End-of-season influenza vaccine effectiveness during the Southern Hemisphere 2022 influenza season - Chile, Paraguay, and Uruguay.

OBJECTIVES: This study estimated the 2022 end-of-season influenza vaccine effectiveness (VE) against severe acute respiratory illness (SARI) hospitalization in Chile, Paraguay, and Uruguay. METHODS: We pooled surveillance data from SARI cases in 18 sentinel surveillance hospitals in Chile (n = 9), Paraguay (n = 2), and Uruguay (n = 7) from March 16-November 30, 2022. VE was estimated using a test-negative design and logistic regression models adjusted for country, age, sex, presence of ≥1 comorbidity, and week of illness onset. VE estimates were stratified by influenza virus type and subtype (when available) and influenza vaccine target population, categorized as children, individuals with comorbidities, and older adults, defined per countries' national immunization policies. RESULTS: Among the 3147 SARI cases, there were 382 (12.1%) influenza test-positive case patients; 328 (85.9%) influenza case patients were in Chile, 33 (8.6%) were in Paraguay, and 21 (5.5%) were in Uruguay. In all countries, the predominant subtype was influenza A(H3N2) (92.6% of influenza cases). Adjusted VE against any influenza-associated SARI hospitalization was 33.8% (95% confidence interval: 15.3%, 48.2%); VE against influenza A(H3N2)-associated SARI hospitalization was 30.4% (95% confidence interval: 10.1%, 46.0%). VE estimates were similar across target populations. CONCLUSION: During the 2022 influenza season, influenza vaccination reduced the odds of hospitalization among those vaccinated by one-third. Health officials should encourage influenza vaccination in accordance with national recommendations.

A multiplex-NGS approach to identifying respiratory RNA viruses during the COVID-19 pandemic.

A methodological approach based on reverse transcription (RT)-multiplex PCR followed by next-generation sequencing (NGS) was implemented to identify multiple respiratory RNA viruses simultaneously. A convenience sampling from respiratory surveillance and SARS-CoV-2 diagnosis in 2020 and 2021 in Montevideo, Uruguay, was analyzed. The results revealed the cocirculation of SARS-CoV-2 with human rhinovirus (hRV) A, B and C, human respiratory syncytial virus (hRSV) B, influenza A virus, and metapneumovirus B1. SARS-CoV-2 coinfections with hRV or hRSV B and influenza A virus coinfections with hRV C were identified in adults and/or children. This methodology combines the benefits of multiplex genomic amplification with the sensitivity and information provided by NGS. An advantage is that additional viral targets can be incorporated, making it a helpful tool to investigate the cocirculation and coinfections of respiratory viruses in pandemic and post-pandemic contexts.

Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay.

The genetic variability of SARS-CoV-2 (genus Betacoronavirus, family Coronaviridae) has been scrutinized since its first detection in December 2019. Although the role of structural variants, particularly deletions, in virus evolution is little explored, these genome changes are extremely frequent. They are associated with relevant processes, including immune escape and attenuation. Deletions commonly occur in accessory ORFs and might even lead to the complete loss of one or more ORFs. This scenario poses an interesting question about the origin and spreading of extreme structural rearrangements that persist without compromising virus viability. Here, we analyze the genome of SARS-CoV-2 in late 2021 in Uruguay and identify a Delta lineage (AY.20) that experienced a large deletion (872 nucleotides according to the reference Wuhan strain) that removes the 7a, 7b, and 8 ORFs. Deleted viruses coexist with wild-type (without deletion) AY.20 and AY.43 strains. The Uruguayan deletion is like those identified in Delta strains from Poland and Japan but occurs in a different Delta clade. Besides providing proof of the circulation of this large deletion in America, we infer that the 872-deletion arises by the consecutive occurrence of a 6-nucleotide deletion, characteristic of delta strains, and an 866-nucleotide deletion that arose independently in the AY.20 Uruguayan lineage. The largest deletion occurs adjacent to transcription regulatory sequences needed to synthesize the nested set of subgenomic mRNAs that serve as templates for transcription. Our findings support the role of transcription sequences as a hotspot for copy-choice recombination and highlight the remarkable dynamic of SARS-CoV-2 genomes.

Increased Detection of Carbapenemase-Producing Enterobacterales Bacteria in Latin America and the Caribbean during the COVID-19 Pandemic.

During 2020-2021, countries in Latin America and the Caribbean reported clinical emergence of carbapenemase-producing Enterobacterales that had not been previously characterized locally, increased prevalence of carbapenemases that had previously been detected, and co-production of multiple carbapenemases in some isolates. These increases were likely fueled by changes related to the COVID-19 pandemic, including empirical antibiotic use for potential COVID-19-related bacterial infections and healthcare limitations resulting from the rapid rise in COVID-19 cases. Strengthening antimicrobial resistance surveillance, epidemiologic research, and infection prevention and control programs and antimicrobial stewardship in clinical settings can help prevent emergence and transmission of carbapenemase-producing Enterobacterales.

