Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 23:56:e0146-2022.
doi: 10.1590/0037-8682-0146-2022. eCollection 2023.

SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil

Ludmila Fiorenzano Baethgen  1 , Ana Beatriz Gorini da Veiga  2 , Richard Steiner Salvato  1 , Talita Giacomet de Carvalho  3 , Thaiane Rispoli  4 , Sun Hee Schiefelbein  4 , Letícia Garay Martins  5 ; CEVS-COVID-19 Team; Zenaida Marion Alves Nunes  1 , Anelise Praetzel Schaurich  6 , Loeci Natalina Timm  1 , Rosane Campanher Ramos  1 , Cynthia Goulart Molina Bastos  7 , Tatiana Schäffer Gregianini  1
Affiliations

SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil

Ludmila Fiorenzano Baethgen et al. Rev Soc Bras Med Trop. .

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.

PubMed Disclaimer

Conflict of interest statement

Conflict of Interest: The authors have no conflicts of interest to declare. All co-authors have seen and agree with the contents of the manuscript and there is no financial interest to report. We certify that the submission is original work and is not under review at any other publication.

Figures

FIGURE 1:
FIGURE 1:. COVID-19 cases occurred in RS in 2020. The monthly SARS-CoV-2 positive cases analyzed at LACEN-RS (black) and monthly confirmed cases of SARS-CoV-2 infection in RS, according to the Ministry of Health criteria (grey).
FIGURE 2:
FIGURE 2:. RT-qPCR tests performed in 2020 at LACEN-RS for diagnosis of SARS-CoV-2 infection and the positivity rate (PR).
FIGURE 3:
FIGURE 3:. RT-qPCR tests performed according to age group and positivity rate (PR) for LACEN-RS and RS notified cases.
FIGURE 4:
FIGURE 4:. RT-qPCR tests performed according to 18 Regional Health Coordinators.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. World Health Organization (WHO) COVID-19 - China. Off Ctry City, Wuhan Prov Hubei Seafood, Huanan Munic Wuhan Comm Heal. 2020. pp. 1–3.https://www.who.int/docs/default-source/coronaviruse/situation-reports/2...
    1. World Health Organization (WHO) WHO Director-General’s remarks at the media briefing on 2019-nCoV on 11 February. WHO Dir Gen Statement; 2020. https://www.who.int/director-general/speeches/detail/who-director-genera...
    1. World Health Organization (WHO) Naming the coronavirus disease (COVID-19) and the virus that causes it. 2020. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technica...
    1. World Health Organization (WHO) Laboratory testing for 2019 novel coronavirus (2019-nCoV) in suspected human cases. WHO - Interim Guid; [2020]. 2019. pp. 1–7.
    1. Johns Hopkins University and Medicine Coronavirus resource center. 2021. [2021 Aug 24]. Available from: https://coronavirus.jhu.edu/map.html .