Cov2clusters: genomic clustering of SARS-CoV-2 sequences

BackgroundThe COVID-19 pandemic remains a global public health concern. Advances in sequencing technologies has allowed for high numbers of SARS-CoV-2 whole genome sequence (WGS) data and rapid sharing of sequences through global repositories to enable almost real-time genomic analysis of the pathogen. WGS data has been used previously to group genetically similar viral pathogens to reveal evidence of transmission, including methods that identify distinct clusters on a phylogenetic tree. Identifying clusters of linked cases can aid in the regional surveillance and management of the disease. In this study, we present a novel method for producing stable genomic clusters of SARS-CoV-2 cases, cov2clusters, and compare the sensitivity and stability of our approach to previous methods used for phylogenetic clustering using real-world SARS-CoV-2 sequence data obtained from British Columbia, Canada, ResultsWe found that cov2clusters produced more stable clusters than previously used phylogenetic clustering methods when adding sequence data through time, mimicking an increase in sequence data through the pandemic. Our method also showed high sensitivity when compared to epidemiologically informed clusters. ConclusionsOur new approach allows for the identification of stable clusters of SARS-CoV-2 from WGS data. Producing high-resolution SARS-CoV-2 clusters from sequence data alone can a challenge and, where possible, both genomic and epidemiological data should be used in combination.

Essential Medications for Patients With Suspected or Confirmed Ebola Virus Disease in Resource-Limited Environments.

BACKGROUND: In 2014, the U.S. Public Health Service (USPHS) Commissioned Corps deployed to Monrovia, Liberia, to operate a 25-bed Ebola treatment unit (ETU) constructed by the U.S. Military. The ETU was named the Monrovia Medical Unit (MMU) and was constructed from an U.S. Air Force Expeditionary Medical Support (EMEDS) unit with modifications on the basis of consultation from Médecins Sans Frontières, the World Health Organization, and expert panels from the U.S. Department of Defense and Department of Health and Human Services. From November 12, 2014, to April 30, 2015, 42 patients (18 confirmed Ebola virus disease [EVD] and 24 suspected EVD) from nine countries were treated by USPHS providers at the MMU. The medications used in the MMU were primarily procured from the EMEDS 25-bed pharmacy cache. However, specific formulary additions were made for treatment of EVD. METHODS: Using the MMU pharmacy dispensing data, we compared and contrasted the medications used in the MMU with recommendations in published EVD treatment guidelines for austere settings. FINDINGS: After comparing and contrasting the MMU pharmacy dispensing data with publications with EVD medication recommendations applicable to resource-limited settings, 101 medications were included in the USPHS Essential Medications for the Management of EVD List (EML) for an austere, isolated clinical environment. DISCUSSION/IMPACT/RECOMMENDATIONS: Because Ebola outbreaks often occur in remote areas, proactive planning, improved preparedness, and optimal patient care for EVD are needed, especially in the context of austere environments with a scarcity of resources. We developed the EML to assist in the planning for future Ebola outbreaks in a remote clinical environment and to provide a list of medications that have been used in an ETU. The EML is a comprehensive medication list that builds on the existing publications with EVD treatment recommendations applicable to supply-constrained clinical environments. As well, it is a resource for the provision of medications when evaluating donations, procurement, and may help inform estimates for product inventory requirements for an ETU. We hope the EML will improve readiness and enhance the capabilities of local and regional international responders.

Low utility of Oncotype DX® in the clinic.

Precision medicine tools are currently making their way into the clinic and being utilized to diagnose, prognose, and individualize cancer care. The multi-gene expression-based assay, Oncotype DX® (ODX), is a genomic tumor profiling tool that determines the expression of 21 tumor- associated genes; it helps determine the risk for distant recurrence and whether chemotherapy is an appropriate course of treatment in patients with early stage, estrogen receptor (ER) positive, HER2 negative, and lymph node negative (or 1-3 positive lymph nodes) invasive BCa. The aim of this study was to determine the overall utilization and uptake of the ODX genomic test in a cross-sectional analysis of the Virginia Tumor registry, compare utilization in African Americans (AAs) and Caucasian Americans (CAs), and determine the profile of patients referred for testing. Caucasian (89.7%) patients made up the majority of the ODX testers compared to AAs (10.3%) (P < 0.0001). Those who received ODX testing were less likely to have higher grade and higher stage tumors, and were less likely to be ER negative (RR = 0.21, 95% CI: 0.01-0.31), progesterone receptor (PR) negative (RR = 0.35, 95% CI: 0.27-0.45), HER2 amplified (RR = 0.27, 95% CI: 0.17-0.43), or triple negative (RR = 0.21, 95% CI: 0.14-0.33). Of the patients that were eligible (n = 3924), 10.5% (n = 412) received ODX testing. Specifically, 11.7% of the Caucasian patients and 5.1% of AAs patients received ODX testing (P < 0.001). Our analysis confirmed that the utilization of ODX was low and that AAs were much less likely to receive ODX testing.

In vivo imaging, tracking, and targeting of cancer stem cells.

BACKGROUND: There is increasing evidence that solid cancers contain cancer-initiating cells (CICs) that are capable of regenerating a tumor that has been surgically removed and/or treated with chemotherapy and/or radiation therapy. Currently, cell surface markers, like CD133 or CD44, are used to identify CICs in vitro; however, these markers cannot be used to identify and track CICs in vivo. The 26S proteasome is the main regulator of many processes within a proliferating cell, and its activity may be altered depending on the phenotype of a cell. METHODS: Human glioma and breast cancer cells were engineered to stably express ZsGreen fused to the carboxyl-terminal degron of ornithine decarboxylase, resulting in a fluorescent fusion protein that accumulates in cells in the absence of 26S proteasome activity; activities of individual proteases were monitored in a plate reader by detecting the cleavage of fluorogenic peptide substrates. Proteasome subunit expression in cells expressing the fusion protein was assessed by quantitative reverse transcription-polymerase chain reaction, and the stem cell phenotype of CICs was assessed by a sphere formation assay, by immunohistochemical staining for known stem cell markers in vitro, and by analyzing their tumorigenicity in vivo. CICs were tracked by in vivo fluorescence imaging after radiation treatment of tumor-bearing mice and targeted specifically via a thymidine kinase-degron fusion construct. All P values were derived from two-sided tests. RESULTS: Cancer cells grown as sphere cultures in conditions, which enrich for cancer stem cells (CSCs), had decreased proteasome activity relative to the respective monolayers (percent decrease in chymotryptic-like activity of sphere cultures relative to monolayers--U87MG: 26.64%, 95% confidence interval [CI] = 10.19 to 43.10, GL261, 52.91%, 95% CI = 28.38 to 77.43). The cancer cells with low proteasome activity can thus be monitored in vitro and in vivo by the accumulation of a fluorescent protein (ZsGreen) fused to a degron that targets it for 26S proteasome degradation. In vitro, ZsGreen-positive cells had increased sphere-forming capacity, expressed CSC markers, and lacked differentiation markers compared with ZsGreen-negative cells. In vivo, ZsGreen-positive cells were approximately 100-fold more tumorigenic than ZsGreen-negative cells when injected into nude mice (ZsGreen positive, 30 mice per group; ZsGreen negative, 31 mice per group), and the number of CICs in tumors increased after 72 hours post radiation treatment. CICs were selectively targeted via a proteasome-dependent suicide gene, and their elimination in vivo led to tumor regression. CONCLUSION: Our results demonstrate that reduced 26S proteasome activity is a general feature of CICs that can easily be exploited to identify, track, and target them in vitro and in vivo.