Evolution and epidemic spread of SARS-CoV-2 in Brazil
Open accessPublished version of a preprint
Abstract
The spread of SARS-CoV-2 in Brazil: Brazil has been hard-hit by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Candido et al. combined genomic and epidemiological analyses to investigate the impact of nonpharmaceutical interventions (NPIs) in the country. By setting up a network of genomic laboratories using harmonized protocols, the researchers found a 29% positive rate for SARS-CoV-2 among collected samples. More than 100 international introductions of SARS-CoV-2 into Brazil were identified, including three clades introduced from Europe that were already well established before the implementation of NPIs and travel bans. The virus spread from urban centers to the rest of the country, along with a 25% increase in the average distance traveled by air passengers before travel bans, despite an overall drop in short-haul travel. Unfortunately, the evidence confirms that current interventions remain insufficient to keep virus transmission under control in Brazil. Science , this issue p. 1255
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?
Viral genetic diversity, evolution, variable infectivity, or co-pathogenesis might contribute to infectivity and fatality but not much to COVID-19 disease heterogeneity.
“Numerous mutations identified so far by thousands of viral sequences obtained during the first 9 months of the pandemic (Candido et al., 2020; Oude Munnink et al., 2020) suggest that viral genetic diversity, genetic evolution, variable infectivity, or co-pathogenesis might contribute to infectivity and fatality, but not so much to disease heterogeneity observed for COVID-19.”
From COVID-19 and the human innate immune system (2021) · cites this paper as Candido et al., 2020
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
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
A new coronavirus associated with human respiratory disease in China
Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2008-3 · Cited by 11,688 · 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-citationApplication of Phylogenetic Networks in Evolutionary Studies
Huson, D. H., & Bryant, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj030 · Cited by 8,751 · 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
Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR
Corman, V. M., Landt, O., Kaiser, M., Molenkamp, R., Meijer, A., Chu, D. K. W., Bleicker, T., Brünink, S., Schneider, J. A., Schmidt, M. L., et al. (2020) · Eurosurveillance · doi:10.2807/1560-7917.es.2020.25.3.2000045 · Cited by 7,266 · see citing works
The proximal origin of SARS-CoV-2
Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020) · Nature Medicine · doi:10.1038/s41591-020-0820-9 · Cited by 5,081 · see citing works
Self-citationBayesian 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-citationEstimates of the severity of coronavirus disease 2019: a model-based analysis
Verity, R., Okell, L. C., Dorigatti, I., Winskill, P., Whittaker, C., Imai, N., Cuomo-Dannenburg, G., Thompson, H., Walker, P. G. T., Fu, H., et al. (2020) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30243-7 · Cited by 3,660 · see citing works
Self-citationRDP4: Detection and analysis of recombination patterns in virus genomes
Martin, D. P., Murrell, B., Golden, M., Khoosal, A., & Muhire, B. M. (2015) · Virus Evolution · doi:10.1093/ve/vev003 · Cited by 3,295 · see citing works
The reproductive number of COVID-19 is higher compared to SARS coronavirus
Liu, Y., Gayle, A. A., Wilder‐Smith, A., & Rocklöv, J. (2020) · Journal of Travel Medicine · doi:10.1093/jtm/taaa021 · Cited by 3,169 · see citing works
Estimating 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
The effect of human mobility and control measures on the COVID-19 epidemic in China
Kraemer, M. U. G., Yang, C.-H., Gutiérrez, B., Wu, C., Klein, B., Pigott, D. M., open COVID-19 data working group, du Plessis, L., Faria, N. R., Li, R., et al. (2020) · Science · doi:10.1126/science.abb4218 · Cited by 2,950 · 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-citationQuantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing
Ferretti, L., Wymant, C., Kendall, M., Zhao, L., Nurtay, A., Abeler-Dörner, L., Parker, M., Bonsall, D., & Fraser, C. (2020) · Science · doi:10.1126/science.abb6936 · Cited by 2,512 · see citing works
Mizumoto, K., Kagaya, K., Zarebski, A., & Chowell, G. (2020) · Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · doi:10.2807/1560-7917.es.2020.25.10.2000180 · Cited by 2,336 · see citing works
Exploring 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-citationPresymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility
Arons, M. M., Hatfield, K. M., Reddy, S. C., Kimball, A. A., James, A. E., Jacobs, J. R., Taylor, J., Spicer, K. B., Bardossy, A. C., Oakley, L. P., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2008457 · Cited by 2,051 · see citing works
Tian, H., Liu, Y., Li, Y., Wu, C.-H., Chen, B., Kraemer, M. U. G., Li, B., Cai, J., Xu, B., Yang, Q., et al. (2020) · Science · doi:10.1126/science.abb6105 · Cited by 2,010 · see citing works
Self-citationBayesian Phylogeography Finds Its Roots
Lemey, P., Rambaut, A., Drummond, A. J., & Suchard, M. A. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000520 · Cited by 1,790 · see citing works
Self-citationA Simple and Robust Statistical Test for Detecting the Presence of Recombination
Bruen, T. C., Philippe, H., & Bryant, D. (2006) · Genetics · doi:10.1534/genetics.105.048975 · Cited by 1,365 · see citing works
Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China
Wu, J. T. K., Leung, K. S. M., Bushman, M., Kishore, N., Niehus, R., Salazar, P. M. D., Cowling, B. J., Lipsitch, M., & Leung, G. M. (2020) · Nature Medicine · doi:10.1038/s41591-020-0822-7 · Cited by 1,308 · see citing works
Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., Oliveira, G., Robles-Sikisaka, R., Rogers, T. F., Beutler, N. A., et al. (2017) · Nature Protocols · doi:10.1038/nprot.2017.066 · Cited by 1,190 · see citing works
Self-citationSuppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo’
Lavezzo, E., Franchin, E., Ciavarella, C., Cuomo-Dannenburg, G., Barzon, L., Vecchio, C. D., Rossi, L., Manganelli, R., Loregian, A., Navarin, N., et al. (2020) · Nature · doi:10.1038/s41586-020-2488-1 · Cited by 1,050 · see citing works
Self-citationThe early spread and epidemic ignition of HIV-1 in human populations
Faria, N. R., Rambaut, A., Suchard, M. A., Baele, G., Bedford, T., Ward, M. J., Tatem, A. J., de Sousa, J. D., Arinaminpathy, N., Pépin, J., et al. (2014) · Science · doi:10.1126/science.1256739 · Cited by 739 · 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-citationPhylogeography Takes a Relaxed Random Walk in Continuous Space and Time
Lemey, P., Rambaut, A., Welch, J. J., & Suchard, M. A. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq067 · Cited by 688 · 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
Improving 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-citationMAFFT: Iterative Refinement and Additional Methods
Katoh, K., & Standley, D. M. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-646-7_8 · Cited by 520 · see citing works
Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform
Thao, T. T. N., Labroussaa, F., Ebert, N., V’kovski, P., Stalder, H., Portmann, J., Kelly, J. N., Steiner, S., Holwerda, M., Kratzel, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2294-9 · Cited by 485 · see citing works
Russell, T., Hellewell, J., Jarvis, C. I., van Zandvoort, K., Abbott, S., Ratnayake, R., CMMID COVID-19 working group, Flasche, S., Eggo, R. M., Edmunds, W. J., et al. (2020) · Eurosurveillance · doi:10.2807/1560-7917.es.2020.25.12.2000256 · Cited by 462 · see citing works
Epidemiological 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-citationIntroductions and early spread of SARS-CoV-2 in the New York City area
Gonzalez-Reiche, A. S., Hernandez, M. M., Sullivan, M. J., Ciferri, B., Alshammary, H., Obla, A., Fabre, S., Kleiner, G., Polanco, J., Khan, Z., et al. (2020) · Science · doi:10.1126/science.abc1917 · Cited by 386 · see citing works
Temporal signal and the phylodynamic threshold of SARS-CoV-2
Duchêne, S., Featherstone, L. A., Haritopoulou-Sinanidou, M., Rambaut, A., Lemey, P., & Baele, G. (2020) · Virus Evolution · doi:10.1093/ve/veaa061 · Cited by 385 · see citing works
Self-citationCotten, M. L., Watson, S. J., Kellam, P., Al-Rabeeah, A. A., Makhdoom, H. Q., Assiri, A. M., Al‐Tawfiq, J. A., Alhakeem, R. F., Madani, H., Alrabiah, F. A., et al. (2013) · The Lancet · doi:10.1016/s0140-6736(13)61887-5 · Cited by 322 · see citing works
Self-citationSuppression of COVID-19 outbreak in the municipality of Vo’, ItalyPreprint
Lavezzo, E., Franchin, E., Ciavarella, C., et al. (2020) · medRxiv · doi:10.1101/2020.04.17.20053157 · Cited by 312 · see citing works
Bayesian analysis of elapsed times in continuous‐time Markov chains
Ferreira, M. A. R., & Suchard, M. A. (2008) · Canadian Journal of Statistics · doi:10.1002/cjs.5550360302 · Cited by 300 · see citing works
Moderate mutation rate in the SARS coronavirus genome and its implications
Zhao, Z., Li, H., Wu, X., Zhong, Y., Zhang, K., Zhang, Y.-P., Boerwinkle, E., & Fu, Y.-X. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-21 · Cited by 286 · see citing works
Counting labeled transitions in continuous-time Markov models of evolution
Minin, V. N., & Suchard, M. A. (2007) · Journal of Mathematical Biology · doi:10.1007/s00285-007-0120-8 · Cited by 282 · see citing works
Croda, J., de Oliveira, W. K., Frutuoso, R. L., Mandetta, L. H., Baía-da-Silva, D. C., Brito-Sousa, J. D., Monteiro, W. M., & Lacerda, M. (2020) · Revista da Sociedade Brasileira de Medicina Tropical · doi:10.1590/0037-8682-0167-2020 · Cited by 270 · see citing works
Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
Cotten, M. L., Watson, S. J., Zumla, A. I., Makhdoom, H. Q., Palser, A. L., Ong, S. H., Rabeeah, A. A. A., Alhakeem, R. F., Assiri, A. M., Al‐Tawfiq, J. A., et al. (2014) · mBio · doi:10.1128/mbio.01062-13 · Cited by 267 · see citing works
Self-citationMERS-CoV spillover at the camel-human interface
Dudas, G., Carvalho, L. M., Rambaut, A., Bedford, T., Somily, A. M., Barry, M., Subaie, S. S. A., BinSaeed, A. A., Alzamil, F. A., Zaher, W., et al. (2018) · eLife · doi:10.7554/elife.31257 · Cited by 260 · see citing works
Self-citationResposta imediata da Vigilância em Saúde à epidemia da COVID-19
Croda, J., & García, L. P. (2020) · Epidemiologia e Serviços de Saúde · doi:10.5123/s1679-49742020000100021 · Cited by 257 · see citing works
Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China
Lu, J., du Plessis, L., Liu, Z., Hill, V., Kang, M., Lin, H., Sun, J., François, S., Kraemer, M. U. G., Faria, N. R., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.023 · Cited by 247 · see citing works
Self-citationA dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiologyPreprint
Rambaut, A., Holmes, E. C., Hill, V., O’Toole, A. N., McCrone, J., Ruis, C., du Plessis, L., & Pybus, O. G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.17.046086 · Cited by 218 · see citing works
