Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
Open accessPublished version of a preprint
Abstract
Unmitigated spread in Brazil: Despite an extensive network of primary care availability, Brazil has suffered profoundly during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Using daily data from state health offices, Castro et al. analyzed the pattern of spread of COVID-19 cases and deaths in the country from February to October 2020. Clusters of deaths before cases became apparent indicated unmitigated spread. SARS-CoV-2 circulated undetected in Brazil for more than a month as it spread north from Sã o Paulo. In Manaus, transmission reached unprecedented levels after a momentary respite in mid-2020. Faria et al. tracked the evolution of a new, more aggressive lineage called P.1, which has 17 mutations, including three (K417T, E484K, and N501Y) in the spike protein. After a period of accelerated evolution, this variant emerged in Brazil during November 2020. Coupled with the emergence of P.1, disease spread was accelerated by stark local inequalities and political upheaval, which compromised a prompt federal response. Science , abh1558 and abh2644, this issue p. 821 and p. 815
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?
Four SARS-CoV-2 variants of concern (Alpha, Beta, Gamma and Delta) emerged in the past several months.
“The past several months have witnessed the emergence of four SArS-cov-2 variants of concern (Alpha, beta, Gamma and Delta)”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [19]
The Gamma variant contains the RBD mutations N501Y, E484K and K417T.
“The Gamma variant contains the RBD mutations N501Y, E484K and K417T (ref. 19 ).”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [19]
As the Gamma variant was associated with a surge of infections in a region of Brazil estimated to have achieved a high infection rate, it is suspected of being able to infect and cause illness in persons previously infected with other variants.
“As the Gamma variant was associated with a surge of infections in a region of Brazil estimated to have achieved a high infection rate, it is suspected of being able to infect and cause illness in persons previously infected with other variants 19,29,30 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [19]
The Gamma variant was estimated to result in virus levels 3-4 times higher than earlier variants and to be responsible for an estimated 1.1-fold to 1.8-fold higher mortality.
“It was estimated to result in virus levels 3-4 times higher than earlier variants and to be responsible for an estimated 1.1-fold to 1.8-fold higher mortality 19 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [19]
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
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873 · see citing works
Posterior summarization in Bayesian phylogenetics using tracer 1.7
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy032 · Cited by 11,159 · see citing works
Self-citationEvolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032 · see citing works
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687 · see citing works
Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor
Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., et al. (2020) · Nature · doi:10.1038/s41586-020-2180-5 · Cited by 5,983 · see citing works
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
Suchard, M. A., Lemey, P., Baele, G., Ayres, D. L., Drummond, A. J., & Rambaut, A. (2018) · Virus Evolution · doi:10.1093/ve/vey016 · Cited by 3,810 · see citing works
Self-citationEstimating the effects of non-pharmaceutical interventions on COVID-19 in Europe
Flaxman, S., Mishra, S., Gandy, A., Unwin, H., Mellan, T., Coupland, H., Whittaker, C., Zhu, H., Berah, T., Eaton, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2405-7 · Cited by 3,072 · see citing works
Self-citationGISAID: Global initiative on sharing all influenza data – from vision to reality
Shu, Y., & McCauley, J. (2017) · Eurosurveillance · doi:10.2807/1560-7917.es.2017.22.13.30494 · Cited by 3,039 · see citing works
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960 · see citing works
HyPhy: hypothesis testing using phylogenies
Pond, S. L. K., Frost, S. D. W., & Muse, S. V. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti079 · Cited by 2,866 · see citing works
Self-citationA dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0770-5 · Cited by 2,543 · see citing works
Self-citationDetection 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-citationExploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
Rambaut, A., Lam, T. T., Carvalho, L. M., & Pybus, O. G. (2016) · Virus Evolution · doi:10.1093/ve/vew007 · Cited by 2,073 · see citing works
Self-citationStarr, T. N., Greaney, A. J., Hilton, S. K., Ellis, D., Crawford, K. H. D., Dingens, A. S., Navarro, M. J., Bowen, J. E., Tortorici, M. A., Walls, A. C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.012 · Cited by 1,956 · see citing works
Detecting Individual Sites Subject to Episodic Diversifying Selection
Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Kosakovsky Pond, S. L. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002764 · Cited by 1,811 · see citing works
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
The COVID-19 Genomics UK (COG-UK) consortium, Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., et al. (2021) · Nature · doi:10.1038/s41586-021-03470-x · Cited by 1,611 · see citing works
Self-citationPiccoli, L., Park, Y.-J., Tortorici, M. A., Czudnochowski, N., Walls, A. C., Beltramello, M., Silacci-Fregni, C., Pinto, D., Rosen, L. E., Bowen, J. E., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.037 · Cited by 1,395 · see citing works
mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C. O., Finkin, S., Schaefer-Babajew, D., Cipolla, M., Gaebler, C., Lieberman, J. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03324-6 · Cited by 1,343 · see citing works
Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants
Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C., Muecksch, F., Rutkowska, M., Hoffmann, H.-H., Michailidis, E., et al. (2020) · eLife · doi:10.7554/elife.61312 · Cited by 1,308 · see citing works
Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host
Choi, B., Choudhary, M. C., Regan, J., Sparks, J. A., Padera, R. F., Qiu, X., Solomon, I. H., Kuo, H.-H., Boucau, J., Bowman, K., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmc2031364 · Cited by 1,246 · see citing works
Greaney, A. J., Loes, A. N., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.003 · Cited by 1,178 · see citing works
Greaney, A. J., Loes, A. N., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D. (2021) · doi:10.1101/2020.12.31.425021 · Cited by 1,178 · cited 2× · see citing works
“Moreover, E484K is associated with reduced antibody neutralisation (6, 56-58).”
BackgroundSARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01285-x · Cited by 1,147 · see citing works
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O’Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, F. F., et al. (2021) · Cell · doi:10.1016/j.cell.2020.11.020 · Cited by 1,006 · see citing works
Self-citationEvidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera
Zhou, D., Dejnirattisai, W., Supasa, P., Liu, C., Mentzer, A. J., Ginn, H. M., Zhao, Y., Duyvesteyn, H. M. E., Tuekprakhon, A., Nutalai, R., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.037 · Cited by 992 · see citing works
Receptor and viral determinants of SARS‐coronavirus adaptation to human ACE2
Li, W., Zhang, C., Sui, J., Kuhn, J. H., Moore, M. J., Luo, S., Wong, S.-K., Huang, I., Xu, K., Vasilieva, N. Y., et al. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600640 · Cited by 976 · see citing works
Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence
Sabino, E. C., Buss, L. F., Carvalho, M. P. S., Prete, C. A., Crispim, M. A. E., Fraiji, N. A., Pereira, R. H. M., Parag, K. V., da Silva Peixoto, P., Kraemer, M. U. G., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00183-5 · Cited by 758 · see citing works
Self-citationAyres, D. L., Darling, A. E., Zwickl, D. J., Beerli, P., Holder, M. T., Lewis, P. O., Huelsenbeck, J. P., Ronquist, F., Swofford, D. L., Cummings, M. P., et al. (2011) · Systematic Biology · doi:10.1093/sysbio/syr100 · Cited by 707 · see citing works
Self-citationAvanzato, V. A., Matson, M. J., Seifert, S. N., Pryce, R., Williamson, B. N., Anzick, S. L., Barbian, K., Judson, S. D., Fischer, E. R., Martens, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.049 · Cited by 703 · see citing works
Self-citationCross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human
Song, H., Tu, C., Zhang, G., Wang, S., Zheng, K. C., Lei, L., Chen, Q., Gao, Y., Zhou, H., Xiang, H., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409608102 · Cited by 683 · see citing works
Self-citationTablet-next generation sequence assembly visualization.
Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F., & Marshall, D. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp666 · Cited by 666 · see citing works
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
Network for Genomic Surveillance in South Africa, Cele, S., COMMIT-KZN Team, Gazy, I., Jackson, L., Hwa, S.-H., Tegally, H., Lustig, G., Giandhari, J., Pillay, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03471-w · Cited by 651 · 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
Evolution and epidemic spread of SARS-CoV-2 in Brazil
Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., Mellan, T. A., du Plessis, L., Pereira, R. H. M., Sales, F. C. S., et al. (2020) · Science · doi:10.1126/science.abd2161 · Cited by 573 · see citing works
Self-citationImproving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci
Gill, M. S., Lemey, P., Faria, N. R., Rambaut, A., Shapiro, B., & Suchard, M. A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss265 · Cited by 555 · see citing works
Self-citationWrobel, A. G., Benton, D. J., Xu, P., Roustan, C., Martin, S. R., Rosenthal, P. B., Skehel, J. J., & Gamblin, S. J. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0468-7 · Cited by 544 · 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
Self-citationCOVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
Naveca, F. G., do Nascimento, V. A., de Souza, V. C., Corado, A. D. L. G., Nascimento, F., Silva, G., Costa, Á., Duarte, D., Pessoa, K., Mejía, M., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01378-7 · Cited by 474 · see citing works
Self-citationBayesian random local clocks, or one rate to rule them all
Drummond, A. J., & Suchard, M. A. (2010) · BMC Biology · doi:10.1186/1741-7007-8-114 · Cited by 429 · see citing works
Self-citationEpidemiological and clinical characteristics of the COVID-19 epidemic in Brazil
de Souza, W. M., Buss, L., Cândido, D. D. S., Carrera, J., Li, S., Zarebski, A. E., Pereira, R. H. M., Junior, C. A. P., Santos, A. A. D. S., Parag, K. V., et al. (2020) · Nature Human Behaviour · doi:10.1038/s41562-020-0928-4 · Cited by 429 · see citing works
Self-citationEstablishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
du Plessis, L., McCrone, J. T., Zarebski, A. E., Hill, V., Ruis, C., Gutiérrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T. R., et al. (2021) · Science · doi:10.1126/science.abf2946 · Cited by 408 · see citing works
Self-citationHallal, P. C., Hartwig, F. P., Horta, B. L., da Silveira, M. F., Struchiner, C. J., Vidaletti, L. P., Neumann, N. A., Pellanda, L. C., Dellagostin, O. A., Burattini, M. N., et al. (2020) · The Lancet Global Health · doi:10.1016/s2214-109x(20)30387-9 · Cited by 398 · see citing works
Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil
Voloch, C. M., Silva F, R. D., de Almeida, L. G. P., Cardoso, C. C., Brustolini, O. J., Gerber, A. L., Guimarães, A. P. D. C., Mariani, D., Costa, R. M. D., Ferreira, O. C., et al. (2020) · doi:10.1101/2020.12.23.20248598 · Cited by 372 · see citing works
Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil
Voloch, C. M., da Silva Francisco, R., de Almeida, L. G. P., Cardoso, C. C., Brustolini, O. J., Gerber, A. L., Guimarães, A. P. D. C., Mariani, D., da Costa, R. M., Ferreira, O. C., et al. (2021) · Journal of Virology · doi:10.1128/jvi.00119-21 · Cited by 372 · see citing works
Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanoporePreprint
Tyson, J. R., James, P. L., Stoddart, D., Sparks, N., Wickenhagen, A., Hall, G., Choi, J. H., Lapointe, H. R., Kamelian, K., Smith, A. D., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.04.283077 · Cited by 356 · see citing works
Self-citationTransmission of COVID-19 in 282 clusters in Catalonia, Spain: a cohort study
Marks, M., Millat-Martínez, P., Ouchi, D., Roberts, C. H., Alemany, A., Corbacho‐Monné, M., Ubals, M., Tobı́as, A., Tebé, C., Ballana, E., et al. (2021) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30985-3 · Cited by 342 · see citing works
On the Integral Equation of Renewal Theory
Feller, W. (1941) · The Annals of Mathematical Statistics · doi:10.1214/aoms/1177731708 · Cited by 340 · see citing works
Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States
Washington, N. L., Gangavarapu, K., Zeller, M., Bolze, A., Cirulli, E. T., Barrett, K. M. S., Larsen, B. B., Anderson, C., White, S., Cassens, T., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.052 · Cited by 328 · see citing works
Self-citationOn the Integral Equation of Renewal Theory
Feller, W. (1977) · Biomathematics · doi:10.1007/978-3-642-81046-6_16 · Cited by 267 · see citing works
Open access epidemiological data from the COVID-19 outbreak
Xu, B., Kraemer, M. U. G., Xu, B., Gutierrez, B., Mekaru, S. R., Sewalk, K. C., Loskill, A., Wang, L., Cohn, E. L., Hill, S., et al. (2020) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30119-5 · Cited by 251 · see citing works
Self-citationEstimating epidemiologic dynamics from cross-sectional viral load distributions
Hay, J. A., Kennedy-Shaffer, L., Kanjilal, S., Lennon, N., Gabriel, S., Lipsitch, M., & Mina, M. (2020) · Science · doi:10.1126/science.abh0635 · Cited by 242 · see citing works
Self-citationKidd, M., Richter, A., Best, A., Cumley, N., Mirza, J., Percival, B., Mayhew, M., Megram, O., Ashford, F., White, T., et al. (2021) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiab082 · Cited by 237 · see citing works
1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America
Worobey, M., Watts, T. D., McKay, R. A., Suchard, M. A., Granade, T. C., Teuwen, D. E., Koblin, B. A., Heneine, W., Lemey, P., & Jaffe, H. W. (2016) · Nature · doi:10.1038/nature19827 · Cited by 221 · see citing works
Self-citationTracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch
O’Toole, A. N., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., Messina, J. P., Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Tegally, H., et al. (2021) · Wellcome Open Research · doi:10.12688/wellcomeopenres.16661.2 · Cited by 213 · see citing works
Self-citationTracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2
O'Toole, Á., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., Messina, J. P., The COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, et al. (2021) · Wellcome Open Research · doi:10.12688/wellcomeopenres.16661.1 · Cited by 192 · see citing works
Self-citationNovel SARS-CoV-2 Variant in Travelers from Brazil to Japan
Fujino, T., Nomoto, H., Kutsuna, S., Ujiie, M., Suzuki, T., Sato, R., Fujimoto, T., Kuroda, M., Wakita, T., & Ohmagari, N. (2021) · Emerging infectious diseases · doi:10.3201/eid2704.210138 · Cited by 178 · see citing works
Routes for COVID-19 importation in Brazil
Cândido, D. D. S., Watts, A., Abade, L., Kraemer, M. U. G., Pybus, O. G., Croda, J., de Oliveira, W. K., Khan, K., Sabino, É. C., & Faria, N. R. (2020) · Journal of Travel Medicine · doi:10.1093/jtm/taaa042 · Cited by 175 · see citing works
