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.

Genetic and phenotypic traits of children and adolescents with cystic fibrosis in Southern Brazil / Características genéticas e fenotípicas de crianças e adolescentes com fibrose cística no Sul do Brasil

ABSTRACT Objectives: To characterize the main identified mutations on cystic fibrosis transmembrane conductance regulator (CFTR) in a group of children and adolescents at a cystic fibrosis center and its association with the clinical and laboratorial characteristics. Method: Descriptive cross-sectional study including patients with cystic fibrosis who had two alleles identified with CFTR mutation. Clinical, anthropometrical, laboratorial and pulmonary function (spirometry) data were collected from patients' records in charts and described with the results of the sample genotyping. Results: 42 patients with cystic fibrosis were included in the study. The most frequent mutation was F508del, covering 60 alleles (71.4%). The second most common mutation was G542X (six alleles, 7.1%), followed by N1303K and R1162X mutations (both with four alleles each). Three patients (7.14%) presented type III and IV mutations, and 22 patients (52.38%) presented homozygous mutation for F508del. Thirty three patients (78.6%) suffered of pancreatic insufficiency, 26.2% presented meconium ileus, and 16.7%, nutritional deficit. Of the patients in the study, 59.52% would be potential candidates for the use of CFTR-modulating drugs. Conclusions: The mutations of CFTR identified more frequently were F508del and G542X. These are type II and I mutations, respectively. Along with type III, they present a more severe cystic fibrosis phenotype. More than half of the sample (52.38%) presented homozygous mutation for F508del, that is, patients who could be treated with Lumacaftor/Ivacaftor. Approximately 7% of the patients (7.14%) presented type III and IV mutations, therefore becoming candidates for the treatment with Ivacaftor.

RESUMO Objetivos: Caracterizar as principais mutações identificadas no cystic fibrosis transmembrane conductance regulator (CFTR) em um grupo de crianças e adolescentes de um centro multidisciplinar de tratamento de fibrose cística e sua associação com características clínicas e laboratoriais. Método: Estudo transversal descritivo que incluiu pacientes com fibrose cística que possuíam dois alelos identificados com mutação no CFTR. Dados clínicos, antropométricos, laboratoriais e de função pulmonar (espirometria) foram coletados de registros em prontuários e descritos com os resultados de genotipagem da amostra. Resultados: Foram incluídos 42 pacientes com fibrose cística. A mutação mais frequente foi a F508del, abrangendo 60 alelos (71,4%). A segunda mutação mais comum foi a G542X (seis alelos, 7,1%), seguida das mutações N1303K e R1162X (ambas com quatro alelos cada uma). Três pacientes (7,14%) apresentaram mutações de classes III e IV, e 22 pacientes (52,38%), homozigose para F508del. Trinta e três pacientes (78,6%) tinham insuficiência pancreática, 11 (26,2%) apresentaram íleo meconial e sete (16,7%) déficit nutricional. Dos pacientes do estudo, 59,52% seriam potenciais candidatos ao uso de fármacos moduladores de CFTR. Conclusões: As mutações do CFTR identificadas com mais frequência foram F508del e G542X, as quais são mutações pertencentes às classes II e I, respectivamente, e que, juntamente à classe III, conferem um fenótipo de fibrose cística com mais gravidade. Mais da metade (52,38%) da amostra apresentava F508del em homozigose, população candidata ao novo tratamento com Lumacaftor/Ivacaftor. Aproximadamente 7% dos pacientes apresentavam mutações de classes III e IV, sendo candidatos ao tratamento com Ivacaftor.