Self-citationRoutes 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-citationSERAPHIM: studying environmental rasters and phylogenetically informed movements
Dellicour, S., Rose, R., Faria, N. R., Lemey, P., & Pybus, O. G. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw384 · Cited by 170 · see citing works
Self-citationCoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation
Singer, J., Gifford, R., Cotten, M., & Robertson, D. (2020) · doi:10.20944/preprints202006.0225.v1 · Cited by 167 · see citing works
Fast, accurate and simulation-free stochastic mapping
Minin, V. N., & Suchard, M. A. (2008) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2008.0176 · Cited by 165 · see citing works
State-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-citationGoogle COVID-19 Community Mobility Reports: Anonymization Process Description (version 1.1)Preprint
Aktay, A., Bavadekar, S., Cossoul, G., et al. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2004.04145 · Cited by 157 · see citing works
Kissler, S. M., Kishore, N., Prabhu, M., Goffman, D., Beilin, Y., Landau, R., Gyamfi-Bannerman, C., Bateman, B. T., Snyder, J., Razavi, A. S., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18271-5 · Cited by 129 · 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-citationLearning to Count: Robust Estimates for Labeled Distances between Molecular Sequences
O'Brien, J. D., Minin, V. N., & Suchard, M. A. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp003 · Cited by 107 · 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-citationTriplex Real-Time RT-PCR for Severe Acute Respiratory Syndrome Coronavirus 2
Waggoner, J. J., Stittleburg, V. D., Pond, R., Saklawi, Y., Sahoo, M. K., Babiker, A., Hussaini, L., Kraft, C. S., Pinsky, B. A., Anderson, E. J., et al. (2020) · Emerging infectious diseases · doi:10.3201/eid2607.201285 · Cited by 95 · see citing works
Dellicour, S., Durkin, K., Hong, S. L., Vanmechelen, B., Martí‐Carreras, J., Gill, M. S., Meex, C., Bontems, S., André, E., Gilbert, M., et al. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa284 · Cited by 92 · see citing works
Self-citationPhylodynamic assessment of intervention strategies for the West African Ebola virus outbreak
Dellicour, S., Baele, G., Dudas, G., Faria, N. R., Pybus, O. G., Suchard, M. A., Rambaut, A., & Lemey, P. (2018) · Nature Communications · doi:10.1038/s41467-018-03763-2 · Cited by 67 · see citing works
Self-citationTemporal signal and the phylodynamic threshold of SARS-CoV-2Preprint
Duchêne, S., Featherstone, L. A., Haritopoulou-Sinanidou, M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.04.077735 · Cited by 66 · see citing works
do 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
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
Epidemiological and clinical characteristics of the early phase of the COVID-19 epidemic in BrazilPreprint
de Souza, W. M., Buss, L., Cândido, D. D. S., et al. (2020) · medRxiv · doi:10.1101/2020.04.25.20077396 · Cited by 37 · see citing works
Self-citationState-level tracking of COVID-19 in the United States
Unwin, H. J. T., Mishra, S., Bradley, Gandy, A., Mellan, T. A., Coupland, H., Ish-Horowicz, J., Vollmer, M., Whittaker, C., Filippi, S. L., et al. (2020) · Spiral (Imperial College London) · doi:10.25561/79231 · Cited by 37 · see citing works
Self-citationDellicour, S., Durkin, K., Hong, S. L., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.05.078758 · Cited by 29 · see citing works
Self-citationResende, P. C., Delatorre, E. O., Gräf, T., Mir, D., Motta, F. C., Appolinario, L., Paixão, A. C. D., Ogrzewalska, M., Caetano, B. C., dos Santos, M. C., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.17.158006 · Cited by 25 · see citing works
Self-citationMonitoring Social Distancing and SARS-CoV-2 Transmission in Brazil Using Cell Phone Mobility DataPreprint
de Oliveira, S. B., Pôrto, V. B. G., Ganem, F., Mendes, F. M., Almirón, M., de Oliveira, W. K., Fantinato, F. F. S. T., de Almeida, W. A. F., Borges, A. P. D. M., Pinheiro, H. N. B., et al. (2020) · SSRN Electronic Journal · doi:10.1101/2020.04.30.20082172 · Cited by 20 · see citing works
Self-citationWuhan coronavirus (2019-nCoV) real-time RT-PCR N gene 2020 (Wuhan-N) v1Preprint
Northill, J. A., & Mackay, I. M. (2020) · doi:10.17504/protocols.io.ba86ihze · Cited by 2 · see citing works
Data from: Evolution and epidemic spread of SARS-CoV-2 in Brazil
Cândido, D. D. S., Claro, I. M., de Jesus, J. G., de Souza, W. M., Moreira, F. R. R., Dellicour, S., Mellan, T. A., du Plessis, L., Pereira, R. H. M., Sales, F. C. D. S., et al. (2020) · ePrints Soton (University of Southampton) · doi:10.5061/dryad.rxwdbrv5z · Cited by 1 · see citing works
Self-citationWuhan coronavirus (2019-nCoV) real-time RT-PCR N gene 2020 (Wuhan-N) v1Preprint
Northill, J. A., & Mackay, I. M. (2020) · doi:10.17504/protocols.io.bbudins6 · Cited by 1 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Infectious disease in an era of global change
Baker, R. E., Mahmud, A. S., Miller, I. F., Rajeev, M., Rasambainarivo, F., Rice, B. L., Takahashi, S., Tatem, A. J., Wagner, C. E., Wang, L.-F., et al. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00639-z · Cited by 2,059 · see citing works
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
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., et al. (2021) · Science · doi:10.1126/science.abh2644 · Cited by 1,461 · see citing works
Self-citationTransmission of SARS-CoV-2 on mink farms between humans and mink and back to humans
