Evolution and epidemic spread of SARS-CoV-2 in Brazil
The spread of SARS-CoV-2 in Brazil
Abstract
Challenges of real-time assessment of transmission
Mobility-driven changes in R
Spatially representative sequencing efforts
Phylogenetic analyses and international introductions
Modeling spatiotemporal spread within Brazil
Discussion
Acknowledgments
Supplementary Material
Summary
Resources
References and Notes
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4 September 2020
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- Darlan S. Candido et al.
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- Dynamics of Early Establishment of SARS-CoV-2 VOC Omicron Lineages in Minas Gerais, Brazil, Viruses, 15, 2, (585), (2023).https://doi.org/10.3390/v15020585
- Retrospective Insights of the COVID-19 Epidemic in the Major Latin American City, São Paulo, Southeastern Brazil, Viruses, 15, 2, (327), (2023).https://doi.org/10.3390/v15020327
- Comparative analysis of the features of organizing measures to combat the COVID-19 pandemic in the health systems of the Russian Federation and foreign countries, Bulletin of the Russian Military Medical Academy, 24, 4, (775-788), (2023).https://doi.org/10.17816/brmma114757
- Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings, PLOS Global Public Health, 3, 2, (e0001455), (2023).https://doi.org/10.1371/journal.pgph.0001455
- Spatio-temporal Graph Learning for Epidemic Prediction, ACM Transactions on Intelligent Systems and Technology, 14, 2, (1-25), (2023).https://doi.org/10.1145/3579815
- Origin and evolution of SARS-CoV-2, The European Physical Journal Plus, 138, 2, (2023).https://doi.org/10.1140/epjp/s13360-023-03719-6
- High mobility group box 1, ATP , lipid mediators, and tissue factor are elevated in COVID ‐19 patients: HMGB1 as a biomarker of worst prognosis , Clinical and Translational Science, (2023).https://doi.org/10.1111/cts.13475
- Genomic surveillance of SARS-CoV-2 in mainland China after ending the zero-COVID policy, December 2022–January 2023, Journal of Infection, (2023).https://doi.org/10.1016/j.jinf.2023.02.040
- Environment and COVID-19 incidence: A critical review, Journal of Environmental Sciences, 124, (933-951), (2023).https://doi.org/10.1016/j.jes.2022.02.016
- Big Data Technology in Infectious Diseases Modeling, Simulation and Prediction After the COVID-19 Outbreak: A Survey, Intelligent Medicine, (2023).https://doi.org/10.1016/j.imed.2023.01.002
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RE: HYMN FOR HELP: Once again, Government inaction against COVID-19 in Brazil
In the Report "Evolution and epidemic spread of SARS-CoV-2 in Brazil", Candido et al.1 discuss that Brazil is one of the countries with the fastest-growing number of cases of infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The national anthem refers to a heroic people with a loud shout, however the shouts are only the sound of desperate people that cry over nearly 250 thousand COVID-19 associated deaths, reaching an alarming lethality rate of 10%. Sadly, not only does the government neglect COVID-19 pandemic, they are also using this crisis to create legal bypasses of governmental interests, such as simplifying and undermining Brazilian environmental legislation, which have contributed to the greatest registered loss of the Pantanal biome2. Government inaction has also been observed in the oil spill that hit the Brazilian coastline in August 2019, as discussed by Brum et al.3
Since the beginning of the pandemic in Brazil, "the sun of freedom, in bright rays" has no longer shined in the sky of the motherland. A work by Ventura & Reis4, entitled "An unprecedented attack on human rights in Brazil: the timeline of the federal government's strategy to spread Covid-19", clearly states that the Federal Government, throughout the year of 2020, used "propaganda against public health, in addition to fake news and technical information without scientific verification, with the purpose of discrediting health authorities, weakening popular adherence to science-based recommendations required to contain the spread of Covid-19". The Ministry of Health has been ruled by an army general experienced in Logistics, since May 15th, after the president dismissed two medical doctors as Ministers. In June, the data on COVID-19 associated deaths were removed from public domain for hours and also from the platform of Johns Hopkins University, which has monitored the progress of the virus since the beginning of the pandemic. Not to mention that, by the end of December, a new variant of concern (VOC) P1 was described in Manaus, Amazon state, by Naveca et al.5, which may be responsible for re-infections and higher transmissibility. Finally, with the imminent expiration of millions of COVID-19 tests6, the lack of action and miscoordination seem to have reached their apices, on January 14th, 2021, when Brazil and the world watched in amazement patients suffocating in hospitals in the Amazon city of Manaus, due to the lack of oxygen supply in the state of Amazon7. The crisis, however, could have been avoided, as the multinational White Martins oxygen supplier and the attorneys in Manaus claim to have warned the government7. In this scenario of horror, lots of patients asked to go home to die next to their beloved ones. Some were transferred to other states and others took their own risk, and traveled to other cities to get health aid.
