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1.
Giovanetti, M.; Slavov, S. N.; Fonseca, V.; Wilkinson, E.; Tegally, H.; Patané, J. S. L.; Viala, V. L.; San, E. J.; Rodrigues, E. S.; Santos, E. V.; Aburjaile, F.; Xavier, J.; Fritsch, H.; Adelino, T. E. R.; Pereira, F.; Leal, A.; Iani, F. C. M.; de Carvalho Pereira, G.; Vazquez, C.; Sanabria, G. M. E.; Oliveira, E. C.; Demarchi, L.; Croda, J.; Dos Santos Bezerra, R.; Paola Oliveira de Lima, L.; Martins, A. J.; Renata Dos Santos Barros, C.; Marqueze, E. C.; de Souza Todao Bernardino, J.; Moretti, D. B.; Brassaloti, R. A.; de Lello Rocha Campos Cassano, R.; Mariani, Pdsc, Kitajima, J. P.; Santos, B.; Proto-Siqueira, R.; Cantarelli, V. V.; Tosta, S.; Nardy, V. B.; Reboredo de Oliveira da Silva, L.; Gómez, M. K. A.; Lima, J. G.; Ribeiro, A. A.; Guimarães, N. R.; Watanabe, L. T.; Barbosa Da Silva, L.; da Silva Ferreira, R.; da Penha, M. P. F.; Ortega, M. J.; de la Fuente, A. G.; Villalba, S.; Torales, J.; Gamarra, M. L.; Aquino, C.; Figueredo, G. P. M.; Fava, W. S.; Motta-Castro, A. R. C.; Venturini, J.; do Vale Leone de Oliveira, S. M.; Gonçalves, C. C. M.; do Carmo Debur Rossa, M.; Becker, G. N.; Giacomini, M. P.; Marques, N. Q.; Riediger, I. N.; Raboni, S.; Mattoso, G.; Cataneo, A. D.; Zanluca, C.; Duarte Dos Santos, C. N.; Assato, P. A.; Allan da Silva da Costa, F.; Poleti, M. D.; Lesbon, J. C. C.; Mattos, E. C.; Banho, C. A.; Sacchetto, L.; Moraes, M. M.; Grotto, R. M. T.; Souza-Neto, J. A.; Nogueira, M. L.; Fukumasu, H.; Coutinho, L. L.; Calado, R. T.; Neto, R. M.; Bispo de Filippis, A. M.; Venancio da Cunha, R.; Freitas, C.; Peterka, C. R. L.; de Fátima Rangel Fernandes, C.; Navegantes, W.; do Carmo Said, R. F.; Campelo de, A. E. Melo C. F.; Almiron, M.; Lourenço, J.; de Oliveira, T.; Holmes, E. C.; Haddad, R.; Sampaio, S. C.; Elias, M. C.; Kashima, S.; Junior de Alcantara, L. C.; Covas, D. T..
Nat Microbiol ; 2022.
Article in English | PubMed | ID: covidwho-1991610

