Genetic Clues in the Goop of a COVID Swab

The components of certain things are meant to remain mysterious. The ingredients of sausage. A burger’s slimy secret sauce. The recipe for Coke or Kentucky Fried Chicken.

Researchers from Stanford University are tackling the make-up of another entity, something rather new to our world: the stuff retrieved from swabs shoved up nostrils to sample genetic material from SARS-CoV-2, the virus behind COVID-19. A swab actually samples much more than the virus’s RNA, required for diagnosis.

Super Swabs

John Gorzynski and colleagues describe the “multi-omic data repositories” from deployed swabs in a preprint (not yet peer-reviewed) and at the recent virtual annual meeting of The American Society of Human Genetics.

“A single nasopharyngeal swab can reveal substantial host and viral genomic information in a high-throughput manner that will facilitate public health pandemic tracking and research into the mechanisms underlying virus-host interactions,” they write.

That’s a mouthful. I’ll just call them super swabs.

Amplifying Viral Sequences

Extracting clues from the stuff on the swabs is a little like collecting evidence at a crime scene. Several things happen.

The polymerase chain reaction (PCR) rapidly ramps up the number of viral genomes to detectable levels, copying the RNA like documents flying out of an old-fashioned Xerox machine. At least 32 PCR cycles must run to yield enough genome copies to register as a positive test, a metric called cycle threshold (CT) value. A low CT can lead to a false negative test result.

The Stanford technology also scrutinizes swabs for genetic material from 40 other respiratory viruses. The list of usual suspects includes rhinoviruses, respiratory syncytial viruses, influenza viruses and other coronaviruses, which are RNA-based, as well as common cold DNA-based adenovirus, and a few others.

Considering Our Genomes and More

Next from the super swabs comes a quickie genome sequencing of the “host” – the person attached to the nose being probed. Cells lining the nose and throat, sloughed off and floating amidst the mucus, provide the genomes. A shortcut technology requires only a brief and limited amplification of the DNA.

Human genome information will become important once we figure out which genes control susceptibility to and severity of COVID-19. A few candidates are popping up in multiple investigations: a section of chromosome 3 found in Neanderthals and some of us; a variant of a gene near the one that determines ABO blood type; and genes that encode antibody parts and interferon receptors.

Swab analysis pays special attention to eleven genes that encode proteins called the human leukocyte antigens. The HLA proteins dot cell surfaces and are traditionally used in tissue typing for transplants. For COVID, HLA typing can be used to predict and monitor the immune response – possibly life-or-death information.

Beyond health associations, our DNA on swabs also indicates how people are related, which could be important in contact tracing. Our gene and genome sequences reflect ancestry. These data, when synced with electronic health records, might point to population groups at elevated risk of severe COVID, likely confirming what we already know from epidemiology and just looking at what’s happening at hospitals.

The swabs also yield human RNA, aka the transcriptome. This is the set of mRNAs present in a specific cell, which indicates the genes that are actively instructing the cell to synthesize their encoded proteins. Host transcriptomes hold clues to the specific choreography of COVID in an individual. In the virus, RNA is the genetic material, but in us, it is the purveyor of the information in the DNA.

Back to the Virus

The original use of a nasopharyngeal swab – to detect SARS-CoV-2 RNA – continues. But researchers are also using the RNA sequences to chart the evolution of the pandemic, paying special attention to mutations. The best studied mutation is D614G, which increases transmissibility.

The D614G mutation has entered the US on several occasions, from Europe. It partly explains why the number of cases has been slowly rising and now is skyrocketing, even as the percentage of deaths decreases. The now notorious mutation alters a single DNA base in a place that changes a critical amino acid in the spike protein, which is what the virus uses to latch onto our cells. The rather unglamorous name D614G is code for the location of the glitch in the viral spike gene.

D614G isn’t the only mutation. The genome of SARS-CoV-2 is changing, as all genomes do. Mutation is a normal consequence of errors in replication of genetic material. But most mutations do no harm. The effect depends upon what part of a protein a mutation perturbs.

Researchers compare different versions of a genome – those with different mutations – to deduce which begat which, connecting viral strains (and the animals that carry them) by their shared mutations, essentially building family trees. This computational approach, called phylodynamic tracking, comes from decades of evolutionary biology research. Now with the more pressing goal of handling pandemic dynamics at local levels, viral tree-building is enabling public health systems to prepare.

Fertilizer for building the viral family trees comes from the data of newly-sequenced SARS-CoV-2 strains posted frequently to a website called the GISAID Initiative. The speed at which the database is building is astonishing.

The first genome sequence of the “novel coronavirus” was published on January 10. When I posted “COVID Genomes Paint Portrait of an Evolving Pathogen” on July 30, GISAID listed 75,000 viral genomes. Now it’s nearing 200,000!

Comparing viral genomes over time has been critical in tracking and predicting outbreaks. Frantic physicians in Washington State, back at the beginning of the pandemic, were initially alerted to community spread from asymptomatic individuals from viral genome sequences.

The information held in seemingly low-tech nasal swabs can serve as a crystal ball during this most challenging of times. And that’s crucial because future infectious disease outbreaks, epidemics, and pandemics are inevitable, the Stanford team warns.

Maybe next time we’ll be better prepared.