Most of this patient trafficking was performed without the proper biosafety care, contributing to the spread of the new VOC P1, which has already been detected in several other states in Brazil: Pará, Roraima, Ceará, Paraíba, Piauí, Bahia, São Paulo, Rio de Janeiro, Espírito Santo, Santa Catarina, and Rio Grande do Sul. Moreover, one cannot forget about the industrial district in Manaus that did not stop its activities. According to the Federal Court of Accounts, Brazilian government prioritized the economic protection, even though the country surpassed 200.000 deaths in January 20214. Business workers from all over the world come back and forth to Manaus, which may also have been a very important source of dissemination of SARS-CoV-2 variants.
One can ask if barriers are sufficient to stop viral dissemination. Is it possible to stop international business? China declared to have one case of a patient with pneumonia-like illness in Wuhan in December 2019, however only in January 9th 2020, WHO8 declared that the pathogen responsible is a novel or new coronavirus identified by gene sequencing9. After one year, Brazil is known worldwide not only because of its high number of deaths, but also by having a new P1 variant of the virus.
Sequencing has been the major tool for genomic surveillance. The United Kingdom and United States of America sequenced more than 50% of their first 1000 cases, however there are countries with high numbers of cases but few sequence data, which might create bias to elucidate new variants and global transmission dynamics of SARS-CoV-210. To help these efforts, our group found that SARS-CoV-2 samples from Ceará state, Norteastern Brazil, obtained from June to December 2020, already had the non-synonymous D614G mutation, in the replacement of aspartic acid with glycine at position 614 of the viral spike protein, enhancing viral cell entry and infectivity. We were the first group to show this widespread mutation in the state of Ceará, even though this mutation has been known since the beginning of 2020.
One can ask why it took so long to detect it, since it is a well-known mutation present in variants from UK and South Africa. The budget for scientific research to combat COVID-19 in 2020 was US$ 0.1 billion in Brazil, whereas in the United States it reached US$ 6,1 billion. Furthermore, the budget available for investments by the Ministry of Science, Technology and Innovations (MCTI) for this year in Brazil is only U$ 690 million, and the government's proposal for 2021 is to further reduce this amount to U$ 500 million11,12. These numbers can explain why Brazil has a low number of sequences deposited in GISAID database (www.gisaid.org) and, when specifically looking at Ceará state, one can find only 41 deposited sequences. It is a priority to monitor SARS-CoV-2 variants, which demands improvement of the surveillance through global sequencing and sharing of variant-specific PCR primers13. Only a global scientific effort, contributing to global genomic surveillance can ensure faster responsiveness to control COVID-19 pandemic.
References and Notes:
1. Candido DS, Claro IM, de Jesus JG, et al. Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science. 369, 1255-1260 (2020). doi: 10.1126/science.abd2161.
2. Nugent C. Brazil Is Burning—and President Bolsonaro's 'Terminator' Environment Minister Is Rolling Back More Protections (2020) (available at https://time.com/5895167/brazil-fires-ricardo-salles-environment/?utm_so...).
3. Brum HD, Campos-Silva JV, Oliveira EG. Brazil oil spill response: Government inaction. Science. 367, 155-156 (2020). doi: 10.1126/science.aba0369.
4. Ventura D, Reis R. An unprecedented attack on human rights in Brazil: the timeline of the federal government's strategy to spread Covid-19. Offprint. Bulletin Rights in the Pandemic. São Paulo, Brazil, CEPEDISA/USP and Conectas Human Rights (2021) (available at https://www.conectas.org/wp/wp-content/uploads/2021/01/10boletimcovid_en...).
5. Naveca F, Costa C, Nascimento V, et al. SARS-CoV-2 reinfection by the new Variant of Concern (VOC) P.1 in Amazonas, Brazil (2021) (available at https://virological.org/t/sars-cov-2-reinfection-by-the-new-variant-of-c...)
6. Machado R. Pazuello diz que estoque de 6,86 milhões de testes para Covid prestes a vencer é adequado ao Brasil (2020) (available at https://folha.com/zkwrjhc9) [in Portuguse]
7. Sassine V. Governo Bolsonaro ignorou alertas em série sobre falta de oxigênio em Manaus (2021) (available at: https://folha.com/ti9go84p). [in Portuguse]
8. World Health Organization. WHO Statement regarding cluster of pneumonia cases in Wuhan, China (2020) (available at: https://www.who.int/china/news/detail/09-01-2020-who-statement-regarding...)
9. Zhou P, Yang XL, Wang, XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020). doi: 10.1038/s41586-020-2012-7.
10. Furuse Y. Genomic sequencing effort for SARS-CoV-2 by country during the pandemic. Int J Infect Dis (2021) 103, 305-307. doi: 10.1016/j.ijid.2020.12.034.
11. Westin, R. Corte de verbas da ciência prejudica reação à pandemia e desenvolvimento do país (2020). (available at: https://www12.senado.leg.br/noticias/infomaterias/2020/09/corte-de-verba...) [in Portuguse]
12. Pires B. Ciência brasileira sofre com cortes de verbas e encara cenário dramático para pesquisas em 2021 (2020). (available at: https://brasil.elpais.com/brasil/2020-12-31/ciencia-brasileira-sofre-com...) [in Portuguse]
13. Fontanet A, Autran B, Lina B, et al. SARS-CoV-2 variants and ending the COVID-19 pandemic. Lancet (2021). doi: 10.1016/S0140-6736(21)00370-6.