Self-citationState-level tracking of COVID-19 in the United States
Unwin, H. J. T., Mishra, S., Bradley, V. C., Gandy, A., Mellan, T. A., Coupland, H., Ish-Horowicz, J. S., Vollmer, M., Whittaker, C., Filippi, S. L., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19652-6 · Cited by 163 · see citing works
Self-citationQu, X., Hao, P., Song, X., Jiang, S., Liu, Y., Wang, P., Rao, X., Song, H., Wang, S., Zuo, Y., et al. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m500662200 · Cited by 159 · see citing works
The SAFER Investigators and Field Study Team, Hellewell, J., CMMID COVID-19 working group, Russell, T., Beale, R. C. L., Kelly, G. P., Houlihan, C. F., Nastouli, E., & Kucharski, A. J. (2021) · BMC Medicine · doi:10.1186/s12916-021-01982-x · Cited by 141 · see citing works
On Age-Dependent Binary Branching Processes
Bellman, R., & Harris, T. E. (1952) · Annals of Mathematics · doi:10.2307/1969779 · Cited by 132 · see citing works
Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking
McGough, S. F., Johansson, M. A., Lipsitch, M., & Menzies, N. A. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007735 · Cited by 121 · see citing works
Peixoto, P. S., Marcondes, D., Peixoto, C., de Queiroz, L., Gouveia, R., Delgado, A., & Oliva, S. M. (2020) · PLoS ONE · doi:10.1371/journal.pone.0235732 · Cited by 115 · see citing works
Self-citationFrancisco, R. D. S., Benites, L. F., Lamarca, A. P., de Almeida, L. G. P., Hansen, A. W., Gularte, J. S., Demoliner, M., Gerber, A. L., Guimarães, A. P. D. C., Eisen, A. K. A., et al. (2021) · Virus Research · doi:10.1016/j.virusres.2021.198345 · Cited by 115 · see citing works
Washington, N., Gangavarapu, K., Zeller, M., et al. (2021) · medRxiv · doi:10.1101/2021.02.06.21251159 · Cited by 106 · see citing works
Report 21: Estimating COVID-19 cases and reproduction number in BrazilPreprint
Mellan, T. A., Hoeltgebaum, H., Mishra, S., Whittaker, C., Schnekenberg, R. P., Gandy, A., Unwin, H. J. T., Vollmer, M., Coupland, H., Hawryluk, I., et al. (2020) · medRxiv · doi:10.25561/78872 · Cited by 105 · see citing works
Self-citationImportation and early local transmission of COVID-19 in Brazil, 2020
de Jesus, J. G., Sacchi, C. T., Cândido, D. D. S., Claro, I. M., Sales, F. C. D. S., Manuli, E. R., da Silva, D. B. B., de Paiva, T. M., Pinho, M. A. B., Santos, K. C. D. O., et al. (2020) · Revista do Instituto de Medicina Tropical de São Paulo · doi:10.1590/s1678-9946202062030 · Cited by 98 · see citing works
Self-citationHall, V. J., Foulkes, S., Charlett, A., Atti, A., Monk, E., Simmons, R., Wellington, E., Cole, M., Saei, A., Oguti, B., et al. (2021) · medRxiv · doi:10.1101/2021.01.13.21249642 · Cited by 94 · see citing works
Borremans, B., Gamble, A., Prager, K. C., Helman, S. K., McClain, A. M., Cox, C., Savage, V., & Lloyd‐Smith, J. O. (2020) · eLife · doi:10.7554/elife.60122 · Cited by 89 · see citing works
Álvarez-Antonio, C., Meza‐Sánchez, G., Calampa, C., Casanova, W., Carey, C., Alava, F., Rodríguez, H., & Quispe, A. M. (2021) · The Lancet Global Health · doi:10.1016/s2214-109x(21)00173-x · Cited by 88 · see citing works
Report 34: COVID-19 infection fatality ratio: estimates from seroprevalence
Brazeau, N., Verity, R., Jenks, S. J., Fu, H. J., Whittaker, C., Winskill, P., Dorigatti, I., Walker, P. G. T., Riley, S., Schnekenberg, R. P., et al. (2020) · Spiral (Imperial College London) · doi:10.25561/83545 · Cited by 86 · see citing works
Self-citationNaveca, F. G., do Nascimento, V. A., Souza, V., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-275494/v1 · Cited by 79 · see citing works
Self-citationWang, Y. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.739524179.793585051 · Cited by 76 · see citing works
The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis?
Farfour, É., Lesprit, P., Visseaux, B., Pascreau, T., Jolly, É., Houhou, N., Mazaux, L., Asso‐Bonnet, M., & Vasse, M. (2020) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-020-03930-8 · Cited by 72 · see citing works
Genomic sequencing of SARS-CoV-2 : A guide to implementation for maximum impact on public health
Hill, S. C., Perkins, M. D., von Eije, K. J., Benschop, K., Faria, N. R., Golubchik, T., Holmes, E. C., Kafetzopoulou, L. E., Lemey, P., Mak, T. M., et al. (2021) · Cited by 67 · see citing works
Self-citationEstimating epidemiologic dynamics from cross-sectional viral load distributionsPreprint
Hay, J. A., Kennedy‐Shaffer, L., Kanjilal, S., et al. (2020) · medRxiv · doi:10.1101/2020.10.08.20204222 · Cited by 66 · see citing works
Self-citationdo Nascimento, V. A., Corado, A. D. L. G., Nascimento, F., Costa, Á., Duarte, D., Luz, S. L. B., Gonçalves, L. M. F., de Jesus, M. S., da Costa, C. F., Delatorre, E. O., et al. (2020) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/0074-02760200310 · Cited by 64 · see citing works
Self-citationKissler, S. M., Fauver, J. R., Mack, C. D., Tai, C. G.-L., Breban, M. I., Watkins, A. E., Samant, R. M., Anderson, D. J., Ho, D. D., Grubaugh, N. D., et al. (2021) · Digital Access to Scholarship at Harvard (DASH) (Harvard University) · Cited by 60 · see citing works
Martins, A. F., Zavascki, A. P., Wink, P. L., Volpato, F. C. Z., Monteiro, F. L., Rosset, C., de Paris, F., Ramos, Á., & Barth, A. L. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.12.2100276 · Cited by 60 · see citing works
Hall, V. J., Foulkes, S., Charlett, A., Atti, A., Monk, E. J. M., Simmons, R., Wellington, E., Cole, M. J., Saei, A., Oguti, B., et al. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3768524 · Cited by 59 · see citing works
Xavier, J., Giovanetti, M., Adelino, T., Fonseca, V., da Costa, A. V. B., Ribeiro, A. A., Felicio, K. N., Guerra-Duarte, C., Silva, M. V. F., Salgado, Á., et al. (2020) · Emerging Microbes & Infections · doi:10.1080/22221751.2020.1803146 · Cited by 51 · see citing works
Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020
Claro, I. M., Sales, F. C. D. S., Ramundo, M. S., Cândido, D. D. S., da Silva, C. A. M., de Jesus, J. G., Manuli, E. R., de Oliveira, C. M., Scarpelli, L. C., Campana, G., et al. (2021) · Emerging infectious diseases · doi:10.3201/eid2703.210038 · Cited by 51 · see citing works
Self-citationLiotti, F. M., Menchinelli, G., Marchetti, S., Morandotti, G. A., Sanguinetti, M., Posteraro, B., & Cattani, P. (2020) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-020-04025-0 · Cited by 49 · see citing works
Paiva, M. H. S., Guedes, D. R. D., Docena, C., Bezerra, M. F., Dezordi, F. Z., Machado, L. C., Krokovsky, L., Helvécio, E., da Silva, A. F., Vasconcelos, L. R. S., et al. (2020) · Viruses · doi:10.3390/v12121414 · Cited by 49 · see citing works
Self-citationSARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity
Siqueira, J. D., Goes, L. R., Alves, B. M., de Carvalho, P. S., Cicala, C., Arthos, J. A., Viola, J. P. B., de Melo, A. C., & Soares, M. A. (2021) · Virus Evolution · doi:10.1093/ve/veab013 · Cited by 41 · see citing works
