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Reducing Transmission with Early Detection Through Wastewater Monitoring with UCSD

Blaine Perdue
| December 12, 2021

Estimated reading time: 4 minutes

University of California San Diego has done a remarkable job containing the on-campus spread of the virus that causes COVID-19. They have done so by utilizing an innovative and proactive approach to virus detection. Dr. Andrew Bartko, Executive Director for the Center for Microbiome Innovation, describes the processes involved and the results achieved, as well as the potential for further public health monitoring tools.

Adam Marko, Director of Life Science Solutions at Panasas, follows up Dr. Bartko’s presentation with a brief talk about the Panasas alternative to traditional multi-tier models of separate storage systems. As data latency and access requirements become more important to HPC, Adam explains how Panasas’ storage solutions can provide optimized results for customers.

 

Panasas Helps Control Covid-19 at UC San Diego

The procedure implemented at UC San Diego aims to reduce the amount of time required to identify an infection outbreak and quickly pinpoint infection locations even before students and staff become symptomatic. This is accomplished by establishing wastewater monitoring points at buildings on campus and testing for the presence of viral DNA. When a positive result is found, occupants of the affected building can be quickly tested and, if infected, quarantined.

The UC San Diego campus currently has 100 sampling sites located at various manhole covers leading to wastewater pipes connected to monitored buildings. Daily samples are taken from each site and quantitative PCR assays are run to test for SARS-CoV-2 viral components. As Dr. Bartko explains, this also presents an opportunity for his lab to test for the presence of and study other components within the samples, such as differences in other microbial composition and quantity that could also point to infection and other microbial anomalies.

Once samples have been collected and analyzed, Dr. Bartko’s team presents the data in a dashboard displaying monitored sites and test results and informs buildings with positive results so that occupants can be told and tested. When done at the building level, this method can quickly narrow down infected students and staff even while they’re still asymptomatic.

This testing procedure has proven incredibly effective. According to Dr. Bartko, the infection rate on campus is 10 times less than the surrounding communities. Panasas has helped make these results possible with its Ultra hardware and fast parallel file system, PanFS. Dr. Bartko credits Panasas with his team’s ability “to look at massive amounts of data in a very timely manner”.

 

Panasas vs. Conventional Tiered Storage

Adam Marko is the Director of Life Science Solutions at Panasas, where he focuses on both helping customers and potential customers understand Panasas’ products and helping engineers understand what customers want. Adam has a background in bioinformatics analysis and research IT consulting.

Adam explains how one of the main pain points in conventional tiered storage solutions is inherent in the tiering structure itself. Different storage media that hold data based on time-based criteria can lead to unacceptable latency for all but the most recently written or accessed data. Other solutions use NVMe drives to store hot files, HDDs for long-term storage, SATA SSDs for everything in between, and possibly tape archives for cold file storage.

While Panasas uses NVMe SSDs, SATA SSDs, and SATA HDDs, PanFS does not separate data by chronological tiers. Rather, PanFS stores all data in a single namespace. File metadata is placed on ultra-low latency NVMe drives to allow the system to find files as quickly as possible. Small files are written to the SATA SSD, while large files are placed on the HDDs. PanFS dynamically manages all data across all drives to provide large-capacity storage with the speed of a high-performance flash solution. Since PanFS is designed to optimize storage performance, users do not need to configure file location rules nor consider where they are going to manually store files or when to transfer them to other media.

The adaptability of PanFS to changing workloads is ideal for Life Science applications. Adam wraps up with two case studies talking about Panasas’ performance and capacity compared to cost versus other vendors.


Watch the video here:

Connect with Adam to learn how Panasas can advance your research efforts.