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Mallmann L, Hermann BS, Schallenberger K, Demoliner M, Eisen AKA, Heldt FH, Gularte JS, Hansen AW, de Almeida PR, Weber MN, Spilki FR, Fleck JD. Proteinase K treatment in absence of RNA isolation classical procedures is a quick and cheaper alternative for SARS-CoV-2 molecular detection. J Virol Methods 2021; 293:114131. [PMID: 33798606 PMCID: PMC8008826 DOI: 10.1016/j.jviromet.2021.114131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/22/2022]
Abstract
The World Health Organization (WHO) has declared a pandemic of COVID-19, the disease caused by the recently described SARS-CoV-2. The relevance and importance of mass diagnosis in order to find the asymptomatic individuals is widely recognized as a mandatory tool to reinforce the control measures for monitoring virus circulation and reduce the spreading of SARS-CoV-2. Here, we described quickness and cheaper strategies of direct RT-qPCR (in the absence of RNA isolation) and compared the results to those obtained using standard RNA isolation procedure. The tests varied using pure, diluted samples, combined with Proteinase K (PK) or Lysis Buffer. Our findings showed consistently that PK pre-treated samples in the absence of RNA extraction procedures presents similar results to those obtained by standard RNA isolation procedures. On average, 16 samples extracted with the MagMAX™ CORE Kit, take around 2 h, costing an average of USD 5, the pre-treatment of samples using PK, on the other hand, would cut the value to less than USD 0.30 and reduce the time of procedure in more than 1 ½ hours. The present study suggests the use of PK treatment instead of RNA isolation in order to reduce costs and time in processing samples for molecular diagnosis of SARS-CoV-2.
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Affiliation(s)
- L Mallmann
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - B S Hermann
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - K Schallenberger
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - M Demoliner
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - A K A Eisen
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - F H Heldt
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - J S Gularte
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - A W Hansen
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - P R de Almeida
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - M N Weber
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - F R Spilki
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - J D Fleck
- Laboratório De Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil.
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Francisco RDS, Benites LF, Lamarca AP, de Almeida LGP, Hansen AW, Gularte JS, Demoliner M, Gerber AL, de C Guimarães AP, Antunes AKE, Heldt FH, Mallmann L, Hermann B, Ziulkoski AL, Goes V, Schallenberger K, Fillipi M, Pereira F, Weber MN, de Almeida PR, Fleck JD, Vasconcelos ATR, Spilki FR. Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Virus Res 2021; 296:198345. [PMID: 33631222 PMCID: PMC7898980 DOI: 10.1016/j.virusres.2021.198345] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [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: 01/13/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/24/2022]
Abstract
Emergence of novel SARS-CoV-2 lineages are under the spotlight of the media, scientific community and governments. Recent reports of novel variants in the United Kingdom, South Africa and Brazil (B.1.1.28-E484K) have raised intense interest because of a possible higher transmission rate or resistance to the novel vaccines. Nevertheless, the spread of B.1.1.28 (E484K) and other variants in Brazil is still unknown. In this work, we investigated the population structure and genomic complexity of SARS-CoV-2 in Rio Grande do Sul, the southernmost state in Brazil. Most samples sequenced belonged to the B.1.1.28 (E484K) lineage, demonstrating its widespread dispersion. We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations. In light of the evidence for E484K dispersion, co-infection and emergence of VUI-NP13 L in Rio Grande do Sul, we reaffirm the importance of establishing strict and effective social distancing measures to counter the spread of potentially more hazardous SARS-CoV-2 strains.
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Affiliation(s)
| | - L Felipe Benites
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Alessandra P Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Luiz G P de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | | | - Meriane Demoliner
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Alexandra L Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Ana Paula de C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | | | - Fagner Henrique Heldt
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Larissa Mallmann
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Bruna Hermann
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Ana Luiza Ziulkoski
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Vyctoria Goes
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | | | - Micheli Fillipi
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Francini Pereira
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | | | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil.