Divergence dating using mixed effects clock modelling: An application to HIV-1
Bletsa, M., Suchard, M. A., Ji, X., Gryseels, S., Vrancken, B., Baele, G., Worobey, M., & Lemey, P. (2019) · Virus Evolution · doi:10.1093/ve/vez036 · Cited by 36 · see citing works
Self-citationGenomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil
Franceschi, V. B., Caldana, G. D., Mayer, A. D. M., Cybis, G. B., Neves, C. A. M., Ferrareze, P. A. G., Demoliner, M., de Almeida, P. R., Gularte, J. S., Hansen, A. W., et al. (2021) · BMC Genomics · doi:10.1186/s12864-021-07708-w · Cited by 35 · see citing works
MacLean, O. A., Lytras, S., Weaver, S., Singer, J. B., Boni, M. F., Lemey, P., Pond, S. L. K., & Robertson, D. L. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.28.122366 · Cited by 33 · see citing works
Self-citationInference of COVID-19 epidemiological distributions from Brazilian hospital data
Hawryluk, I., Mellan, T. A., Hoeltgebaum, H., Mishra, S., Schnekenberg, R. P., Whittaker, C., Zhu, H., Gandy, A., Donnelly, C. A., Flaxman, S. R., et al. (2020) · Journal of The Royal Society Interface · doi:10.1098/rsif.2020.0596 · Cited by 30 · see citing works
Self-citationHellewell, J., Russell, T., The SAFER Investigators and Field Study Team, CMMID COVID-19 working group, Beale, R. C. L., Kelly, G. P., Houlihan, C. F., Nastouli, E., & Kucharski, A. J. (2020) · medRxiv · doi:10.1101/2020.11.24.20229948 · Cited by 30 · see citing works
Suchard, M. A., Weiss, R. E., & Sinsheimer, J. S. (2003) · Systematic Biology · doi:10.1080/10635150390132713 · Cited by 22 · see citing works
Self-citationQuantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infectionPreprint
Borremans, B., Gamble, A., Prager, K. C., Helman, S. K., McClain, A. M., Cox, C., Savage, V. M., & Lloyd‐Smith, J. O. (2020) · medRxiv · doi:10.1101/2020.05.15.20103275 · Cited by 22 · see citing works
Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans
(2020) · TUScholarShare (Temple University) · doi:10.34944/dspace/225 · Cited by 14 · see citing works
Siqueira, J. D., Goes, L. R., Alves, B. M., de Carvalho, P. S., Cicala, C., Arthos, J. A., Viola, J. P. B., de Melo, A. C., Soares, M. A., & on behalf of the INCA COVID-19 Task Force (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.26.267831 · Cited by 14 · see citing works
Gaussian Process Nowcasting: Application to COVID-19 Mortality ReportingPreprint
Hawryluk, I., Hoeltgebaum, H., Mishra, S., Miscouridou, X., Schnekenberg, R. P., Whittaker, C., Vollmer, M., Flaxman, S. R., Bhatt, S., & Mellan, T. A. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2102.11249 · Cited by 11 · see citing works
Self-citationGenomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, BrazilPreprint
Franceschi, V. B., Caldana, G. D., Mayer, A. D. M., et al. (2021) · medRxiv · doi:10.1101/2021.01.21.21249906 · Cited by 10 · see citing works
Seroprevalence of Anti-SARS-CoV-2 Antibodies in Iquitos, Loreto, PeruPreprint
Álvarez-Antonio, C., Meza‐Sánchez, G., Calampa, C., Casanova, W., Carey, C., Alava, F., Rodríguez, H., & Quispe, A. M. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3759629 · Cited by 7 · see citing works
Seroprevalence of anti-SARS-CoV-2 antibodies in Iquitos, Loreto, PeruPreprint
Álvarez-Antonio, C., Meza‐Sánchez, G., Calampa, C., et al. (2021) · medRxiv · doi:10.1101/2021.01.17.21249913 · Cited by 6 · see citing works
MOLECULAR EPIDEMIOLOGY TO UNDERSTAND THE SARS-CoV-2 EMERGENCE IN THE BRAZILIAN AMAZON REGIONPreprint
dos Santos, M. C., Sousa, E. C., Ferreira, J. D. A., da Silva, S. P., de Souza, M. P. C., Cardoso, J. F., Silva, A. M., Barbagelata, L. S., das Chagas, W. D., Ferreira, J. L., et al. (2020) · medRxiv · doi:10.1101/2020.09.04.20184523 · Cited by 2 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [83]83. T. H. Jukes, C. R. Cantor, in Mammalian Protein Metabolism, H. N. Munro, Ed. (Academic Press, 1969), pp. 21132.
Cited by
Sorted by citations
SARS-CoV-2 variants, spike mutations and immune escape
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., COVID-19 Genomics UK (COG-UK) Consortium, et al. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00573-0 · Cited by 3,528 · see citing works
Self-citationFeatures, Evaluation and Treatment Coronavirus (COVID-19)
Cascella, M., Rajnik, M., Cuomo, A., Dulebohn, S. C., & Napoli, R. D. (2020) · StatPearls · Cited by 3,351 · see citing works
Mechanisms of SARS-CoV-2 entry into cells
Jackson, C. B., Farzan, M., Chen, B., & Choe, H. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00418-x · Cited by 3,082 · see citing works
Rapid 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-citationAirborne transmission of respiratory viruses
Wang, C. C., Prather, K. A., Sznitman, J., Jimenez, J. L., Lakdawala, S. S., Tüfekçi, Z., & Marr, L. C. (2021) · Science · doi:10.1126/science.abd9149 · Cited by 1,551 · see citing works
SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion
Mlcochova, P., Kemp, S. A., Dhar, M. S., Papa, G., Meng, B., Ferreira, I. A. T. M., Datir, R., Collier, D. A., Albecka, A., Singh, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03944-y · Cited by 1,337 · see citing works
Self-citationSARS-CoV-2 variant biology: immune escape, transmission and fitness
Carabelli, A. M., Peacock, T. P., Thorne, L., Harvey, W. T., Hughes, J., de Silva, T. I., Peacock, S. J., Barclay, W., de Silva, T. I., Towers, G. J., et al. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00841-7 · Cited by 1,293 · see citing works
Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2
Liu, L., Iketani, S., Guo, Y., Chan, J. F.-W., Wang, M., Liu, L., Luo, Y., Chu, H., Huang, Y., Nair, M. S., et al. (2022) · Nature · doi:10.1038/s41586-021-04388-0 · Cited by 1,290 · see citing works
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
Tregoning, J. S., Flight, K. E., Higham, S. L., Wang, Z., & Pierce, B. F. (2021) · Nature reviews. Immunology · doi:10.1038/s41577-021-00592-1 · Cited by 1,110 · see citing works
The biological and clinical significance of emerging SARS-CoV-2 variants
Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00408-x · Cited by 1,009 · see citing works
Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021
Alizon, S., Haïm‐Boukobza, S., Foulongne, V., Verdurme, L., Trombert‐Paolantoni, S., Lecorché, E., Roquebert, B., & Sofonea, M. T. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.28.2100573 · Cited by 867 · see citing works
Fiolet, T., Kherabi, Y., MacDonald, C.-J., Ghosn, J., & Peiffer-Smadja, N. (2022) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.10.005 · Cited by 911 · see citing works
Tarke, A., Sidney, J., Methot, N., Yu, E. D., Zhang, Y., Dan, J. M., Goodwin, B., Rubiro, P., Sutherland, A., Wang, E., et al. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100355 · Cited by 706 · see citing works
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
Network for Genomic Surveillance in South Africa, Cele, S., COMMIT-KZN Team, Gazy, I., Jackson, L., Hwa, S.-H., Tegally, H., Lustig, G., Giandhari, J., Pillay, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03471-w · Cited by 651 · see citing works
