1 Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270-273, doi:10.1038/s41586-020-2012-7 (2020).
2 Drosten, C. et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348, 1967-1976, doi:10.1056/NEJMoa030747 (2003).
3 Li, W. et al. Bats are natural reservoirs of SARS-like coronaviruses. Science 310, 676-679, doi:10.1126/science.1118391 (2005).
4 Lau, S. K. et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci U S A 102, 14040-14045 (2005).
5 Wacharapluesadee, S. et al. Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia. Nat Commun 12, 972, doi:10.1038/s41467-021-21240-1 (2021).
6 Delaune, D. et al. A novel SARS-CoV-2 related coronavirus in bats from Cambodia. Nat Commun 12, 6563, doi:10.1038/s41467-021-26809-4 (2021).
7 Ge, X. Y. et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503, 535-538, doi:10.1038/nature12711 (2013).
8 Hu, B. et al. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog 13, e1006698, doi:10.1371/journal.ppat.1006698 (2017).
9 Lam, T. T. et al. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 583, 282-285, doi:10.1038/s41586-020-2169-0 (2020).
10 Harvey, W. T. et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol 19, 409-424, doi:10.1038/s41579-021-00573-0 (2021).
11 Wang, P. et al. Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization. Cell Host Microbe 29, 747-751 e744, doi:10.1016/j.chom.2021.04.007 (2021).
12 Wang, P. et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature 593, 130-135, doi:10.1038/s41586-021-03398-2 (2021).
13 Chen, R. E. et al. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat Med 27, 717-726, doi:10.1038/s41591-021-01294-w (2021).
14 McCallum, M. et al. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science 373, 648-654, doi:10.1126/science.abi7994 (2021).
15 McCallum, M. et al. Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. Science 374, 1621-1626, doi:10.1126/science.abl8506 (2021).
16 Planas, D. et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature 596, 276-280, doi:10.1038/s41586-021-03777-9 (2021).
17 Mlcochova, P. et al. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 599, 114-119, doi:10.1038/s41586-021-03944-y (2021).
18 Saito, A. et al. Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nature, doi:10.1038/s41586-021-04266-9 (2021).
19 Cao, Y. et al. Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature, doi:https://doi.org/10.1038/s41586-021-04385-3 (2021).
20 Schmidt, F. et al. Plasma neutralization properties of the SARS-CoV-2 Omicron variant. medRxiv, doi:10.1101/2021.12.12.21267646 (2021).
21 Collie, S., Champion, J., Moultrie, H., Bekker, L. G. & Gray, G. Effectiveness of BNT162b2 Vaccine against Omicron Variant in South Africa. N Engl J Med, doi:10.1056/NEJMc2119270 (2021).
22 Cele, S. et al. Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization. Nature, doi:10.1038/s41586-021-04387-1 (2021).
23 Tan, C. W. et al. Pan-Sarbecovirus Neutralizing Antibodies in BNT162b2-Immunized SARS-CoV-1 Survivors. N Engl J Med 385, 1401-1406, doi:10.1056/NEJMoa2108453 (2021).
24 Tan, C. W. et al. A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2-spike protein-protein interaction. Nat Biotechnol 38, 1073-1078, doi:10.1038/s41587-020-0631-z (2020).
25 Chandler, J. C. et al. SARS-CoV-2 exposure in wild white-tailed deer (Odocoileus virginianus). Proc Natl Acad Sci U S A 118, doi:10.1073/pnas.2114828118 (2021).
26 Perera, R. et al. Evaluation of a SARS-CoV-2 Surrogate Virus Neutralization Test for Detection of Antibody in Human, Canine, Cat, and Hamster Sera. J Clin Microbiol 59, doi:10.1128/JCM.02504-20 (2021).
27 Chia, W. N. et al. Dynamics of SARS-CoV-2 neutralising antibody responses and duration of immunity: a longitudinal study. Lancet Microbe 2, e240-e249, doi:10.1016/S2666-5247(21)00025-2 (2021).
28 Chia, P. Y. et al. Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine breakthrough infections: a multicentre cohort study. Clin Microbiol Infect, doi:10.1016/j.cmi.2021.11.010 (2021).
29 Piccoli, L. et al. Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology. Cell 183, 1024-1042 e1021, doi:10.1016/j.cell.2020.09.037 (2020).
30 Premkumar, L. et al. The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients. Sci Immunol 5, doi:10.1126/sciimmunol.abc8413 (2020).
31 Zhu, F. et al. WHO international standard for SARS-CoV-2 antibodies to determine markers of protection. Lancet Microbe, doi:10.1016/S2666-5247(21)00307-4 (2021).
32 Smith, D. J. et al. Mapping the antigenic and genetic evolution of influenza virus. Science 305, 371-376, doi:10.1126/science.1097211 (2004).
33 Kendra, J. A., Tohma, K., Ford-Siltz, L. A., Lepore, C. J. & Parra, G. I. Antigenic cartography reveals complexities of genetic determinants that lead to antigenic differences among pandemic GII.4 noroviruses. Proc Natl Acad Sci U S A 118, doi:10.1073/pnas.2015874118 (2021).
34 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, doi:10.1038/s41591-021-01377-8 (2021).
35 Nemet, I. et al. Third BNT162b2 Vaccination Neutralization of SARS-CoV-2 Omicron Infection. N Engl J Med, doi:10.1056/NEJMc2119358 (2021).
36 Lewnard, J. A. et al. Clinical outcomes among patients infected with Omicron (B.1.1.529) SARS-CoV-2 variant in southern California. MedRxiv, doi:https://doi.org/10.1101/2022.01.11.22269045 (2022).
37 Davies, M. et al. Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa. medRxiv, doi:https://doi.org/10.1101/2022.01.12.22269148 (2022).
38 Boni, M. F. et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 5, 1408-1417, doi:10.1038/s41564-020-0771-4 (2020).
39 Zhou, H. et al. A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Curr Biol 30, 3896, doi:10.1016/j.cub.2020.09.030 (2020).
40 Kemp, S. A. et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature 592, 277-282, doi:10.1038/s41586-021-03291-y (2021).
41 Choi, B. et al. Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host. N Engl J Med 383, 2291-2293, doi:10.1056/NEJMc2031364 (2020).
42 Avanzato, V. A. et al. Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer. Cell 183, 1901-1912 e1909, doi:10.1016/j.cell.2020.10.049 (2020).
43 Hale, V. L. et al. SARS-CoV-2 infection in free-ranging white-tailed deer. Nature, doi:10.1038/s41586-021-04353-x (2021).
44 Oreshkova, N. et al. SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 25, doi:10.2807/1560-7917.ES.2020.25.23.2001005 (2020).
45 Schmidt, F. et al. Plasma Neutralization of the SARS-CoV-2 Omicron Variant. N Engl J Med, doi:10.1056/NEJMc2119641 (2021).
46 Yu, M. et al. Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species. J Immunol Methods 331, 1-12, doi:10.1016/j.jim.2007.11.009 (2008).