SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil
ABSTRACT Background: Brazil has one of the highest numbers of COVID-19 cases and deaths. Rio Grande do Sul (RS) in southern Brazil is one of the leading states in terms of case numbers. As part of the national public health network, the State Central Laboratory (LACEN-RS) changed its routine in 20...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Sociedade Brasileira de Medicina Tropical (SBMT)
2023-01-01
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| Series: | Revista da Sociedade Brasileira de Medicina Tropical |
| Subjects: | |
| Online Access: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0037-86822023000100300&lng=en&tlng=en |
| _version_ | 1797944924611543040 |
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| author | Ludmila Fiorenzano Baethgen Ana Beatriz Gorini da Veiga Richard Steiner Salvato Talita Giacomet de Carvalho Thaiane Rispoli Sun Hee Schiefelbein Letícia Garay Martins Zenaida Marion Alves Nunes Anelise Praetzel Schaurich Loeci Natalina Timm Rosane Campanher Ramos Cynthia Goulart Molina Bastos Tatiana Schäffer Gregianini |
| author_facet | Ludmila Fiorenzano Baethgen Ana Beatriz Gorini da Veiga Richard Steiner Salvato Talita Giacomet de Carvalho Thaiane Rispoli Sun Hee Schiefelbein Letícia Garay Martins Zenaida Marion Alves Nunes Anelise Praetzel Schaurich Loeci Natalina Timm Rosane Campanher Ramos Cynthia Goulart Molina Bastos Tatiana Schäffer Gregianini |
| author_sort | Ludmila Fiorenzano Baethgen |
| collection | DOAJ |
| description | ABSTRACT Background: Brazil has one of the highest numbers of COVID-19 cases and deaths. Rio Grande do Sul (RS) in southern Brazil is one of the leading states in terms of case numbers. As part of the national public health network, the State Central Laboratory (LACEN-RS) changed its routine in 2020 to focus on the diagnosis of COVID-19. This study evaluated the laboratory surveillance of COVID-19 suspected cases analyzed at the LACEN-RS in 2020. Methods: Viral detection was performed using RT-qPCR in samples from patients with respiratory infection who met the study criteria. Viral RNA was isolated using commercial manual kits or automated extractors, and SARS-CoV-2 RT-qPCR was performed using the Bio-Manguinhos/Rio de Janeiro, IBMP/Paraná, or Allplex 2019-nCoV assay. In total, 360 representative SARS-CoV-2 samples were sequenced using the Illumina platform. Results: In total, 31,197 of 107,578 (positivity rate = 29%) tested positive for SARS-CoV-2. The number of RT-qPCR tests performed per month followed the COVID-19 epidemic curve observed for the state, with peaks in July-August and December. Females accounted for 63% of the samples, whereas the positivity rate was higher among males (33.1% males vs. 26.5% females). The positivity rate was higher in adults aged 50-79 years compared to the overall positivity rate. The majority of cases were observed in the capital, Porto Alegre, and the metropolitan region. Ten distinct lineages were identified, with B.1.1.28, B.1.1.33, and P.2 being the most frequent. Conclusions: Here, we describe laboratory surveillance of COVID-19 to identify priorities for epidemiological surveillance actions in RS. |
| first_indexed | 2024-04-10T20:46:13Z |
| format | Article |
| id | doaj.art-bb95884791eb496db2a5a546ef5c96bb |
| institution | Directory Open Access Journal |
| issn | 1678-9849 |
| language | English |
| last_indexed | 2024-04-10T20:46:13Z |
| publishDate | 2023-01-01 |
| publisher | Sociedade Brasileira de Medicina Tropical (SBMT) |
| record_format | Article |
| series | Revista da Sociedade Brasileira de Medicina Tropical |