Li, B., Deng, A., Li, K., Hu, Y., Li, Z., Shi, Y., Xiong, Q., Liu, Z., Guo, Q., Zou, L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28089-y · Cited by 566 · see citing works
Self-citationTransmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
Deng, X., Garcia-Knight, M. A., Khalid, M. M., Servellita, V., Wang, C., Morris, M. K., Sotomayor-González, A., Glasner, D. R., Reyes, K. R., Gliwa, A. S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.025 · Cited by 651 · see citing works
Starr, T. N., Greaney, A. J., Dingens, A. S., & Bloom, J. D. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100255 · Cited by 470 · see citing works
SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape
Starr, T. N., Czudnochowski, N., Liu, Z., Zatta, F., Park, Y., Addetia, A., Pinto, D., Beltramello, M., Hernandez, P., Greaney, A. J., et al. (2021) · Nature · doi:10.1038/s41586-021-03807-6 · Cited by 495 · see citing works
The emergence and epidemic characteristics of the highly mutated SARS‐CoV‐2 Omicron variant
Tian, D., Sun, Y., Xu, H., & Ye, Q. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27643 · Cited by 461 · see citing works
COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
Naveca, F. G., do Nascimento, V. A., de Souza, V. C., Corado, A. D. L. G., Nascimento, F., Silva, G., Costa, Á., Duarte, D., Pessoa, K., Mejía, M., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01378-7 · Cited by 474 · see citing works
Self-citationMapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies
Greaney, A. J., Starr, T. N., Barnes, C. O., Weisblum, Y., Schmidt, F., Caskey, M., Gaebler, C., Cho, A., Agudelo, M., Finkin, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24435-8 · Cited by 433 · see citing works
After the pandemic: perspectives on the future trajectory of COVID-19
Telenti, A., Arvin, A. M., Corey, L., Corti, D., Diamond, M., García‐Sastre, A., Garry, R. F., Holmes, E. C., Pang, P. S., & Virgin, H. W. (2021) · Nature · doi:10.1038/s41586-021-03792-w · Cited by 440 · see citing works
Long-term complications of COVID-19
Desai, A. D., Lavelle, M. P., Boursiquot, B. C., & Wan, E. Y. (2021) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00375.2021 · Cited by 427 · see citing works
Gangavarapu, K., Latif, A. A., Mullen, J. L., Alkuzweny, M., Hufbauer, E. C., Tsueng, G., Haag, E., Zeller, M., Aceves, C. M., Zaiets, K., et al. (2023) · Nature Methods · doi:10.1038/s41592-023-01769-3 · Cited by 393 · see citing works
Self-citationEmerging Variants of SARS-CoV-2 And Novel Therapeutics Against Coronavirus (COVID-19)
Aleem, A., Samad, A., & Slenker, A. K. (2021) · Europe PMC (PubMed Central) · Cited by 398 · see citing works
Ong, S. W. X., Chiew, C. J., Ang, L. W., Mak, T. M., Cui, L., Toh, M. P. H., Lim, Y. D., Lee, P. H., Lee, T. H., Chia, P. Y., et al. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab721 · Cited by 418 · see citing works
SARS-CoV-2 Variants and Vaccines
Krause, P. R., Fleming, T. R., Longini, I. M., Peto, R., Briand, S. C., Heymann, D. L., Beral, V., Snape, M. D., Rees, H., Ropero, A. M., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmsr2105280 · Cited by 352 · see citing works
Low-dose mRNA-1273 COVID-19 vaccine generates durable memory enhanced by cross-reactive T cells
(2021) · doi:10.1126/science.abj9853 · Cited by 327 · see citing works
“…to immune memory of persons infected with SARS-CoV-2 is of value, as studies have indicated natural immunity is 93% to 100% protective against symptomatic reinfection for 7–8 months (16–19), though natural immunity protection against certain variants of concern (VOCs) is likely to be lower (20).”
Ranzani, O., Hitchings, M. D. T., Dorión, M., D’Agostini, T. L., de Paula, R. C., de Paula, O. F. P., Villela, E. F. D. M., Torres, M. S. S., de Oliveira, S. B., Schulz, W. L., et al. (2021) · BMJ · doi:10.1136/bmj.n2015 · Cited by 348 · see citing works
Novel SARS-CoV-2 variants: the pandemics within the pandemic
Boehm, E., Kronig, I., Neher, R. A., Eckerle, I., Vetter, P., & Kaiser, L. (2021) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.05.022 · Cited by 341 · see citing works
Spatiotemporal pattern of COVID-19 spread in Brazil
Castro, M. C., Kim, S., Barberia, L., Ribeiro, A. F., Gurzenda, S., Ribeiro, K. B., Abbott, E., Blossom, J. C., Rache, B., & Singer, B. H. (2021) · Science · doi:10.1126/science.abh1558 · Cited by 345 · see citing works
SARS-CoV-2 breakthrough infections in vaccinated individuals: measurement, causes and impact
Lipsitch, M., Krammer, F., Regev‐Yochay, G., Lustig, Y., & Balicer, R. D. (2021) · Nature reviews. Immunology · doi:10.1038/s41577-021-00662-4 · Cited by 340 · see citing works
The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic
Otto, S. P., Day, T., Arino, J., Colijn, C., Dushoff, J. G., Li, M., Mechai, S., Domselaar, G. V., Wu, J., Earn, D. J. D., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.06.049 · Cited by 316 · see citing works
SARS-CoV-2 Variants, Vaccines, and Host Immunity
Mistry, P., Barmania, F., Mellet, J., Peta, K. T., Strydom, A., Viljoen, I. M., James, W., Gordon, S., & Pepper, M. S. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2021.809244 · Cited by 293 · see citing works
Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant
Zhang, J., Xiao, T., Cai, Y., Lavine, C. L., Peng, H., Zhu, H., Anand, K., Tong, P., Gautam, A. K., Mayer, M. L., et al. (2021) · Science · doi:10.1126/science.abl9463 · Cited by 282 · see citing works
Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India
Dhar, M. S., Marwal, R., Radhakrishnan, V. S., Ponnusamy, K., Jolly, B., Bhoyar, R. C., Sardana, V., Naushin, S., Rophina, M., Mellan, T. A., et al. (2021) · Science · doi:10.1126/science.abj9932 · Cited by 291 · see citing works
Self-citationGenomic characterization and Epidemiology of an emerging SARS-CoV-2 variant in Delhi, India
Dhar, M. S., Marwal, R., Radhakrishnan, V., Ponnusamy, K., Jolly, B., Bhoyar, R. C., Sardana, V., Naushin, S., Rophina, M., Mellan, T. A., et al. (2021) · doi:10.1101/2021.06.02.21258076 · Cited by 296 · see citing works
Self-citationSARS-CoV-2 Variants of Concern
Choi, J. Y., & Smith, D. M. (2021) · Yonsei Medical Journal · doi:10.3349/ymj.2021.62.11.961 · Cited by 297 · see citing works
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
Martin, D. P., Weaver, S., Tegally, H., San, J. E., Shank, S. D., Wilkinson, E., Lucaci, A. G., Giandhari, J., Naidoo, S., Pillay, Y., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.003 · Cited by 273 · see citing works
“, 2021), increased transmissibility (V1, V2, and V3) (Althaus et al., 2021; Faria et al., 2021; Lubinski et al., 2021; Pearson et al., 2021; Public Health England, 2020; Volz et al., 2021), substantially increased capacity to overcome prior infection and/or vaccination-induced immunity (V2 and V3) (Cele et al.”