[Epidemiological and clinical characteristics of children with COVID-19 cared for in a private health provider in Uruguay]. / Características epidemiológicas y clínicas de los niños con COVID-19 asistidos en un prestador de salud privado de Uruguay.

BACKGROUND: After the detection of the first cases of SARS-CoV-2 and the declaration of a health emergency in the country, community transmission of the virus remained low to moderate until November 2020, later becoming medium and high. Children under 15 years of age constitute the least affected group. The diagnosis is confirmed by RT-qPCR. The usefulness of the CT (cycle threshold) is discussed. AIM: To describe the epidemiological and clinical characteristics of children infected with SARS-CoV-2 and the relationship between the CT value and clinical presentation. METHOD: A descriptive, retrospective study was carried out in patients under 16 years of age with SARS-CoV-2 infection, assisted by a health provider in Montevideo between epidemiological week (EW) 3 of2020 and EW 9 of2021. Clinical variables, epidemiological notion, severity and evolution were described. The CT value at diagnosis was recorded and compared with the presence of symptoms. RESULTS: Patients under 16 years of age represented 16.6% of the total infected (794 in 4,792). 70% of the cases occurred between the months of January and February 2021. 67.6% presented intradomiciliary contact. The mean age was 7.5 ± 4.1 years, 51% were male. 55% presented symptoms and 45% were asymptomatic; no significant differences were observed in the mean, mode and age range of both groups. None presented comorbidities. In the group of 440 symptomatic patients, 55% presented fever: 32% associated with other symptoms, mainly upper respiratory symptoms, and 23% as the only symptom. The CT value was obtained in 536 of the 794 patients (67.5%). The mean CT was 29.7+5.8 in the symptomatic group vs. 31.5 ± 5.7 in asymptomatic patients (p > 0.05). Three patients were hospitalized, none required intensive care and none died. CONCLUSIONS: The prevalence and incidence of SARS-CoV-2 infection in children accompany that of adults and the majority had mild or asymptomatic forms, without complications. In this series, the CT value was not different in symptomatic and asymptomatic children. Close household contact was the main source of infection.

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.

Características epidemiológicas y clínicas de los niños con COVID-19 asistidos en un prestador de salud privado de Uruguay / Epidemiological and clinical characteristics of children with COVID-19 cared for in a private health provider in Uruguay

INTRODUCCIÓN: Tras la detección de los primeros casos de SARS-CoV-2 y declararse la emergencia sanitaria en el país, la transmisión comunitaria del virus se mantuvo baja a moderada hasta noviembre de 2020 pasando luego a ser media y alta. Los niños bajo 15 años de edad constituyen el grupo menos afectado. El diagnóstico se confirma mediante RT-qPCR. La utilidad del CT (cycle threshold) es discutida. Objetivo: Describir las características epidemiológicas y clínicas de los niños infectados con SARS-CoV-2 y la relación entre el valor del CT y la presentación clínica. METODOLOGÍA: Se realizó un estudio descriptivo, retrospectivo, en pacientes bajo 16 años de edad con infección por SARS-CoV-2, asistidos en un prestador de salud de Montevideo entre la semana epidemiológica (S.E.) 3 del 2020 y la SE 9 del 2021. Se describieron variables clínicas, noción epidemiológica, gravedad y evolución. Se consignó el valor del CT al diagnóstico y se comparó con la presencia de síntomas. RESULTADOS: Los pacientes bajo 16 años representaron el 16,6% del total de infectados (794 en 4.792). El 70% de los casos ocurrió entre los meses de enero y febrero de 2021. El 67,6% presentó contacto intradomiciliario. La media de edad fue 7,5 ± 4,1 años, 51% de sexo masculino. Presentaron síntomas 55% y fueron asintomáticos 45%; no se observaron diferencias significativas en la media, moda y rango de edades de ambos grupos. Ninguno presentó comorbilidades. En el grupo de los 440 pacientes sintomáticos, 55% presentaron fiebre: 32% asociada con otros síntomas, principalmente respiratorios altos y 23% como único síntoma. El valor de CT se obtuvo en 536 de los 794 pacientes (67,5%). La media de CT fue 29,7 ± 5,8 en el grupo de sintomáticos vs. 31,5 ± 5,7 en asintomáticos (p > 0,05). Se hospitalizaron tres pacientes, ninguno requirió cuidados intensivos ni falleció. CONCLUSIONES: La prevalencia e incidencia de la infección por SARS-CoV-2 en niños acompañan a la de adultos y la mayoría cursó formas leves o asintomáticas, sin complicaciones. En esta serie, el valor de CT no fue diferente en niños sintomáticos y asintomáticos. El contacto estrecho intradomiciliario fue la principal fuente de infección.