ABSTRACT

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

2.
Giovanetti, M.; Slavov, S. N.; Fonseca, V.; Wilkinson, E.; Tegally, H.; Patané, J. S. L.; Viala, V. L.; San, J. E.; Rodrigues, E. S.; Vieira Santos, E.; Aburjaile, F.; Xavier, J.; Fritsch, H.; Ribeiro Adelino, T. E.; Pereira, F.; Leal, A.; Campos de Melo Iani, F.; de Carvalho Pereira, G.; Vazquez, C.; Mercedes Estigarribia Sanabria, G.; de Oliveira, E. C.; Demarchi, L.; Croda, J.; Dos Santos Bezerra, R.; Oliveira de Lima, L. P.; Martins, A. J.; Dos Santos Barros, C. R.; Marqueze, E. C.; de Souza Todao Bernardino, J.; Moretti, D. B.; Brassaloti, R. A.; de Lello Rocha Campos Cassano, R.; Drummond Sampaio Corrêa Mariani, P.; Kitajima, J. P.; Santos, B.; Proto-Siqueira, R.; Cantarelli, V. V.; Tosta, S.; Brandão Nardy, V.; Reboredo de Oliveira da Silva, L.; Astete Gómez, M. K.; Lima, J. G.; Ribeiro, A. A.; Guimarães, N. R.; Watanabe, L. T.; Barbosa Da Silva, L.; da Silva Ferreira, R.; MP, F. da Penha, Ortega, M. J.; Gómez de la Fuente, A.; Villalba, S.; Torales, J.; Gamarra, M. L.; Aquino, C.; Martínez Figueredo, G. P.; Fava, W. S.; Motta-Castro, A. R. C.; Venturini, J.; do Vale Leone de Oliveira, S. M.; Cavalheiro Maymone Gonçalves, C.; Debur Rossa, M. D. C.; Becker, G. N.; Presibella, M. M.; Marques, N. Q.; Riediger, I. N.; Raboni, S.; Coelho, G. M.; Cataneo, A. H. D.; Zanluca, C.; Dos Santos, C. N. D.; Assato, P. A.; Allan da Silva da Costa, F.; Poleti, M. D.; Chagas Lesbon, J. C.; Mattos, E. C.; Banho, C. A.; Sacchetto, L.; Moraes, M. M.; Tommasini Grotto, R. M.; Souza-Neto, J. A.; Nogueira, M. L.; Fukumasu, H.; Coutinho, L. L.; Calado, R. T.; Neto, R. M.; Bispo de Filippis, A. M.; Venancio da Cunha, R.; Freitas, C.; Leonel Peterka, C. R.; Rangel Fernandes, C. F.; de Araújo, W. N.; do Carmo Said, R. F.; Almiron, M.; Campelo de Albuquerque, E. Melo C. F.; Lourenço, J.; de Oliveira, T.; Holmes, E. C.; Haddad, R.; Sampaio, S. C.; Elias, M. C.; Kashima, S.; de Alcantara, L. C. J.; Covas, D. T..
PubMed; 2022.
Preprint in English | PubMed | ID: ppcovidwho-332259

ABSTRACT

Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

3.
34th IEEE International Symposium on Computer-Based Medical Systems, CBMS 2021 ; 2021-June:324-329, 2021.
Article in English | Scopus | ID: covidwho-1334347

ABSTRACT

This case study outlines the agile development of a web information system, called Leitos, to manage the ICU and semi-ICU beds assigned to COVID-19 patients. This system aims to aid the State Health Department of Rio Grande do Norte (SESAP/RN)'s actions in response to Brazil's coronavirus outbreak. The purpose of this study is threefold. First, we intend to present the methodology and strategies used to develop and implement the Leitos system. Second, we describe the adaptations we have made to the agile practices to cope with the urgency of pandemic times and the remote teams. Lastly, we present the main characteristics of the Leitos system. The case study describes a real scenario, where the SESAP/RN requested us to rapidly develop a technology to integrate ICU beds and patient data related explicitly to COVID-19 from 61 health units (hospitals and clinics) spread across the state. With a small remote team of volunteers, we heavily relied on the Agile Scrum Methodology, where the first sprint took only one week and covered approximately 70% of the system's requirements. By the end of October 2020, 215 government agents and clinical unit staff have used this system, which suggests the efforts described in this article were crucial to support SESAP/RN's decisions on public health during the earliest stages of coronavirus pandemic in Rio Grande do Norte. As the main contribution, this article provides valuable insights into the impact of COVID-19 outbreak and the remote work in real agile teams. © 2021 IEEE.

4.
2020 Ieee Symposium on Computers and Communications ; : 842-845, 2020.
Article in English | Web of Science | ID: covidwho-1271178

ABSTRACT

With the world pandemic generated by Covid-19, many places in the world are not able to rapidly measure the number of intensive care unit (ICU) beds existing and available in a city, state, or country. Knowing precisely the number of ICU beds in real-time is very important to estimate the health system collapse and to create strategies for the government to provide new ICU beds for patients. Thus, at Rio Grande do Norte, a state in Brazil, the State Health Department requested us to rapidly develop a technology to integrate ICU beds and patient data related explicitly to Covid-19 from the 58 health units (hospitals and clinics) in the state. Thus, this article presents the methodology and strategies used for the development and implementation of a web information system, called Leitos, for the management of ICU and semi-ICU beds assigned to Covid-19 patients. Nowadays, more than 200 government agents and clinical unit staff are using this system that presents the real-time situation of the ICU beds in this state.

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