This paper could have used more precise wordings.
The authors wrote: "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel betacoronavirus with a 30-kb genome that was first reported in December 2019 in Wuhan, China" and "SARS-CoV-2 was declared a public health emergency of international concern on 30 January 2020". While COVID-19 (named later) was first reported in December 2019, the pathogen was not identified until in early January 2020. And WHO declared COVID-19 or the virus outbreak, not the virus, as a public health emergency of international concern on January 30, 2020.
RE: From chloroquine to anal ozone: how ignorance has helped to kill more than 100,000 Brazilians by COVID-19
Brazil has been facing a 'pandemic of ignorance' in the last two years that is materialized by scientific negationism and by the institutionalization of fake news, which has created internal and external crises, constraining the country in different ways. Regrettably, President Bolsonaro himself has fervently defended aspects that escape any reasonableness and his followers embark on a battle of counter-science that is detrimental to normality of civilized life (1). It is true that this movement is not exclusive to Brazil, since the wave of scientific negationism is worldwide, but here it takes on the contours of cruelty, since ignorance cannot be best tool to facing COVID-19 outbreak (2). Terribly this week Brazil has reached the sad mark of 100,000 deaths due COVID-19 waging fruitless discussions about the use of chloroquine (CLQ) and hydroxychloroquine (HLQ) as drugs that cure the disease .
The COVID-19 outbreak has become much more of a political platform than a serious public health crisis and the politicization of facing the disease has won the defense even of associations of doctors, which is in itself embarrassing, after all, it should defend best practices and scientific evidence and not as a weapon in the party political field (2). Although it is an unquestionable fact that the off-label drugs uses, such as CLQ and HLQ, in medicine is a common practice, as long as there is clear agreement from the patient (3), but the treatment of COVID-19 with off-label drugs uses should be treated as such, and not as a 'miraculous cure' because it is a dangerous and counterproductive decoy (1). Recently, the new 'cure' for COVID-19 seems to be the application of ozone by the rectal route, procedure without any scientific evidence, but which was defended by politicians in another embarrassing episode for Brazil. In the United States, the Food and Drug Administration (FDA) prohibited the ozone therapy, with the justification of being dangerous and due the lack of scientific evidence (4).
These episodes linked to scientific negationism seem to be the creation of smoke curtains to cover the Brazilian government's troubled action in confronting COVID-19 outbreak, including the trivialization of the death of patients, thus 100,000 deaths seems to be just a number and not lives lost, lives that should matter. These deaths are reflection of a government that underestimated the seriousness of the pandemic.
The negationism as a state policy represents the most cruel face of intolerance. Besides to rejecting those who think differently, it seeks to undermine reason, the pillar of science, destroying the dialogue channels, which presuppose the capacity for convincing through rationality. Associated with this scenario, there is the fragility caused by the significant reduction of governmental investments in science and technology experienced since 2015 which led to a technological dependence in the country both in the search for a vaccine, as in development of drugs (or drug repurposing) and equipment for facing COVID-19. According to Knowledge Observatory, a non-governmental entity, the Brazilian budget for science and technology was impaired from R$ 10.7 billion, in 2015, to R$ 3.7 billion, in 2019. Scientific agency Finep (the most important governmental agency that finances infrastructure for research) decreased the investments from R$ 2.38 billion, in 2015, to R$ 422 million, in 2019 (5). Even in the face of this catastrophic scenario for promoting of Brazilian research, despite the 2020 Annual Budget Law foresees R$ 4.8 billion available for R&D, the government restricted R$ 4.2 billion, releasing only R$ 600 million for investment in science and technology (6). If such a scenario persists for Brazil, while the population is dying abandoned, the science will die of starvation.
Competing Interests: None declared.
References
(1) Stargardter, G., Paraguassu, L. Special Report: Bolsonaro bets 'miraculous cure' for COVID-19 can save Brazil - and his life. 2020. Available in: https://www.reuters.com/article/us-health-coronavirus-brazil-hydroxychlo...
(2) Martins-Filho, P.R. Facing the COVID-19 epidemic in Brazil: Ignorance cannot be our new best friend. 2020. eLetter. Available in: https://science.sciencemag.org/content/368/6490/493/tab-e-letters
(3) Shojaei A, Salari P. COVID-19 and off label use of drugs: an ethical viewpoint. Daru. 2020;1-5. doi:10.1007/s40199-020-00351-y
(4) Code of Federal Regulations Title 21 Sec. 801.415 Maximum acceptable level of ozone (FDA Website). 2003. Available in: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?f...
(5) Carta de Campinas. Governo federal retira da ciência brasileira mais de R$ 5 bilhões em apenas dois anos. 2019. Available in: https://cartacampinas.com.br/2019/04/governo-federal-retira-da-ciencia-b...
(6) ABC. Conselho diretor do FNDCT pede descontingenciamento total. 2020. Available in: http://www.abc.org.br/2020/04/04/conselho-diretor-do-fndct-pede-desconti...