Using an Unsupervised Clustering Model to Detect the Early Spread of SARS-CoV-2 Worldwide.

Deciphering the population structure of SARS-CoV-2 is critical to inform public health management and reduce the risk of future dissemination. With the continuous accruing of SARS-CoV-2 genomes worldwide, discovering an effective way to group these genomes is critical for organizing the landscape of the population structure of the virus. Taking advantage of recently published state-of-the-art machine learning algorithms, we used an unsupervised deep learning clustering algorithm to group a total of 16,873 SARS-CoV-2 genomes. Using single nucleotide polymorphisms as input features, we identified six major subtypes of SARS-CoV-2. The proportions of the clusters across the continents revealed distinct geographical distributions. Comprehensive analysis indicated that both genetic factors and human migration factors shaped the specific geographical distribution of the population structure. This study provides a different approach using clustering methods to study the population structure of a never-seen-before and fast-growing species such as SARS-CoV-2. Moreover, clustering techniques can be used for further studies of local population structures of the proliferating virus.

Resilience, Anxiety, Stress, and Substance Use Patterns During COVID-19 Pandemic in the Miami Adult Studies on HIV (MASH) Cohort.

We evaluated mental health and substance use during the COVID-19 pandemic in 196 participants from the Miami Adult Studies on HIV (MASH) Cohort. A survey was administered between July-August of 2020, including validated measures of resilience and anxiety, a scale to measure COVID-19-related worry, and self-reported substance use. Compared to HIV-uninfected participants (n = 80), those living with HIV (n = 116) reported fewer anxiety symptoms, less COVID-19-related worry, and higher resilience. Those with more anxiety symptoms and lower resilience engaged in more frequent alcohol consumption, binge drinking, and cocaine use. Alcohol misuse was more common among HIV-uninfected participants. Cocaine use was reported by 21% fewer participants during the pandemic compared with 7.3 ± 1.5 months earlier. Possibly due to their experiences with HIV, PLWH responded with higher resilience and reduced worry and anxiety to the adversities brought by the COVID-19 pandemic.