Munnink, B. B. O., Sikkema, R. S., Nieuwenhuijse, D. F., Molenaar, R. J., Münger, E., Molenkamp, R., van der Spek, A. N., Tolsma, P., Rietveld, A., Brouwer, M., et al. (2020) · Science · doi:10.1126/science.abe5901 · Cited by 1,087 · 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
COVID-19 and the human innate immune system
Schultze, J. L., & Aschenbrenner, A. C. (2021) · Cell · doi:10.1016/j.cell.2021.02.029 · Cited by 714 · 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-citationNon-pharmaceutical interventions during the COVID-19 pandemic: A review
Perra, N. (2021) · Physics Reports · doi:10.1016/j.physrep.2021.02.001 · Cited by 518 · see citing works
Ranzani, O., Bastos, L. D. S. L., Gelli, J. G. M., Marchesi, J. F., Baião, F., Hamacher, S., & Bozza, F. A. (2021) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(20)30560-9 · Cited by 517 · 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
Epidemiological 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-citationThe emergence, genomic diversity and global spread of SARS-CoV-2
Li, J., Lai, S., Gao, G. F., & Shi, W. (2021) · Nature · doi:10.1038/s41586-021-04188-6 · Cited by 408 · 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
Self-citationImprovements 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-citationSpatiotemporal 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
Zoonotic spillover: Understanding basic aspects for better prevention
Ellwanger, J. H., & Chies, J. A. B. (2021) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2020-0355 · Cited by 261 · see citing works
The 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
Liu, R., Wu, P., Ogrodzki, P., Mahmoud, S., Liang, K., Liu, P., Francis, S. S., Khalak, H. G., Liu, D., Li, J., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-92851-3 · Cited by 204 · see citing works
The SARS-CoV-2 mutations versus vaccine effectiveness: New opportunities to new challenges
Malik, J. A., Ahmed, S., Aroosa, M., Shinde, M., Bender, O., Alshammari, F., Ansari, M., & Anwar, S. (2022) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2021.12.014 · Cited by 201 · see citing works
Spatiotemporal 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 200 · see citing works
Self-citationWeigang, S., Fuchs, J., Zimmer, G., Schnepf, D., Kern, L., Beer, J., Luxenburger, H., Ankerhold, J., Falcone, V., Kemming, J. S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26602-3 · Cited by 180 · 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
Self-citationKuzmina, A., Khalaila, Y., Voloshin, O., Keren-Naus, A., Boehm-Cohen, L., Raviv, Y., Shemer-Avni, Y., Rosenberg, E., & Taube, R. (2021) · Cell Host and Microbe · doi:10.1016/j.chom.2021.03.008 · Cited by 188 · see citing works
Control and prevention of infectious diseases from a One Health perspective
Ellwanger, J. H., da Veiga, A. B. G., Kaminski, V. D. L., Valverde-Villegas, J. M., de Freitas, A. W. Q., & Chies, J. A. B. (2021) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2020-0256 · Cited by 183 · see citing works
An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants
Chan, K. K., Tan, T. J. C., Narayanan, K. K., & Procko, E. (2021) · Science Advances · doi:10.1126/sciadv.abf1738 · Cited by 152 · see citing works
Attwood, S. W., Hill, S. C., Aanensen, D. M., Connor, T. R., & Pybus, O. G. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00483-8 · Cited by 150 · see citing works
Self-citationYu, F., Pan, T. S., Huang, F., Ying, R., Liu, J., Fan, H., Zhang, J., Liu, W., Lin, Y., Yuan, Y., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.884034 · Cited by 151 · see citing works
Long, S., Olsen, R., Christensen, P. A., Bernard, D. W., Davis, J. J., Shukla, M., Nguyen, M., Saavedra, M., Yerramilli, P., Pruitt, L., et al. (2020) · mBio · doi:10.1128/mbio.02707-20 · Cited by 121 · see citing works
Excesso de mortes durante a pandemia de COVID-19: subnotificação e desigualdades regionais no Brasil
Orellana, J. D. Y., da Cunha, G. M., Marrero, L., Moreira, R. I., Leite, I. D. C., & Horta, B. L. (2021) · Cadernos de Saúde Pública · doi:10.1590/0102-311x00259120 · Cited by 146 · see citing works
Self-citationda Silva, L. L. S., Lima, A. F. R., Polli, D. A., Razia, P. F. S., Pavão, L. F. A., Cavalcanti, M. A. F. D. H., & Toscano, C. M. (2020) · Cadernos de Saúde Pública · doi:10.1590/0102-311x00185020 · Cited by 145 · see citing works
dos Santos, L. A., Filho, P. G. D. G., Silva, A. M. F., dos Santos, J. V. G., Santos, D. S., Aquino, M. M., de Jesus, R. M., Almeida, M. L. D., Silva, J. S., Altmann, D. M., et al. (2021) · Journal of Infection · doi:10.1016/j.jinf.2021.01.020 · Cited by 136 · 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
COVID-19 pandemic and pediatric dentistry: Fear, eating habits and parent’s oral health perceptions
Campagnaro, R., Collet, G. D. O., de Andrade, M. P., Salles, J. P. D. S. L., Fracasso, M. D. L. C., Scheffel, D. L. S., de Freitas, K. M. S., & Santin, G. C. (2020) · Children and Youth Services Review · doi:10.1016/j.childyouth.2020.105469 · Cited by 131 · see citing works
Park, J., & Chung, E. (2020) · World Development · doi:10.1016/j.worlddev.2020.105198 · Cited by 125 · see citing works
An Overview of Anthropogenic Actions as Drivers for Emerging and Re-Emerging Zoonotic Diseases
Tazerji, S. S., Nardini, R., Safdar, M., Shehata, A. A., & Duarte, P. M. (2022) · Pathogens · doi:10.3390/pathogens11111376 · Cited by 134 · see citing works
Cali, D. S., Kalsi, G. S., Bingöl, Z., Fırtına, C., Subramanian, L., Kim, J. S., Ausavarungnirun, R., Alser, M., Gómez-Luna, J., Boroumand, A., et al. (2020) · IEEE/ACM International Symposium on Microarchitecture (MICRO) · doi:10.1109/micro50266.2020.00081 · Cited by 25 · see citing works
