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Jesus JGD, Sacchi C, Candido DDS, Claro IM, Sales FCS, Manuli ER, Silva DBBD, Paiva TMD, Pinho MAB, Santos KCDO, Hill SC, Aguiar RS, Romero F, Santos FCPD, Gonçalves CR, Timenetsky MDC, Quick J, Croda JHR, Oliveira WD, Rambaut A, Pybus OG, Loman NJ, Sabino EC, Faria NR. Importation and early local transmission of COVID-19 in Brazil, 2020. Rev Inst Med Trop Sao Paulo 2020; 62:e30. [PMID: 32401959 PMCID: PMC7232955 DOI: 10.1590/s1678-9946202062030] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 11/26/2022] Open
Abstract
We conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil.
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Affiliation(s)
- Jaqueline Goes de Jesus
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Claudio Sacchi
- Laboratório Estratégico, Instituto Adolfo Lutz, São Paulo, São Paulo, Brazil
| | | | - Ingra Morales Claro
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Erika Regina Manuli
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | - Filipe Romero
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro,, Brazil
| | | | | | | | - Joshua Quick
- University of Birmingham, Birmingham, United Kingdom
| | - Julio Henrique Rosa Croda
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil.,Universidade Federal da Grande Dourados, Laboratório de Pesquisa em Ciências da Saúde, Dourados, Mato Grosso do Sul, Brazil,Fundação Osvaldo Cruz Campo Grande, Mato Grosso do Sul, Brazil
| | - Wanderson de Oliveira
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Andrew Rambaut
- University of Edinburgh, Institute of Evolutionary Biology, Edinburgh, United Kingdom
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Nuno Rodrigues Faria
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Department of Zoology, University of Oxford, Oxford, United Kingdom.,Imperial College, School of Public Health, Department of Infectious Disease Epidemiology, London, United Kingdom
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Silva PE, Figueiredo CA, Luchs A, de Paiva TM, Pinho MAB, Paulino RS, da Silva DBB, de Oliveira Santos KC, Afonso AMS, de Oliveira MI. Human bocavirus in hospitalized children under 5 years with acute respiratory infection, São Paulo, Brazil, 2010. Arch Virol 2018; 163:1325-1330. [PMID: 29392492 PMCID: PMC7087275 DOI: 10.1007/s00705-017-3694-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/13/2017] [Indexed: 12/19/2022]
Abstract
The aims of this study were to investigate the human bocavirus (HBoV) frequency and genotypes in hospitalized children <5 years presenting acute respiratory infections (ARI) within the São Paulo metropolitan area. Nasopharyngeal samples from 300 patients, previously screened for common respiratory viruses, were tested by qPCR for the NSP1 and NP-1 genes. The VP1/2 gene in positive samples was then amplified by PCR and sequenced. A total of 49 positive HBoV cases (16.3%; mean Ct value of 34.41) were detected with the mean age being 18.1 months (range 1 month to 5 years) and the median age being 1 year of age. Children aged between 0 and 12 months had higher detection rates of HBoV (69.4%; 34/49; mean Ct = 34.45) than children from other age groups (30.6%; 15/49; mean Ct = 34.34). No significant differences were observed between HBoV Ct levels and clinical illness. The occurrence was more frequently associated with fall (38.8%; 19/49) and spring (36.7%; 18/49). All 12 sequenced isolates were identified as HBoV-1, displaying minor genetic variation compared to the Swedish reference strains ST1 and ST2 (99.1–99.7% nt). The sole identification of HBoV-1 supports the hypothesis that this particular genotype is strongly related to ARI, and contributes to the role of this virus in the aetiology of respiratory diseases.
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Affiliation(s)
- Patricia Evelin Silva
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Respiratórias, Av. Dr. Arnaldo, 355, São Paulo, CEP 01246-902, Brazil
| | - Cristina Adelaide Figueiredo
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Respiratórias, Av. Dr. Arnaldo, 355, São Paulo, CEP 01246-902, Brazil
| | - Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr. Arnaldo, 355, São Paulo, CEP 01246-902, Brazil
| | - Terezinha Maria de Paiva
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Respiratórias, Av. Dr. Arnaldo, 355, São Paulo, CEP 01246-902, Brazil
| | - Margarete Aparecida Benega Pinho
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Respiratórias, Av. Dr. Arnaldo, 355, São Paulo, CEP 01246-902, Brazil
| | - Renato Sousa Paulino
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Respiratórias, Av. Dr. Arnaldo, 355, São Paulo, CEP 01246-902, Brazil
| | | | - Katia Corrêa de Oliveira Santos
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Respiratórias, Av. Dr. Arnaldo, 355, São Paulo, CEP 01246-902, Brazil
| | - Ana Maria Sardinha Afonso
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Respiratórias, Av. Dr. Arnaldo, 355, São Paulo, CEP 01246-902, Brazil
| | - Maria Isabel de Oliveira
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Respiratórias, Av. Dr. Arnaldo, 355, São Paulo, CEP 01246-902, Brazil.
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Borborema SET, Silva DBBD, Silva KCO, Pinho MAB, Curti SP, Paiva TMD, Santos CLS. Molecular characterization of influenza B virus outbreak on a cruise ship in Brazil 2012. Rev Inst Med Trop Sao Paulo 2014; 56:185-9. [PMID: 24878994 PMCID: PMC4085868 DOI: 10.1590/s0036-46652014000300001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 10/08/2013] [Indexed: 11/22/2022] Open
Abstract
In February 2012, an outbreak of respiratory illness occurred on the
cruise ship MSC Armonia in Brazil. A 31-year-old female crew member was hospitalized
with respiratory failure and subsequently died. To study the etiology of the
respiratory illness, tissue taken at necropsy from the deceased woman and respiratory
specimens from thirteen passengers and crew members with respiratory symptoms were
analyzed. Influenza real-time RT-PCR assays were performed, and the full-length
hemagglutinin (HA) gene of influenza-positive samples was sequenced. Influenza B
virus was detected in samples from seven of the individuals, suggesting that it was
the cause of this respiratory illness outbreak. The sequence analysis of the HA gene
indicated that the virus was closely related to the B/Brisbane/60/2008-like virus,
Victoria lineage, a virus contained in the 2011-12 influenza vaccine for the Southern
Hemisphere. Since the recommended composition of the influenza vaccine for use during
the 2013 season changed, an intensive surveillance of viruses circulating worldwide
is crucial. Molecular analysis is an important tool to characterize the pathogen
responsible for an outbreak such as this. In addition, laboratory disease
surveillance contributes to the control measures for vaccine-preventable
influenza.
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Affiliation(s)
| | | | | | | | - Suely Pires Curti
- Respiratory Diseases Division, Virology Center, Adolfo Lutz Institute, Sao Paulo, SP, Brazil
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