ABSTRACT
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.
ABSTRACT
Since its detection in December of 2020, the SARS-CoV2 lineage P.1, descendent of B.1.1.28 lineage, has been identified in several places in Brazil and abroad. This Variant of Concern was considered highly prevalent in Northern Brazil and now is rapidly widening its geographical range. Here, we present epidemiological and genomic information of the first case of P1 lineage in Rio Grande do Sul state, in a patient without reported travel history and a tracked transmission chain. These findings occurred in a tourist destination representing an important hub receiving tourists from diverse places.(AU)
Desde a sua detecção em dezembro de 2020, a linhagem P.1 do SARS-CoV2, descendente da linhagem B.1.1.28, foi identificada em diversos locais no Brasil e no mundo. Essa variante de preocupação era considerada altamente frequente no Norte do Brasil e agora está ampliando rapidamente sua distribuição geográfica. Aqui, apresentamos informações epidemiológicas e genômicas do primeiro caso da linhagem P.1 no Rio Grande do Sul em um paciente sem histórico de viagens relatado e com cadeia de transmissão identificada. Esses achados ocorreram em um destino turístico que representa um importante pólo de recepção de turistas de diversas localidades.(AU)
Desde su detección en diciembre de 2020, del linaje P.1 del SARS-CoV2, derivada de la B.1.1.28, hay sido ampliamente identificada en Brasil y en todo el mundo. Esta variante preocupante es muy frecuente en el norte de Brasil y ahora está ampliando rápidamente su distribución geográfica. Aquí, presentamos información epidemiológica y genómica del primer caso de P.1 en Rio Grande do Sul en un paciente sin antecedentes de viaje y con una cadena de transmisión identificada. Estos datos se han obtenido en un destino turístico que representa un importante centro de acogida de turistas de diferentes lugares.(AU)