Smith, T., Flaxman, S. R., Gallinat, A. S., Kinosian, S. P., Stemkovski, M., Unwin, H. J. T., Watson, O. J., Whittaker, C., Cattarino, L., Dorigatti, I., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2019284118 · Cited by 119 · see citing works
Alteri, C., Cento, V., Piralla, A., Costabile, V., Tallarita, M., Colagrossi, L., Renica, S., Giardina, F., Novazzi, F., Gaiarsa, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20688-x · Cited by 118 · see citing works
Geoghegan, J. L., Ren, X., Storey, M., Hadfield, J., Jelley, L., Jefferies, S., Sherwood, J., Paine, S., Huang, Q. S., Douglas, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-20235-8 · Cited by 120 · see citing works
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil
Giovanetti, M., Slavov, S. N., Fonseca, V., Wilkinson, E., Tegally, H., Patané, J. S. L., Viala, V. L., San, J. E., Rodrigues, E. S., Santos, E. V., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01191-z · Cited by 108 · see citing works
Self-citationMathematical modeling of COVID-19 in 14.8 million individuals in Bahia, Brazil
de Oliveira, J. F., Jorge, D. C. P., Veiga, R., Rodrigues, M. M. D. S., Torquato, M. F., da Silva, N. B., Fiaccone, R. L., Cardim, L. L., Pereira, F. A., de Castro, C. P., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-19798-3 · Cited by 99 · see citing works
Nicolelis, M. A. L., Raimundo, R. L. G., Peixoto, P. S., & de Andreazzi, C. S. (2021) · Scientific Reports · doi:10.1038/s41598-021-92263-3 · Cited by 95 · see citing works
Self-citationGenomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia
Komissarov, A. B., Safina, K. R., Garushyants, S. K., Fadeev, A. V., Sergeeva, M. V., Ivanova, A. A., Danilenko, D., Lioznov, D. A., Shneider, O. V., Shvyrev, N., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20880-z · Cited by 92 · see citing works
Troyano-Hernáez, P., Reinosa, R., & Holguín, Á. (2021) · Viruses · doi:10.3390/v13020243 · Cited by 92 · see citing works
Engineered ACE2 decoy mitigates lung injury and death induced by SARS-CoV-2 variants
Zhang, L., Dutta, S., Xiong, S., Chan, M. C., Chan, K. K., Fan, T. M., Bailey, K. L., Lindeblad, M. O., Cooper, L. M., Rong, L., et al. (2022) · Nature Chemical Biology · doi:10.1038/s41589-021-00965-6 · Cited by 85 · see citing works
Mulder, M., der Vegt, D. S. J. M. V., Munnink, B. B. O., GeurtsvanKessel, C. H., van de Bovenkamp, J. H. B., Sikkema, R. S., Jacobs, E. M. G., Koopmans, M., & Wegdam-Blans, M. C. A. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa1538 · Cited by 87 · see citing works
Three SARS-CoV-2 reinfection cases by the new Variant of Concern (VOC) P.1/501Y.V3Preprint
Naveca, F. G., da Costa, C. F., do Nascimento, V. A., de Souza, V. C., Corado, A. D. L. G., Nascimento, F., Costa, Á., Duarte, D., Silva, G., Mejía, M., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-318392/v1 · Cited by 81 · see citing works
Marques, C. D. L., Kakehasi, A. M., Pinheiro, M. M., da Mota, L. M. H., de Albuquerque, C. P., Silva, C. R., Santos, G. P. J., dos Reis-Neto, E. T., Matos, P., Devidé, G., et al. (2021) · RMD Open · doi:10.1136/rmdopen-2020-001461 · Cited by 78 · see citing works
Self-citationCOVID-19 no Nordeste brasileiro: sucessos e limitações nas respostas dos governos dos estados
Kerr, L. R. F. S., Kendall, C., da Sílva, A. A. M., Aquino, E. M. L., Pescarini, J. M., de Almeida, R. L. F., Ichihara, M. Y., de Oliveira, J. F., de Araújo, T. V. B., Santos, C. A. D. S. T., et al. (2020) · Ciência & Saúde Coletiva · doi:10.1590/1413-812320202510.2.28642020 · Cited by 78 · see citing works
Self-citationModelling and optimal control of multi strain epidemics, with application to COVID-19
Arruda, E. F., Das, S. S., Dias, C. M., & Pastore, D. H. (2021) · PLoS ONE · doi:10.1371/journal.pone.0257512 · Cited by 76 · see citing works
Pan, T. S., Chen, R., He, X., Yuan, Y., Deng, X., Li, R., Yan, H., Yan, S., Liu, J., Zhang, Y., et al. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00848-1 · Cited by 72 · see citing works
The global transmission of new coronavirus variants
Zhao, Y., Huang, J., Zhang, L., Chen, S., Gao, J., & Jiao, H. (2021) · Environmental Research · doi:10.1016/j.envres.2021.112240 · Cited by 75 · see citing works
A multipurpose machine learning approach to predict COVID-19 negative prognosis in São Paulo, Brazil
Fernandes, F. T., de Oliveira, T. A., Teixeira, C. E., Batista, A. F. D. M., Costa, G. D., & Filho, A. D. P. C. (2021) · Scientific Reports · doi:10.1038/s41598-021-82885-y · Cited by 75 · see citing works
Introduction of Brazilian SARS-CoV-2 484K.V2 related variants into the UK
Toovey, O. T. R., Harvey, K. N., Bird, P. W., & Tang, J. W.-T. (2021) · Journal of Infection · doi:10.1016/j.jinf.2021.01.025 · Cited by 74 · see citing works
Origin and evolution of SARS-CoV-2
Pagani, I., Ghezzi, S., Alberti, S., Poli, G., & Vicenzi, E. (2023) · The European Physical Journal Plus · doi:10.1140/epjp/s13360-023-03719-6 · Cited by 74 · see citing works
SARS-CoV-2 uses CD4 to infect T helper lymphocytes
Brunetti, N. S., Davanzo, G. G., de Moraes, D., Ferrari, A., de Souza, G. F., Muraro, S. P., Knittel, T. L., Boldrini, V. D. O., Monteiro, L. D. B., Virgílio-da-Silva, J. V., et al. (2023) · eLife · doi:10.7554/elife.84790 · Cited by 74 · see citing works
Self-citationLison, A., Banholzer, N., Sharma, M., Mindermann, S., Unwin, H. J. T., Mishra, S., Stadler, T., Bhatt, S., Ferguson, N. M., Brauner, J., et al. (2023) · The Lancet Public Health · doi:10.1016/s2468-2667(23)00046-4 · Cited by 71 · see citing works