BACKGROUND: After the detection of the first cases of SARS-CoV-2 and the declaration of a health emergency in the country, community transmission of the virus remained low to moderate until November 2020, later becoming medium and high. Children under 15 years of age constitute the least affected group. The diagnosis is confirmed by RT-qPCR. The usefulness of the CT (cycle threshold) is discussed. AIM: To describe the epidemiological and clinical characteristics of children infected with SARS-CoV-2 and the relationship between the CT value and clinical presentation. METHOD: A descriptive, retrospective study was carried out in patients under 16 years of age with SARS-CoV-2 infection, assisted by a health provider in Montevideo between epidemiological week (EW) 3 of2020 and EW 9 of2021. Clinical variables, epidemiological notion, severity and evolution were described. The CT value at diagnosis was recorded and compared with the presence of symptoms. RESULTS: Patients under 16 years of age represented 16.6% of the total infected (794 in 4,792). 70% of the cases occurred between the months of January and February 2021. 67.6% presented intradomiciliary contact. The mean age was 7.5 ± 4.1 years, 51% were male. 55% presented symptoms and 45% were asymptomatic; no significant differences were observed in the mean, mode and age range of both groups. None presented comorbidities. In the group of 440 symptomatic patients, 55% presented fever: 32% associated with other symptoms, mainly upper respiratory symptoms, and 23% as the only symptom. The CT value was obtained in 536 of the 794 patients (67.5%). The mean CT was 29.7+5.8 in the symptomatic group vs. 31.5 ± 5.7 in asymptomatic patients (p > 0.05). Three patients were hospitalized, none required intensive care and none died. CONCLUSIONS: The prevalence and incidence of SARS-CoV-2 infection in children accompany that of adults and the majority had mild or asymptomatic forms, without complications. In this series, the CT value was not different in symptomatic and asymptomatic children. Close household contact was the main source of infection.

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.

Genome Sequences of SARS-CoV-2 P.1 (Variant of Concern) and P.2 (Variant of Interest) Identified in Uruguay.

Two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants associated with increased transmission and immune evasion, P.1 and P.2, emerged in Brazil and spread throughout South America. Here, we report genomes corresponding to these variants that were recently detected in Uruguay. These P.1 and P.2 genomes share all substitutions that are characteristic of these variants.

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.

Community strains of methicillin-resistant Staphylococcus aureus as potential cause of healthcare-associated infections, Uruguay, 2002-2004.

Community-associated MRSA (CA-MRSA) strains have emerged in Uruguay. We reviewed Staphylococcus aureus isolates from a large healthcare facility in Montevideo (center A) and obtained information from 3 additional hospitals on patients infected with CA-MRSA. An infection was defined as healthcare-onset if the culture was obtained >48 hours after hospital admission. At center A, the proportion of S. aureus infections caused by CA-MRSA increased from 4% to 23% over 2 years; the proportion caused by healthcare-associated MRSA (HA-MRSA) decreased from 25% to 5%. Of 182 patients infected with CA-MRSA, 38 (21%) had healthcare-onset infections. Pulsed-field gel electrophoresis determined that 22 (92%) of 24 isolates were USA1100, a community strain. CA-MRSA has emerged in Uruguay and appears to have replaced HA-MRSA strains at 1 healthcare facility. In addition, CA-MRSA appears to cause healthcare-onset infections, a finding that emphasizes the need for infection control measures to prevent transmission within healthcare settings.

Prevalencia del síndrome metabólico en una población adulta

RESUMEN Objetivo: determinar la prevalencia de síndrome metabólico en la población adulta y su asociación con variables de estilo de vida potencialmente modificables. Métodos: se estimó la prevalencia de síndrome metabólico de acuerdo a la definición del Programa Nacional de Educación en Colesterol (ATP III) de Estados Unidos, entre 1.411 participantes del estudio epidemiológico que se desarrolla desde 1995 en una muestra representativa de los asociados adultos de la institución. Se realizó ajuste por edad y por sexo de acuerdo a la composición de la población uruguaya. Resultados: la prevalencia no ajustada de síndrome metabólico fue 27,7% y la prevalencia ajustada fue 19,7%. En hombres la prevalencia ajustada fue 23,1% y en mujeres 18,1%. La obesidad o el sobrepeso estuvieron presentes en 93% de los portadores de síndrome metabólico. El 75% de quienes presentan la entidad no realizan actividad física regular. La prevalencia de acuerdo al nivel educativo fue 35,9%, 30,6% y 17,9% (p<0,0001) entre quienes tenían <=6 años, 6 a 12 y >12 años de estudio. La prevalencia entre individuos activos fue 25,2%, siendo de 32,3% y de 30,0% en jubilados y en desocupados (p =0,02). Conclusiones: el síndrome metabólico tiene alta prevalencia en la población estudiada, la que es particularmente elevada en los hombres. El sedentarismo, el sobrepeso y la obesidad son altamente prevalentes entre los portadores de esta entidad. Es necesario identificar a los pacientes con síndrome metabólico y optimizar su estilo de vida para prevenir el desarrollo de enfermedad coronaria. Las estrategias para promover el cambio de estilo de vida deben poner especial énfasis en los grupos de mayor prevalencia.

