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Filippi M, Demoliner M, Gularte JS, de Abreu Goes Pereira VM, da Silva MS, Girardi V, Hansen AW, Spilki FR. Relative frequency of genomic mutations in SARS-CoV-2 recovered from southern Brazilian cases of COVID-19 through the Gamma, Delta and Omicron waves. Infect Genet Evol 2024; 120:105590. [PMID: 38574833 DOI: 10.1016/j.meegid.2024.105590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/06/2024]
Abstract
The presence of different mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can be related to changes in coronavirus disease (COVID-19) infection. Besides, these viral alterations associated with factors such as massive number of positive cases, vaccination and reinfections can be important in the viral evolution process. As well as, mutations found at low frequencies may have a more neutral action and consequently be less inclined to negative selection, facilitating their spread through the population. Related to that, we aimed to present mutations that are possibly relevant in the process of viral evolution found in 115 SARS-CoV-2 sequences from samples of individuals residing in the metropolitan region of Porto Alegre in the state of Rio Grande do Sul, Brazil. The genome from clinical samples was sequenced using High-Throughput Sequencing (HTS) and analyzed using a workflow to map reads and find variations/SNPs. The samples were separated into 3 groups considering the sample lineage. Of the total number of analyzed sequences, 35 were from the Gamma lineage, 35 from Delta and 45 from Omicron. Amino acid changes present in frequencies lower than 80% of the reads in the sequences were evaluated. 11 common mutations among the samples were found in the Gamma lineage, 1 in the ORF1ab gene, 7 in the S gene, 2 in the ORF6 gene and 1 in the ORF7a gene. While in the Delta lineage, a total of 11 mutations distributed in the ORF1ab, S, ORF7a and N genes, 2, 7, 1 and 1 mutation were found in each gene, respectively. And finally, in the Omicron, 16 mutations were identified, 2 in the ORF1ab gene, 12 in the S gene and 2 in the M gene. In conclusion, we emphasize that genomic surveillance can be a useful tool to assess how mutations play a key role in virus adaptation, and its process of susceptibility to new hosts showing the possible signs of viral evolution.
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Affiliation(s)
- Micheli Filippi
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil.
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Viviane Girardi
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
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Rhoden J, Hoffmann AT, Stein JF, da Silva MS, Gularte JS, Filippi M, Demoliner M, Girardi V, Spilki FR, Fleck JD, Rigotto C. Diversity of Omicron sublineages and clinical characteristics in hospitalized patients in the southernmost state of Brazil. BMC Infect Dis 2024; 24:193. [PMID: 38350887 PMCID: PMC10863127 DOI: 10.1186/s12879-024-09089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 02/02/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Omicron has become the dominant variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since first reported in November 2021. From the initially detected Wuhan lineage, sublineages BA.2, BA.4, BA.5, BQ, XAG, and XBB have emerged over time and are dominant in many countries. Therefore, the aim is to evaluate which variants are circulating and the clinical characteristics of inpatients infected with the Omicron variant. METHODS This retrospective cohort study selected hospitalized patients admitted with respiratory symptoms to a hospital in the state of Rio Grande do Sul, Brazil, between June and July 2022. SARS-CoV-2 results were analyzed together with clinical outcomes and vaccination status. A viral genome library was prepared and forwarded to the Illumina MiSeq Platform for sequencing. RESULTS In total, 37 genomes were sequenced. Concerning the Omicron sublineages, our study detected: BA.1 (21 K), BA.2 (21 L), BA.4 (22A), BA.5 (22B), BA.2.12.1 (22C), BQ.1 (22E), XBB (22F), and XAG recombinant. Omicron BA.5 (30%), BA.2 (19%), and BQ.1 (19%) were the most frequent sublineages, respectively. In total, 38% of patients present hypertension, and the most common symptoms were coughing (62%). Analyzing the COVID-19 vaccination, 30% of patients were fully vaccinated, 49% had a partial vaccination status, and 21% were unvaccinated (no dose). CONCLUSIONS BA.5 was the most prevalent sublineage in our study and surpassed the predominance of BA.2, as reported by the national genomic surveillance program. BQ.1 was diagnosed earlier in this study than it was officially reported in the state. Current data have demonstrated that the Omicron variant causes less severe infections, with the high rate of transmissibility and mutational landscape causing the rapid emergence of new sublineages.
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Affiliation(s)
- Jaqueline Rhoden
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil.
- Santa Casa de Misericórdia de Porto Alegre, Hospital Dom Vicente Scherer, Centro Histórico. Av. Independência, n. 155, CEP 90035-074, Porto Alegre, Rio Grande do Sul, Brazil.
| | - Andressa Taíz Hoffmann
- Santa Casa de Misericórdia de Porto Alegre, Hospital Dom Vicente Scherer, Centro Histórico. Av. Independência, n. 155, CEP 90035-074, Porto Alegre, Rio Grande do Sul, Brazil
| | - Janaína Franciele Stein
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Viviane Girardi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Caroline Rigotto
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, n. 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, Rio Grande do Sul, Brazil
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Weber MN, da Silva MS. Corona- and Paramyxoviruses in Bats from Brazil: A Matter of Concern? Animals (Basel) 2023; 14:88. [PMID: 38200819 PMCID: PMC10778288 DOI: 10.3390/ani14010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Chiroptera are one of the most diverse mammal orders. They are considered reservoirs of main human pathogens, where coronaviruses (CoVs) and paramyxoviruses (PMVs) may be highlighted. Moreover, the growing number of publications on CoVs and PMVs in wildlife reinforces the scientific community's interest in eco-vigilance, especially because of the emergence of important human pathogens such as the SARS-CoV-2 and Nipha viruses. Considering that Brazil presents continental dimensions, is biologically rich containing one of the most diverse continental biotas and presents a rich biodiversity of animals classified in the order Chiroptera, the mapping of CoV and PMV genetics related to human pathogens is important and the aim of the present work. CoVs can be classified into four genera: Alphacoronavirus, Betacoronavirus, Deltacoronavirus and Gammacoronavirus. Delta- and gammacoronaviruses infect mainly birds, while alpha- and betacoronaviruses contain important animal and human pathogens. Almost 60% of alpha- and betacoronaviruses are related to bats, which are considered natural hosts of these viral genera members. The studies on CoV presence in bats from Brazil have mainly assayed phyllostomid, molossid and vespertilionid bats in the South, Southeast and North territories. Despite Brazil not hosting rhinophilid or pteropodid bats, which are natural reservoirs of SARS-related CoVs and henipaviruses, respectively, CoVs and PMVs reported in Brazilian bats are genetically closely related to some human pathogens. Most works performed with Brazilian bats reported alpha-CoVs that were closely related to other bat-CoVs, despite a few reports of beta-CoVs grouped in the Merbecovirus and Embecovirus subgenera. The family Paramyxoviridae includes four subfamilies (Avulavirinae, Metaparamyxovirinae, Orthoparamyxovirinae and Rubulavirinae), and bats are significant drivers of PMV cross-species viral transmission. Additionally, the studies that have evaluated PMV presence in Brazilian bats have mainly found sequences classified in the Jeilongvirus and Morbillivirus genera that belong to the Orthoparamyxovirinae subfamily. Despite the increasing amount of research on Brazilian bats, studies analyzing these samples are still scarce. When surveying the representativeness of the CoVs and PMVs found and the available genomic sequences, it can be perceived that there may be gaps in the knowledge. The continuous monitoring of viral sequences that are closely related to human pathogens may be helpful in mapping and predicting future hotspots in the emergence of zoonotic agents.