Self-citationResende, P. C., Delatorre, E. O., Gräf, T., Mir, D., Motta, F. C., Appolinario, L., Paixão, A. C. D., Mendonça, A. C. D. F., Ogrzewalska, M., Caetano, B. C., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.615280 · Cited by 70 · see citing works
Self-citationRelax, Keep Walking — A Practical Guide to Continuous Phylogeographic Inference with BEAST
Dellicour, S., Gill, M. S., Faria, N. R., Rambaut, A., Pybus, O. G., Suchard, M. A., & Lemey, P. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab031 · Cited by 68 · see citing works
Self-citationPerfil clínico e fatores associados ao óbito de pacientes COVID-19 nos primeiros meses da pandemia
Pontes, L., Danski, M. T. R., Piubello, S. M. N., Pereira, J. D. F. G., Jantsch, L. B., Costa, L. B., dos Santos, J. D. O., & Arrué, A. M. (2021) · Escola Anna Nery · doi:10.1590/2177-9465-ean-2021-0203 · Cited by 67 · see citing works
Spatial pattern of COVID-19 deaths and infections in small areas of Brazil
de Lima, E. E. C., Gayawan, E., Baptista, E. A., & Queiroz, B. L. (2021) · PLoS ONE · doi:10.1371/journal.pone.0246808 · Cited by 65 · see citing works
One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages
Gónzález‐Candelas, F., Shaw, M., Phan, T. G., Kulkarni‐Kale, U., Paraskevis, D. N., Luciani, F., Kimura, H., & Sironi, M. (2021) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2021.104869 · Cited by 65 · see citing works
Layan, M., Müller, N. F., Dellicour, S., Maio, N. D., Bourhy, H., Cauchemez, S., & Baele, G. (2023) · Virus Evolution · doi:10.1093/ve/vead010 · Cited by 65 · see citing works
Self-citationNonaka, C. K. V., Gräf, T., Barcia, C. A. D. L., Costa, V. F., de Oliveira, J. L., Passos, R. D. H., Bastos, I. N., de Santana, M. C. B., Santos, I. M., de Sousa, K. A. F., et al. (2021) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2021.08.003 · Cited by 63 · see citing works
Banho, C. Á., Sacchetto, L., Campos, G. R. F., Bittar, C., Possebon, F. S., Ullmann, L. S., Marques, B. D. C., da Silva, G. C. D., Moraes, M. M., Parra, M. C. P., et al. (2022) · Communications Medicine · doi:10.1038/s43856-022-00108-5 · Cited by 63 · see citing works
Self-citationSARS-CoV-2 variants – Evolution, spike protein, and vaccines
Chen, K.-W. K., Huang, D. T., & Huang, L. (2022) · Biomedical Journal · doi:10.1016/j.bj.2022.04.006 · Cited by 61 · see citing works
Environment and COVID-19 incidence: A critical review
Han, J., Yin, J., Wu, X., Wang, D., & Li, C. (2022) · Journal of Environmental Sciences · doi:10.1016/j.jes.2022.02.016 · Cited by 60 · see citing works
López, M. G., Chiner‐Oms, Á., de Viedma, D. G., Ruiz-Rodríguez, P., Bracho, M. A., Cancino‐Muñoz, I., D’Auria, G., Marco, G. D., García‐González, N., Goig, G. A., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00936-6 · Cited by 57 · see citing works
Pradhan, N. A., Samnani, A. A., Abbas, K., & Rizvi, N. (2023) · Health Research Policy and Systems · doi:10.1186/s12961-023-01031-4 · Cited by 67 · see citing works
Castelli, E. C., de Castro, M. V., Naslavsky, M. S., Scliar, M. O., Silva, N. D. S. B., Andrade, H. S., Souza, A. S., Pereira, R. N., Castro, C. F. B., Mendes‐Junior, C. T., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.742881 · Cited by 57 · see citing works
Self-citationPopulation-based seroprevalence of SARS-CoV-2 and the herd immunity threshold in Maranhão
da Sílva, A. A. M., Neto, L. G. L., de Azevedo, C. D. M. P. E. S., da Costa, L. M. M., Bragança, M. L. B. M., Filho, A. K. D. B., Wittlin, B. B., de Souza, B. F., de Oliveira, B. L. C. A., de Carvalho, C. A., et al. (2020) · Revista de Saúde Pública · doi:10.11606/s1518-8787.2020054003278 · Cited by 55 · see citing works
Self-citationInsights into SARS-CoV-2 Persistence and Its Relevance
Desimmie, B. A., Raru, Y., Awadh, H., He, P., Teka, S., & Willenburg, K. S. (2021) · Viruses · doi:10.3390/v13061025 · Cited by 54 · see citing works
Pondé, R. A. D. A. (2022) · Virology · doi:10.1016/j.virol.2022.05.003 · Cited by 52 · see citing works
Griffiths, E., Timme, R., Mendes, C. I., Page, A. J., Alikhan, N.-F., Fornika, D., Maguire, F., Campos, J., Park, D. J., Olawoye, I. B., et al. (2022) · GigaScience · doi:10.1093/gigascience/giac003 · Cited by 55 · see citing works
Self-citationJorge, D. C. P., Rodrigues, M. M. D. S., Silva, M. S., Cardim, L. L., da Silva, N. B., da Silveira, I. H., da Silva, V. A. F., Pereira, F. A., de Azevedo, A. R., Amad, A. A. S., et al. (2021) · Epidemics · doi:10.1016/j.epidem.2021.100465 · Cited by 50 · see citing works
Tracking the onset date of the community spread of SARS-CoV-2 in western countries
Delatorre, E. O., Mir, D., Gräf, T., & Bello, G. (2020) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/0074-02760200183 · 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-citationA comparison of five epidemiological models for transmission of SARS-CoV-2 in India
Purkayastha, S., Bhattacharyya, R., Bhaduri, R., Kundu, R., Gu, X., Salvatore, M., Ray, D., Mishra, S., & Mukherjee, B. (2021) · BMC Infectious Diseases · doi:10.1186/s12879-021-06077-9 · Cited by 49 · see citing works
Self-citationPaiva, 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
Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong
Gu, H., Xie, R., Adam, D. C., Tsui, J. L.-H., Chu, D. K. W., Chang, L. D. J., Cheuk, S. S. Y., Gurung, S., Krishnan, P., Ng, D. Y. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28420-7 · Cited by 46 · see citing works
Lin, X., Glier, M. B., Kuchinski, K. S., Mierlo, T. R.-V., McVea, D., Tyson, J. R., Prystajecky, N., & Ziels, R. M. (2021) · mSystems · doi:10.1128/msystems.01068-21 · Cited by 44 · see citing works