InfluentialSelf-citationGlobal disparities in SARS-CoV-2 genomic surveillance
Brito, A. F., Semenova, E., Dudas, G., Hassler, G. W., Kalinich, C. C., Kraemer, M. U. G., Ho, J., Tegally, H., Githinji, G., Agoti, C. N., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33713-y · Cited by 351 · see citing works
Self-citationCrotty, S. (2021) · Science · doi:10.1126/science.abj2258 · Cited by 267 · see citing works
Immunological memory to SARS‐CoV ‐2 infection and COVID ‐19 vaccines
Sette, A., & Crotty, S. (2022) · Immunological Reviews · doi:10.1111/imr.13089 · Cited by 266 · see citing works
Broad sarbecovirus neutralization by a human monoclonal antibody
Tortorici, M. A., Czudnochowski, N., Starr, T. N., Marzi, R., Walls, A. C., Zatta, F., Bowen, J. E., Jaconi, S., di Iulio, J., Wang, Z., et al. (2021) · Nature · doi:10.1038/s41586-021-03817-4 · Cited by 251 · see citing works
A COVID-19 peptide vaccine for the induction of SARS-CoV-2 T cell immunity
Heitmann, J. S., Bilich, T., Tandler, C., Nelde, A., Maringer, Y., Marconato, M., Reusch, J., Jäger, S., Denk, M., Richter, M., et al. (2021) · Nature · doi:10.1038/s41586-021-04232-5 · Cited by 255 · see citing works
Rapid 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:10.1101/2021.12.19.21268028 · Cited by 250 · see citing works
Self-citationCOVID-19 and metabolic disease: mechanisms and clinical management
Steenblock, C., Schwarz, P. E. H., Ludwig, B., Linkermann, A., Zimmet, P., Kulebyakin, K. Y., Va, T., Markov, A. G., Lehnert, H., de Angelis, M. H., et al. (2021) · The Lancet Diabetes & Endocrinology · doi:10.1016/s2213-8587(21)00244-8 · Cited by 248 · see citing works
Hoffmann, M., Hofmann-Winkler, H., Krüger, N., Kempf, A., Nehlmeier, I., Graichen, L., Arora, P., Sidarovich, A., Moldenhauer, A.-S., Winkler, M. S., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109415 · Cited by 258 · see citing works
Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants
Xu, J., Xu, K. Y., Jung, S., Conte, A., Lieberman, J. A., Muecksch, F., Lorenzi, J. C. C., Park, S., Schmidt, F., Wang, Z., et al. (2021) · Nature · doi:10.1038/s41586-021-03676-z · Cited by 225 · see citing works
Estimating epidemiologic dynamics from cross-sectional viral load distributions
Hay, J. A., Kennedy-Shaffer, L., Kanjilal, S., Lennon, N., Gabriel, S., Lipsitch, M., & Mina, M. (2020) · Science · doi:10.1126/science.abh0635 · Cited by 242 · see citing works
Self-citationThe next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology
Munnink, B. B. O., Worp, N., Nieuwenhuijse, D. F., Sikkema, R. S., Haagmans, B. L., Fouchier, R. A. M., & Koopmans, M. (2021) · Nature Medicine · doi:10.1038/s41591-021-01472-w · Cited by 229 · see citing works
Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York
Annavajhala, M. K., Mohri, H., Wang, P., Nair, M. S., Zucker, J. E., Sheng, Z., Gomez‐Simmonds, A., Kelley, A. L., Tagliavia, M., Huang, Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03908-2 · Cited by 226 · see citing works
The Disease Severity and Clinical Outcomes of the SARS-CoV-2 Variants of Concern
Lin, L., Liu, Y., Tang, X., & He, D. (2021) · Frontiers in Public Health · doi:10.3389/fpubh.2021.775224 · Cited by 228 · see citing works
Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2
Wu, H., Xing, N., Meng, K., Fu, B., Xue, W., Dong, P., Tang, W., Xiao, Y., Liu, G., Luo, H., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.11.005 · Cited by 224 · see citing works
“These mutations are carried by the increasingly frequent lineages B.1.1.7 (Alpha) (Collier et al., 2021; C. Caserta et al., 2021) and P.1 (Gamma) (Dejnirattisai et al., 2021; Faria et al., 2021).”
InfluentialEarly detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC
Jahn, K., Dreifuss, D., Topolsky, I., Kull, A., Ganesanandamoorthy, P., Fernández-Cassi, X., Bänziger, C., Devaux, A. J., Stachler, E. N., Caduff, L., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01185-x · Cited by 212 · see citing works
SARS-CoV-2 infection generates tissue-localized immunological memory in humans
Poon, M. M. L., Rybkina, K., Kato, Y., Kubota, M., Matsumoto, R., Bloom, N. I., Zhang, Z., Hastie, K. M., Grifoni, A., Weiskopf, D., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abl9105 · Cited by 214 · see citing works
Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe
Thakur, V., Bhola, S., Thakur, P., Patel, S. K. S., Kulshrestha, S., Ratho, R. K., & Kumar, P. (2022) · Infection · doi:10.1007/s15010-021-01734-2 · Cited by 210 · see citing works
Ribeiro, A. C. D. M., Aikawa, N. E., Saad, C. G. S., Yuki, E. F. N., Pedrosa, T. D. N., Fusco, S. R. G., Rojo, P. T., Pereira, R. M. R., Shinjo, S. K., Andrade, D. C. O., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01469-5 · Cited by 197 · see citing works
Self-citationSpatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence
Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutiérrez, B., et al. (2021) · Science · doi:10.1126/science.abj0113 · Cited by 188 · see citing works
Self-citationExperimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants
Laffeber, C., de Koning, K., Kanaar, R., & Lebbink, J. (2021) · bioRxiv · doi:10.1016/j.jmb.2021.167058 · Cited by 195 · see citing works
The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape
Tian, D., Sun, Y., Zhou, J., & Ye, Q. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.751778 · Cited by 192 · see citing works
Hitchings, M. D. T., Ranzani, O., Torres, M. S. S., de Oliveira, S. B., Almirón, M., Said, R., Borg, R., Schulz, W. L., de Oliveira, R. D., da Silva, P. V., et al. (2021) · The Lancet Regional Health - Americas · doi:10.1016/j.lana.2021.100025 · Cited by 200 · see citing works
“The World Health Organisation declared the amma variant as a Variant of Concern [5] given the evidence for ts increased transmissibility [3] and mutations shared with other ariants of concern.”
BackgroundInfluentialCOVID-19: Unmasking Emerging SARS-CoV-2 Variants, Vaccines and Therapeutic Strategies
Raman, R., Patel, K. J., & Ranjan, K. (2021) · Biomolecules · doi:10.3390/biom11070993 · Cited by 186 · see citing works
Implications of diversity in sperm size and function for sperm competition and fertility
Gomendio, M., & Roldán, E. R. S. (2008) · The International Journal of Developmental Biology · doi:10.1387/ijdb.082595mg · Cited by 185 · see citing works
Predicting the mutational drivers of future SARS-CoV-2 variants of concern
Maher, M. C., Bartha, I., Weaver, S., di Iulio, J., Ferri, E., Soriaga, L. B., Lempp, F. A., Hie, B., Bryson, B. D., Berger, B., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abk3445 · Cited by 179 · see citing works
Self-citationThe evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Tegally, H., San, J. E., Cotten, M. L., Moir, M., Tegomoh, B., Mboowa, G., Martin, D. P., Baxter, C., Lambisia, A. W., Diallo, A. B., et al. (2022) · Science · doi:10.1126/science.abq5358 · Cited by 184 · see citing works
“The remaining VOC, Gamma (14), originated in Brazil and had a limited influence in Africa, with only four recorded sequenced cases.”
