1. Palacios R, Batista AP, Nascimento Albuquerque CS, et al. Efficacy and safety of a COVID-19 inactivated vaccine in healthcare professionals in Brazil: The PROFISCOV study. SSRN 2021.
2. Sadoff J, Gray G, Vandebosch A, et al. Safety and Efficacy of Single-Dose Ad26.COV2.S Vaccine against Covid-19. New England Journal of Medicine 2021.
3. Ranzani OT, Hitchings M, Dorion Neto M, et al. Effectiveness of the CoronaVac vaccine in the elderly population during a P.1 variant-associated epidemic of COVID-19 in Brazil: A test-negative case-control study. medRxiv 2021: 2021.05.19.21257472.
4. Dagan N, Barda N, Kepten E, et al. BNT162b2 mRNA Covid-19 Vaccine in a Nationwide Mass Vaccination Setting. New England Journal of Medicine 2021; 384(15): 1412-23.
5. Bernal JL, Andrews N, Gower C, et al. Early effectiveness of COVID-19 vaccination with BNT162b2 mRNA vaccine and ChAdOx1 adenovirus vector vaccine on symptomatic disease, hospitalisations and mortality in older adults in England. medRxiv 2021: 2021.03.01.21252652.
6. Emary KRW, Golubchik T, Aley PK, et al. Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial. Lancet 2021; 397(10282): 1351-62.
7. Hall VJ, Foulkes S, Saei A, et al. COVID-19 vaccine coverage in health-care workers in England and effectiveness of BNT162b2 mRNA vaccine against infection (SIREN): a prospective, multicentre, cohort study. The Lancet 2021.
8. Madhi SA, Baillie VL, Cutland CL, et al. Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351 variant in South Africa. medRxiv 2021: 2021.02.10.21251247.
9. Novavax. Novavax COVID-19 Vaccine Demonstrates 89.3% Efficacy in UK Phase 3 Trial. News Release. 2021.
10. Johnson and Johnson. Johnson & Johnson Announces Single-Shot Janssen COVID-19 Vaccine Candidate Met Primary Endpoints in Interim Analysis of its Phase 3 ENSEMBLE Trial. 2021. https://www.prnewswire.com/news-releases/johnson--johnson-announces-single-shot-janssen-covid-19-vaccine-candidate-met-primary-endpoints-in-interim-analysis-of-its-phase-3-ensemble-trial-301218035.html (accessed 1 May 2021.
11. Kustin T, Harel N, Finkel U, et al. Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals. medRxiv 2021: 2021.04.06.21254882.
12. . https://ourworldindata.org/coronavirus/country/brazil (accessed 20th April 2021.
13. Buss LF, Prete CA, Abrahim CMM, et al. Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic. Science (New York, NY) 2021; 371(6526): 288.
14. Voloch CM, Silva F Rd, de Almeida LGP, et al. Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil. medRxiv 2020: 2020.12.23.20248598.
15. Faria NR, Mellan TA, Whittaker C, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science (New York, NY) 2021: eabh2644.
16. Sabino EC, Buss LF, Carvalho MPS, et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. The Lancet 2021; 397(10273): 452-5.
17. Hall VJ, Foulkes S, Charlett A, et al. SARS-CoV-2 infection rates of antibody-positive compared with antibody-negative health-care workers in England: a large, multicentre, prospective cohort study (SIREN). The Lancet 2021; 397(10283): 1459-69.
18. Naveca FG, da Costa C, Nascimento V, et al. SARS-CoV-2 reinfection by the new Variant of Concern (VOC) P.1 in Amazonas, Brazil. 2021. https://virological.org/t/sars-cov-2-reinfection-by-the-new-variant-of-concern-voc-p-1-in-amazonas-brazil/596 (accessed 3 May 2021.
19. Vasques Nonaka CK, Miranda Franco M, Graf T, et al. Genomic Evidence of a Sars-Cov-2 Reinfection Case With E484K Spike Mutation in Brazil. Preprints 2021.
20. Jangra S, Ye C, Rathnasinghe R, et al. SARS-CoV-2 spike E484K mutation reduces antibody neutralisation. The Lancet Microbe.
21. Widera M, Wilhelm A, Hoehl S, et al. Bamlanivimab does not neutralize two SARS-CoV-2 variants carrying E484K in vitro. medRxiv 2021: 2021.02.24.21252372.
22. Wang P, Wang M, Yu J, et al. Increased Resistance of SARS-CoV-2 Variant P.1 to Antibody Neutralization. bioRxiv 2021.