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3
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Gularte JS, Staggemeier R, Demoliner M, Heck TMS, Heldt FH, Ritzel RGF, Rigotto C, Henzel A, Spilki FR. Human adenovirus in tissues of freshwater snails living in contaminated waters. Environ Monit Assess 2017; 189:276. [PMID: 28523581 DOI: 10.1007/s10661-017-5979-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/18/2016] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
Human adenovirus (HAdV) is resistant to environment and can be used as a marker to detect fecal contamination. Considering the importance of freshwater snails in the aquatic environment, their use as concentrators for HAdV is a complementary tool for viral analysis of water. The goal of the study was to detect HAdV in snails and surface water collected from wetlands of the Sinos River (Rio Grande do Sul, Brazil) basin and to compare rates and viral loads found in both samples. HAdV was detected through real-time PCR. Total and fecal coliforms were detected by Colilert® kit, and viral infectivity of positive samples of the DNA genome was performed in A549 human cell line. All wetlands presented bacterial and viral contamination, but no viral particle was considered viable. The wetland that showed lower fecal coliform mean was Campo Bom, and São Leopoldo (both cities in Rio Grande do Sul) was representative of the highest mean. HAdV was detected in water samples (53%), gastropods' hemolymph (31%) and tissues (16%). Wetlands proved to be environments already altered by human action. Water samples exhibited a higher frequency of HAdV detection; however, in some instances, the target viral genomes were only found in gastropod biological samples. This was a pioneer study in the use of freshwater snails for human enteric viral assessment thus demonstrating that the human organism can retain fecal contamination, complementing and assisting in microbiological water analyzes.
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Affiliation(s)
- J S Gularte
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2 Andar, Sala 205 RS 239, n 2755, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93352-000, Brazil
| | - R Staggemeier
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2 Andar, Sala 205 RS 239, n 2755, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93352-000, Brazil
| | - M Demoliner
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2 Andar, Sala 205 RS 239, n 2755, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93352-000, Brazil
| | - T M S Heck
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2 Andar, Sala 205 RS 239, n 2755, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93352-000, Brazil
| | - F H Heldt
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2 Andar, Sala 205 RS 239, n 2755, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93352-000, Brazil
| | - R G F Ritzel
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2 Andar, Sala 205 RS 239, n 2755, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93352-000, Brazil
| | - C Rigotto
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2 Andar, Sala 205 RS 239, n 2755, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93352-000, Brazil
| | - A Henzel
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2 Andar, Sala 205 RS 239, n 2755, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93352-000, Brazil.
| | - F R Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2 Andar, Sala 205 RS 239, n 2755, Vila Nova, Novo Hamburgo, Rio Grande do Sul, CEP 93352-000, Brazil
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Heldt FH, Staggmeier R, Gularte JS, Demoliner M, Henzel A, Spilki FR. Hepatitis E Virus in Surface Water, Sediments, and Pork Products Marketed in Southern Brazil. Food Environ Virol 2016; 8:200-5. [PMID: 27169536 DOI: 10.1007/s12560-016-9243-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 01/15/2016] [Accepted: 05/03/2016] [Indexed: 05/25/2023]
Abstract
Hepatitis E virus (HEV) is an emerging causative agent of food and waterborne hepatitis in human beings. HEV circulates among human populations and swine herds, and may be found in water contaminated by swine feces, as well as in pork. In the present study, 68 sediment samples and 250 water samples collected from the Sinos River tributaries, as well as 50 samples of pork products (pâté and blood sausage) marketed in the Sinos River watershed region, Brazil, were tested for the presence of HEV genome. Reverse-transcriptase polymerase chain reaction followed by nucleotide sequencing was used for detection and characterization of HEV genomes. Overall, 36 % of food samples tested positive for HEV (genotype 3). No sediment or water samples were positive. These results suggest that contaminated pork products may be a source of HEV infection within this region and indicate a need for better monitoring of food safety and swine herds.
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Affiliation(s)
- F H Heldt
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2° Andar, Sala 205 RS 239, nº 2755, Novo Hamburgo, RS, Brazil
| | - R Staggmeier
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2° Andar, Sala 205 RS 239, nº 2755, Novo Hamburgo, RS, Brazil
| | - J S Gularte
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2° Andar, Sala 205 RS 239, nº 2755, Novo Hamburgo, RS, Brazil
| | - M Demoliner
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2° Andar, Sala 205 RS 239, nº 2755, Novo Hamburgo, RS, Brazil
| | - A Henzel
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2° Andar, Sala 205 RS 239, nº 2755, Novo Hamburgo, RS, Brazil.
| | - F R Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Prédio Vermelho 2° Andar, Sala 205 RS 239, nº 2755, Novo Hamburgo, RS, Brazil
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