ABSTRACT
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.
ABSTRACT
Introducción: las infecciones respiratorias agudas bajas (IRAB) son la primer causa de hospitalización a lo largo del año. La etiología viral es la más frecuente. El Metapneumovirus humano (MNVh) ha sido vinculado a las IRAB con aspirado negativo para Virus respiratorio sincicial (VRS) y Adenovirus (AD). Objetivo: determinar la prevalencia, epidemiología, clínica y severidad de las infecciones por MNVh, e intentar detectar un patrón radiológico relacionado con el mismo. Métodos: se estudiaron niños entre 0 y 2 años de edad internados por IRAB en el Centro Hospitalario Pereira Rossell, Hospital Central de las Fuerzas Armadas, Hospital Policial, Hospital Británico y Asociación Española Primera de Socorros Mutuos en el período 1 de abril al 30 de noviembre de 2006. Los aspirados nasofaríngeos fueron analizados en la Sección Virología de la Facultad de Ciencias. Resultados: se estudiaron 185 pacientes, obteniéndose 17 resultados positivos para MNVh (9,2%), con 9 coinfecciones con VRS. La mayoría de los pacientes tenían 6 meses o menos de edad. Las manifestaciones clínicas principales fueron polipnea, tirajes y sibilancias. Los principales hallazgos radiológicos fueron infiltrado intersticial difuso e hiperinsuflación. Ningún paciente requirió internación en unidad de cuidados intensivos y no hubo casos fatales. Conclusiones: la prevalencia, características clínicas y evolutivas de las infecciones por MNVh no mostraron diferencias frente a las producidas por el VRS.
Subject(s)
Humans , Paramyxoviridae Infections/epidemiology , Metapneumovirus , Child, Hospitalized , PrevalenceABSTRACT
The variability of the G glycoprotein from human respiratory syncytial viruses (HRSV) (groups A and B) isolated during 17 consecutive epidemics in Montevideo, Uruguay have been analyzed. Several annual epidemics were studied, where strains from groups A and B circulated together throughout the epidemics with predominance of one of them. Usually, group A predominates, but in some epidemics group B is more frequently detected. To analyse the antigenic diversity of the strains, extracts of cells infected with different viruses of group A were tested with a panel of anti-G monoclonal antibodies (MAbs). The genetic variability of both groups was analyzed by sequencing the C-terminal third of the G protein gene. The sequences obtained together with previously published sequences were used to perform phylogenetic analyses. The data from Uruguayan isolates, together with those from the rest of the world provide information regarding worldwide strain circulation. Phylogenetic analyses of HRSV from groups A and B show a model of evolution analogous to the one proposed for influenza B viruses providing information that would be beneficial for future immunization programs and to design safe vaccines.