Durability of SARS-CoV-2 Antibodies from Natural Infection in Children and Adolescents

Background. Recent data suggest the SARS-CoV-2 Delta (B.1.617.2) variant is more transmissible among children compared to the Alpha (B.1.1.7) variant. The true incidence and longitudinal presence of antibody response to SARS-CoV-2 infection is not known, however. We provided estimates of antibody response using Texas Coronavirus Antibody REsponse Survey (Texas CARES) data, a prospective population-based seroprevalence project designed to assess antibody status over time among the general population throughout the state. Methods. In October 2020 Texas CARES began enrolling adults (aged 20-80 years) and children (aged 5-19 years). Participants were offered a series of three SARS-CoV-2 antibody tests over 6-8 months, or every 2-3 months that includes the immunoassay for detection of antibodies to the SARS-CoV-2 nucleocapsid protein (Roche N-test). Descriptive characteristics and COVID-19 infection-related symptom status was determined by questionnaire at the time of enrollment and prior to each successive blood draw. This analysis included participants ages 5-to-19 years old who have completed all three antibody assessments. Results. From our sample (n=159; mean age 12.5 years, SD 3.6), 96% of those with evidence of nucleocapsid antibodies at baseline assessment continued to have antibodies > six months later (mean 7.0 months, SD 0.97). There was no difference in the presence of antibodies by symptom status (asymptotic versus symptomatic) or severity (mild-moderate versus severe), sex, age group, or body mass index group (underweight, healthy weight, overweight, obesity) over the three antibody measurement timepoints. Conclusions. These results suggest that infection-induced antibodies persist and thus may provide some protection against future infection for at least half a year. 57.9% of the sample were negative for infection-induced antibodies at their third measurement point, suggesting a significant proportion of children have still not acquired natural infection.

ToKSA - Tokenized Key Sentence Annotation - a Novel Method for Rapid Approximation of Ground Truth for Natural Language Processing

ABSTRACTObjectiveIdentifying phenotypes and pathology from free text is an essential task for clinical work and research. Natural language processing (NLP) is a key tool for processing free text at scale. Developing and validating NLP models requires labelled data. Labels are generated through time-consuming and repetitive manual annotation and are hard to obtain for sensitive clinical data. The objective of this paper is to describe a novel approach for annotating radiology reports.Materials and MethodsWe implemented tokenized key sentence-specific annotation (ToKSA) for annotating clinical data. We demonstrate ToKSA using 180,050 abdominal ultrasound reports with labels generated for symptom status, gallstone status and cholecystectomy status. Firstly, individual sentences are grouped together into a term-frequency matrix. Annotation of key (i.e. the most frequently occurring) sentences is then used to generate labels for multiple reports simultaneously. We compared ToKSA-derived labels to those generated by annotating full reports. We used ToKSA-derived labels to train a document classifier using convolutional neural networks. We compared performance of the classifier to a separate classifier trained on labels based on the full reports.ResultsBy annotating only 2,000 frequent sentences, we were able to generate labels for symptom status for 70,000 reports (accuracy 98.4%), gallstone status for 85,177 reports (accuracy 99.2%) and cholecystectomy status for 85,177 reports (accuracy 100%). The accuracy of the document classifier trained on ToKSA labels was similar (0.1-1.1% more accurate) to the document classifier trained on full report labels.ConclusionToKSA offers an accurate and efficient method for annotating free text clinical data.

Stepwise endo-/epicardial catheter ablation for atrial fibrillation: the Mediterranea approach