Noureddine, F. Y., Chakkour, M., Roz, A. E., Reda, J., Sahily, R. A., Assi, A., Joma, M., Salami, H. A., Hashem, S. J., Harb, B., et al. (2021) · Medical Sciences · doi:10.3390/medsci9020040 · Cited by 46 · see citing works
Using Seismic Noise Levels to Monitor Social Isolation: An Example From Rio de Janeiro, Brazil
Dias, F. L., de Assumpção, M. S., Peixoto, P. S., Bianchi, M., Collaço, B., & Calhau, J. (2020) · Geophysical Research Letters · doi:10.1029/2020gl088748 · Cited by 45 · see citing works
Self-citationGarushyants, S. K., Rogozin, I. B., & Koonin, E. V. (2021) · Communications Biology · doi:10.1038/s42003-021-02858-9 · Cited by 45 · see citing works
SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants
Hattab, D., Amer, M. F. A., Al‐Alami, Z. M., & Bakhtiar, A. (2024) · Infection · doi:10.1007/s15010-024-02223-y · Cited by 44 · see citing works
Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread
Moreno, G. K., Braun, K. M., Riemersma, K. K., Martin, M. A., Halfmann, P., Crooks, C. M., Prall, T. M., Baker, D., Baczenas, J. J., Heffron, A. S., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19346-z · Cited by 44 · see citing works
Dataset on SARS-CoV-2 non-pharmaceutical interventions in Brazilian municipalities
Santos, A. A. D. S., Cândido, D. D. S., de Souza, W. M., Buss, L., Li, S. L., Pereira, R. H. M., Wu, C., Sabino, É. C., & Faria, N. R. (2021) · Scientific Data · doi:10.1038/s41597-021-00859-1 · Cited by 44 · see citing works
Self-citationSARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay
Elizondo, V., Harkins, G. W., Mabvakure, B. M., Smidt, S., Zappile, P., Marier, C., Maurano, M. T., Perez, V., Mazza, N., Beloso, C., et al. (2020) · Emerging Microbes & Infections · doi:10.1080/22221751.2020.1863747 · Cited by 43 · see citing works
Self-citationStange, M., Mari, A., Roloff, T. C., Seth-Smith, H. M. B., Schweitzer, M., Brunner, M., Leuzinger, K., Søgaard, K. K., Gensch, A., Tschudin‐Sutter, S., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009374 · Cited by 43 · see citing works
Resende, P. C., Bezerra, J. F., Vasconcelos, R. H. T., Arantes, I., Appolinario, L., Mendonça, A. C. D. F., Paixão, A. C. D., Duarte, A. C., Silva, T., da Rocha, A. S. B., et al. (2021) · Emerging infectious diseases · doi:10.3201/eid2707.210401 · Cited by 42 · see citing works
Resende, P. C., Gräf, T., Paixão, A. C. D., Appolinario, L., Lopes, R. S., Mendonça, A. C. D. F., da Rocha, A. S. B., Motta, F. C., Neto, L. G. L., Khouri, R., et al. (2021) · Viruses · doi:10.3390/v13050724 · Cited by 43 · see citing works
Lekagul, A., Chattong, A., Rueangsom, P., Waleewong, O., & Tangcharoensathien, V. (2022) · Globalization and Health · doi:10.1186/s12992-022-00861-1 · Cited by 44 · see citing works
Banholzer, N., Lison, A., Özcelik, D., Stadler, T., Feuerriegel, S., & Vach, W. (2022) · European Journal of Epidemiology · doi:10.1007/s10654-022-00908-y · Cited by 42 · see citing works
Pomorska‐Mól, M., Włodarek, J., Gogulski, M., & Rybska, M. (2021) · animal · doi:10.1016/j.animal.2021.100272 · Cited by 40 · see citing works
SARS-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
Mortalidade por COVID-19 padronizada por idade nas capitais das diferentes regiões do Brasil
Silva, G. A. E., Jardim, B. C., & Lotufo, P. A. (2021) · Cadernos de Saúde Pública · doi:10.1590/0102-311x00039221 · Cited by 40 · see citing works
Costa, C. S., Pitombo, C. S., & de Souza, F. L. U. (2022) · Sustainability · doi:10.3390/su14084573 · Cited by 40 · see citing works
Savaris, R. F., Guilherme Pumi, A., Dalzochio, J., & Kunst, R. (2021) · Scientific Reports · doi:10.1038/s41598-021-84092-1 · Cited by 37 · see citing works
RetractedSlavov, S. N., Patané, J. S. L., Bezerra, R. D. S., Giovanetti, M., Fonseca, V., Martins, A. J., Viala, V. L., Rodrigues, E. S., Santos, E. V., Barros, C. R. S., et al. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27190 · Cited by 39 · see citing works
COVID-19 mortality and exposure to airborne PM2.5: A lag time correlation
Shao, L., Cao, Y., Jones, T. P., Santosh, M., Silva, L. F. O., Ge, S., da Boit, K., Feng, X., Zhang, M., & BéruBé, K. (2021) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.151286 · Cited by 39 · see citing works
Yu, Y., Esposito, D., Kang, Z., Lü, J., Remaley, A. T., Giorgi, V. D., Chen, L. N., West, K. A., & Cao, L. (2022) · Scientific Reports · doi:10.1038/s41598-022-06629-2 · Cited by 38 · see citing works
- Authors
- 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., Manuli, E. R., Thézé, J., Almeida, L., Menezes, M. T., Voloch, C. M., Fumagalli, M. J., Coletti, T. M., da Silva, C. A. M., Ramundo, M. S., Amorim, M. R., Hoeltgebaum, H. H., Mishra, S., Gill, M. S., Carvalho, L. M., Buss, L. F., Prete, C. A., Ashworth, J., Nakaya, H. I., Peixoto, P. S., Brady, O. J., Nicholls, S. M., Tanuri, A., Rossi, Á. D., Braga, C. K. V., Gerber, A. L., de C. Guimarães, A. P., Gaburo, N., Alencar, C. S., Ferreira, A. C. S., Lima, C. X., Levi, J. E., Granato, C., Ferreira, G. M., Francisco, R. S., Granja, F., Garcia, M. T., Moretti, M. L., Perroud, M. W., Castiñeiras, T. M. P. P., Lazari, C. S., Hill, S. C., de Souza Santos, A. A., Simeoni, C. L., Forato, J., Sposito, A. C., Schreiber, A. Z., Santos, M. N. N., de Sá, C. Z., Souza, R. P., Resende-Moreira, L. C., Teixeira, M. M., Hubner, J., Leme, P. A. F., Moreira, R. G., Nogueira, M. L., Brazil-UK Centre for Arbovirus Discovery, D., Ferguson, N. M., Costa, S. F., Proenca-Modena, J. L., Vasconcelos, A. T. R., Bhatt, S., Lemey, P., Wu, C.-H., Rambaut, A., Loman, N. J., Aguiar, R. S., Pybus, O. G., Sabino, E. C., & Faria, N. R.