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Affiliation(s)
- Matheus Nunes Weber
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93525-075, RS, Brazil;
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Gularte JS, Sacchetto L, Demoliner M, Girardi V, da Silva MS, Filippi M, Pereira VMDAG, Hansen AW, da Silva LL, Fleck JD, de Almeida PR, Nogueira ML, Spilki FR. DENV-1 genotype V linked to the 2022 dengue epidemic in Southern Brazil. J Clin Virol 2023; 168:105599. [PMID: 37751628 DOI: 10.1016/j.jcv.2023.105599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/31/2023] [Accepted: 09/20/2023] [Indexed: 09/28/2023]
Abstract
Even though Brazil is a country where the dengue virus (DENV) is endemic, until recently, Southern states did not have significant viral circulation, such as Rio Grande do Sul (RS), and some municipalities were even considered dengue-free. During 2022, these places have shown a sharp increase in the incidence of the disease, apparently following a worldwide growth pattern. Therefore, in this study, we monitor and characterize the genetic diversity of DENV circulating in southern Brazil through next-generation sequencing during an outbreak in 2022. We generated 70 DENV-1 genome sequences, all characterized as genotype V, divided into two clade clusters in the L1 lineage. Furthermore, unique mutations have been described in each clade of L1 lineage. Our results are essential in managing outbreaks since these data provide important information during the emergence of DENV circulation in RS. Since the south of Brazil has a lower viral circulation when compared to other Brazilian states, RS still lacks data that can help in understanding the transmission, dissemination, and evolution of the dengue virus. Hence, genomic surveillance efforts are essential to increase the accuracy of preventive actions and to control viral dissemination.
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Affiliation(s)
- Juliana Schons Gularte
- Universidade Feevale, Laboratório de Microbiologia Molecular, Rodovia ERS-239, n° 2755, Vila Nova, CEP 93525-075, Novo Hamburgo, RS, Brazil.
| | - Lívia Sacchetto
- Faculdade de Medicina de São José do Rio Preto, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Laboratório de Pesquisas em Virologia. Avenida Brigadeiro Faria Lima, 5416, Vila São José, CEP 15090000, São José do Rio Preto, SP, Brazil
| | - Meriane Demoliner
- Universidade Feevale, Laboratório de Microbiologia Molecular, Rodovia ERS-239, n° 2755, Vila Nova, CEP 93525-075, Novo Hamburgo, RS, Brazil
| | - Viviane Girardi
- Universidade Feevale, Laboratório de Microbiologia Molecular, Rodovia ERS-239, n° 2755, Vila Nova, CEP 93525-075, Novo Hamburgo, RS, Brazil
| | - Mariana Soares da Silva
- Universidade Feevale, Laboratório de Microbiologia Molecular, Rodovia ERS-239, n° 2755, Vila Nova, CEP 93525-075, Novo Hamburgo, RS, Brazil
| | - Micheli Filippi
- Universidade Feevale, Laboratório de Microbiologia Molecular, Rodovia ERS-239, n° 2755, Vila Nova, CEP 93525-075, Novo Hamburgo, RS, Brazil
| | | | - Alana Witt Hansen
- Universidade Feevale, Laboratório de Microbiologia Molecular, Rodovia ERS-239, n° 2755, Vila Nova, CEP 93525-075, Novo Hamburgo, RS, Brazil
| | | | - Juliane Deise Fleck
- Universidade Feevale, Laboratório de Microbiologia Molecular, Rodovia ERS-239, n° 2755, Vila Nova, CEP 93525-075, Novo Hamburgo, RS, Brazil
| | - Paula Rodrigues de Almeida
- Universidade Feevale, Laboratório de Microbiologia Molecular, Rodovia ERS-239, n° 2755, Vila Nova, CEP 93525-075, Novo Hamburgo, RS, Brazil
| | - Maurício Lacerda Nogueira
- Faculdade de Medicina de São José do Rio Preto, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Laboratório de Pesquisas em Virologia. Avenida Brigadeiro Faria Lima, 5416, Vila São José, CEP 15090000, São José do Rio Preto, SP, Brazil; Department of Pathology, The University of Texas Medical Branch, Galveston, TX, United States of America
| | - Fernando Rosado Spilki
- Universidade Feevale, Laboratório de Microbiologia Molecular, Rodovia ERS-239, n° 2755, Vila Nova, CEP 93525-075, Novo Hamburgo, RS, Brazil
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Girardi V, Gularte JS, Demoliner M, da Silva MS, Filippi M, de Abreu Góes Pereira VM, Hansen AW, Rosa RB, Fleck JD, Spilki FR. Reinfection by SARS-CoV-2 by divergent Omicron sublineages, 16 days apart. Braz J Microbiol 2023; 54:1847-1851. [PMID: 37269428 PMCID: PMC10239041 DOI: 10.1007/s42770-023-01018-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/09/2023] [Indexed: 06/05/2023] Open
Abstract
Since the beginning of the SARS-CoV-2 pandemic, studies on the variants and sublineages stand out, mainly in the cases of reinfection in a short period. In this study, we describe a case of infection by BA.1.1 sublineage in an individual from Southern Brazil. The same patient acquired reinfection with sublineage BA.2 within 16 days after the first detection. The viral extraction and RT-qPCR were performed on the samples LMM72045 (collected in May 2022) and LMM72044 (collected in June 2022). After the confirmation of SARS-CoV-2 infection, we conducted the sequencing and viral genome analysis. This case of reinfection affected a 52-year-old male patient, without comorbidities, with three doses of vaccines against COVID-19, showing symptoms on May 19. These symptoms lasted for approximately six days. The patient returned to work activities on May 30. However, on June 4, the patient felt a new round of clinical signs that lasted for approximately seven days. Analysis of the viral genomes recovered from patients' clinical samples revealed that the two COVID-19 episodes were related to two divergent VOC Omicron sublineages, namely, BA.1.1 for the first round of symptoms and BA.2 for the second infection. Based on our findings, we can say that the present case of reinfection is the shortest described so far.
