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.

Consecutive deletions in a unique Uruguayan SARS-CoV-2 lineage evidence the genetic variability potential of accessory genes.

Deletions frequently occur in the six accessory genes of SARS-CoV-2, but most genomes with deletions are sporadic and have limited spreading capability. Here, we analyze deletions in the ORF7a of the N.7 lineage, a unique Uruguayan clade from the Brazilian B.1.1.33 lineage. Thirteen samples collected during the early SARS-CoV-2 wave in Uruguay had deletions in the ORF7a. Complete genomes were obtained by Illumina next-generation sequencing, and deletions were confirmed by Sanger sequencing and capillary electrophoresis. The N.7 lineage includes several individuals with a 12-nucleotide deletion that removes four amino acids of the ORF7a. Notably, four individuals underwent an additional 68-nucleotide novel deletion that locates 44 nucleotides downstream in the terminal region of the same ORF7a. The simultaneous occurrence of the 12 and 68-nucleotide deletions fuses the ORF7a and ORF7b, two contiguous accessory genes that encode transmembrane proteins with immune-modulation activity. The fused ORF retains the signal peptide and the complete Ig-like fold of the 7a protein and the transmembrane domain of the 7b protein, suggesting that the fused protein plays similar functions to original proteins in a single format. Our findings evidence the remarkable dynamics of SARS-CoV-2 and the possibility that single and consecutive deletions occur in accessory genes and promote changes in the genomic organization that help the virus explore genetic variations and select for new, higher fit changes.

A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay.

The analysis of genetic diversity in SARS-CoV-2 is the focus of several studies, providing insights into how the virus emerged and evolves. Most common changes in SARS-CoV-2 are single or point nucleotide substitutions; meanwhile, insertions and deletions (indels) have been identified as a less frequent source of viral genetic variability. Here, we report the emergence of a 12-nucleotide deletion in ORF7a, resulting in a 4-amino acid in-frame deletion. The Δ12 variant was identified in viruses from patients of a single outbreak and represents the first report of this deletion in South American isolates. Phylogenetic analysis revealed that Δ12 strains belong to the lineage B.1.1 and clustered separated from the remaining Uruguayan strains. The ∆12 variant was detected in 14 patients of this outbreak by NGS sequencing and/or two rapid and economic methodologies: Sanger amplicon sequencing and capillary electrophoresis. The presence of strong molecular markers as the deletion described here are useful for tracking outbreaks and reveal a significant aspect of the SARS-CoV-2 evolution on the robustness of the virus to keep its functionality regardless loss of genetic material.

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.

Deletion of the Correia element in the mtr gene complex of Neisseria meningitidis.

The mtr gene complex in Neisseria meningitidis encodes an efflux pump that is responsible for export of antibacterial hydrophobic agents. The promoter region of the mtrCDE operon harbours an insertion sequence known as a Correia element, and a binding site for the integration host factor (IHF) is present at the centre of the Correia element. It has been suggested that the expression of the mtrCDE operon in meningococci is subject to transcriptional regulation by the IHF and post-transcriptional regulation by cleavage in the inverted repeat of the Correia element. The promoter region of the mtrCDE operon as well as the association of changes at that point with decreased susceptibility to antimicrobial drugs in 606 Neisseria meningitidis strains were analysed in this study. Two different deletions were present in the analysed region. The first one, found in seven strains, corresponded to absence of the Correia element. The second one, affecting the -10 region and first 100 bp of the mtrR gene and present in 57 isolates, was only found in ST-1624 isolates. None of the deletions were associated with decreased susceptibility to antimicrobial drugs. Although most of the meningococcal strains carry the Correia element at that position, its deletion is not an exception.

Molecular characterization of invasive serogroup Y Neisseria meningitidis strains isolated in the Latin America region.