OLIVEIRA, E. A., Colosimo, E. A., Silva, A. C. S. E., MAK, R. H. K., Martelli, D. R. B., Silva, L. R., Martelli‐Júnior, H., & Oliveira, M. C. L. (2021) · The Lancet Child & Adolescent Health · doi:10.1016/s2352-4642(21)00134-6 · Cited by 166 · see citing works
Guo, L., Wang, G., Wang, Y., Zhang, Q., Ren, L., Gu, X., Huang, T., Zhong, J., Wang, Y., Wang, X., et al. (2022) · The Lancet Microbe · doi:10.1016/s2666-5247(22)00036-2 · Cited by 169 · see citing works
Reduction in life expectancy in Brazil after COVID-19
Castro, M. C., Gurzenda, S., Turra, C. M., Kim, S., Andrasfay, T., & Goldman, N. (2021) · Nature Medicine · doi:10.1038/s41591-021-01437-z · Cited by 164 · see citing works
Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York
Annavajhala, M. K., Mohri, H., Wang, P., Nair, M., Zucker, J. E., Sheng, Z., Gomez-Simmonds, A., Kelley, A. L., Tagliavia, M., Huang, Y., et al. (2021) · doi:10.1101/2021.02.23.21252259
The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity
Zhou, Y., Zhi, H., & Teng, Y. (2022) · Journal of Medical Virology · doi:10.1002/jmv.28138 · Cited by 155 · see citing works
Victora, C. G., Castro, M. C., Gurzenda, S., de Medeiros, A. C., de França, G. V. A., & Barros, A. J. D. (2021) · EClinicalMedicine · doi:10.1016/j.eclinm.2021.101036 · Cited by 154 · see citing works
Interferon resistance of emerging SARS-CoV-2 variants
Guo, K., Barrett, B. S., Morrison, J. H., Mickens, K. L., Vladar, E. K., Hasenkrug, K. J., Poeschla, E. M., & Santiago, M. L. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2203760119 · Cited by 136 · see citing works
Moodley, A., Stegger, M., BAĞCIGİL, A. F., Baptiste, K. E., Loeffler, A., Lloyd, D. H., Williams, N. J., Leonard, N., Abbott, Y., Skov, R. L., et al. (2006) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkl394 · Cited by 146 · see citing works
The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK
Hill, V., du Plessis, L., Peacock, T. P., Aggarwal, D., Colquhoun, R., Carabelli, A. M., Ellaby, N. A. F., Gallagher, E., Groves, N., Jackson, B., et al. (2022) · Virus Evolution · doi:10.1093/ve/veac080 · Cited by 138 · see citing works
Self-citationWang, Z., Muecksch, F., Cho, A., Gaebler, C., Hoffmann, H.-H., Ramos, V., Zong, S., Cipolla, M., Johnson, B., Schmidt, F., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.04.003 · Cited by 142 · see citing works
“…supersite are mutated in several variants of concern including Beta, Gamma, and Omicron—the latter of which carries 3 deletions, 4 amino acid substitutions, and an insertion in the NTD that render antibodies to the supersite ineffective (Callaway, 2021; Faria et al., 2021; Tegally et al., 2021).”
Striking Antibody Evasion Manifested by the Omicron Variant of SARS-CoV-2Preprint
Liu, L., Iketani, S., Guo, Y., Chan, J. F., Wang, M., Liu, L., Luo, Y., Chu, H., Huang, Y., Nair, M. S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.14.472719 · Cited by 142 · see citing works
Lustig, Y., Zuckerman, N. S., Nemet, I., Atari, N., Kliker, L., Regev‐Yochay, G., Sapir, E., Mor, O., Alroy‐Preis, S., Mendelson, E., et al. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.26.2100557 · Cited by 143 · see citing works
“The Gamma isolate was kindly provided by the Tropical Medicine Institute, Sao Paulo University (Brazil) [6].”
MethodZeiser, F. A., Donida, B., da Costa, C. A., Ramos, G. D. O., Scherer, J. N., Barcellos, N. T., Alegretti, A. P., Ikeda, M. L. R., Müller, A. P. W. C., Bohn, H. C., et al. (2021) · The Lancet Regional Health - Americas · doi:10.1016/j.lana.2021.100107 · Cited by 141 · see citing works
COVID-19 in patients with hematologic malignancy
Langerbeins, P., & Hallek, M. J. (2022) · Blood · doi:10.1182/blood.2021012251 · Cited by 141 · see citing works
Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants
Sun, C., Xie, C., Bu, G., Zhong, L., & Zeng, M. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01039-2 · Cited by 139 · see citing works
Moriyama, S., Adachi, Y., Sato, T., Tonouchi, K., Sun, L., Fukushi, S., Yamada, S., Kinoshita, H., Nojima, K., Kanno, T., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.06.015 · Cited by 133 · see citing works
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains
Rella, S. A., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. A. (2021) · Scientific Reports · doi:10.1038/s41598-021-95025-3 · Cited by 136 · see citing works
Two Years into the COVID-19 Pandemic: Lessons Learned
da Silva, S. J. R., do Nascimento, J. C. F., Mendes, R. P. G., Guarines, K. M., da Silva, C. T. A., da Silva, P. G., de Magalhães, J. J. F., Vigar, J. R. J., Silva‐Júnior, A., Kohl, A., et al. (2022) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.2c00204 · Cited by 140 · see citing works
Self-citationPango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences
O’Toole, A. N., Pybus, O. G., Abram, M. E., Kelly, E. J., & Rambaut, A. (2022) · BMC Genomics · doi:10.1186/s12864-022-08358-2 · Cited by 135 · see citing works
Self-citationFast-spreading SARS-CoV-2 variants: challenges to and new design strategies of COVID-19 vaccines
Zhou, W., & Wang, W. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00644-x · Cited by 132 · see citing works
da Silva, S. J. R., & Pena, L. (2021) · One Health · doi:10.1016/j.onehlt.2021.100287 · Cited by 138 · see citing works
“Using a dynamical model, a recent study has demonstrated that the gamma variant is more transmissible (estimated to be 1.7 to 2.4) when compared to non-gamma lineages, which may have accelerated the rapid propagation around the world [18].”
InfluentialModel-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant
Coutinho, R. M., Marquitti, F. M. D., Ferreira, L. S., Borges, M. E., Lopes, R., Canton, O., Portella, T. P., Poloni, S., Franco, C. F. J., Pluciński, M. M., et al. (2021) · Communications Medicine · doi:10.1038/s43856-021-00048-6 · Cited by 129 · see citing works
SARS-CoV-2 evolution in the Omicron era
Roemer, C., Sheward, D. J., Hisner, R., Gueli, F., Sakaguchi, H., Frohberg, N., Schoenmakers, J., Sato, K., O’Toole, A. N., Rambaut, A., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01504-w · Cited by 129 · see citing works
“Examples of variants that are extremely different include the VOCs Alpha, Beta, Gamma and the Omicron lineages (for example, BA.1, BA.2 and BA.5) 10,12–14 The first generation of SARS-CoV-2 VOCs (Alpha, Beta, Gamma, Delta and Omicron) each evolved from pre-VOC ancestors and sequentially replaced…”
BackgroundSelf-citationEarly introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States
Alpert, T., Brito, A. F., Lasek‐Nesselquist, E., Rothman, J. E., Valesano, A. L., MacKay, M. J., Petrone, M. E., Breban, M. I., Watkins, A. E., Vogels, C. B. F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.061 · Cited by 120 · see citing works
Aggarwal, A., Stella, A. O., Walker, G. J., Akerman, A., Esneau, C., Milogiannakis, V., Burnett, D. L., McAllery, S., Silva, M. R., Lu, Y., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01135-7 · Cited by 121 · see citing works
Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis
Thye, A. Y.-K., Law, J. W., Pusparajah, P., Letchumanan, V., Chan, K., & Lee, L. (2021) · Biomedicines · doi:10.3390/biomedicines9101303 · Cited by 116 · see citing works
A look into the future of the COVID-19 pandemic in Europe: an expert consultation [viewpoint].