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Affiliation(s)
- Viviane Girardi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil.
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Vyctoria Malayhka de Abreu Góes Pereira
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Raquel Borba Rosa
- Secretaria Municipal de Saúde, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, N° 2755, Prédio Vermelho, Piso 1, Sala 103, Vila Nova, CEP, Novo Hamburgo, RS, 93525-075, Brazil
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Gregianini TS, Salvato RS, Barcellos RB, Godinho FM, Ruivo AP, de Melo VH, Schroder JA, Martiny FL, Möllmann EB, Favreto C, Baethgen LF, Ferreira VP, de Lima LE, Piazza CF, Machado TRM, Becker IM, Ramos RR, Frölich GC, Rossetti AF, Almeida LDC, Rodrigues TMA, Bragança IT, Campos AAS, Manzoni VB, Machado LC, da Silva LMI, de Oliveira ALS, Paiva MHS, Nunes ZMA, de Almeida PR, Demoliner M, Gularte JS, da Silva MS, Filippi M, Pereira VMDAG, Spilki FR, da Veiga ABG, Wallau GL. Chikungunya virus infection in the southernmost state of Brazil was characterised by self-limited transmission (2017-2019) and a larger 2021 outbreak. Mem Inst Oswaldo Cruz 2023; 118:e220259. [PMID: 37531506 PMCID: PMC10392894 DOI: 10.1590/0074-02760220259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Chikungunya is a mosquito-borne virus that has been causing large outbreaks in the Americas since 2014. In Brazil, Asian-Caribbean (AC) and East-Central-South-African (ECSA) genotypes have been detected and lead to large outbreaks in several Brazilian states. In Rio Grande do Sul (RS), the southernmost state of Brazil, the first cases were reported in 2016. OBJECTIVES AND METHODS We employed genome sequencing and epidemiological investigation to characterise the Chikungunya fever (CHIKF) burden in RS between 2017-2021. FINDINGS We detected an increasing CHIKF burden linked to travel associated introductions and communitary transmission of distinct lineages of the ECSA genotype during this period. MAIN CONCLUSIONS Until 2020, CHIKV introductions were most travel associated and transmission was limited. Then, in 2021, the largest outbreak occurred in the state associated with the introduction of a new ECSA lineage. CHIKV outbreaks are likely to occur in the near future due to abundant competent vectors and a susceptible population, exposing more than 11 million inhabitants to an increasing infection risk.
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Affiliation(s)
- Tatiana Schäffer Gregianini
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Richard Steiner Salvato
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Regina Bones Barcellos
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Fernanda Marques Godinho
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Amanda Pellenz Ruivo
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Viviane Horn de Melo
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Júlio Augusto Schroder
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Fernanda Letícia Martiny
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Erica Bortoli Möllmann
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Cátia Favreto
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Divisão de Vigilância Epidemiológica, Porto Alegre, RS, Brasil
| | - Ludmila Fiorenzano Baethgen
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Vithoria Pompermaier Ferreira
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Lívia Eidt de Lima
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Cláudia Fasolo Piazza
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Taís Raquel Marcon Machado
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Irina Marieta Becker
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Raquel Rocha Ramos
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Guilherme Carey Frölich
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Alana Fraga Rossetti
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Lucas da Cunha Almeida
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Tahiana Machado Antunes Rodrigues
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Isabella Tabelli Bragança
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Aline Alves Scarpellini Campos
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Divisão de Vigilância Ambiental, Porto Alegre, RS, Brasil
| | - Verônica Baú Manzoni
- Prefeitura de São Nicolau, Secretaria Municipal de Saúde, São Nicolau, RS, Brasil
| | - Lais Ceschini Machado
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Entomologia e Núcleo de Bioinformática, Recife, PE, Brasil
| | - Luisa Maria Inácio da Silva
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Entomologia e Núcleo de Bioinformática, Recife, PE, Brasil
| | - André Luiz Sá de Oliveira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Núcleo de Estatística e Geoprocessamento, Recife, PE, Brasil
| | - Marcelo Henrique Santos Paiva
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Entomologia e Núcleo de Bioinformática, Recife, PE, Brasil
| | - Zenaida Marion Alves Nunes
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | | | - Meriane Demoliner
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, RS, Brasil
| | | | | | - Micheli Filippi
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, RS, Brasil
| | | | | | | | - Gabriel Luz Wallau
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Entomologia e Núcleo de Bioinformática, Recife, PE, Brasil
- National Reference Centre for Tropical Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Department of Arbovirology, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany
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7
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Filippi M, Ribeiro Amorim M, Soares da Silva M, Schons Gularte J, Demoliner M, Girardi V, de Abreu Goes Pereira VM, Witt Hansen A, Fleck JD, Frohlich J, de-Paris F, Motta Rodrigues G, Aparecida Risczik Arruda Correa J, Machado Arlindo De Mattos E, Minuto Paiva R, Deutschendorf C, Soares Falcetta F, Proença Modena JL, Rosado Spilki F. Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child. Pediatr Infect Dis J 2023; 42:212-217. [PMID: 36728777 PMCID: PMC9935232 DOI: 10.1097/inf.0000000000003782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/30/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND With the progression of the Coronavirus disease pandemic, the number of mutations in the viral genome has increased, showing the adaptive evolution of severe acute respiratory syndrome coronavirus 2 in humans and intensification in transmissibility. Long-term infections also allow the development of viral diversity. In this study, we report the case of a child with severe combined immu presenting a prolonged severe acute respiratory syndrome coronavirus 2 infection. We aimed to analyze 3 naso-oropharyngeal swab samples collected between August and December 2021 to describe the amino acid changes present in the sequence reads that may have a role in the emergence of new viral variants. METHODS The whole genome from clinical samples was sequenced through high throughput sequencing and analyzed using a workflow to map reads and then find variations/single-nucleotide polymorphisms. In addition, the samples were isolated in cell culture, and a plaque forming units assay was performed, which indicates the presence of viable viral particles. RESULTS The results obtained showed that the virus present in all samples is infectious. Also, there were 20 common mutations among the 3 sequence reads, found in the ORF1ab and ORF10 proteins. As well, a considerable number of uncommon mutations were found. CONCLUSIONS In conclusion, we emphasize that genomic surveillance can be a useful tool to assess possible evolution signals in long-term patients.
