Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion.

BACKGROUND: Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES: We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. METHODS: Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. FINDINGS: We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. MAIN CONCLUSIONS: Our findings provide evidence for the origin and spread of deletion variants and emphasise indels' importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.

Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion

BACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. METHODS Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. FINDINGS We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. MAIN CONCLUSIONS Our findings provide evidence for the origin and spread of deletion variants and emphasise indels' importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.

Valoración del enzimoinmunoanálisis de micropartículas para diagnóstico de la toxoplasmosis / Assessment of microparticle enzyme inmunoassay for the diagnosis of toxoplasmosis

Se realiza una evaluación de la técnica de enzimoinmunoanálisis de micropartículas (MEIA), para diagnóstico de toxoplasmosis, mediante estudio de 322 sueros correspondientes a pacientes sin infección, y con diferentes etapas de ella. Se seleccionaron estos sueros según los resultados obtenidos previamente mediante la aplicación de inmunofluorescencia indirecta, e inmunofluorescencia indirecta para IgM. Se aplicó MEIA IgM y MEIA IgM, procesándose mediante un sistema auto-analizador de inmunoensayo totalmente automatizado. Se obtuvo para MEIA IgG: sensibilidad 95,12 por ciento, especificidad 98,25 por ciento, predictibilidad positiva 97,50 por ciento y predictibilidad negativa 96,57 por ciento. Para MEIA IgM se obtuvo: sensibilidad 100 por ciento, especificidad 91,13 por ciento, predictibilidad positiva 56,14 por ciento y predictibilidad negativa 100 por ciento. Se concluye que la técnica MEIA, es un método sensible y específico, pero la baja predictibilidad positiva de la investigación de la IgM, no permite afirmar por sí sola la actividad de la infección, debiendo ser confirmada por otras técnicas, como la inmunofluorescencia IgM