23. FDA News Release. Coronavirus (COVID-19) Update: FDA Revokes Emergency Use Authorization for Monoclonal Antibody Bamlanivimab. 2021.
24. Tegally H, Wilkinson E, Giovanetti M, et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv 2020: 2020.12.21.20248640.
25. Public Health England. Investigation of SARS-CoV-2 variants of concern in England 13 February 2021. 2021. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/961299/Variants_of_Concern_VOC_Technical_Briefing_6_England-1.pdf (accessed 2 May 2021.
26. COG consortium. COG-UK report on SARS-CoV-2 Spike mutations of interest in the UK 2021. https://www.cogconsortium.uk/wp-content/uploads/2021/01/Report-2_COG-UK_SARS-CoV-2-Mutations.pdf (accessed 30th April 2021.
27. Rambaut A LN, Pybus O, Barclay W, Barrett J, Carabelli A, Connor T, Peacock T, Robertson DL, Volz E on behalf of COVID-19 Genomics Consortium UK (COG-UK). Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. 2020.
28. Davies NG, Jarvis CI, van Zandvoort K, et al. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature 2021.
29. Davies NG, Abbott S, Barnard RC, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science (New York, NY) 2021; 372(6538): eabg3055.
30. Supasa P, Zhou D, Dejnirattisai W, et al. Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell 2021.
31. Wang P, Nair MS, Liu L, et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature 2021.
32. Zhou D, Dejnirattisai W, Supasa P, et al. Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Cell 2021; 184(9): 2348-61 e6.
33. Dejnirattisai W, Zhou D, Supasa P, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell 2021.
34. Voysey M, Clemens SAC, Madhi SA, et al. Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK. Lancet 2021; 397(10269): 99-111.
35. Voysey M, Costa Clemens SA, Madhi SA, 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 2021; 397(10277): 881-91.
36. Folegatti PM, Ewer KJ, Aley PK, 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 2020; 396(10249): 467-78.
37. Marshall JC, Murthy S, Diaz J, et al. A minimal common outcome measure set for COVID-19 clinical research. The Lancet Infectious Diseases 2020; 20(8): e192-e7.
38. Rubin DB. Multiple Imputation for Nonresponse in Surveys: New York: John Wiley & Sons; 1987.
39. Rubin DB. Inference and missing data. Biometrika 1976; 63(3): 581-92.
40. Abu-Raddad LJ, Chemaitelly H, Butt AA, National Study Group for C-V. Effectiveness of the BNT162b2 Covid-19 Vaccine against the B.1.1.7 and B.1.351 Variants. The New England journal of medicine 2021.
41. Shinde V, Bhikha S, Hoosain Z, et al. Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant. The New England journal of medicine 2021; 384(20): 1899-909.
42. Madhi SA, Baillie V, Cutland CL, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine 2021.
43. Fischer RJ, van Doremalen N, Adney DR, et al. ChAdOx1 nCoV-19 (AZD1222) protects hamsters against SARS-CoV-2 B.1.351 and B.1.1.7 disease. bioRxiv 2021: 2021.03.11.435000.
44. Collier DA, De Marco A, Ferreira I, et al. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature 2021; 593(7857): 136-41.
45. Naveca FG, Nascimento V, de Souza VC, et al. COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence. Nature Medicine 2021.
46. Hay JA, Kennedy-Shaffer L, Kanjilal S, et al. Estimating epidemiologic dynamics from cross-sectional viral load distributions. medRxiv 2021: 2020.10.08.20204222.
47. Cao L, Zhao S, Lou J, et al. Genetic mismatch explains sizable variation of COVID-19 vaccine efficacy in clinical trials. medRxiv 2021: 2021.04.22.21254079.
48. Graf T, Belio G, Martins Venas TM, et al. Identification of SARS-CoV-2 P.1-related lineages in Brazil provides new insights about the mechanisms of emergence of Variants of Concern. Virologicalorg 2021.
49. Lythgoe KA, Hall M, Ferretti L, et al. SARS-CoV-2 within-host diversity and transmission. Science (New York, NY) 2021; 372(6539).
50. Wymant C, Blanquart F, Golubchik T, et al. Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver. Virus Evol 2018; 4(1): vey007.
51. Katoh K, Standley DM. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution 2013; 30(4): 772-80.
52. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Molecular Biology and Evolution 2015; 32(1): 268-74.
53. Ratcliff J, Nguyen D, Fish M, et al. Virological and serological characterization of critically ill patients with COVID-19 in the UK: a special focus on variant detection. medRxiv 2021: 2021.02.24.21251989.