Enabling Local SARS-CoV-2 Genomic Surveillance Efforts

As SARS-CoV-2 continues to spread across the globe, random mutations to the 30kb genome introduced during replication have given rise to new variants of the virus. Although many of these have not yet shown a notable increase in transmissibility or virulence of the pathogen, a small subset, classified as variants of concern (VOC), may have a significant epidemiological impact and are currently being monitored closely. The United Kingdom was the first to identify the B.1.1.7 lineage of SARS-CoV-2 through the country’s national genome sequencing initiative, having discovered a subset of alterations to the spike protein which appear to increase infectivity of the virus by as much as 50 percent. With the introduction of additional VOCs, including the B.1.351 strain first identified in South Africa and the P.1 strain from Brazil, questions around the lack of robust national, regional and local genome surveillance programs in much of the world have come to light.

In January of this year, the United States was ranked 43rd globally in the percentage of positive cases sequenced at around 0.3%, even though the country represents approximately 25% of all positive coronavirus cases globally. Although efforts have been taken to increase the number of positive cases sequenced on a national level, there continue to be many states and regions that remain under-represented due to limitations in resources and expertise. As of February 12, the state of Tennessee had sequenced a total of 153 cases, representing 0.02% of all positives in the state, Drs Dawn Richards and Elizabeth Forester at the Baylor Esoteric and Molecular Laboratory at Baylor School are committed to significantly improving regional surveillance efforts. Affiliated with a private secondary school located in the city of Chattanooga, Tenn., the CLIA certified lab has already been instrumental in providing qPCR-based testing for the population of Hamilton county. After identifying one the county’s first cases of the B.1.1.7 strain, the decision was made to expand the lab’s capabilities through the use of next-generation sequencing (NGS). Establishing an integrated workflow to continuously monitor prevalence and emergence of new variants in the population of the surrounding Chattanooga area was the goal, though providing that information to local health authorities in time to assist with critical decisions requires rapid turnaround time. Dr. Forrester, faculty member at the Baylor School and co-director of the Baylor Esoteric and Molecular Laboratory is well aware of those challenges and immediately recognized the significance of the Ion Torrent Genexus System in the context of regional surveillance. “If we were to outsource samples to a reference lab, it would take weeks to get results. With the Genexus system, we’ll be able to share sequencing results with local health systems and public health officials in 24-48 hours.” Using the Ion AmpliSeq SARS-CoV-2 research assay on their Genexus system along with the integrated SARS-CoV-2 analysis workflow, the lab now has the ability to go from extracted sample to consensus sequence of the complete viral genome in less than one day.

The laboratory at Baylor is at the forefront of establishing genome surveillance programs at a local level, but they’re not alone in this effort to build a network of rapid response labs across the U.S. Although large, centralized sequencing efforts will continue to provide information at a national and global scale, states, counties and communities like Chattanooga will only benefit from access to real-time information enabled through decentralization of technologies like NGS and passionate scientists and healthcare professionals like Dr. Richards and Dr. Forrester.