The Emerging Viral Threat (EVT) Lab at LSU Health Shreveport has now sequenced a total 651 Louisiana SARS-CoV-2 virus genomes making them the largest contributor to date of genetic data on SARS-CoV-2 in the state. SARS-CoV-2, which is short for ‘Severe Acute Respiratory Syndrome Coronavirus-2,’ is the virus that causes COVID-19, and viral genome sequencing is contributing to a worldwide effort to fight the ongoing pandemic.
LSU Health Shreveport is working closely with GISAID which after years of experience with influenza epidemics, has now also emerged as the world’s go-to data resource, exclusively enabling real-time data analyses that drive crucial results for targeted responses to the SARS-CoV-2. Responses to date include but are not limited to identification of potential drug and vaccine targets, evidence that the virus has not drifted to a significant strain difference, and development of diagnostic kits for future mutations of COVID-19. Scientists can rapidly and openly access data through GISAID’s extensive network of researchers providing the timely generation of curated genomic data through a collaborative effort. “Dr. Jeremy Kamil and his colleagues at LSU Health Shreveport are much respected for their quality work in genome sequencing and their interactions with GISAID’s data curation teams placed across the globe”, says GISAID’s Cheryl Bennett.
GISAID is currently reporting 1,361 total virus genomes from Louisiana, of which 651 (48 %) are from LSU Health Shreveport. Others submitting genome sequencing data for Louisiana are Tulane, Scripps, BioInfo Experts, LSU Baton Rouge, Gingko Bioworks, the CDC, and University of Washington.
There are numerous reasons why genomic sequencing of SARS-CoV-2, the virus that causes COVID-19, is important. These include being able to tell how many times the virus has been introduced into a nursing home, school, or workplace, helping public health officials determine if control measures such as social/physical distancing are working, or whether an outbreak is due to a so-called “super-spreader” event. Sequencing also provides critical surveillance for whether any mutations are emerging that could allow the virus to escape antibodies or vaccines.
“We have found only one mutant so far, a spike mutation called F490L, that might help the virus resist the protective effects of antibodies. But the fact we’ve only seen it once suggests it is either detrimental to the virus or at least does not provide any real-world advantage for the virus,” shared Jeremy Kamil, PhD, a virologist and lead in genomic sequencing at LSUHS. As the virus replicates, new mutations occur. “Most of the mutations detected during sequencing are harmless to the virus and do not impact the clinical course of the disease it causes. However, these mutations provide a unique “bar code” to allow scientists to trace SARS-CoV-2 outbreak clusters. Dr. Kamil likens a unique “bar code” to a misspelled word in a book chapter, which can be identified by that mistake every time the book is photocopied. Specific combinations of mutations in a given genome are passed along every time the virus infects a new person, and can be used to trace transmission chains. On a larger scale, keeping track of the “sub-strains” or “variants” and their mutations, by sequencing the virus from patient samples, is essential for understanding how it is spreading in the region and around the world. For instance, this type of genetic data allowed scientists to discern that SARS-CoV-2 mostly came to the United States via Europe and not from China directly. With the EVT Lab processing more than 8,000 COVID-19 test samples per week, sequencing of the virus from COVID-19 positive samples is helping scientists understand how SARS-CoV-2 is spreading within our community.
The nursing home COVID testing program is being led by LSUHS physician scientist John Vanchiere, MD, PhD. This testing has been instrumental to genomic sequencing in north Louisiana and has resulted in one of the lowest nursing home positivity rates in the nation at an average of 2%.
THE LSUHS COVID-19 sequencing has been a collaborative effort with MiGS, the Microbial Genome Sequencing Center of Pittsburgh, PA, which sequences viral genomes directly from patient RNA samples purified by Dr. Rona Scott, Professor of Microbiology and Immunology.
To visualize sequences, go to https://nextstrain.org/community/emmahodcroft/south-usa-sarscov2/south-central?f_division=Louisiana