Background Outcomes of catheter ablation (CA) among patients with non-paroxysmal atrial fibrillation (AF) are largely disappointing. Purpose We sought to evaluate the feasibility, effectiveness, and safety of a single-stage stepwise endo-/epicardial approach in patients with persistent/longstanding-persistent AF. Methods We enrolled 25 consecutive patients with symptomatic persistent (n=4) or longstanding-persistent (n=21) AF and at least one prior endocardial procedure, who underwent CA using an endo-/epicardial approach. Our anatomical stepwise protocol included multiple endocardial as well as epicardial (Bachmann's bundle [BB] and ligament of Marshall ablations) components, and entailed ablation of atrial tachycardias emerging during the procedure. The primary outcome was freedom from any AF/atrial tachycardia episode after a 3-month blanking period. The secondary outcome was patients' symptom status during follow-up. Results The stepwise endo-/epicardial approach allowed sinus rhythm restoration in 72% of patients, either directly (n=6, 24%) or after AF organization into atrial tachycardia (n=12, 48%). BB's ablation was commonly implicated in arrhythmia termination. After a median follow-up of 266 days (interquartile range, 96 days), survival free from AF/atrial tachycardia was 88%. Antiarrhythmic drugs could be discontinued in 22 patients (88%). As compared to baseline, more patients were asymptomatic at 9-month follow-up (0% vs- 56%, p=0.02). Five patients (20%) developed mild medical complications, whereas one subject (4%) had severe kidney injury requiring dialysis. Conclusion A single-stage endo-/epicardial CA resulted in favorable rhythm and symptom outcomes in a cohort of patients with symptomatic persistent/longstanding-persistent AF and one or more prior endocardial procedures. Epicardial ablation of BB was commonly implicated in procedural success. FUNDunding Acknowledgement Type of funding sources: None.

The Impact of New SARS-CoV-2 Variants on Vaccine Breakthrough: a pilot study on spreading infection in the communities

Background: Coronavirus disease 2019 (COVID-19) vaccines are effective at helping protect against severe disease and death from variants; however, incident of breakthrough infection in vaccinated patients has been increased. Therefore, we aimed to assess the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) new variants of concern in the communities and investigate vaccine breakthrough cases on our laboratory (Ayass Bioscience LLC) confirmed detection of COVID-19 variants in Dallas-Fort Worth (DFW), Texas. Methods: Epidemiologic study has been performed at our laboratory. We studied the viral whole-genome sequence and genotyping analysis on 166 symptomatic cases of COVID-19 which were randomly selected from nasal swab positive cases assessed from June 1st to August 30th, 2021, by reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (CT) values. COVID-19 variants were identified to be dominated by B.1.617.2 (89.2%) and followed by AY.3 (1.8%), B.1.1.7 (4.8%), a combination of B.1.526.1 and B.1.617.2 (3%), B.1.621 (0.6%), and P.2 (0.6%). Result: The CT values showed significant difference among the three age groups: <30 years, 31-60 years, and >60 years by one-way ANOVA (N1: F (2, 118) =4.96, p=0.009; N2: F (2, 118) =4.95, p=0.009). No significant difference was observed by symptom, status of immunization, or vaccine manufacturer. A two-way ANOVA was performed to examine the effect of gender and variant group (Delta and other variants) on the CT values. The analyses revealed a statistically significant interaction between the effect of gender and variant group (N1, F (1.117) = 3.906, p = 0.05; N2, F (1, 117) = 7.402, p = 0.008). Conclusion: Our study shows that Delta, the dominant variant of COVID-19, is spreading in the communities, and vaccine breakthrough cases occurred in the majority of Delta variant (91%) followed by AY.3 (5%), B.1.1.7 (2%) and 2% of the double variant of B.1.526.1 and B.1.617.2. The incidence of the breakthrough cases was not linked to a specific manufacturer. The CT value is likely to associate with age. This study also supports our laboratory's ongoing efforts to sequence the SARS-CoV-2 virus from positive patient samples to identify the new viral variants and possible vaccine breakthrough mutations in the community.

Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2

Background Community surveys of SARS-CoV-2 RT-PCR swab-positivity provide prevalence estimates largely unaffected by biases from who presents for routine case testing. The REal-time Assessment of Community Transmission-1(REACT-1) has estimated swab-positivity approximately monthly since May 2020 in England from RT-PCR testing of self-administered throat and nose swabs in random non-overlapping cross-sectional community samples. Estimating infection incidence from swab-positivity requires an understanding of the persistence of RT-PCR swab positivity in the community. Methods During round 8 of REACT-1 from 6 January to 22 January 2021, of the 2,282 participants who tested RT-PCR positive, we recruited 896 (39%) from whom we collected up to two additional swabs for RT-PCR approximately 6 and 9 days after the initial swab. We estimated sensitivity and duration of positivity using an exponential model of positivity decay, for all participants and for subsets by initial N-gene cycle threshold (Ct) value, symptom status, lineage and age. Estimates of infection incidence were obtained for the entire duration of the REACT-1 study using P-splines. Results We estimated the overall sensitivity of REACT-1 to detect virus on a single swab as 0.79 (0.77, 0.81) and median duration of positivity following a positive test as 9.7 (8.9, 10.6) days. We found greater median duration of positivity where there was a low N-gene Ct value, in those exhibiting symptoms, or for infection with the Alpha variant. The estimated proportion of positive individuals detected on first swab, P0, was found to be higher for those with an initially low N-gene Ct value and those who were pre-symptomatic. When compared to swab-positivity, estimates of infection incidence over the duration of REACT-1 included sharper features with evident transient increases around the time of key changes in social distancing measures. Discussion Home self-swabbing for RT-PCR based on a single swab, as implemented in REACT-1, has high overall sensitivity. However, participants' time-since-infection, symptom status and viral lineage affect the probability of detection and the duration of positivity. These results validate previous efforts to estimate incidence of SARS-CoV-2 from swab-positivity data, and provide a reliable means to obtain community infection estimates to inform policy response.

COVID-19 Projections for K12 Schools in Fall 2021: Significant Transmission without Interventions

Background: Millions of primary school students across the United States are about to return to in-person learning. Amidst circulation of the highly infectious Delta variant, there is danger that without the appropriate safety precautions, substantial amount of school-based spread of COVID-19 may occur. Methods: We used an extended Susceptible-Infected-Recovered computational model to estimate the number of new infections during 1 semester among a student population under different assumptions about mask usage, routine testing, and levels of incoming protection. Our analysis considers three levels of incoming protection (30%, 40%, or 50%; denoted as "low", "mid", or "high"). Universal mask usage decreases infectivity by 50%, and weekly testing may occur among 50% of the student population; positive tests prompt quarantine until recovery, with compliance contingent on symptom status. Results: Without masking and testing, more than 75% of susceptible students become get infected within three months in all settings. With masking, this values decreases to 50% for "low" incoming protection settings ("mid"=35%, "high"=24%). Testing half the masked population ("testing") further drops infections to 22% (16%, 13%). Conclusion: Without interventions in place, the vast majority of susceptible students will become infected through the semester. Universal masking can reduce student infections by 26-78%, and biweekly testing along with masking reduces infections by another 50%. To prevent new infections in the community, limit school absences, and maintain in-person learning, interventions such as masking and testing must be implemented widely, especially among elementary school settings in which children are not yet eligible for the vaccine.

A Real-World Comparison of SARS-CoV-2 Rapid Antigen vs. Polymerase Chain Reaction Testing in Florida

Background The reported sensitivity of rapid, antigen-based diagnostics for SARS-CoV-2 infection varies. Few studies have evaluated rapid antigen tests in real-world settings or among large populations. Methods Beginning October 2020, Florida offered individuals presenting for SARS-CoV-2 testing polymerase chain reaction (PCR) testing if they tested positive by the Abbott BinaxNOW TM COVID-19 Ag Card, were symptomatic, or required or requested PCR testing. We compared test results among individuals who received both types of tests at four publicly-accessible testing sites across Florida. We calculated the positive percent agreement (PPA) between the two test types by symptom status. Subsequently, we evaluated the PPA among individuals regardless of symptoms with lower cycle threshold values (<30). Results Overall, 18,457 individuals were tested via both methods, of which 3,153 (17.1%) were positive by PCR. The PPA for the Abbott BinaxNOW TM COVID-19 Ag Card using the PCR comparator was 49.2% (95% CI 47.4%-50.9%). That performance was moderately improved among symptomatic individuals (51.9%; 95% CI 49.7%-54.0%). When restricted to positive PCR tests with a cycle threshold value <30, regardless of symptom status, the PPA was 75.3% (95% CI 72.8%-77.6%). Conclusion The PPA of the Abbott BinaxNOW TM COVID-19 Ag Card with PCR was lower than among previous reports. Our findings may reflect the performance of the BinaxNOW TM antigen test in real-world settings.