Continuous genomic diversification of long polynucleotide fragments drives the emergence of new SARS-CoV-2 variants of concern

Wearable Devices and Explainable Unsupervised Learning for COVID-19 Detection and Monitoring

Despite the declining COVID-19 cases, global healthcare systems still face significant challenges due to ongoing infections, especially among fully vaccinated individuals, including adolescents and young adults (AYA). To tackle this issue, cost-effective alternatives utilizing technologies like Artificial Intelligence (AI) and wearable devices have emerged for disease screening, diagnosis, and monitoring. However, many AI solutions in this context heavily rely on supervised learning techniques, which pose challenges such as human labeling reliability and time-consuming data annotation. In this study, we propose an innovative unsupervised framework that leverages smartwatch data to detect and monitor COVID-19 infections. We utilize longitudinal data, including heart rate (HR), heart rate variability (HRV), and physical activity measured via step count, collected through the continuous monitoring of volunteers. Our goal is to offer effective and affordable solutions for COVID-19 detection and monitoring. Our unsupervised framework employs interpretable clusters of normal and abnormal measures, facilitating disease progression detection. Additionally, we enhance result interpretation by leveraging the language model Davinci GPT-3 to gain deeper insights into the underlying data patterns and relationships. Our results demonstrate the effectiveness of unsupervised learning, achieving a Silhouette score of 0.55. Furthermore, validation using supervised learning techniques yields high accuracy (0.884 ± 0.005), precision (0.80 ± 0.112), and recall (0.817 ± 0.037). These promising findings indicate the potential of unsupervised techniques for identifying inflammatory markers, contributing to the development of efficient and reliable COVID-19 detection and monitoring methods. Our study shows the capabilities of AI and wearables, reflecting the pursuit of low-cost, accessible solutions for addressing health challenges related to inflammatory diseases, thereby opening new avenues for scalable and widely applicable health monitoring solutions.

Quantifying the immunological distinctiveness of emerging SARS-CoV-2 variants in the context of prior regional herd exposure

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 epidemiological 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 (Area Under the Curve, AUC = 0.88 [95% confidence interval 0.86 to 0.90]). 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.