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Affiliation(s)
- Micheli Filippi
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Mariene Ribeiro Amorim
- Laboratório de Vírus Emergentes, Departamento de Genética, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Mariana Soares da Silva
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Meriane Demoliner
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Viviane Girardi
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | - Alana Witt Hansen
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliane Deise. Fleck
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Júlia Frohlich
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernanda de-Paris
- Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | | | | | | | | | - José Luiz Proença Modena
- Laboratório de Vírus Emergentes, Departamento de Genética, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Fernando Rosado Spilki
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
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8
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Hoffmann AT, da Silva MS, Gularte JS, Pasqualotto AC, Proença Módena JL, Hansen AW, Stadñik CMB, Sukienik TCT, Demoliner M, Heldt FH, Filippi M, Pereira VMDAG, de Marques CG, Kohler II, Quevedo DMD, Spilki FR. Dynamics of nosocomial SARS-CoV-2 transmissions: Facing the challenge of variants of concern in a Brazilian reference hospital. J Med Virol 2023; 95:e28446. [PMID: 36579775 PMCID: PMC9880750 DOI: 10.1002/jmv.28446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/12/2022] [Accepted: 12/18/2022] [Indexed: 12/30/2022]
Abstract
The hospital environment can be considered a high risk for the occurrence of SARS-CoV-2 transmission outbreaks, either for health professionals who are directly involved in the care of suspected or confirmed cases of the disease, or for patients, for being in an environment more vulnerable to the acquisition of nosocomial infections. In this molecular epidemiology study, we aimed to analyze the occurrence and transmission dynamics of SARS-CoV-2 in outbreaks and local chains of transmission in a large tertiary teaching hospital in southern Brazil, in addition to verifying circulating strains and their epidemiological relation in the local context, from September 21, 2020 to October 5, 2021. Positive samples involved in COVID-19 clusters or outbreaks were analyzed using clinical, epidemiological and genomic data. Different lineages and sublineages among patients in the same room were observed. Most patients had their first clinical manifestation, evidence of suspicion, and diagnostic confirmation within 7-14 days or >14 days after hospital admission. The patients who have contact with confirmed cases of COVID-19 spent, on average, 6.28 days in the same environment until the positive test. There was a significant association between the outcome and the number of vaccine doses (p < 0.05), where those who received two doses presented a lower occurrence of death. There was a total replacement of variant of concern (VOC) Gamma by VOC Delta from August 2021 at the study site. Although the epidemiological analysis indicates nosocomial infections, through genomic sequencing, it was established that most of the hospital outbreaks had different origins. These findings highlight the utility of integrating epidemiological and genomic data to identify possible routes of viral entry and dissemination.
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Affiliation(s)
- Andressa Taíz Hoffmann
- Controle de Infecção HospitalarSanta Casa de Misericórdia de Porto AlegrePorto AlegreRio Grande do SulBrazil
| | - Mariana Soares da Silva
- Laboratório de Microbiologia MolecularUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | - Juliana Schons Gularte
- Laboratório de Microbiologia MolecularUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | | | | | - Alana Witt Hansen
- Laboratório de Microbiologia MolecularUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | | | | | - Meriane Demoliner
- Laboratório de Microbiologia MolecularUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | - Fágner Henrique Heldt
- Laboratório de Microbiologia MolecularUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | - Micheli Filippi
- Laboratório de Microbiologia MolecularUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
| | | | | | - Ionara Ines Kohler
- Laboratório de Análises ClínicasSanta Casa de Misericórdia de Porto AlegrePorto AlegreBrazil
| | | | - Fernando Rosado Spilki
- Laboratório de Microbiologia MolecularUniversidade FeevaleNovo HamburgoRio Grande do SulBrazil
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9
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Demoliner M, Filippi M, Gularte JS, da Silva MS, de Almeida PR, Pereira VMDAG, Heldt FH, Spilki FR. Genome of a husavirus from Southern Brazil. Rev Inst Med Trop Sao Paulo 2023; 65:e5. [PMID: 36651466 PMCID: PMC9870242 DOI: 10.1590/s1678-9946202365005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/05/2022] [Accepted: 11/21/2022] [Indexed: 01/18/2023] Open
Abstract
New viruses of the Picornavirales order have been discovered with the increase in the number of sequences obtained by high-throughput sequencing, as well as human stool-associated RNA virus (husavirus [HuV]), found in human stool samples. However, there is much to be clarified about HuV. Its cellular host, evolutionary history, and other biological characteristics are still unknown. Therefore, samples collected from human beings and environmental samples in a watershed in Southern Brazil were processed for the metagenomic library. Upon metagenomic analysis, we identified a HuV (husavirus LMM_67754 OP019707) genome with 8,846 bp, which was reported for the first time in Southern Brazil. The new genome presents only 37% of nucleotide identity with Brazilian strains and more than 90% with genomes from China, Vietnam, Venezuela, and the Netherlands. The HuV phylogeny presents significant differences among genomes, probably because multiple introductions of the virus may have occurred. Many questions still need to be answered about HuV. Therefore, more sequences and studies on this virus are necessary to improve the comprehension of the unknown origin of Picornavirales.
