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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.
J Hosp Infect ; 122: 187-193, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1652629

ABSTRACT

BACKGROUND: Healthcare-associated infections (HAIs) impact morbidity, mortality, and hospitalization costs. The contribution of viruses to the overall burden of HAIs is not well described. AIM: To evaluate the prevalence and clinical findings in patients with HAIs caused by respiratory viruses. METHODS: An observational, analytical, cross-sectional study was conducted to evaluate patients with a viral nosocomial respiratory infection, occurring between January 2013 and December 2019. Outcomes, comorbidities, cause of hospitalization, seasonality, and presence of bacterial co-infection were assessed. FINDINGS: In all, 161 cases of HAIs with community respiratory viruses (CRVs) were identified through six years; 76.4% of patients had a median age of 2.8 years (interquartile range: 0.28-15.4 years). The main comorbidities in immunosuppressed patients were haematologic neoplasia (46.5%), myelodysplastic syndrome (33.8%), and haematopoietic stem cell transplantation (18.3%). In non-immunosuppressed patients, the most prevalent comorbidities were prematurity (49.1%), respiratory tract diseases (21.0%), and congenital malformations (19.3%). The viruses detected were human rhinovirus (36.6%), respiratory syncytial virus (21.7%), and the parainfluenza group (18.6%). The fatality rate was low (4.6%), and a higher incidence of HAIs occurred in the CRV seasonality period in southern Brazil. CONCLUSION: CRV circulation in the hospital environment is frequent, and likely involves healthcare workers and visitors as well as patients. More guidance on preventive measures in healthcare settings is required. In addition, care teams should consider these aetiologic agents in the differential diagnosis of patients with nosocomial pneumonia, giving opportunities to limit antibiotic use.


Subject(s)
Cross Infection , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Viruses , Adolescent , Child , Child, Preschool , Cross Infection/complications , Cross Infection/epidemiology , Cross-Sectional Studies , Delivery of Health Care , Humans , Infant
4.
International Journal of Environmental Research & Public Health [Electronic Resource] ; 18(7):06, 2021.
Article in English | MEDLINE | ID: covidwho-1209042

ABSTRACT

SARS-CoV-2 environmental monitoring can track the rate of viral contamination and can be used to establish preventive measures. This study aimed to detect by RT-PCR the presence of SARS-CoV-2 from inert surface samples in public health settings with a literature review about surface contamination and its burden on spread virus. Samples were collected from health settings in Curitiba, Brazil, between July and December 2020. A literature review was conducted using PRISMA. A total of 711 environmental surface samples were collected from outpatient areas, dental units, doctors' offices, COVID-19 evaluation areas, and hospital units, of which 35 (4.9%) were positive for SARS-CoV-2 RNA. The frequency of environmental contamination was higher in primary care units than in hospital settings. The virus was detected on doctors' personal items. Remarkably, the previously disinfected dental chair samples tested positive. These findings agree with those of other studies in which SARS-CoV-2 was found on inanimate surfaces. Detection of SARS-CoV-2 RNA on surfaces in public health settings, including those not meant to treat COVID-19, indicates widespread environmental contamination. Therefore, the intensification of disinfection measures for external hospital areas may be important for controlling community COVID-19 dissemination.

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