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 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.

Chikungunya virus infection in the southernmost state of Brazil was characterised by self-limited transmission (2017-2019) and a larger 2021 outbreak

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.

Epidemiological investigation reveals local transmission of SARS-CoV-2 lineage P. 1 in Southern Brazil / Investigação epidemiológica revela transmissão local da variante P. 1 do SARS-CoV-2 no Sul do Brasil / Una investigación epidemiológica revela la transmisión local de la variante P. 1 del SARS-CoV-2 en el sur de Brasil

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)

Outbreak of rubella after mass vaccination of children and adult women: challenges for rubella elimination strategies / Brote epidémico de rubéola tras la vacunación masiva de niños y mujeres adultas: un reto para las estrategias de eliminación de la rubéola

OBJECTIVE: To describe rubella outbreaks and control strategies in the Brazilian state of Rio Grande do Sul before rubella elimination. METHODS: We analyzed rubella and congenital rubella syndrome surveillance data for the state of Rio Grande do Sul and calculated age- and gender-specific incidence of confirmed rubella cases in 2007. We obtained data on measles-rubella doses administered during the outbreak from the state immunization program and reviewed the timing of suspect case notification and implementation of control measures. RESULTS: Of 2 842 confirmed rubella cases reported to the state health department in 2007, 2 145 (75.5 percent) were in males (39.5 cases per 100 000 population) and 697 (24.5 percent) were in females (12.3 per 100 000 population). Incidence among 15- to 39-year-olds was 1.8 to 5.5 times higher in males than in females. Rubella genotype 2B was detected in nasopharyngeal specimens from 13 patients from multiple chains of transmission. Eight children were born with congenital rubella syndrome (5.9 cases per 100 000 births in 2008). Delayed notification of initial cases hampered early control efforts, resulting in outbreak spread throughout the state. Rubella transmission was interrupted after mass vaccination of adult men and women as part of a national vaccination campaign. CONCLUSIONS: Routine vaccination strategies and mass vaccination of adolescents and adults for accelerated rubella control and elimination should target men and women.

OBJETIVO: Describir los brotes de rubéola y las estrategias para el control de la enfermedad anteriores a la eliminación de la rubéola en el estado brasileño de Rio Grande do Sul. MÉTODOS: Se analizaron los datos de vigilancia epidemiológica sobre la rubéola y el síndrome de rubéola congénita del estado de Rio Grande do Sul y se calculó la incidencia específica por edad y sexo de los casos confirmados de rubéola en el 2007. A partir del programa de vacunación estatal se obtuvieron datos sobre las dosis de vacunación antisarampionosa y antirrubeólica administradas durante el brote y se analizaron el momento de notificación de los casos sospechosos y la puesta en práctica de medidas de control. RESULTADOS: De los 2842 casos confirmados de rubéola notificados al departamento de salud estatal en el 2007, 2 145 (75,5 por ciento) correspondieron a hombres (39,5 casos por 100000 habitantes) y 697 (24,5 por ciento) a mujeres (12,3 por 100000 habitantes). La incidencia en las personas de 15 a 39 años de edad fue de 1,8 a 5,5 veces mayor en los varones que en las mujeres. En 13 pacientes provenientes de distintas cadenas de transmisión se detectó el genotipo 2B del virus de la rubéola en muestras obtenidas de la nasofaringe. Nacieron 8 niños con síndrome de rubéola congénita (5,9 casos por 100000 nacimientos en el 2008). La demora en la notificación de los casos iniciales obstaculizó la adopción temprana de medidas de control, lo que hizo que el brote se propagara a todo el estado. La transmisión de la rubéola se interrumpió después de la vacunación masiva de varones y mujeres adultos como parte de una campaña nacional de vacunación. CONCLUSIONES: Las estrategias de vacunación sistemática y la vacunación masiva de adolescentes y adultos tendientes a acelerar el control y la eliminación de la rubéola deben dirigirse tanto a varones como a mujeres.