SUMMARY Objective: to determine prevalence of the metabolic syndrome in an adult population and its association with varying lifestyles. Methods: prevalence of the metabolic syndrome was estimated following the National Cholesterol Education Program (ATP III), United States, among 1 411 adult users of a health-center since 1995. Age and sexe adjustments were done according to the Uruguayan population. Results: unadjusted prevalence of the metabolic syndrome was 27,7% and adjusted prevalence was 19,7%. Adjusted prevalence among men was 23,1%, among women, 18,1%. Obesity and overweight were seen in 93% of the metabolic syndrome carriers. Regular physical activity was practiced by 25%. Prevalence according to educational level was 35,9%, 30,6% y 17,9% (p<0,0001) among those with 6 years, 6 to 12 and >12 years of education. Prevalence among active adults was 25,2%, while among retired and unemployed people, 32,3% and 30,0% respectively (p=0,02). Conclusions: prevalence of the metabolic syndrome was high among the studied population, particularly among men. Sedentarism, overweight and obesity are particularly prevalent among metabolic syndrome carriers. Carriers of metabolic syndrome should be identify in order to optimize their lifestyles and consequently to prevent coronary disease.

Comparison of hepatitis C viral loads in patients with or without coinfection with different genotypes.

Hepatitis C virus genotyping was assessed for 257 chronic hepatitis C patients with viral loads above 1,000 IU/ml. Twelve patients were coinfected with more than one genotype. Their median viral loads did not differ significantly from those observed for monoinfected patients, which in turn did not vary significantly among different genotypes.

Acute respiratory infections in children from a derived urban population from Uruguay

Para obter informacao basica sobre a incidencia, duracao, caracteristicas clinicas e etiologia das infeccoes respiratorias agudas (IRA), foram observadas 276 criancas de familias pobres que moram em Montevideo durante 32 meses. A populacao alvo foi dividida em dois grupos para analise dos resultados: Criancas com menos de 12 meses e acima dessa idade. Durante o periodo de seguimento foram registrados 1056 episodios de IRA. A incidencia de IRA foi 5.2 por crianca/ano. Foi 87 por cento mais alta nos lactentes do que nos grupos de mais idade, com duracao maior dos episodios. A maioria das infeccoes foi pouco grave...

Serotipos y susceptibilidad a los antibacterianos de S. pneumoniae aislados de poblaciones infantiles (1987-1990) / Serotypes and susceptibility of the antibacterians of S. pneumoneal isolated from infantile populations (1987-1990)

Cepas de S. pneumoniae aisladas entre 1987 y 1990, de niños con neumonía, otitis media aguda o ambos, de la nasofaringe de pacientes con esas patologías y de controles sanos, fueron tipificadas y estudiada su susceptibilidad a la penicilina y cotrimoxazol. Se determinó la presencia y frecuencia de los 83 serotipos de S. pneumoniae en las cepas invasivas (n= 70), en las que producían infecciones localizadas (n= 12) y en las que colonizaban la orofaringe (n= 98). El serotipo 14 predominó entre las cepas invasivas (34.3 por ciento ). Conjuntamente con los tipos 9V, 1, 3 y 5 constituyeron la mayoría (75.7 por ciento ). En escaso número de pacientes, los serotipos de cepas aisladas de la sangre o de derrame pleural, coincidieron con los resultados de los cultivos de la orofaringe. La resistencia a la penicilina fue baja en el total de cepas tipificadas (4.6 por ciento ) y menor aún en las cepas invasivas (2.6 por ciento ). Sólo 68.7 por ciento de las cepas fueron sensibles al cotrimoxazol. Las cepas resistentes a los fármacos mencionados no se asociaron a ningún serotipo en especial. Se concluye que son pocos los serotipos que se asocian a las neumonías del niño, y que la resistencia a la penicilina, hasta el momento, no constituye una limitación para su uso