/ml (Table 1), and they did not differ from HIV-uninfected individuals in terms of SARS-CoV-2 shedding (Fig. 3A-B). Table 1: PHIRST-C study June 2020 C August 2021, characteristics of the population and SARS-CoV-2 infections at two study sites, South Africa.*PLWH: persons living with HIV values. We found that individuals were more infectious in the RNA proliferation than clearance stage. Prior to the emergence of Omicron, substantial population immunity had accumulated through prior infection, with high and durable protection against symptomatic and asymptomatic reinfection, in line with prior findings ( test used to determine statistical significance. For regression analyses of risk factors for SARS-CoV-2 infection and re-infection, we used mixed-effects Poisson regression (Materials and Methods Section 2.5), and two-tailed z-tests to determine statistical significance. We also present a sensitivity analysis of risk factors associated with SARS-CoV-2 infection using mixed-effects logistic regression (Materials and Methods Section 2.5), with two-tailed z-tests to determine statistical significance. P 0.05 was considered significant. All regression analysis were performed SDZ 205-557 HCl using R package lme4 version 1.1-27.1 under R version 4.1.2. Details on the SARS-CoV-2 transmission models and calibration procedures to project the trajectory of the Omicron and post-Omicron waves can be found in Materials and Methods Section 3-5. Acknowledgments Funding: This work was supported by the National Institute for Communicable Diseases of the National Health Laboratory Service and the U.S. Centers for Disease Control and Prevention [cooperative agreement number: 6 U01IP001048] and Wellcome Trust (grant number 221003/Z/20/Z) in collaboration with the Foreign, Commonwealth and Development Office, United Kingdom. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the NIH or the U.S. Centers for Disease Control and Mst1 Prevention. Author contributions: KS, ST, JK, AvG, MLM, NW, JM, NAM, KK, STo, LL, CV, CC designed the experiments. CC, JK, and ST accessed and verified the underlying data. ST, JK, AvG, MLM, NW, JNB, JM, MdP, MC, AB, NAM, KK, STo, LL, FW, JdT, FXG, FSD, TMK, CC collected the data and performed laboratory experiments. KS, ST, JK, AvG, MLM, NW, JNB, JM, MdP, MC, AB, NAM, KK, STo, LL, FW, JdT, FXG, FSD, TMK, CV, and CC analyzed the data and interpreted the results. KS, ST, JK, AvG, CV, and CC drafted the manuscript. All authors critically reviewed the article and had access to all the data reported in the SDZ 205-557 HCl study. Competing interests: CC has received grant support from Sanofi Pasteur, Advanced Vaccine Initiative, and payment of travel costs from Parexel. AvG has received grant support from Sanofi Pasteur, Pfizer related to pneumococcal vaccine, CDC and the Bill & Melinda Gates Foundation. NW reports grants from Sanofi Pasteur SDZ 205-557 HCl and the Bill & Melinda Gates Foundation. NAM has received a grant to his institution from Pfizer to conduct research in patients with pneumonia and from Roche to collect specimens to assess a TB assay. JM has received grant support from Sanofi Pasteur. Data and materials availability: All data associated with this study are present in the paper or supplementary materials. Code and aggregate data to reproduce the figures, regression analyses, and transmission model for the Omicron wave are available at 10.5281/zenodo.6544507. To access data, including individual participant data and a data dictionary defining each field in the data set, please submit a proposal to Professor Cheryl Cohen. These data can.