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Affiliation(s)
- Meriane Demoliner
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Micheli Filippi
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Mariana Soares da Silva
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | | | - Fágner Henrique Heldt
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernando Rosado Spilki
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
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10
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Molossi FA, de Cecco BS, de Almeida BA, Henker LC, da Silva MS, Mósena ACS, Canal CW, Brandalise L, Simão GMR, Vanucci F, Pavarini SP, Driemeier D. PCV3-associated reproductive failure in pig herds in Brazil. Trop Anim Health Prod 2022; 54:293. [PMID: 36097231 DOI: 10.1007/s11250-022-03282-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/31/2022] [Indexed: 11/24/2022]
Abstract
Porcine circovirus type 3 (PCV3) has been widely detected worldwide in healthy and sick pigs. Recently its association with clinical disease and reproductive failure has been proven through the detection of intralesional viral mRNA in affected pigs. This study aims to describe the occurrence of PCV3-associated reproductive failure (abortions) in sow herds in southern Brazil. Eleven fetuses from five different litters from two herds were analyzed. These herds reported an increase in the rate of late-gestation abortions, stillbirths, and the percentage of mummified piglets. At gross examination, six of the fetuses had large caudally rotated ears and one fetus was mummified. Microscopically, multisystemic vasculitis, lymphocytic interstitial pneumonia, myocarditis, and encephalitis were observed. These six fetuses with gross and histological lesions were positive in qPCR analysis for PCV3, and PCV3 transcription was shown through in situ hybridization (ISH-RNA) within the histologic lesions. Samples from all 11 fetuses tested negative in PCR exam for Porcine Circovirus type 1 and 2, Porcine Reproductive and Respiratory Syndrome, Porcine Parvovirus, and Atypical Porcine Pestivirus. Furthermore, based on the ORF2 analysis, the PCV3a clade was identified. This is the first report of PCV3a-associated reproductive failure in pig herds in South America.
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Affiliation(s)
- Franciéli Adriane Molossi
- Setor de Patologia Veterinária, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil.
| | - Bianca Santana de Cecco
- Setor de Patologia Veterinária, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Bruno Albuquerque de Almeida
- Setor de Patologia Veterinária, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Luan Cleber Henker
- Setor de Patologia Veterinária, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Mariana Soares da Silva
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Ana Cristina Sbaraini Mósena
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Cláudio Wageck Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | | | | | - Fabio Vanucci
- University of Minnesota Veterinary Diagnostic Laboratory, St. Paul, MN, USA
| | - Saulo P Pavarini
- Setor de Patologia Veterinária, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - David Driemeier
- Setor de Patologia Veterinária, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
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11
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Alves RS, do Canto Olegário J, Weber MN, da Silva MS, Canova R, Sauthier JT, Baumbach LF, Witt AA, Varela APM, Mayer FQ, da Fontoura Budaszewski R, Canal CW. Detection of coronavirus in vampire bats (Desmodus rotundus) in southern Brazil. Transbound Emerg Dis 2022; 69. [PMID: 33977671 PMCID: PMC8242716 DOI: 10.1111/tbed.14150+10.1111/tbed.14150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The vampire bat (Desmodus rotundus) is a haematophagous animal that feeds exclusively on the blood of domestic mammals. Vampire bat feeding habits enable their contact with mammalian hosts and may enhance zoonotic spillover. Moreover, they may carry several pathogenic organisms, including coronaviruses (CoVs), for which they are important hosts. The human pathogens that cause severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV) and possibly coronavirus disease 2019 (SARS-CoV-2) all originated in bats but required bridge hosts to spread into human populations. To monitor the presence of potential zoonotic viruses in bats, the present work evaluated the presence of CoVs in vampire bats from southern Brazil. A total of 101 vampire bats were captured and euthanized between 2017 and 2019 in Rio Grande do Sul state, southern Brazil. The brain, heart, liver, lungs, kidneys and intestines were collected and macerated individually. The samples were pooled and submitted to high-throughput sequencing (HTS) using the Illumina MiSeq platform and subsequently individually screened using a pancoronavirus RT-PCR protocol. We detected CoV-related sequences in HTS, but only two (2/101; 1.98%) animals had CoV detected in the intestines by RT-PCR. Partial sequences of RdRp and spike genes were obtained in the same sample and the RdRp region in the other sample. The sequences were classified as belonging to Alphacoronavirus. The sequences were closely related to alphacoronaviruses detected in vampire bats from Peru. The continuous monitoring of bat CoVs may help to map and predict putative future zoonotic agents with great impacts on human health.
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Affiliation(s)
- Raquel Silva Alves
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Juliana do Canto Olegário
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia MolecularInstituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoBrazil
| | - Mariana Soares da Silva
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Raissa Canova
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Jéssica Tatiane Sauthier
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Letícia Ferreira Baumbach
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - André Alberto Witt
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
- Secretaria Estadual de AgriculturaPecuária e Desenvolvimento Rural (SEAPDR)Rio Grande do Sul Rio Grande do SulBrazil
| | - Ana Paula Muterle Varela
- Centro de Pesquisa em Saúde AnimalInstituto de Pesquisas Veterinárias Desidério Finamor (IPVDF)Departamento de Diagnóstico e Pesquisa Agropecuária (DDPA)Secretaria da AgriculturaPecuária e Desenvolvimento Rural (SEAPDR)Rio Grande do SulBrazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde AnimalInstituto de Pesquisas Veterinárias Desidério Finamor (IPVDF)Departamento de Diagnóstico e Pesquisa Agropecuária (DDPA)Secretaria da AgriculturaPecuária e Desenvolvimento Rural (SEAPDR)Rio Grande do SulBrazil
| | | | - Cláudio Wageck Canal
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
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12
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Gularte JS, da Silva MS, Filippi M, Demoliner M, Schallenberger K, Hansen AW, de Abreu Góes Pereira VM, Heldt FH, Girardi V, Weber MN, de Almeida PR, Abbadi BL, Dornelles M, Bizarro CV, Machado P, Basso LA, Dellagostin OA, Fleck JD, Spilki FR. Viral isolation allows characterization of early samples of SARS-CoV-2 lineage B1.1.33 with unique mutations (S: H655Y and T63N) circulating in Southern Brazil in 2020. Braz J Microbiol 2022; 53:1313-1319. [PMID: 35778549 PMCID: PMC9428868 DOI: 10.1007/s42770-022-00789-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/06/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Abstract
Different approaches are in use to improve our knowledge about the causative agent of coronavirus disease (COVID-19). Cell culture-based methods are the better way to perform viral isolation, evaluate viral infectivity, and amplify the virus. Furthermore, next-generation sequencing (NGS) have been essential to analyze a complete genome and to describe new viral species and lineages that have arisen over time. Four naso-oropharyngeal swab samples, collected from April to July of 2020, were isolated and sequenced aiming to produce viral stocks and analyze the mutational profile of the found lineage. B.1.1.33 was the lineage detected in all sequences. Although the samples belong to the same lineage, it was possible to evaluate different mutations found including some that were first described in these sequences, like the S:H655Y and T63N. The results described here can help to elicit how the pandemic started to spread and how it has been evolving in south Brazil.
