ABSTRACT
IMPORTANCE: In December 2019, an infectious disease caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) emerged. There remains limited information regarding the epidemiology and clinical features of pediatric patients affected by COVID-19, particularly in the pulmonary sub-population. OBJECTIVE: Describe the clinical course of pediatric pulmonary patients with COVID-19 throughout the initial wave of infection at a single pediatric center. METHODS: Retrospective chart review was conducted on 1,350 patients, ≤ 35 years who tested positive for SARS-CoV-2 infection between March 1 and August 31, 2020. Patients followed by our pulmonary group, and evaluated at least once in the three years preceding study completion, were identified for additional chart review. Demographics, pulmonary diagnoses, co-morbidities, presenting symptoms, clinical course and management were collected for analysis. RESULTS: 70 pulmonary patients (mean age 8.3 years, range 8 months to 23 years;45% male;44% Black of African American;29% Hispanic or Latino) were identified from 1,350 patients who tested positive for COVID-19 via nasopharyngeal PCR testing through our hospital system. Most frequently reported symptoms were fever (49%), cough (49%), and nasal congestion (29%). Thirteen patients (19%, mean age 9.2 years, range 12 months to 18 years) required inpatient treatment for symptoms related to SARS-CoV-2 infection, one asymptomatic patient tested positive while admitted. Most common pulmonary diagnoses of those requiring admission were asthma (57%), prematurity (29%), sleepdisordered breathing (29%), and respiratory disorders with positive pressure requirement (29%). For those requiring inpatient care, extra-pulmonary co-morbidities included chronic neurological disorders (71%), gastrointestinal disease (43%), and allergic rhinitis (36%). Disease severity was defined as asymptomatic (17%), mild (67%), moderate (6%), severe (6%), or critical (3%). Mild disease was defined as cases managed outpatient or those admitted for observation and supportive care;moderate as those admitted for medical intervention or respiratory support via supplemental oxygen or high-flow nasal cannula;severe as those who received noninvasive ventilation or an increase in baseline respiratory support;critical were patients who received mechanical ventilation. Inpatient complications associated with SARS-CoV-2 included superinfection, thrombosis, refractory hypoxemia and tracheostomy placement. Seven experienced complications and required intensive care unit services;two required tracheostomy. No deaths were reported. CONCLUSIONS: Patients followed by our pediatric pulmonary group presented with similar symptoms compared to the general pediatric population. The majority of our patients were managed outpatient, however the rate of hospitalization was higher than those of the general pediatric population in existing studies. Of those admitted, few required invasive mechanical ventilation.
ABSTRACT
Background: As the pandemic SARS-CoV-2 virus has spread globally its genome has diversified and distinct clones can now be recognized, tracked, and traced. Identifying clonal groups allows for assessment of geographic spread, transmission events, and identification of more virulent or transmissible emerging strains. Methods: All SARS-CoV-2 genomes (n=17,504) that are complete and high coverage were downloaded from GISAID on May 17th 2020. We developed a GNU-based Virus IDentification (GNUVID) tool that implements a whole genome multilocus sequence typing (wgMLST) scheme composed of all ten ORFs in the SARS-CoV-2 genome. The 10,422 genomes that passed our quality check were fed to the GNUVID tool, which assigned a ST profile to each genome. Global optimum eBURST was then used to cluster the STs in clonal complexes (CCs). Results: Our ST/CC analysis uncovered strong associations of ST/CCs with certain geographical regions but also dynamic local changes in ST/CC prevalence. We also identified several unexpected putative global transmission events (e.g., from the US to the Middle East and reintroduction to China later in the pandemic). We have made our tool (GNUVID) available so that new WG sequences can be rapidly assigned to an ST/CC (https://github.com/ahmedmagds/GNUVID). Conclusion: Our sequence typing system uncovered previously unappreciated transmission events and waves of expansion and replacement of SARS-CoV-2 STs and CCs in different geographical locations, suggesting complex dynamics in viral populations that previously seemed monomorphic. Because, our tool can be rapidly updated with new sequencing data it can track emerging clones and identifying new hotspots.