Wouters, O. J. et al. Challenges in ensuring global access to COVID-19 vaccines: production, affordability, allocation and deployment. Lancet 397, 1023–1034 (2021).
Forni, G. & Mantovani, A. COVID-19 vaccines: where we stand and challenges ahead. Cell Death Differ. 28, 626–639 (2021).
Shrotri, M., Swinnen, T., Kampmann, B. & Parker, E. P. K. An interactive website tracking COVID-19 vaccine development. Lancet Glob. Health 9, e590–e592 (2021).
Koup, R. A. et al. A government-led effort to identify correlates of protection for COVID-19 vaccines. Nat. Med. 27, 1493–1494 (2021).
Saad-Roy, C. M. et al. Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes. Science 372, 363–370 (2021).
Bubar, K. M. et al. Model-informed COVID-19 vaccine prioritization strategies by age and serostatus. Science 371, 916–921 (2021).
Voysey, M. et al. Single-dose administration and the influence of the timing of the booster dose on immunogenicity and efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine: a pooled analysis of four randomised trials. Lancet 397, 881–891 (2021).
Garg, A. K., Mittal, S., Padmanabhan, P., Desikan, R. & Dixit, N. M. Increased B cell selection stringency in germinal centers can explain improved COVID-19 vaccine efficacies with low dose prime or delayed boost. Front. Immunol. 12, 776933 (2021).
Tauzin, A. et al. Strong humoral immune responses against SARS-CoV-2 spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. Cell Host Microbe 30, 97–109 (2022).
Baden, L. R. et al. Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine. N. Engl. J. Med. 384, 403–416 (2021).
Polack, F. P. et al. Safety and efficacy of the BNT162b2 mRNA COVID-19 Vaccine. N. Engl. J. Med. 383, 2603–2615 (2020).
Logunov, D. Y. et al. Safety and efficacy of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine: an interim analysis of a randomised controlled phase 3 trial in Russia. Lancet 397, 671–681 (2021).
Ella, R. et al. Efficacy, safety, and lot-to-lot immunogenicity of an inactivated SARS-CoV-2 vaccine (BBV152): interim results of a randomised, double-blind, controlled, phase 3 trial. Lancet 398, 2173–2184 (2021).
Jara, A. et al. Effectiveness of an inactivated SARS-CoV-2 vaccine in Chile. N. Engl. J. Med. 385, 875–884 (2021).
Sadoff, J. et al. Safety and efficacy of single-dose Ad26.COV2.S vaccine against COVID-19. N. Engl. J. Med. 384, 2187–2201 (2021).
Heath, P. T. et al. Safety and efficacy of NVX-CoV2373 COVID-19 vaccine. N. Engl. J. Med. 385, 1172–1183 (2021).
Khoury, D. S. et al. Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection. Nat. Med. 27, 1205–1211 (2021).
Earle, K. A. et al. Evidence for antibody as a protective correlate for COVID-19 vaccines. Vaccine 39, 4423–4428 (2021).
Feng, S. et al. Correlates of protection against symptomatic and asymptomatic SARS-CoV-2 infection. Nat. Med. 27, 2032–2040 (2021).
Barrett, J. R. et al. Phase 1/2 trial of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 with a booster dose induces multifunctional antibody responses. Nat. Med. 27, 279–288 (2021).
Israelow, B. et al. Adaptive immune determinants of viral clearance and protection in mouse models of SARS-CoV-2. Sci. Immunol. 6, eabl4509 (2021).
Gilbert, P. B. et al. Immune correlates analysis of the mRNA-1273 COVID-19 vaccine efficacy clinical trial. Science 375, 43–50 (2022).
Addetia, A. et al. Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with a high attack rate. J. Clin. Microbiol. 58, e02107–e02120 (2020).
Lumley, S. F. et al. Antibody status and incidence of SARS-CoV-2 infection in health care workers. N. Engl. J. Med. 384, 533–540 (2020).
Callow, K. A. Effect of specific humoral immunity and some non-specific factors on resistance of volunteers to respiratory coronavirus infection. J. Hyg. 95, 173–189 (1985).
Liu, L. et al. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature 584, 450–456 (2020).
Robbiani, D. F. et al. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature 584, 437–442 (2020).
Folegatti, P. M. et al. Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial. Lancet 396, 467–478 (2020).
Perelson, A. S. & Oster, G. F. Theoretical studies of clonal selection: minimal antibody repertoire size and reliability of self-non-self discrimination. J. Theor. Biol. 81, 645–670 (1979).
Chi, X. et al. A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science 369, 650–655 (2020).
Wang, C. et al. A human monoclonal antibody blocking SARS-CoV-2 infection. Nat. Commun. 11, 2251 (2020).