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Affiliation(s)
- Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil.
| | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
| | - Karoline Schallenberger
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
| | | | - Fágner Henrique Heldt
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
| | - Viviane Girardi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
| | - Paula Rodrigues de Almeida
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
| | - Bruno Lopes Abbadi
- Centro de Pesquisas Em Biologia Molecular E Funcional (CPBMF), Pontifícia Universidade Católica Do Rio Grande Do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre, RS, CEP 90619900, Brazil
| | - Maiele Dornelles
- Centro de Pesquisas Em Biologia Molecular E Funcional (CPBMF), Pontifícia Universidade Católica Do Rio Grande Do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre, RS, CEP 90619900, Brazil
| | - Cristiano Valim Bizarro
- Centro de Pesquisas Em Biologia Molecular E Funcional (CPBMF), Pontifícia Universidade Católica Do Rio Grande Do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre, RS, CEP 90619900, Brazil
| | - Pablo Machado
- Centro de Pesquisas Em Biologia Molecular E Funcional (CPBMF), Pontifícia Universidade Católica Do Rio Grande Do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre, RS, CEP 90619900, Brazil
| | - Luiz Augusto Basso
- Centro de Pesquisas Em Biologia Molecular E Funcional (CPBMF), Pontifícia Universidade Católica Do Rio Grande Do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre, RS, CEP 90619900, Brazil
| | - Odir Antonio Dellagostin
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Campus Universitário, Pelotas, RS, CEP 96010-900, Brazil
| | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, nº 2755, Vila Nova, Novo Hamburgo, RS, CEP 93525-075, Brazil
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13
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Alves RS, do Canto Olegário J, Weber MN, da Silva MS, Canova R, Sauthier JT, Baumbach LF, Witt AA, Varela APM, Mayer FQ, da Fontoura Budaszewski R, Canal CW. Detection of coronavirus in vampire bats (Desmodus rotundus) in southern Brazil. Transbound Emerg Dis 2022; 69. [PMID: 33977671 PMCID: PMC8242716 DOI: 10.1111/tbed.14150 10.1111/tbed.14150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The vampire bat (Desmodus rotundus) is a haematophagous animal that feeds exclusively on the blood of domestic mammals. Vampire bat feeding habits enable their contact with mammalian hosts and may enhance zoonotic spillover. Moreover, they may carry several pathogenic organisms, including coronaviruses (CoVs), for which they are important hosts. The human pathogens that cause severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV) and possibly coronavirus disease 2019 (SARS-CoV-2) all originated in bats but required bridge hosts to spread into human populations. To monitor the presence of potential zoonotic viruses in bats, the present work evaluated the presence of CoVs in vampire bats from southern Brazil. A total of 101 vampire bats were captured and euthanized between 2017 and 2019 in Rio Grande do Sul state, southern Brazil. The brain, heart, liver, lungs, kidneys and intestines were collected and macerated individually. The samples were pooled and submitted to high-throughput sequencing (HTS) using the Illumina MiSeq platform and subsequently individually screened using a pancoronavirus RT-PCR protocol. We detected CoV-related sequences in HTS, but only two (2/101; 1.98%) animals had CoV detected in the intestines by RT-PCR. Partial sequences of RdRp and spike genes were obtained in the same sample and the RdRp region in the other sample. The sequences were classified as belonging to Alphacoronavirus. The sequences were closely related to alphacoronaviruses detected in vampire bats from Peru. The continuous monitoring of bat CoVs may help to map and predict putative future zoonotic agents with great impacts on human health.
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Affiliation(s)
- Raquel Silva Alves
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Juliana do Canto Olegário
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia MolecularInstituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoBrazil
| | - Mariana Soares da Silva
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Raissa Canova
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Jéssica Tatiane Sauthier
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Letícia Ferreira Baumbach
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - André Alberto Witt
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil,Secretaria Estadual de AgriculturaPecuária e Desenvolvimento Rural (SEAPDR)Rio Grande do Sul Rio Grande do SulBrazil
| | - Ana Paula Muterle Varela
- Centro de Pesquisa em Saúde AnimalInstituto de Pesquisas Veterinárias Desidério Finamor (IPVDF)Departamento de Diagnóstico e Pesquisa Agropecuária (DDPA)Secretaria da AgriculturaPecuária e Desenvolvimento Rural (SEAPDR)Rio Grande do SulBrazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde AnimalInstituto de Pesquisas Veterinárias Desidério Finamor (IPVDF)Departamento de Diagnóstico e Pesquisa Agropecuária (DDPA)Secretaria da AgriculturaPecuária e Desenvolvimento Rural (SEAPDR)Rio Grande do SulBrazil
| | | | - Cláudio Wageck Canal
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
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14
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Witt AA, Alves RS, do Canto Olegário J, de Camargo LJ, Weber MN, da Silva MS, Canova R, Mosena ACS, Cibulski SP, Varela APM, Mayer FQ, Canal CW, da Fontoura Budaszewski R. The virome of the white-winged vampire bat Diaemus youngi is rich in circular DNA viruses. Virus Genes 2022; 58:214-226. [PMID: 35366197 PMCID: PMC8976263 DOI: 10.1007/s11262-022-01897-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/25/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022]
Abstract
In the Neotropical region, the white-winged vampire bat (Diaemus youngi) is the rarest of the three species of vampire bats. This bat species feeds preferentially on bird blood, and there is limited information on the viruses infecting D. youngi. Hence, this study aimed to expand the knowledge about the viral diversity associated with D. youngi by sampling and pooling the lungs, liver, kidneys, heart, and intestines of all animals using high-throughput sequencing (HTS) on the Illumina MiSeq platform. A total of three complete and 10 nearly complete circular virus genomes were closely related to gemykrogvirus (Genomoviridae family), smacovirus (Smacoviridae family), and torque teno viruses (TTVs) (Anelloviridae family). In addition, three sequences of bat paramyxovirus were detected and found to be closely related to viruses reported in Pomona roundleaf bats and rodents. The present study provides a snapshot of the viral diversity associated with white-winged vampire bats and provides a baseline for comparison to viruses detected in future outbreaks.
