Outbreak investigation hinges on DNA matches
April 1, 2008 3 minutes read
Outbreak investigation hinges on DNA matches
Pattern of letters will make the match
Appropriately enough in Las Vegas, the largest patient look-back investigation in history will come down to something akin to a high-stakes bingo game.
The fate of clinicians who may be criminally charged and civilly sued — and certainly the fate of patients who are matched together as outbreak cases — will be in large part determined by a series of representative letters gleaned from the rapidly mutating hepatitis C virus (HCV). The process is called DNA (deoxyribonucleic acid) sequencing. Combined with shoe-leather epidemiology, the high-tech process already has shown that six HCV infected patients — particularly five treated on the same day — are so closely linked that transmission must have occurred between them or from a common source. They are officially a cluster, identified by epidemiology detectives and "fingerprinted" by lab researchers at the Centers for Disease Control and Prevention. As the 40,000 patients treated at the endoscopy clinic are tested, positive results reported to state officials will be forwarded to the CDC for genetic analysis and sequencing.
"We subject the specimen to an extraction process to take out the RNA and the DNA, which are collectively called nucleic acids," explains Chong-Gee Teo, MD, PhD, chief of the viral hepatitis lab at the CDC. "Usually, a polymerase chain reaction [PCR] technique is used to define as much of the sequence of interest [as possible]. The identified segments of the viral genome are then processed through a sequencing machine that provides read-outs of the various nucleotides that constitute the sequence of any particular origin."
The sequence will appear in some order of representative letters used to identify various genetic components. The order of the sequence of genetic information that is being passed along may appear in some repetitive pattern and be given a numerical value as part of the analysis. It may closely match another sequence from another patient, suggesting transmission or common source exposure. The trained eye can find the matches, but with HCV the phrase "perfect match" is no more likely to be shouted in the lab than "Bingo."
"For rapidly evolving viruses like hepatitis C or HIV, very seldom do we find a perfect match," Teo tells Hospital infection Control. "Because once a virus enters a host it undergoes a route of evolution that is different from host to host. We look for how closely related one sequence is with another."
Powerful evidence
When matches are found, they stand out dramatically from background sequences representing national HCV strains. Teo declined to give a percentage estimate of "certainty" or comment on the specific patients in Las Vegas, but he made it clear that genetic findings linked with epidemiological investigation combine to form powerful evidence that transmission has occurred. "They cluster closest to each other," he says. "To make an inference that these sequences [are a cluster] we have to have 100% concordance with the epidemiological [investigation]."
Though some have noted that the investigation may be undermined as pre-existing viral infections are found in the clinic patients, Teo says discernment should not be difficult. "It has been our experience that [cases] epidemiologically linked to each other — whether one infected the other or whether they were infected by a common source — always cluster to each other and not to non-linked sequences," he says. "For this investigation we already have sequences from the initial cluster, so other [identified cases] will be related to the outbreak itself. The others that are not related or linked at all will fall outside the cluster."
As clinic patients are tested for HIV, the issues in molecular epidemiology will be very similar to HCV. However, the slower-mutating HBV will be less distinctly defined from background viruses. "HCV and HIV are very 'light' viruses and they mutate very fast," he says. "Hepatitis B is a slowly evolving virus and instances where specimens are collected from a single outbreak there is higher likelihood of having identical matches." Bingo.
Appropriately enough in Las Vegas, the largest patient look-back investigation in history will come down to something akin to a high-stakes bingo game.You have reached your article limit for the month. Subscribe now to access this article plus other member-only content.
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