Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus.

Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 5'-UTR-1a-1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3'UTR were predicted. The relative frequencies of missense: silent SNPs were calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in descending order were E, 3b, 5'UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5'UTR did not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of 0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes produced by genetic drift is questioned.

2009 H1N1 fatalities: the New Mexico experience.

Histopathologic features of New Mexico 2009 H1N1 fatalities have not been representative of those reported nationwide. We retrospectively reviewed medical records of all New Mexico 2009 pandemic influenza A (pH1N1) fatalities (n = 50). In cases in which autopsy was performed (n = 12), histologic sections and culture results were examined. In contrast to previously published studies, the majority of our fatalities did not have diffuse alveolar damage (DAD) (2/12; 16.7%). Common findings included pulmonary interstitial inflammation and edema, tracheobronchitis, and pneumonia. Two cases had significant extra-pulmonary manifestations: myocarditis and cerebral edema with herniation. The majority had a rapid disease course: range from 1 to 12 days (median, 2 days), and Native Americans were disproportionately represented among fatalities. These findings suggest that New Mexico H1N1 fatalities generally did not survive long enough to develop the classic picture of DAD. Pathologists should be aware that H1N1 may cause extra-pulmonary pathology and perform postmortem cultures and histologic sampling accordingly.

Acute lower respiratory tract infections by adenovirus in children: histopathologic findings in 18 fatal cases.

Adenoviruses (Ads) are the 2nd-most common cause of acute lower respiratory tract infections of viral etiology in immunocompetent children who require hospitalization in Argentina. A new pathogenic genomic variant, Ad7h, has been identified and was associated with severe sequelae and a high mortality rate. A retrospective observational study was conducted in hospitalized children with acute lower respiratory tract infections between March 1988 and May 2005. Nasopharyngeal or tracheal aspirates, bacteriological analysis on blood samples and pleural fluids, and histopathologic studies on autopsies were performed. A total of 415 children were included in the study. Sixty-two patients died in the acute stage of illness (1-8 weeks), and postmortem examination was performed on 18 of them. Mean age was 8.25 months. The male to female ratio was 1.3∶1. The Ad was genome typed in 9% of all children, of whom 29 corresponded to the Ad7h variant. This genome type was diagnosed in 7 of the autopsies performed. Necrotizing bronchitis and bronchiolitis with abundant typical adenoviral inclusion nuclear cells and diffuse alveolar damage were the most important findings. Superimposed bacterial infection occurred in 11 cases, and cytomegalovirus was found in 1. In our population, Ad respiratory infection was found to have a severe course with sequelae or death. No differences were observed between lesions caused by other previously described genome types and those found in cases in which Ad7h was identified.

Laringotraqueobronquitis en niños hospitalizados: características clínicas / Laryngotracheobronchitis in hospitalized children: clinical features

Introducción: Laringotraqueobronquitis (LTB) es una condición frecuente en niños, con escasos estudios publicados en la literatura nacional. Objetivo: Caracterizar los episodios de LTB en nuestra institución. Método: Estudio retrospectivo descriptivo del 2001 al 2003. Resultados: 68 pacientes sufrieron 72 episodios de LTB. La edad promedio fue 16,5 meses, 62 por ciento eran varones. La mayoría de los ingresos ocurrieron en otoño (65 por ciento). El número de días promedio de síntomas previo al ingreso fue 2, siendo los más frecuentes estridor (85 por ciento), tos seca (78 por ciento) y fiebre (72 por ciento). La estadía promedio duró 1 día. Se identificó virus Parainfluenza en 12 de 23 inmunofluorescencias. La terapia incluyó adrenalina (100 por ciento), corticoides (96 por ciento), oxígeno (15 por ciento), salbutamol (11 por ciento) y antibióticos (11 por ciento). Las complicaciones fueron neumonía (3 por ciento) y traqueitis bacteriana (2 por ciento). Conclusión: En nuestra serie, LTB fue más frecuente en varones y menores de 2 años, con clara estacionalidad, estadías hospitalarias cortas y un bajo riesgo de complicaciones.

Etiologia viral en afecciones broncopulmonares agudas y recidivantes de la infancia / Viral etiology in acute bronchopulmonary and recidivant diseases in childhood

Se estudiaron 289 casos clínicos diagnosticados como: bronquiolitis, bronquitis obstructiva recidivante y neumonitis durante los años 1974 y desde 1978 hasta 1982 inclusive. La edad se distribuyó desde 1 mes a preescolares y todos fueron casos hospitalizados. Los casos de bronquiolitis se encontraron en el grupo menor de 6 meses; las bronquitis obstructivas recidivantes predominaron en el grupo de 6-11 meses y las neumonitis en los dos grupos menores de 1 año de edad. Se estudiaron los sueros pareados, agudo y convalesciente de dichos casos, reacciones de microtécnica de inhibición de la hemaglutinación y fijación de complemento para una batería de antígenos virales respiratorios y M. Pneumoniae. En 141 casos se obtuvo un alza diagnóstica destacando como agente principal el VRS, en los 3 diagnósticos estudiados, seguido de parainfluenza y virus influenza A y B. En menor grado se encontraron casos de adenovirus y de M. pneumoniae