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PremiseTransposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long‐read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. Unfortunately, TE annotation currently represents a bottleneck in the annotation of genome assemblies.Methods and ResultsWe present a new functionality of the Next‐Generation Sequencing Experience Platform (NGSEP) to perform efficient homology‐based TE annotation. Sequences in a reference library are treated as long reads and mapped to an input genome assembly. A hierarchical annotation is then assigned by homology using the annotation of the reference library. We tested the performance of our algorithm on genome assemblies of different plant species, including Arabidopsis thaliana, Oryza sativa, Coffea humblotiana, and Triticum aestivum (bread wheat). Our algorithm outperforms traditional homology‐based annotation tools in speed by a factor of three to >20, reducing the annotation time of the T. aestivum genome from months to hours, and recovering up to 80% of TEs annotated with RepeatMasker with a precision of up to 0.95.ConclusionsNGSEP allows rapid analysis of TEs, especially in very large and TE‐rich plant genomes.

Introducción: el COVID-19 en la edad pediátrica se describe con menor severidad, aunque la literatura en este grupo etario es limitada, principalmente en el contexto local. El presente estudio describe las características sociodemográficas, clínicas y desenlaces de los pacientes menores de 18 años hospitalizados con diagnóstico confirmado de COVID-19. Metodos: estudio observacional, descriptivo, de tipo cohorte retrospectiva en pacientes pediátricos diagnosticados con SARS-CoV-2 hospitalizados en la Clínica Infantil Colsubsidio en la ciudad de Bogotá, Colombia durante el periodo transcurrido entre marzo del 2020 y abril del 2021. Resultados: se incluyeron 230 pacientes, con dos picos epidemiológicos: agosto de 2 020 y abril de 2 021; Hubo predominio del género masculino (57.4 %) y la edad menor de 2 años. Los principales síntomas fueron tos (60 %), congestión nasal (33.9 %) y diarrea (22.2 %). La estancia media fue de 7.8 días (DS: 13.9 días) y el 25.2 % requirió manejo en UCIP. El 60 % de los casos presentaron linfopenia y trombocitopenia. El principal hallazgo en la radiografía de tórax fue el engrosamiento peribronquial. El 25.2 % (n=58) recibió esteroides y el 5.2 % (n=12) inmunoglobulina en el contexto de Síndrome Inflamatorio Mulstisistémico Temporalmente Asociado a COVID19 (SIMS-TAC). El 38.3 % tuvo manejo antibiótico por sospecha de coinfección bacteriana. La mortalidad fue del 2.2 %.Conclusión: el COVID-19 en niños tiene particularidades en comparación con los adultos, en nuestro estudio se evidenció mayor severidad a menor rango de edad, predominio del género masculino y una tasa de mortalidad menor a la de los adultos hospitalizados. Se requieren más estudios de contexto local.

Background Pneumococcal conjugate vaccines (PCV) have decreased pneumonia in children. Colombia introduced massive vaccination with PCV10 in 2012. Methods Pneumococcal pneumonia cases from 10 hospitals part of an active surveillance network for invasive pneumococcal disease were included. Two periods were compared, pre-PCV10: 2008-2012 and post-PCV10: 2014-2019. The objective was to compare characteristics and outcomes before and after PCV10. Results 370 cases were included. Serotype 1(15, 11.2%) and 14 (33, 24.6%) were the most frequent in Pre-PCV10, with only 4(3%) 19A and 1(0.7%) serotype 3. Post-PCV10, serotype 1 decreased to 6(3.1%), 14 to 15(7.8%), while 19A increased to 58(30.2%), serotype 3 to 32(16.7%) and 6A to 7(3.6%) (p = < 0.001), (Graph 1). Complicated pneumonia (CN) also increased (13.4% to 31,8%) (p< 0,001). Pre-PVC10, 44% of CN were due to PCV10 serotypes; with no PCV13 serotypes cases. Post-vaccine period, PCV10 explained only 8.2% and PCV13 60.6%(p < 0.001) of CN. Comparing PICU requirement among predominant serotypes on each period; 23.5% of serotypes 14 and 27.2% of serotypes 1 were admitted, while 59.4% of serotypes 3, 56.9 % of 19A and 42.8% of 6A required PICU. The median of hospitalization increased from 8(5.5-15) to 12 (7-22) days (p < 0.001), as well as the frequency of PICU, 32.8% to 51.6 %, (p = 0.001). Penicillin prescription was similar (17.2% -15.7%), with decrease in ampicillin use (28.4% - 3.6%) and increase ampicillin-sulbactam (0.7% to 24%), and ceftriaxone / clindamycin (0.7% to 5.7%) in post-PCV10. The duration of empirical antibiotic treatment was 7(4-11) and increased to 10(6-17) (p = < 0.001). Lethality showed a slight, non-significant increase between periods 7.5% vs. 9.9% (p = 0.57). (Table1) Graph 1. Serotype distribution 2008 - 2019 Year 2012, PCV10 introduced 2 + 1 schedule. Table 1. Outcomes in the Pre-PCV10 and Post-PCV10 Period Conclusion PCV10 significantly decreased vaccine serotypes, with increase in PCV13 serotypes. 19A, 3 and 6A the predominant serotypes had greater severity including PICU admission, CN and more resistance, with an increase in the use of broad-spectrum antibiotics and longer hospitalization. The current data support national and regional evidence on the importance of replacing PCV10 to a higher valence that include 19A, as PCV13, with the aim of reducing the circulation, particularly of this serotype. Disclosures Ivan Felipe Gutiérrez Tobar, n/a, Pfizer and MSD (Advisor or Review Panel member, Research Grant or Support, Speaker’s Bureau, Has received support from Pfizer and MSD for participation in congresses and has received conference payments from Pfizer)Pfizer and MSD (Speaker’s Bureau, Other Financial or Material Support, Has received support from Pfizer for participation in congresses) Cristina Mariño Drews, n/a, Pfizer (Other Financial or Material Support, Has received support from Pfizer for participation in congresses) Sandra Beltran, n/a, Pfizer (Other Financial or Material Support, Has received support from Pfizer for participation in congresses) Aura Lucia Leal Castro, MD, Pfizer and MSD (Research Grant or Support, Speaker’s Bureau, Other Financial or Material Support, Has received support from Pfizer for participation in congresses) Aura Lucia Leal Castro, n/a, Pfizer and MSD (Research Grant or Support, Speaker’s Bureau, Other Financial or Material Support, Has received support from Pfizer for participation in congresses) Jaime alberto Patiño-Niño, n/a, Pfizer (Research Grant or Support, Speaker’s Bureau, Other Financial or Material Support, Has received support from Pfizer for participation in congresses) Martha Isabel Alvarez-Olmos, n/a, Pfizer (Other Financial or Material Support, Has received support from Pfizer for participation in congresses) Rocio Barrero Barreto, n/a, Pfizer and MSD (Other Financial or Material Support, Has received support from Pfizer and MSD for participation in congresses and has received conference payments from Pfizer) Fabio Espinosa, n/a, MSD (Research Grant or Support, Other Financial or Material Support, Has received support from MSD for other research.) Nicolas Ramos, n/a, Pfizer (Other Financial or Material Support, Has received support from Pfizer for participation in congresses) Vivian Marcela Moreno Mejia, n/a, Pfizer (Research Grant or Support)