OBJECTIVES: To improve the understanding of serogroup Y invasive meningococcal disease (IMD) in Latin America, particularly IMD molecular epidemiology; 166 Y serogroup isolates received at the National Reference Laboratories of Argentina, Brazil, Chile, Colombia, and Costa Rica during 2000-2006 were characterized by their molecular markers. METHODS: This analysis included serological assays to determine serogroup/serotype/serosubtype, DNA sequencing and genotyping of the porB and/or porA genes, multilocus sequence typing (MLST) and fetA allele determination. RESULTS: Sixteen different antigenic combinations were observed. Sixty-two (37.3%) isolates were NT:P1.5 and 36 (21.7%) isolates were 14:NST. Thirty-two different STs appeared, but 3 STs (ST-1624, ST-23, and ST-5770) accounted for 69.9% (116) of the strains. Most of the IMD isolates belonged to the ST-23, ST-167 clonal complexes or the group composed by ST-5770 and related STs. CONCLUSIONS: Isolates obtained in Colombia and Costa Rica were similar to that of the United States, in that most sequence types belonged to the ST-23 clonal complex. IMD isolates found in Argentina appear to be the result of an independent event and did not spread from nearby countries, being the sequence type ST-1624 (ST-167 clonal complex) the most frequently found. We were unable to correlate an antigenic shift of outer membrane proteins with an increase of serogroup Y meningococcal cases in our collection of isolates.

Incidencia y transmisión de coqueluche en Buenos Aires, Neuquén, Santa Fe y Tucumán: implicancias de las características socio-sanitarias / Incidence and transmission of pertussis in Buenos Aires, Neuquén, Santa Fe and Tucumán: implicancies of social and health characteristics

INTRODUCCION: Pertussis es una enfermedad inmunoprevenible respiratoria que afecta a la población infantil y a los adolescentes/adultos. Para diseñar estrategias que mejoren el control de la enfermedad, resulta esencial profundizar el conocimiento de su epidemiología.OBJETIVO: Estimar la frecuencia de casos de pertussis en 5 provincias argentinas, analizar la implicancia de las características socio-sanitarias de la población e identificar la fuente más probable de contagio.METODOS: Se realizó un trabajo multidisciplinario y multicéntrico empleando algoritmos consensuados. Se estudió a niños menores de 1 año (caso índice, CI) y sus contactos. Para los análisis, se incorporó la información obtenida durante el período a una base de datos ya existente.RESULTADOS: Durante 2006-2011 se analizaron 18.106 muestras de pacientes con sintomatología compatible con pertussis, y se confirmaron 3.766 casos. La mayor proporción de casos confirmados y de casos fatales (8 a 21 por año) se registró en los menores de 1 año. Un análisis de la epidemiología de 113 grupos familiares, constituidos por al menos un CI y dos contactos, determinó que en más del 50% el caso primario no se correspondió al CI. Análisis preliminares mostraron a los convivientes adultos jóvenes como posible fuente de infección de la población vulnerable. En relación con la implicancia de la situación socio-sanitaria en la epidemiología de pertussis, la evolución de los síntomas y la distribución por edades de los casos confirmados mostraron una desigualdad entre los barrios carecientes y los no carecientes.CONCLUSIONES: Se detectó la presencia de más de un caso de pertussis en los grupos familiares. Los adultos jóvenes convivientes serían los responsables de transmitir la infección a los más pequeños. Por la influencia de las condiciones socio-sanitarias en la epidemiología de pertussis, se detectaron patrones diferenciales en la distribución de casos.

INTRODUCTION: Pertussis is an immune preventable resporatory disease affecting the pediatric population and teens/adults. To design better strategies for the disease control, it is essential to improve epidemiological knowledge.OBJECTIVE: To estimate the frequency of pertussis cases in 5 Argentine provinces, to analyze the implication of the socio-economic characteristics and to identify the most likely source of infection.METHODS: A multidisciplinary, multicenter study was conducted, using consensus algorithms. The analysis was focused on children under 1 year (index cases, IC) and their contacts. The information obtained was incorporated into a previous database.RESULTS: 18.106 samples of patients with symptoms compatible with pertussis were analyzed during 2006-2011. Of these cases, 3.766 were confirmed in the lab. The largest proportion of confirmed cases and fatal cases (8-21 per year) were registered in children under 1 year. An epidemiologic analysis of 113 family units, consisting in at least one IC and two contacts, found that in over 50% the primary case did not correspond to the IC. A preliminary analysis showed that the young and adult cohabitants were the possible source of infection for vulnerable populations. Regarding the implications of the socio-sanitary conditions in the disease epidemiology, the evolution of symptoms and the age group distribution of confirmed cases were unequeal between poor and non-poor neighborhoods.CONCLUSIONS: The study detected the presence of more than one case of pertussis in family units. Young and adult cohabitants would be responsible for transmitting the infection to children. Due to the influence of socio-sanitary conditions in the epidemiology of pertussis, differential patterns were detected in the distribution of cases.

