Precision Medicine Lab Finds Omicron Variant in December
Leslie Capo, Director of Information Services, Originally published December, 2021
Among the 567 new COVID-19 cases reported on December 10, 2021 in Louisiana, two were confirmed cases of the Omicron variant from the New Orleans area found by the LSU Health New Orleans' Precision Medicine Laboratory. Directed by Lucio Miele, MD, PhD, Professor and Chair of Genetics at LSU Health New Orleans School of Medicine, along with Dr. Gordon Love, Professor and Chair of Pathology, the lab sequences samples from positive tests to learn what strains of the virus that causes COVID-19 are infecting patients here. LSU Health New Orleans partners with the Louisiana Department of Health, Ochsner and BioInfoExperts (BIE), a Louisiana company experienced in infectious disease bioinformatics, on the project.
“Sequencing is essentially ‘reading' all the virus's genetic code,” Dr. Miele explains. “The coronavirus genetic code includes approximately 30,000 ‘letters' of RNA that direct the production of all the proteins the virus needs to make copies of itself and infect other cells.”
It's a complex undertaking that starts with patient samples from PCR tests taken with the long swabs that reach so far up the nose that some patients claim touched their brains.
The samples from Ochsner are delivered to LSU Health's CLIA-certified and CAP-inspected Precision Medicine Laboratory that is powered by a $2+ million investment in equipment, including a negative pressure room, extraction robots, 12 PCR amplifiers, a NextSeq550DX and accessory equipment.
“These samples are loaded into a robot that extracts the viral RNA,” adds Miele. “The RNA is then copied into DNA, which is more stable. The DNA is then amplified into many overlapping pieces that are molecularly ‘barcoded' and loaded into a specially designed flow cell. The flow cell is loaded into an automatic sequencer which produces millions of ‘reads' of the overlapping pieces of DNA. The ‘reads' are then assembled into a continuous sequence.”
BIE then compares the sequences produced by LSU Health to the canonical sequence of the original SARS-CoV-2 and all its variants.
“We have seen virtually all Variants of Concern designated by the WHO and CDC at some point in Louisiana,” notes Miele. “Right now, we are monitoring some Delta sub-variants that appear to be particularly adept at infecting vaccinated patients.”
What the Omicron variant will do is a question that does not yet have an answer.
“It contains many of the mutations already seen in other Variants of Concern, but also several brand-new mutations, particularly in the S gene,” Miele points out. “The S gene codes for the Spike protein, which the virus uses to attach to human cells, and it mutates very frequently.”
Omicron may also differ from other variants in another way, a way that concerns scientists around the world.
“Some of the mutations in Omicron suggest that it may be less sensitive to neutralizing antibodies,” Miele says. “These are antibodies that block the virus from entering cells. They recognize specific features of the S protein, and these features are changed in the Omicron variant. There is no published work yet, but it seems that serum from convalescent patients may not neutralize Omicron as well as other variants. This may mean that Omicron will be able to re-infect people who have been infected before or people who are vaccinated. However, we don't really know to what extent this will happen in real life.”
How severe the disease it causes is also unknown at this point.
“Isolated reports from Europe indicate mild symptoms,” says Miele. “However, these cases are either in vaccinated people or in young, healthy patients. We don't really know how dangerous it will be to unvaccinated patients with risk factors for severe COVID-19. We also don't know whether it can cause ‘long COVID' as other variants do.”
Miele says it's even more important now to practice mitigation measures.
“We are also tracking how virus variant diversity follows public health containment measures in the state,” he says. “Put simply, it increases every time restrictions are lifted. Unfortunately, we don't decide when the pandemic is over, and there is no reason to abandon caution at this time. We know what works. Masks, social distancing and vaccines.”
Vaccination rates are key.
“It is critical that vaccination rates increase, not only in the US but globally,” notes Miele. “Individuals who have been recently vaccinated and/or who have received boosters have very high levels of many kinds of antibodies as well as T-cells, and it's likely that they will be protected from severe disease, hospitalization and death, even though they may not be protected from infection.”
He continues, “Vaccine protection is not an all-or-nothing phenomenon. Even if a vaccine doesn't stop infection, it may make the difference between a mild or asymptomatic disease and a fatal or life-threatening one.”
Miele concedes that adjustments are inescapable.
“This is an arms race between the virus and medicine. As the virus mutates, vaccine effectiveness will inevitably decline, as it happens yearly with the influenza virus. However, a great advantage of mRNA vaccines is that they can be readily adapted to new viral variants in a matter of weeks.”
In the meantime, the people of Louisiana can rest assured that Miele and his team are on it.
“We have a state-of-the-art facility operated by highly dedicated professionals who
are devoting most of their time to serving the public by surveying viral variants.”