Lab scientist discusses finding 17 omicron cases in Monroe County


Omicron, the latest COVID-19 variant of concern designated by the World Health Organization, gets its name from a letter in the Greek alphabet. (Photo: Getty Images)

ROCHESTER, N.Y. (WROC) — The omicron variant in Monroe County was first detected by researchers at UR Medicine Labs Laboratory. 

UR Medicine’s Central Laboratory is one of only five labs designed by New York State to preform genomic sequencing of COVID positive samples. Since the start of the pandemic, the lab has been sequencing positive COVID samples, finding variants from Alpha, to Delta, and now Omicron. 

“We receive specimens and the question is: Does this specimen have SARS-CoV-2, the virus that causes COVID 19? And what we do within our laboratories here, we perform PCR for the detection of the virus that causes COVID 19,” said Dwight Hardy, the Director of Clinical Microbiology for UR Medicine Labs. 

Hardy said they look at anywhere from 2,000-3,000 PCR tests a day. Out of those tests, roughly 10-15% come back positive. Out of those positive tests, scientists sequence a couple hundred a week.

“We’ve been sequencing somewhere around at least 200 positive specimens per week, which is a sample of the total number of positives. And this week, we find that from specimens, specimens that we detected as positive by PCR for the SARS-CoV-2 virus, we now see that we have the Omicron variant in our community,” Hardy explained.

The process of sequencing takes time, according to Hardy. His team is working 24/7 and will be working over the holidays.

“There’s instrumentation to help us do this, but it’s still somewhat of a manual process,” Hardy said. “Then once you get sequences, then you have to analyze them against known databases. So the whole process of sequencing approximately 200 specimens takes us three or four days.”

When the scientists found Omicron, they found it in 17 of the 100-200 sequences.

“The specimens that we sequence are selected. There’s a selection process that takes place. So what I’m saying is I’m not testing each and every specimen that is positive. I’m testing, I’m sequencing, a representative sample, and hopefully that representative sample is indeed representative of the larger picture,” Hardy said. 

Hardy said the variant was found mostly in Monroe County residents, due to the area’s larger population. But he also found the variant in one person from Ontario County, one person from Wayne, and a couple others in people who were traveling in the area. 

“Now that we know it’s in our community, we will continue to sequence. And it’s our expectation that we will. So if I say 17 out of approximately in the 100-200 range were Omicron, the balance was delta. But going forward, we expect to see more Omicron and less delta. And the question is just how long will it take for Omicron to displace delta,” Hardy said. 

Hardy said the virus will continue mutating, which presents a challenge for their lab. 

“The virus is quicker than we are. It mutates, and this is why we continue to urge people to get vaccinated, because the vaccines are still effective in reducing severity of disease and hospitalizations and certainly death as well,” Hardy said. 

UR Medicine Labs gets specimens from all over our area, including from different hospitals, emergency departments, urgent cares, nursing homes, and community private practices. 

County health officials say the variant likely arrived in our region between Dec. 1 and Dec. 15.

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