Iftekhar, E. N., Priesemann, V., Balling, R., Bauer, S., Beutels, P., Valdez, A. S. C., Cuschieri, S., Czypionka, T., Dumpis, U., Glaab, E., et al. (2021) · BORIS (University Library Bern) · doi:10.17863/cam.75145 · Cited by 119 · see citing works
Oral prodrug of remdesivir parent GS-441524 is efficacious against SARS-CoV-2 in ferrets
Cox, R. M., Wolf, J. D., Lieber, C. M., Sourimant, J., Lin, M. J., Babusis, D. M., Pont, V. D., Chan, J., Barrett, K., Lye, D. S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26760-4 · Cited by 119 · see citing works
SeyedAlinaghi, S., Mirzapour, P., Dadras, O., Pashaei, Z., Karimi, A., MohsseniPour, M., Soleymanzadeh, M., Barzegary, A., Afsahi, A. M., Vahedi, F., et al. (2021) · European journal of medical research · doi:10.1186/s40001-021-00524-8 · Cited by 117 · see citing works
Chakraborty, C., Bhattacharya, M., & Sharma, A. R. (2022) · Reviews in Medical Virology · doi:10.1002/rmv.2270 · Cited by 111 · see citing works
The Spike of Concern—The Novel Variants of SARS-CoV-2
Winger, A., & Caspari, T. (2021) · Viruses · doi:10.3390/v13061002 · Cited by 114 · see citing works
Bolze, A., Luo, S., White, S. J., Cirulli, E. T., Wyman, D., Rossi, A. D., Machado, H., Cassens, T., Jacobs, S., Barrett, K. M. S., et al. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100564 · Cited by 118 · see citing works
de Souza, W. M., Amorim, M. R., Sesti-Costa, R., Coimbra, L. D., Brunetti, N. S., Toledo-Teixeira, D. A., de Souza, G. D., Muraro, S., Parise, P., Barbosa, P., et al. (2021) · The Lancet Microbe · doi:10.1016/s2666-5247(21)00129-4 · Cited by 98 · see citing works
Self-citationChanging composition of SARS-CoV-2 lineages and rise of Delta variant in England
Mishra, S., Mindermann, S., Sharma, M., Whittaker, C., Mellan, T. A., Wilton, T., Klapsa, D., Mate, R., Fritzsche, M., Zambon, M. C. F. A., et al. (2021) · EClinicalMedicine · doi:10.1016/j.eclinm.2021.101064 · Cited by 108 · see citing works
“1 are more transmissible than ancestral SARS-CoV-2 lineages; [10,13] for B.”
BackgroundInfluentialSelf-citation
- Authors
- Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. D. S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., Hulswit, R. J. G., Franco, L. A. M., Ramundo, M. S., de Jesus, J. G., Andrade, P. S., Coletti, T. M., Ferreira, G. M., Silva, C. A. M., Manuli, E. R., Pereira, R. H. M., Peixoto, P. S., Kraemer, M. U. G., Gaburo, N., Camilo, C. D. C., Hoeltgebaum, H., Souza, W. M., Rocha, E. C., de Souza, L. M., de Pinho, M. C., Araujo, L. J. T., Malta, F. S. V., de Lima, A. B., Silva, J. D. P., Zauli, D. A. G., Ferreira, A. C. D. S., Schnekenberg, R. P., Laydon, D. J., Walker, P. G. T., Schlüter, H. M., dos Santos, A. L. P., Vidal, M. S., Del Caro, V. S., Filho, R. M. F., dos Santos, H. M., Aguiar, R. S., Proença-Modena, J. L., Nelson, B., Hay, J. A., Monod, M., Miscouridou, X., Coupland, H., Sonabend, R., Vollmer, M., Gandy, A., Prete, C. A., Nascimento, V. H., Suchard, M. A., Bowden, T. A., Pond, S. L. K., Wu, C.-H., Ratmann, O., Ferguson, N. M., Dye, C., Loman, N. J., Lemey, P., Rambaut, A., Fraiji, N. A., Carvalho, M. D. P. S. S., Pybus, O. G., Flaxman, S., Bhatt, S., & Sabino, E. C.
- Affiliations
- Universidade de São Paulo (BR)
- Imperial College London (GB)
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (BR)
- University of Edinburgh (GB)
- Centre for Human Genetics (GB)
- Departamento de Epidemiologia, Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, Brazil.
- Universidade Federal de Uberlândia (BR)
- Institute of Applied Economic Research (BR)
- University of Oxford (GB)
- DB Diagnósticos do Brasil, São Paulo, Brazil.
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil.
- Instituto Hermes Pardini, Belo Horizonte, Brazil.
- CDL Laboratório Santos e Vidal, Manaus, Brazil.
- Universidade Federal de Minas Gerais (BR)
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil.
- Instituto Nacional de Pesquisas da Amazônia (BR)
- Harvard University (US)
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil.
- University of California, Los Angeles (US)
- Temple University (US)
- University of Southampton (GB)
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK.
- Rega Institute for Medical Research (BE)
- Royal Veterinary College (GB)
- University of Copenhagen (DK)
- Corresponding author
- Faria, Nuno R.
- Mellan, Thomas A.
- Whittaker, Charles
- Claro, Ingra M.
- Mishra, Swapnil
- Pybus, Oliver G.
- Flaxman, Seth
- Bhatt, Samir
- ORCID
- Faria, Nuno R.
- Mellan, Thomas A.
- Whittaker, Charles
- Claro, Ingra M.
- Candido, Darlan da S.
- Mishra, Swapnil
- Crispim, Myuki A. E.
- Sales, Flavia C. S.
- Hawryluk, Iwona
- McCrone, John T.
- Hulswit, Ruben J. G.
- Franco, Lucas A. M.
- Ramundo, Mariana S.
- de Jesus, Jaqueline G.
- Andrade, Pamela S.
- Coletti, Thais M.
- Ferreira, Giulia M.
- Silva, Camila A. M.
- Manuli, Erika R.
- Pereira, Rafael H. M.
- Peixoto, Pedro S.
- Kraemer, Moritz U. G.
- Gaburo, Nelson
- Camilo, Cecilia da C.
- Hoeltgebaum, Henrique
- Souza, William M.
- Rocha, Esmenia C.
- de Souza, Leandro M.
- de Pinho, Mariana C.
- Araujo, Leonardo J. T.
- Malta, Frederico S. V.
- de Lima, Aline B.
- Silva, Joice do P.
- Zauli, Danielle A. G.
- Ferreira, Alessandro C. de S.
- Schnekenberg, Ricardo P.
- Laydon, Daniel J.
- Walker, Patrick G. T.
- Schlüter, Hannah M.
- dos Santos, Ana L. P.
- Vidal, Maria S.
- Del Caro, Valentina S.
- Aguiar, Renato S.
- Proença-Modena, José L.
- Nelson, Bruce
- Hay, James A.
- Monod, Mélodie
- Coupland, Helen
- Sonabend, Raphael
- Vollmer, Michaela
- Gandy, Axel
- Prete, Carlos A.
- Nascimento, Vitor H.
- Suchard, Marc A.
- Bowden, Thomas A.
- Pond, Sergei L. K.
- Wu, Chieh-Hsi
- Ratmann, Oliver
- Ferguson, Neil M.
- Dye, Christopher
- Loman, Nick J.
- Lemey, Philippe
- Rambaut, Andrew
- Fraiji, Nelson A.
- Carvalho, Maria do P. S. S.
- Pybus, Oliver G.
- Flaxman, Seth
- Bhatt, Samir
- Sabino, Ester C.
- Venue
- Science
- Published
- 2021-05-21
- Volume
- 372
- Issue
- 6544
- Pages
- 815-821
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC8139423
- OpenAlex
- W3156343712
- Cited by
- 1,461
- References
- 93
- Citations by year
- 2026: 48 · 2025: 73 · 2024: 104 · 2023: 227 · 2022: 492 · 2021: 502 · 2020: 1 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 2 · 2013: 2 · 2012: 1
- FWCI
- 105.79
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Science (publishedVersion, cc-by)
- medRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (publishedVersion, cc-by)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (publishedVersion, other-oa)
- Spiral (Imperial College London) (submittedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- ePrints Soton (University of Southampton) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Lirias (KU Leuven) (submittedVersion, other-oa)
- TUScholarShare (Temple University) (submittedVersion, cc-by)
- Funders
- Medical Research Council (MR/S0195/1)
- National Institute for Health Research (203141/Z/16/Z, MR/S007555/1, ALTF 869-2019, OPP1175094, 2018/12579-7 CNP)
- Wellcome Trust and Royal Society (204311/Z/16/Z)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- P.1 lineage, SARS-CoV-2, COVID-19 pandemic, variants of concern, spike protein mutations, E484K, N501Y, ACE2 binding, transmissibility, immune evasion, molecular clock, epidemic resurgence, Manaus, genomic surveillance
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
