External quality assessment of SARS-CoV-2-sequencing: An ESGMD-SSM pilot trial across 15 European laboratories

Objective: This first pilot on external quality assessment (EQA) of SARS-CoV-2 whole genome sequencing, initiated by the ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD) and Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing.Methods: Ten samples with varying viral loads were sent out to 15 clinical laboratories who had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centres were compared on were identification of 1) SNPs and indels, 2) Pango lineages, and 3) clusters between samples.Results: The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to varying depth (up to 100-fold difference across centres). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignment. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data.Conclusions: The pilot EQA was an overall success. It was able to show the high quality of participating labs and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.</p

Feeding habits of coypu (Myocastor coypus Molina 1978) in the wetlands of the Southern region of Brazil

The aim of this study was to determine the diet of coypu (Myocastor coypus) in two areas (Santa Isabel do Sul wetlands – Area 1, and Santa Marta Farm – Area 2) in the Southern region of Brazil, using microhistological analyses of feces. Twenty-four plant species were identified from collected feces samples. Among the identified species, nine are common in the animals’ diet in both areas; the presence of Oriza sativa was not detected in any of the samples. Among the identified species, 84% and 54% of the coypu’s diet from Areas 1 and 2, respectively, are aquatic plants. Poaceae family was most common, being found in 82% of the samples from both areas. Paspalum disthichum (Area 1) and Panicum tricholaenoides (Area 2) were the most frequent species on the coypu’s diet. The diet comparison for both areas indicates that feeding habits vary depending on the type of habitat, environmental conditions and food availability. The absence of rice in our analysis may be an indication for the preservation of native areas around watercourses, so as to prevent coypu from invading irrigated crops.O objetivo deste estudo foi determinar a dieta do ratão-dobanhado (Myocastor coypus), em duas regiões (áreas alagadas em Santa Isabel do Sul – área 1 e Fazenda Santa Marta – área 2), na região sul do Brasil, utilizando microhistological análises de fezes. Foram identificadas 24 espécies de plantas nas amostras de fezes coletadas. Entre as espécies identificadas, nove são comuns a dieta dos animais de ambas as áreas, não sendo detectada a presença de Oriza sativa em nenhuma das amostras. Entre as espécies identificadas, 84% e 54% da dieta do ratão-do-banhado, nas áreas 1 e 2 respectivamente, são plantas aquáticas. A família Poaceae foi a mais abundante, sendo encontrada em 82% das amostras de ambas as áreas. Paspalum disthichum (área 1) e Panicum tricholaenoides (área 2), foram as espécies mais frequentes na dieta do ratão-do-banhado. A comparação da dieta de ambas as áreas mostrou que a alimentação varia dependendo do tipo de habitat, condições ambientais e de disponibilidade alimentar. A ausência de arroz na nossa análise pode ser um indicativo de que a preservação de áreas nativas ao redor de cursos d’água, evita que o ratão-do-banhado utilize as culturas de arroz