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Case Study Shows Power of SARS-CoV-2 Genome Testing to Track Viral Spread, ID Strains

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NEW YORK – As the world begins to get a grip on the COVID-19 pandemic, some countries that seem to have been successful at flattening the infection curve are looking to ease stay-at-home restrictions and slowly reopen their economies. But they're learning that diagnostic testing is only part of the solution when it comes to tracking the virus and clamping down on its transmission. Contact tracing, epidemiological analyses, and genetic studies will also be needed to better understand the mutations the virus undergoes both within the host and between individuals as it spreads between members of a community, how many unique strains of the virus there really are and how they may affect different populations, and what different mutations in these viral strains could mean for how well certain diagnostics and vaccine candidates work.

The large majority of SARS-CoV-2 tests have been PCR-based and work well to give a yes-or-no answer on whether a person is infected. However, they can't really go much further into genetic and epidemiological analyses needed to getting the world back on its feet.

Next-generation sequencing could fill the gap, and a recent case study from the pediatric intensive care unit at Children's Hospital Los Angeles (CHLA) illustrates why NGS is ideal for the more detailed studies that will be needed in the future.

A patient at the hospital's PICU and his mother showed signs of COVID-19 simultaneously with four healthcare workers in the unit, and the hospital was concerned that there was potential for transmission of the virus between patients and frontline healthcare workers.

Researchers at CHLA's Center for Personalized Medicine performed NGS sequencing on samples from all the patients, using Thermo Fisher Scientific's Ion AmpliSeq SARS-CoV-2 Research Panel. The panel is listed as a resource on the US Centers for Disease Control and Prevention website for laboratories that intend to sequence SARS-CoV-2 coronavirus samples. It consists of two pools of amplicons 125 to 275 base pairs in length that cover more than 99 percent of the viral genome. The panel was previously designed to run on the Ion GeneStudio S5 sequencer and was recently optimized to run on the Ion Torrent Genexus system, which can provide results in 24 hours.

The comparative analysis of all the samples showed that although the mother and son had nearly identical strains of the virus, originating in Utah with links to Europe, the four healthcare workers had strains only distantly related to each other and to the family. This confirmed that there was no transmission between the patient family and the healthcare workers, and that the workers had acquired the virus from community spread.

Tim Triche, co-director of the Center for Personalized Medicine at CHLA, said in an email that he and his colleagues were "surprised, pleased, and relieved" at the results of the analysis, adding that it would have been "impossible" to determine the patterns of transmission using a PCR-based test.

"[Finding transmission patterns] is only possible by NGS methods that provide detailed viral sequence data, from which we can decipher who infected whom, or not," he said. "In this case, the information was invaluable for assessing risk of infection and patterns of spread in a hospital environment. Most noteworthy to me was that it unequivocally determined the virus was not being spread on our campus, thus confirming the overall safety of the hospital environment and the need to screen patients and healthcare workers before entering the hospital."

Such information could help to immediately eliminate any kind of hotspot flare-up of the virus in a facility like a hospital, nursing home, or where people would need to be in close contact with each other, he added. NGS testing is uniquely valuable in this regard as opposed to PCR testing, which can't provide information on person-to-person transmission of the virus. Knowing about such outbreaks early on would be the only way to contain the spread.

A number of groups have recently developed high-throughput NGS-based COVID-19 diagnostic tests that they believe can be implemented for large-scale testing. But Triche said he believes there likely won't be a role for NGS-based tests in the rapid diagnosis setting anytime soon.

"Because of the urgent need for rapid turnaround time, sensitive, inexpensive, and reliable testing — especially point-of-care or even home testing currently under development — I don't see a role for NGS-based tests as front-line tests," he said. He compared existing diagnostic SARS-CoV-2 tests to rapid strep tests that provide quick confirmation of suspected cases but are less sensitive, and NGS-based SARS-CoV-2 tests to culture-based antibiotic sensitivity testing that provides more specific and reliable information for patient management.

In his analogy, Triche viewed NGS as a confirmatory test rather than a frontline test because it takes longer, costs more, and requires specialized equipment, and because the results can require specialized skills to interpret. But NGS testing could be used in a multitude of ways, on cases that are demonstrably positive, those that have a clinical presentation that is highly suspicious for COVID-19, or that have borderline PCR testing results because of very low viral load.

"Each example is for a different reason, but in each case, invaluable information is obtained that is not possible by a PCR or serology test," Triche said. "For example, when the PCR result is equivocal from a patient with apparent disease, and we can identify viral sequence that is barely detectable by PCR, we assume the PCR result is positive. If we see no viral sequence, we assume it is not. This is orthogonal validation: two different types of test for the same pathogen, for cross-validation of the result."

A viral genome sequence can also tell a doctor which strain of the virus is infecting a patient and how it compares to other isolates. If two isolates are identical, or nearly identical, one patient likely infected the other, according to Triche. If they are not, the patients were likely infected in the community in unrelated exposures. This allows public health officials to identify a strain's spread within the community, determine whether there are any hotspots of infection, analyze transmission patterns over time, and determine whether new strains have been introduced into the community or have arisen spontaneously.

"As has been widely noted, the so-called D614G strain spontaneously arose in Europe but has since spread to the East Coast and now to the West Coast," Triche said. "That tells us that many new infections in the US were introduced from Europe, not China, for example. Similarly, virtually every viral isolate we have seen so far varies in some small way from the others. The extent of identify and non-identity allows us to compare our isolates with those from around the world and create so-called phylogeny trees, resembling family genealogy trees, that tell us where infections in our patients came from, which in turn allows us to trace new infections as they may occur within the hospital or the community, which is essential for infectious disease control, a key priority for all hospitals and healthcare facilities, and increasingly, for everyone."

If such viral sequence data was paired with clinical data, researchers and healthcare professionals could also correlate viral type with clinical disease, analyze the development of antibodies, compare the rates of new infections for each strain of the virus, and even rate the reliability of molecular diagnostic tests that rely on the presence of a specific viral RNA sequence when, in fact, a new sequence has emerged, Triche noted.

"Most PCR reactions assume a common sequence between strains," he said. "If sequence divergence goes beyond the usual 'hotspots,' that assumption may not be true and the PCR reaction could fail. Sequence divergence and so-called antigenic drift also has important implications for vaccine development."

Following the example of this case study, and to encourage the use of its NGS-based SARS-CoV-2 research panel for mapping coronavirus transmission and epidemiological studies, Thermo Fisher this week launched the SARS-CoV-2 Global Access Sequencing Program for research consortia and industry groups. Under the terms of the program, the company said it will provide 50 units of the Ion Torrent Genexus System at a subsidized price to support global collaborative COVID-19 research.

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