Incidencia y transmisión de coqueluche en Buenos Aires, Neuquén, Santa Fe y Tucumán: implicancias de las características socio-sanitarias / Incidence and transmission of pertussis in Buenos Aires, Neuquén, Santa Fe and Tucumán: implicancies of social and health characteristics

INTRODUCCION: Pertussis es una enfermedad inmunoprevenible respiratoria que afecta a la población infantil y a los adolescentes/adultos. Para diseñar estrategias que mejoren el control de la enfermedad, resulta esencial profundizar el conocimiento de su epidemiología.OBJETIVO: Estimar la frecuencia de casos de pertussis en 5 provincias argentinas, analizar la implicancia de las características socio-sanitarias de la población e identificar la fuente más probable de contagio.METODOS: Se realizó un trabajo multidisciplinario y multicéntrico empleando algoritmos consensuados. Se estudió a niños menores de 1 año (caso índice, CI) y sus contactos. Para los análisis, se incorporó la información obtenida durante el período a una base de datos ya existente.RESULTADOS: Durante 2006-2011 se analizaron 18.106 muestras de pacientes con sintomatología compatible con pertussis, y se confirmaron 3.766 casos. La mayor proporción de casos confirmados y de casos fatales (8 a 21 por año) se registró en los menores de 1 año. Un análisis de la epidemiología de 113 grupos familiares, constituidos por al menos un CI y dos contactos, determinó que en más del 50% el caso primario no se correspondió al CI. Análisis preliminares mostraron a los convivientes adultos jóvenes como posible fuente de infección de la población vulnerable. En relación con la implicancia de la situación socio-sanitaria en la epidemiología de pertussis, la evolución de los síntomas y la distribución por edades de los casos confirmados mostraron una desigualdad entre los barrios carecientes y los no carecientes.CONCLUSIONES: Se detectó la presencia de más de un caso de pertussis en los grupos familiares. Los adultos jóvenes convivientes serían los responsables de transmitir la infección a los más pequeños. Por la influencia de las condiciones socio-sanitarias en la epidemiología de pertussis, se detectaron patrones diferenciales en la distribución de casos.

INTRODUCTION: Pertussis is an immune preventable resporatory disease affecting the pediatric population and teens/adults. To design better strategies for the disease control, it is essential to improve epidemiological knowledge.OBJECTIVE: To estimate the frequency of pertussis cases in 5 Argentine provinces, to analyze the implication of the socio-economic characteristics and to identify the most likely source of infection.METHODS: A multidisciplinary, multicenter study was conducted, using consensus algorithms. The analysis was focused on children under 1 year (index cases, IC) and their contacts. The information obtained was incorporated into a previous database.RESULTS: 18.106 samples of patients with symptoms compatible with pertussis were analyzed during 2006-2011. Of these cases, 3.766 were confirmed in the lab. The largest proportion of confirmed cases and fatal cases (8-21 per year) were registered in children under 1 year. An epidemiologic analysis of 113 family units, consisting in at least one IC and two contacts, found that in over 50% the primary case did not correspond to the IC. A preliminary analysis showed that the young and adult cohabitants were the possible source of infection for vulnerable populations. Regarding the implications of the socio-sanitary conditions in the disease epidemiology, the evolution of symptoms and the age group distribution of confirmed cases were unequeal between poor and non-poor neighborhoods.CONCLUSIONS: The study detected the presence of more than one case of pertussis in family units. Young and adult cohabitants would be responsible for transmitting the infection to children. Due to the influence of socio-sanitary conditions in the epidemiology of pertussis, differential patterns were detected in the distribution of cases.