LSU Health Shreveport Viral Threat Lab helps understanding COVID-19 spread in Louisiana
LSU Health Shreveport’s Emerging Viral Threat Lab processed over 110,000 COVID-19 test samples from multiple public health regions of the state and created over 170,000 test kits that were distributed throughout the state during its first six months of operation.
Based on today’s CDC report that 11,348,492 tests having been processed nationally, LSU Health Shreveport has processed almost 0.1% of all COVID tests in the US during its’ first six months of operation, according to information from LSU Health.
The EVT Lab is currently processing 0.13% of all daily testing in the US based on an average of 1,300 tests per day compared to the US average of 1 million tests being processed each day.
Strategic sample collection in north Louisiana nursing homes by the Emerging Viral Threat Lab Strike Team has utilized the EVT Lab’s strong diagnostic potential to result in one of the lowest nursing home positivity rates in the nation at 2%, as there are currently over 33 states with nursing home positivity rates above 5% with some as high as 20%. This favorable positivity rate is due to the ongoing testing of residents and staff using an efficient and rapid qPCR testing, which is over 99.7% reliable.
Understanding how COVID-19 arrived in Louisiana
Data from the Emerging Viral Threat Lab is also contributing to understanding the COVID-19 mutation in Louisiana, how it arrived as well as sharing key data with the national genome databank.
LSUHS researchers working with sequencing partner, MiGS Center in Pittsburgh, PA, have completed viral genome sequencing of 159 SARS-CoV-2 genomes of which 158 are from Louisiana and 1 from Texas.
These genomes are shared on the Global Initiative on Sharing All Influenza Data (GISIAD) which is the central repository for SARS-CoV-2 coronavirus genome sequencing data.
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Mirroring the global and U.S. trends, virtually all of the LSUHS sequences have the D614G mutation in the viral Spike protein, which is hypothesized by some scientists to increase transmission, although there is no evidence that the mutation affects disease severity.
Interestingly, out of a total of 817 completed genomes from Louisiana, the EVT Lab found the only recorded instance in Louisiana of an ancestral D614 virus. As of today (29 September), the GISAID database shows 27,263 SARS-CoV-2 genome sequences from the United States, and 107,014 worldwide.
LSU Health Shreveport is continuing to sequence the viral genomic RNA from COVID-19 test samples and has an additional 138 sequences in the process. The EVT Lab is collaborating with expert genomic epidemiologists to determine the estimated date the SARS-CoV-2 virus entered Louisiana as well as the most likely routes by which the virus came into the state.
Helping patients in need of plasma
The LSUHS Emerging Viral Threat Lab is also impacting clinical care as the serology testing has made it possible for patients at Ochsner LSU Health Shreveport Academic Medical Center as well as other community hospitals to have access to convalescent plasma. Serology testing is required to match donated plasma from recovered COVID patients with current COVID-19 patients in need of antibodies from plasma.
The EVT Lab continues to bring new technologies to LSUHS and to grow its automated capabilities to increase diagnostic testing capacity. The lab is also developing new testing capabilities that will allow the lab to be prepared for the expected combined increase in Influenza and Coronavirus infections this fall.
The EVT Lab functions as a reference lab serving communities through outreach and public surveillance while simultaneously working closely with public health officials and scientists to provide the most effective and timely diagnostic tools.