Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

During the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and to support rapid experimental examination of genome-informed vaccine and therapeutic designs. Given the broad range of methods applied to generate new viral genomes, it is critical that consensus and variant calling tools yield consistent results across disparate pipelines. Here we examine the impact of sequencing technologies (Illumina and Oxford Nanopore) and 7 different downstream bioinformatic protocols on SARS-CoV-2 variant calling as part of the NIH Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) Tracking Resistance and Coronavirus Evolution (TRACE) initiative, a public-private partnership established to address the COVID-19 outbreak. Our results indicate that bioinformatic workflows can yield consensus genomes with different single nucleotide polymorphisms, insertions, and/or deletions even when using the same raw sequence input datasets. We introduce the use of a specific suite of parameters and protocols that greatly improves the agreement among pipelines developed by diverse organizations. Such consistency among bioinformatic pipelines is fundamental to SARS-CoV-2 and future pathogen surveillance efforts. The application of analysis standards is necessary to more accurately document phylogenomic trends and support data-driven public health responses.

Competitive fitness of emerging SARS-CoV-2 variants is linked to their Distinctiveness relative to preceding lineages from that region

The COVID-19 pandemic has seen the persistent emergence of immune-evasive SARS-CoV-2 variants under the selection pressure of natural and vaccination-acquired immunity. However, it is currently challenging to quantify how immunologically distinct a new variant is compared to all the prior variants to which a population has been exposed. Here we define Distinctiveness of SARS-CoV-2 sequences based on a proteome-wide comparison with all prior sequences from the same geographical region. We observe a correlation between Distinctiveness relative to contemporary sequences and future change in prevalence of a newly circulating lineage (Pearson r = 0.75), suggesting that the Distinctiveness of emergent SARS-CoV-2 lineages is associated with their competitive fitness. We further show that the average Distinctiveness of sequences belonging to a lineage, relative to the Distinctiveness of other sequences that occur at the same place and time (n = 944 location/time data points), is predictive of future increases in prevalence (AUC = 0.88, 0.86-0.90 95% confidence interval). By assessing the Delta variant in India versus Brazil, we show that the same lineage can have different Distinctiveness-contributing positions in different geographical regions depending on the other variants that previously circulated in those regions. Finally, we find that positions that constitute epitopes contribute disproportionately (20-fold higher than the average position) to Distinctiveness. Overall, this study suggests that real-time assessment of new SARS-CoV-2 variants in the context of prior regional herd exposure via Distinctiveness can augment genomic surveillance efforts.

Effects of a classroom-based yoga intervention on cortisol and behavior in second- and third-grade students: a pilot study.

This uncontrolled pilot study examined the effects of a classroom-based yoga intervention on cortisol concentrations and perceived behavior in children. A 10-week Yoga 4 Classrooms intervention was implemented in one second-grade and one third-grade classroom. Students' salivary cortisol responses were assessed at 3 time points. Classroom teachers also documented their perceptions of the effects of the intervention on students' cognitive, social, and emotional skills. Second, but not third, graders showed a significant decrease in baseline cortisol from before to after the intervention. Second and third graders both showed significant decreases in cortisol from before to after a cognitive task, but neither grade showed additional decreases from before to after a single yoga class. The second-grade teacher perceived significant improvements in several aspects his/her students' behavior. The third-grade teacher perceived some, but fewer, improvements in his/her students' behavior. Results suggest that school-based yoga may be advantageous for stress management and behavior.

Redo autograft operations after the Ross procedure.

BACKGROUND: Autograft dilatation after the Ross procedure is the most common cause of late autograft failure. We looked at results after reoperation for autograft dysfunction using autograft sparing and composite root replacement techniques. METHODS: Data were abstracted from our prospectively collected Ross registry for 160 consecutive patients who underwent a Ross procedure by a single surgeon between 1994 and 2008. Follow-up records were obtained, and the last echocardiographic report after reoperation was analyzed. RESULTS: Autograft reoperation was necessary in 17 patients, at a median interval of 6.9 years after the original procedure. Indications for reoperation were insufficiency with autograft dilatation in 16 patients, and without dilatation in 1 patient. Surgical procedures used at reoperation included autograft reimplantation in 6 patients (35.3%), autograft remodeling procedure in 1 patient (5.9%), composite root replacement with mechanical valved conduit in 5 patients (29.4%), composite root replacement with biologic valved conduit in 3 patients (17.6%), and mechanical aortic valve replacement in 2 patients (11.8%). At a median follow-up of 5.0 years after reoperation, freedom from greater than 2+ aortic insufficiency was 100% (17 of 17 patients) in both reimplantation and replacement groups. There was 1 death after reoperation (at >14 years) related to complications from systemic lupus erythematosus. There have been no strokes after autograft reimplantation. CONCLUSIONS: Autograft valve reimplantation and composite aortic root replacement are effective treatments for aortic root dilatation and aortic insufficiency after the Ross procedure. Echocardiographic follow-up demonstrates reasonable short-term function after autograft preservation procedures.