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Affiliation(s)
- André Alberto Witt
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.,Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Porto Alegre, Rio Grande do Sul, Brazil
| | - Raquel Silva Alves
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Juliana do Canto Olegário
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Laura Junqueira de Camargo
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Mariana Soares da Silva
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.,Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Raíssa Canova
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Cristina Sbaraini Mosena
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Samuel Paulo Cibulski
- Centro de Biotecnologia (Cbiotec), Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Ana Paula Muterle Varela
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Eldorado Do Sul, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Eldorado Do Sul, Rio Grande do Sul, Brazil
| | - Cláudio Wageck Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Renata da Fontoura Budaszewski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
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15
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Sartor ITS, Varela FH, Meireles MR, Kern LB, Azevedo TR, Giannini GLT, da Silva MS, Demoliner M, Gularte JS, de Almeida PR, Fleck JD, Zavaglia GO, Fernandes IR, de David CN, Santos AP, de Almeida WAF, Porto VBG, Scotta MC, Vieira GF, Spilki FR, Stein RT, Polese-Bonatto M. Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Diagn Microbiol Infect Dis 2022; 102:115636. [PMID: 35219552 PMCID: PMC8761118 DOI: 10.1016/j.diagmicrobio.2022.115636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/14/2021] [Accepted: 01/09/2022] [Indexed: 11/30/2022]
Abstract
We aimed to describe the SARS-CoV-2 lineages circulating early pandemic among samples with S gene dropout and characterize the receptor-binding domain (RBD) of viral spike protein. Adults and children older than 2 months with signs and symptoms of COVID-19 were prospectively enrolled from May to October in Porto Alegre, Brazil. All participants performed RT-PCR assay, and samples with S gene dropout and cycle threshold < 30 were submitted to high-throughput sequencing (HTS). 484 out of 1,557 participants tested positive for SARS-CoV-2. The S gene dropout was detected in 7.4% (36/484) and a peak was observed in August. The B.1.1.28, B.1.91 and B.1.1.33 lineages were circulating in early pandemic. The RBD novel mutation (Y380Q) was found in one sample occurring simultaneously with C379W and V395A, and the B.1.91 lineage in the spike protein. The Y380Q and C379W may interfere with the binding of neutralizing antibodies (CR3022, EY6A, H014, S304).
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Affiliation(s)
| | - Fernanda Hammes Varela
- Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.
| | - Mariana Rost Meireles
- Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | | | | | - Meriane Demoliner
- Laboratory of Molecular Microbiology, Universidade FEEVALE, Novo Hamburgo, Brazil
| | | | | | - Juliane Deise Fleck
- Laboratory of Molecular Microbiology, Universidade FEEVALE, Novo Hamburgo, Brazil
| | | | | | | | - Amanda Paz Santos
- Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil
| | | | | | - Marcelo Comerlato Scotta
- Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Gustavo Fioravanti Vieira
- Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Post-Graduation Program in Health and Human Development, Universidade La Salle, Canoas, Brazil
| | | | - Renato T Stein
- Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
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16
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Demoliner M, da Silva MS, Gularte JS, Hansen AW, de Almeida PR, Weber MN, Heldt FH, Silveira F, Filippi M, de Abreu Góes Pereira VM, da Silva FP, Mallmann L, Fink P, de Moura Valim AR, Possuelo LG, Fleck JD, Spilki FR. Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. Infect Genet Evol 2021; 96:105134. [PMID: 34763050 PMCID: PMC8575543 DOI: 10.1016/j.meegid.2021.105134] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022]
Abstract
Recently, the highest wave of SARS-CoV-2 epidemic occurred since the beginning of the pandemic in Brazil was registered in Rio Grande do Sul (RS) State, Southern Brazil, considering the number of cases, deaths and hospitalization per day caused by COVID-19. In this study we described which lineages were circulating in the first quarter of 2021 in Southern Brazil to better understand the viral factors involved in the health crisis caused by SARS-CoV-2 in the region, searching also for possible additional SARS-CoV-2 sequence mutations. A total of 70 positive SARS-CoV-2 samples collected between January 28th, 2021 until April 23rd, 2021, were selected to sequencing. Whole genome sequencing of 70 SARS-CoV-2 samples showed a predominance of Gamma lineage (67%, 47/70), followed by P.2 lineage (27%, 19/70) and B.1.1.28 (6%, 4/70). Two Gamma lineage consensus sequences presented a new S:D614A mutation. Newly mutations could be emerging due the quick SARS-CoV-2 spreading. Thus, the greater understanding about immune protection and variants vigilance is essential to the better management of the health SARS-CoV-2 crisis.
