SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis.

RATIONALE: There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear. OBJECTIVES: We aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis. METHODS: Samples were collected during two waves of COVID-19 at the University of California, Davis Medical Center, in COVID-19 patient serving and staff congregation areas. qRT-PCR positive samples were investigated in Vero cell cultures for cytopathic effects and phylogenetically assessed by whole genome sequencing. MEASUREMENTS AND MAIN RESULTS: Improved cleaning and patient management practices between April and August 2020 were associated with a substantial reduction of SARS-CoV-2 qRT-PCR positivity (from 11% to 2%) in hospital surface samples. Even though we recovered near-complete genome sequences in some, none of the positive samples (11 of 224 total) caused cytopathic effects in cultured cells suggesting this nucleic acid was either not associated with intact virions, or they were present in insufficient numbers for infectivity. Phylogenetic analysis suggested that the SARS-CoV-2 genomes of the positive samples were derived from hospitalized patients. Genomic sequences isolated from qRT-PCR negative samples indicate a superior sensitivity of viral detection by sequencing. CONCLUSIONS: This study confirms the low likelihood that SARS-CoV-2 contamination on hospital surfaces contains infectious virus, disputing the importance of fomites in COVID-19 transmission. Ours is the first report on recovering near-complete SARS-CoV-2 genome sequences directly from environmental surface swabs.

Utility of Mid-Upper Arm Circumference in Diagnosing Malnutrition in Children With Cystic Fibrosis.

BACKGROUND: Standardized diagnostic indicators for malnutrition using growth percentile z-scores (weight for length or body mass index [BMI]) and mid-upper arm circumference (MUAC) z-scores are being used in clinical practice; however, their application to the pediatric cystic fibrosis (CF) population is not well described. In this study, we aim to compare growth percentile z-scores and MUAC z-scores in diagnosing and classifying malnutrition in children with CF and assess the relationship between their degree of malnourishment and corresponding pulmonary function tests (PFTs). METHODS: In this retrospective observational outpatient study of 49 pediatric CF patients, data were collected on baseline characteristics, anthropometrics, and PFTs over 12 months. Agreement in malnutrition diagnoses was quantified by Cohen κ statistics. Pearson test assessed the correlation between MUAC and BMI z-scores as well as PFTs and anthropometrics. Serial anthropometrics and PFTs were obtained and compared for a subset of patients (n = 28). RESULTS: Growth percentile and MUAC z-scores were positively correlated in diagnosing malnutrition (Pearson correlation r = 0.87), but MUAC z-scores identified more patients as malnourished compared with growth percentile z-scores (49% vs 12%, Cohen κ of 0.22 [95% CI, 0.04-0.40]). There was no significant relationship between anthropometrics and PFTs. MUAC z-scores increased significantly over time, but BMI z-scores did not show this trend. CONCLUSIONS: Our small-scale data suggest a promising role for MUAC z-scores in classifying malnutrition and in measuring changes in nutrition status over time in pediatric CF.