- Affiliations
- Department of Zoology, University of Oxford, Oxford, UK.
- Universidade de São Paulo (BR)
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
- Centro de Pesquisa em Virologia, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, Brazil.
- Universidade Federal do Rio de Janeiro (BR)
- Université Libre de Bruxelles (BE)
- Imperial College London (GB)
- Institute of Applied Economic Research (BR)
- Université Clermont Auvergne (FR)
- Universidade Estadual de Campinas (UNICAMP) (BR)
- Fundação Getulio Vargas (BR)
- Rega Institute for Medical Research (BE)
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil.
- London School of Hygiene & Tropical Medicine (GB)
- University of Birmingham (GB)
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil.
- Instituto Hermes Pardini, Belo Horizonte, Brazil.
- Universidade Federal de Minas Gerais (BR)
- Fleury S.A. (Brazil) (BR)
- Universidade Federal de Roraima (BR)
- Divisão de Doenças Infecciosas, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, Brazil.
- Hospital Estadual Sumaré, Universidade Estadual de Campinas, Campinas, Brazil.
- Royal Veterinary College (GB)
- University of Oxford, Latin American Centre, Oxford School of Global and Area Studies, Oxford, UK.
- Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, Brazil.
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
- Centro de Saúde da Comunidade, Universidade Estadual de Campinas, Campinas, Brazil.
- Faculdade de Medicina de São José do Rio Preto (BR)
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil.
- University of Southampton (GB)
- University of Edinburgh (GB)
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK.
- Corresponding author
- Faria, Nuno Rodrigues
- ORCID
- Candido, Darlan S.
- Claro, Ingra M.
- de Jesus, Jaqueline G.
- Souza, William M.
- Moreira, Filipe R. R.
- Dellicour, Simon
- Mellan, Thomas A.
- du Plessis, Louis
- Pereira, Rafael H. M.
- Sales, Flavia C. S.
- Manuli, Erika R.
- Thézé, Julien
- Almeida, Luiz
- Menezes, Mariane T.
- Voloch, Carolina M.
- Fumagalli, Marcilio J.
- Coletti, Thaís M.
- da Silva, Camila A. M.
- Ramundo, Mariana S.
- Amorim, Mariene R.
- Hoeltgebaum, Henrique H.
- Mishra, Swapnil
- Gill, Mandev S.
- Carvalho, Luiz M.
- Buss, Lewis F.
- Prete, Carlos A.
- Ashworth, Jordan
- Nakaya, Helder I.
- Peixoto, Pedro S.
- Brady, Oliver J.
- Nicholls, Samuel M.
- Tanuri, Amilcar
- Rossi, Átila D.
- Braga, Carlos K. V.
- Gerber, Alexandra L.
- de C. Guimarães, Ana Paula
- Gaburo, Nelson
- Alencar, Cecila Salete
- Ferreira, Alessandro C. S.
- Lima, Cristiano X.
- Levi, José Eduardo
- Granato, Celso
- Ferreira, Giulia M.
- Francisco, Ronaldo S.
- Granja, Fabiana
- Garcia, Marcia T.
- Perroud, Mauricio W.
- Castiñeiras, Terezinha M. P. P.
- Hill, Sarah C.
- Simeoni, Camila L.
- Forato, Julia
- Sposito, Andrei C.
- Schreiber, Angelica Z.
- Santos, Magnun N. N.
- de Sá, Camila Zolini
- Souza, Renan P.
- Resende-Moreira, Luciana C.
- Teixeira, Mauro M.
- Hubner, Josy
- Leme, Patricia A. F.
- Moreira, Rennan G.
- Nogueira, Maurício L.
- Ferguson, Neil M.
- Costa, Silvia F.
- Proenca-Modena, José Luiz
- Vasconcelos, Ana Tereza R.
- Bhatt, Samir
- Lemey, Philippe
- Wu, Chieh-Hsi
- Rambaut, Andrew
- Loman, Nick J.
- Aguiar, Renato S.
- Pybus, Oliver G.
- Sabino, Ester C.
- Faria, Nuno Rodrigues
- Venue
- Science
- Published
- 2020-09-04
- Volume
- 369
- Issue
- 6508
- Pages
- 1255-1260
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7402630
- OpenAlex
- W3044468596
- Cited by
- 573
- References
- 69
- Citations by year
- 2026: 6 · 2025: 32 · 2024: 46 · 2023: 61 · 2022: 133 · 2021: 227 · 2020: 68
- FWCI
- 16.04
- 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)
- ePrints Soton (University of Southampton) (acceptedVersion)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- HAL (submittedVersion, other-oa)
- Lirias (submittedVersion, cc-by)
- RVC Research Online (Royal Veterinary College) (submittedVersion, cc-by)
- Lirias (submittedVersion, cc-by-nc-nd)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- Spiral (Imperial College London) (submittedVersion, other-oa)
- Funders
- Medical Research Council (MR/S0195/1)
- São Paulo Research Foundation (MR/S0195/1)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, COVID-19 epidemic, Brazil, non-pharmaceutical interventions, reproduction number, viral genome sequencing, air travel, viral evolution, São Paulo, Rio de Janeiro
- MeSH terms
- Betacoronavirus, COVID-19, SARS-CoV-2, COVID-19 Testing, Bayes Theorem, Brazil, Cities, Europe, Humans, Models, Genetic, Phylogeny, Pneumonia, Viral, Travel, Urban Population, Models, Statistical, Genome, Viral, Coronavirus Infections, Evolution, Molecular, Clinical Laboratory Techniques, Basic Reproduction Number, Pandemics, Phylogeography, Spatio-Temporal Analysis
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