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Affiliation(s)
- Meriane Demoliner
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil.
| | - Mariana Soares da Silva
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Alana Witt Hansen
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | - Matheus Nunes Weber
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fágner Henrique Heldt
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Flávio Silveira
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Micheli Filippi
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | - Francini Pereira da Silva
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Larissa Mallmann
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Pietra Fink
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | | | - Juliane Deise Fleck
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernando Rosado Spilki
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
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17
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Gularte JS, da Silva MS, Demoliner M, Hansen AW, Heldt FH, Silveira F, Filippi M, Pereira VMDAG, da Silva FP, Mallmann L, Fink P, Laux JL, Weber MN, de Almeida PR, Fleck JD, Spilki FR. Reinfection cases by closely related SARS-CoV-2 lineages in Southern Brazil. Braz J Microbiol 2021; 52:1881-1885. [PMID: 34562232 PMCID: PMC8475897 DOI: 10.1007/s42770-021-00621-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/19/2021] [Indexed: 11/25/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic that started in late 2019 and still affects people's lives all over the world. Lack of protective immunity after primary infection has been involved with reported reinfection cases by SARS-CoV-2. In this study, we described two cases of reinfection caused by non-VOC (Variants of Concern) strains in southern Brazil, being one patient a healthcare worker. The four samples previously positive for SARS-CoV-2 by real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) were sequenced by a high-performance platform and the genomic analysis confirmed that lineages responsible for infections were B.1.91 and B.1.1.33 (patient 1), and B.1.1.33 and B.1.1.28 (patient 2). The interval between the two positive RT-qPCR for patients 1 and 2 was 45 and 61 days, respectively. This data shows that patients may be reinfected even by very closely related SARS-CoV-2 lineages.
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Affiliation(s)
- Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil.
| | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Fágner Henrique Heldt
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Flávio Silveira
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Vyctoria Malayhka de Abreu Góes Pereira
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Francini Pereira da Silva
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Larissa Mallmann
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Pietra Fink
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Jéssica Luísa Laux
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Paula Rodrigues de Almeida
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93525-075, Brazil
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18
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da Silva MS, Demoliner M, Hansen AW, Gularte JS, Silveira F, Heldt FH, Filippi M, Pereira VMDAG, da Silva FP, Mallmann L, Fink P, da Silva LL, Weber MN, de Almeida PR, Fleck JD, Spilki FR. Early detection of SARS-CoV-2 P.1 variant in Southern Brazil and reinfection of the same patient by P.2. Rev Inst Med Trop Sao Paulo 2021; 63:e58. [PMID: 34231823 PMCID: PMC8266303 DOI: 10.1590/s1678-9946202163058] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 01/16/2023] Open
Abstract
Multiple variants of the Severe Acute Respiratory Syndrome coronavirus 2 virus (SARS-CoV-2) have been constantly reported across the world. The B.1.1.28 lineage has been evolving in Brazil since February 2020 and originated the P.1 variant of concern (VOC), recently named as the Gamma variant by the newly WHO nomenclature proposal, and P.2 as a variant of interest (VOI). Here we describe an early case of P.1 primary infection in Southern Brazil in late November 2020, soon after the emergence of the variant in Manaus, Northern Brazil. The same male patient was reinfected by another B.1.1.28 variant, namely P.2, in March, 2021. The genomic analysis confirmed genetically significant differences between the two viruses recovered in both infections, the P.1 lineage in the first episode and P.2 in the reinfection. Due the very early detection of P.1, we have also investigated the circulation of P.1 in the same region by differential RT-qPCR, showing that this was an isolated case of P.1 at the time of detection, and this variant has disseminated and became prominent from late January to the end of March, 2021. SARS-CoV-2 recent reports of reinfection have raised critical questions on whether and how well a first infection protects against reinfection.
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Affiliation(s)
- Mariana Soares da Silva
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | - Meriane Demoliner
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | - Alana Witt Hansen
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | - Flávio Silveira
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | - Fágner Henrique Heldt
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | - Micheli Filippi
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | | | - Francini Pereira da Silva
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | - Larissa Mallmann
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | - Pietra Fink
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | | | - Matheus Nunes Weber
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | | | - Juliane Deise Fleck
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
| | - Fernando Rosado Spilki
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo
Hamburgo, Rio Grande do Sul, Brazil
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19
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Alves RS, do Canto Olegário J, Weber MN, da Silva MS, Canova R, Sauthier JT, Baumbach LF, Witt AA, Varela APM, Mayer FQ, da Fontoura Budaszewski R, Canal CW. Detection of coronavirus in vampire bats (Desmodus rotundus) in southern Brazil. Transbound Emerg Dis 2021; 69:2384-2389. [PMID: 33977671 PMCID: PMC8242716 DOI: 10.1111/tbed.14150] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 03/29/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022]
Abstract
The vampire bat (Desmodus rotundus) is a haematophagous animal that feeds exclusively on the blood of domestic mammals. Vampire bat feeding habits enable their contact with mammalian hosts and may enhance zoonotic spillover. Moreover, they may carry several pathogenic organisms, including coronaviruses (CoVs), for which they are important hosts. The human pathogens that cause severe acute respiratory syndrome (SARS‐CoV), Middle East respiratory syndrome (MERS‐CoV) and possibly coronavirus disease 2019 (SARS‐CoV‐2) all originated in bats but required bridge hosts to spread into human populations. To monitor the presence of potential zoonotic viruses in bats, the present work evaluated the presence of CoVs in vampire bats from southern Brazil. A total of 101 vampire bats were captured and euthanized between 2017 and 2019 in Rio Grande do Sul state, southern Brazil. The brain, heart, liver, lungs, kidneys and intestines were collected and macerated individually. The samples were pooled and submitted to high‐throughput sequencing (HTS) using the Illumina MiSeq platform and subsequently individually screened using a pancoronavirus RT‐PCR protocol. We detected CoV‐related sequences in HTS, but only two (2/101; 1.98%) animals had CoV detected in the intestines by RT‐PCR. Partial sequences of RdRp and spike genes were obtained in the same sample and the RdRp region in the other sample. The sequences were classified as belonging to Alphacoronavirus. The sequences were closely related to alphacoronaviruses detected in vampire bats from Peru. The continuous monitoring of bat CoVs may help to map and predict putative future zoonotic agents with great impacts on human health.
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Affiliation(s)
- Raquel Silva Alves
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Juliana do Canto Olegário
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Brazil
| | - Mariana Soares da Silva
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Raissa Canova
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Jéssica Tatiane Sauthier
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Letícia Ferreira Baumbach
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - André Alberto Witt
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Rio Grande do Sul Rio Grande do Sul, Brazil
| | - Ana Paula Muterle Varela
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária (DDPA), Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária (DDPA), Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Rio Grande do Sul, Brazil
| | - Renata da Fontoura Budaszewski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Cláudio Wageck Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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