Seydoux, E. et al. Analysis of a SARS-CoV-2-infected individual reveals development of potent neutralizing antibodies with limited somatic mutation. Immunity 53, 98–105 e105 (2020).
Shi, R. et al. A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2. Nature 584, 120–124 (2020).
Wec, A. Z. et al. Broad neutralization of SARS-related viruses by human monoclonal antibodies. Science 369, 731–736 (2020).
Lei, C. et al. Neutralization of SARS-CoV-2 spike pseudotyped virus by recombinant ACE2-Ig. Nat. Commun. 11, 2070 (2020).
Lv, Z. et al. Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody. Science 369, 1505–1509 (2020).
Zost, S. J. et al. Potently neutralizing and protective human antibodies against SARS-CoV-2. Nature 584, 443–449 (2020).
Ju, B. et al. Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature 584, 115–119 (2020).
Cao, Y. et al. Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients’ B cells. Cell 182, 73–84 (2020).
Hansen, J. et al. Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail. Science 369, 1010–1014 (2020).
Rogers, T. F. et al. Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. Science 369, 956–963 (2020).
Barnes, C. O. et al. Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies. Cell 182, 828–842 (2020).
Pinto, D. et al. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature 583, 290–295 (2020).
Hanke, L. et al. An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction. Nat. Commun. 11, 4420 (2020).
Webb, N. E., Montefiori, D. C. & Lee, B. Dose–response curve slope helps predict therapeutic potency and breadth of HIV broadly neutralizing antibodies. Nat. Commun. 6, 8443 (2015).
Padmanabhan, P. & Dixit, N. M. Inhibitors of hepatitis C virus entry may be potent ingredients of optimal drug combinations. Proc. Natl Acad. Sci. USA 114, E4524–E4526 (2017).
Jilek, B. L. et al. A quantitative basis for antiretroviral therapy for HIV-1 infection. Nat. Med. 18, 446–451 (2012).
Isho, B. et al. Persistence of serum and saliva antibody responses to SARS-CoV-2 spike antigens in COVID-19 patients. Sci. Immunol. 5, eabe5511 (2020).
Iyer, A. S. et al. Persistence and decay of human antibody responses to the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 patients. Sci. Immunol. 5, eabe0367 (2020).
Röltgen, K. et al. Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome. Sci. Immunol. 5, eabe0240 (2020).
Shrock, E. et al. Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity. Science 370, eabd4250 (2020).
Yuan, M. et al. Structural basis of a shared antibody response to SARS-CoV-2. Science 369, 1119–1123 (2020).
Meyer, C. T. et al. Quantifying drug combination synergy along potency and efficacy axes. Cell Syst. 8, 97–108 (2019).
Widge, A. T. et al. Durability of responses after SARS-CoV-2 mRNA-1273 vaccination. N. Engl. J. Med. 384, 80–82 (2021).
McMahan, K. et al. Correlates of protection against SARS-CoV-2 in rhesus macaques. Nature 590, 630–634 (2021).
Sette, A. & Crotty, S. Adaptive immunity to SARS-CoV-2 and COVID-19. Cell 184, 861–880 (2021).
Wölfel, R. et al. Virological assessment of hospitalized patients with COVID-2019. Nature 581, 465–469 (2020).
Neant, N. et al. Modeling SARS-CoV-2 viral kinetics and association with mortality in hospitalized patients from the French COVID cohort. Proc. Natl Acad. Sci. USA 118, e2017962118 (2021).
Kissler, S. M. et al. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies. PLoS Biol. 19, e3001333 (2021).
Desikan, R., Raja, R. & Dixit, N. M. Early exposure to broadly neutralizing antibodies may trigger a dynamical switch from progressive disease to lasting control of SHIV infection. PLoS Comput. Biol. 16, e1008064 (2020).
Yu, J. et al. DNA vaccine protection against SARS-CoV-2 in rhesus macaques. Science 369, 806–811 (2020).
Yang, S., Jerome, K. R., Greninger, A. L., Schiffer, J. T. & Goyal, A. Endogenously produced SARS-CoV-2 specific IgG antibodies may have a limited impact on clearing nasal shedding of virus during primary infection in humans. Viruses 13, 516 (2021).
van Gils, M. J. & Sanders, R. W. In vivo protection by broadly neutralizing HIV antibodies. Trends Microbiol. 22, 550–551 (2014).
Fajnzylber, J. et al. SARS-CoV-2 viral load is associated with increased disease severity and mortality. Nat. Commun. 11, 5493 (2020).
Arnaout, R. et al. SARS-CoV2 testing: the limit of detection matters. Preprint at bioRxiv https://doi.org/10.1101/2020.06.02.131144 (2020).