| spelling | doaj.art-bb95884791eb496db2a5a546ef5c96bb2023-01-24T07:35:34ZengSociedade Brasileira de Medicina Tropical (SBMT)Revista da Sociedade Brasileira de Medicina Tropical1678-98492023-01-015610.1590/0037-8682-0146-2022SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern BrazilLudmila Fiorenzano Baethgenhttps://orcid.org/0000-0002-4871-8877Ana Beatriz Gorini da Veigahttps://orcid.org/0000-0003-1462-5506Richard Steiner Salvatohttps://orcid.org/0000-0002-5701-9437Talita Giacomet de Carvalhohttps://orcid.org/0000-0001-6479-9438Thaiane Rispolihttps://orcid.org/0000-0003-4421-8995Sun Hee Schiefelbeinhttps://orcid.org/0000-0001-7212-8036Letícia Garay Martinshttps://orcid.org/0000-0002-5614-6952Zenaida Marion Alves Nuneshttps://orcid.org/0000-0001-5443-7695Anelise Praetzel Schaurichhttps://orcid.org/0000-0002-7530-5568Loeci Natalina Timmhttps://orcid.org/0000-0002-3409-9710Rosane Campanher Ramoshttps://orcid.org/0000-0002-9714-9252Cynthia Goulart Molina Bastoshttps://orcid.org/0000-0002-2504-2915Tatiana Schäffer Gregianinihttps://orcid.org/0000-0002-9912-9060ABSTRACT Background: Brazil has one of the highest numbers of COVID-19 cases and deaths. Rio Grande do Sul (RS) in southern Brazil is one of the leading states in terms of case numbers. As part of the national public health network, the State Central Laboratory (LACEN-RS) changed its routine in 2020 to focus on the diagnosis of COVID-19. This study evaluated the laboratory surveillance of COVID-19 suspected cases analyzed at the LACEN-RS in 2020. Methods: Viral detection was performed using RT-qPCR in samples from patients with respiratory infection who met the study criteria. Viral RNA was isolated using commercial manual kits or automated extractors, and SARS-CoV-2 RT-qPCR was performed using the Bio-Manguinhos/Rio de Janeiro, IBMP/Paraná, or Allplex 2019-nCoV assay. In total, 360 representative SARS-CoV-2 samples were sequenced using the Illumina platform. Results: In total, 31,197 of 107,578 (positivity rate = 29%) tested positive for SARS-CoV-2. The number of RT-qPCR tests performed per month followed the COVID-19 epidemic curve observed for the state, with peaks in July-August and December. Females accounted for 63% of the samples, whereas the positivity rate was higher among males (33.1% males vs. 26.5% females). The positivity rate was higher in adults aged 50-79 years compared to the overall positivity rate. The majority of cases were observed in the capital, Porto Alegre, and the metropolitan region. Ten distinct lineages were identified, with B.1.1.28, B.1.1.33, and P.2 being the most frequent. Conclusions: Here, we describe laboratory surveillance of COVID-19 to identify priorities for epidemiological surveillance actions in RS.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0037-86822023000100300&lng=en&tlng=enMolecular diagnosisSARS-CoV-2SARS-CoV-2 lineagesPandemicPublic health laboratory services |
| spellingShingle | Ludmila Fiorenzano Baethgen Ana Beatriz Gorini da Veiga Richard Steiner Salvato Talita Giacomet de Carvalho Thaiane Rispoli Sun Hee Schiefelbein Letícia Garay Martins Zenaida Marion Alves Nunes Anelise Praetzel Schaurich Loeci Natalina Timm Rosane Campanher Ramos Cynthia Goulart Molina Bastos Tatiana Schäffer Gregianini SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil Revista da Sociedade Brasileira de Medicina Tropical Molecular diagnosis SARS-CoV-2 SARS-CoV-2 lineages Pandemic Public health laboratory services |
| title | SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil |
| title_full | SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil |
| title_fullStr | SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil |
| title_full_unstemmed | SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil |
| title_short | SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil |
| title_sort | sars cov 2 laboratory surveillance during the first year of the covid 19 pandemic in southern brazil |
| topic | Molecular diagnosis SARS-CoV-2 SARS-CoV-2 lineages Pandemic Public health laboratory services |
| url | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0037-86822023000100300&lng=en&tlng=en |
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