Gonçalves, A. et al. Timing of antiviral treatment initiation is critical to reduce SARS-CoV-2 viral load. CPT Pharmacometrics Syst. Pharm. 9, 509–514 (2020).
Goyal, A., Cardozo-Ojeda, E. F. & Schiffer, J. T. Potency and timing of antiviral therapy as determinants of duration of SARS-CoV-2 shedding and intensity of inflammatory response. Sci. Adv. 6, eabc7112 (2020).
Dagan, N. et al. BNT162b2 mRNA COVID-19 vaccine in a nationwide mass vaccination setting. N. Engl. J. Med. 384, 1412–1423 (2021).
Walsh, E. E. et al. Safety and immunogenicity of two RNA-based COVID-19 vaccine candidates. N. Engl. J. Med. 383, 2439–2450 (2020).
Anderson, E. J. et al. Safety and immunogenicity of SARS-CoV-2 mRNA-1273 vaccine in older adult. N. Engl. J. Med. 383, 2427–2438 (2020).
Maisonnasse, P. et al. COVA1-18 neutralizing antibody protects against SARS-CoV-2 in three preclinical models. Nat. Commun. 12, 6097 (2021).
Chigutsa, E., O’Brien, L., Ferguson-Sells, L., Long, A. & Chien, J. Population pharmacokinetics and pharmacodynamics of the neutralizing antibodies bamlanivimab and etesevimab in patients with mild to moderate COVID-19 infection. Clin. Pharmacol. Ther. 110, 1302–1310 (2021).
Saha, A. & Dixit, N. M. Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection. PLoS Comput. Biol. 16, e1008434 (2020).
Krammer, F. A correlate of protection for SARS-CoV-2 vaccines is urgently needed. Nat. Med. 27, 1147–1148 (2021).
Chatterjee, B., Sandhu, H. S. & Dixit, N. M. The relative strength and timing of innate immune and CD8 T-cell responses underlie the heterogeneous outcomes of SARS-CoV-2 infection. Preprint at medRxiv https://doi.org/10.1101/2021.06.15.21258935 (2021).
Padmanabhan, P., Garaigorta, U. & Dixit, N. M. Emergent properties of the interferon-signalling network may underlie the success of hepatitis C treatment. Nat. Commun. 5, 3872 (2014).
Perelson, A. S. & Ke, R. Mechanistic modeling of SARS-CoV-2 and other infectious diseases and the effects of therapeutics. Clin. Pharmacol. Ther. 109, 829–840 (2020).
Baum, A. et al. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science 369, 1014–1018 (2020).
Padmanabhan, P. & Dixit, N. M. Modeling suggests a mechanism of synergy between hepatitis C virus entry inhibitors and drugs of other classes. CPT Pharmacometrics Syst. Pharm. 4, 445–453 (2015).
Chou, T. C. Theoretical basis, experimental design, and computerized simulation of synergism and antagonism in drug combination studies. Pharm. Rev. 58, 621–681 (2006).
Padmanabhan, P., Desikan, R. & Dixit, N. M. Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection. PLoS Comput. Biol. 16, e1008461 (2020).
Brouwer, P. J. M. et al. Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability. Science 369, 643–650 (2020).
Kim, K. S. et al. A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2. PLoS Biol. 19, e3001128 (2021).
Zarnitsyna, V. I. et al. Mathematical model reveals the role of memory CD8 T cell populations in recall responses to influenza. Front. Immunol. 7, 165 (2016).
Benotmane, I. et al. Biomarkers of cytokine release syndrome predict disease severity and mortality from COVID-19 in kidney transplant recipients. Transplantation 105, 158–169 (2021).
Ke, R. et al. Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. Preprint at medRxiv https://doi.org/10.1101/2021.07.12.21260208 (2021).
Golob, J. L., Lugogo, N., Lauring, A. S. & Lok, A. S. SARS-CoV-2 vaccines: a triumph of science and collaboration. JCI Insight 6, e149187 (2021).
Zhang, Y. et al. Safety, tolerability and immunogenicity of an inactivated SARS-CoV-2 vaccine in healthy adults aged 18–59 years: a randomised, double-blind, placebo-controlled, phase 1/2 clinical trial. Lancet Infect. Dis. 21, 181–192 (2021).
Jackson, L. A. et al. An mRNA vaccine against SARS-CoV-2—preliminary report. N. Engl. J. Med. 383, 1920–1931 (2020).
Padmanabhan, P., Desikan, R. & Dixit, N. M. COVID-19 vaccine efficacies. Zenodo https://doi.org/10.5281/zenodo.5879304 (2022).