Immunocompromised Key to Identifying Omicron: IDSA Experts

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Dr Carlos del Rio

Even as officials await more information on the virulence, transmissibility, and vaccine evasion potential of the Omicron variant, one immediate action they recommend is prioritizing the genetic sequencing of positive virus samples, especially from immunocompromised people.

Focusing on this population could make sense, experts said at a December 2 media briefing by the Infectious Diseases Society of America (IDSA).

Some officials believe infection of an immunocompromised person allowed enough time and opportunity for the high number of mutations in the SARS-CoV-2 virus to create the new variant.

“What makes Omicron particularly concerning is the fact that it has a lot of mutations,” Carlos del Rio, MD, said at the briefing. “It appears to be a virus that emerged in a single patient, likely somebody who was severely immunosuppressed who could not clear that infection.”

So in addition to doing a better job of vaccinating the world, “we also need to be more concerned about our immunosuppressed patients because immunosuppressed patients may be where the virus continues to mutate,” said del Rio, president-elect of the IDSA board of directors and professor of global health and epidemiology at the Rollins School of Public Health of Emory University in Atlanta, Georgia.

del Rio relies on colleagues in infectious disease and transplant medicine to flag immunocompromised patients who test positive for SARS-CoV-2 infection. “Just yesterday, we had an HIV patient in our hospital with COVID. Immediately the consultant on the team said, ‘Let’s get the lab to refer this [sample] for genetic surveillance,'” he said.

‘Tis the Season for Testing?



Dr Julie Vaishampayan

Public health officials are ramping up efforts in the face of the many unknowns about Omicron, Julie Vaishampayan, MD, MPH, said during the media briefing.

“We just need more science and information,” she said. Public health is increasing testing, whole-genome sequencing, case investigation, and contact tracing when cases are identified as a result.

The actions are urgent as winter approaches and colder weather brings more people indoors. “We’re at the time of year…when respiratory viruses thrive,” added Vaishampayan, chair of the IDSA Public Health Committee and a Stanislaus County Public Health Officer in Modesto, California.

Individual Americans can do their part as well, she said. Vaishampayan recommended that people use additional layers of protection. Consider more testing, wearing masks in any public space where you do not know everyone’s vaccination status, and “get your flu shot, please.”

Del Rio agreed. “We need to do more testing. I think testing had gone down quite a bit in the US.”

Vaishampayan is not recommending people cancel holiday gatherings. “I’m not saying change your plans. I’m saying look very carefully at what you’re planning to do, and maybe add in a few additional layers.”

US Sequencing Much Improved

Del Rio said the rapid detection of Omicron in South Africa exemplifies the need to do active surveillance for new and circulating variants in the United States as well.

Genomic sequencing of PCR-positive samples has greatly improved in the United States, he said. “We were very far behind with genomic surveillance in the US in 2020. We’ve done a much better job this year.”

An estimated 5% to 7% of positive samples get sequenced nationwide, del Rio said, through a network of university, private, and public health laboratory settings. Furthermore, Vaishampayan estimated one in seven positive samples in California undergoes whole-genome sequencing.

Emory University is working with the Centers for Disease Control and Prevention and the Georgia Department of Health to conduct viral surveillance, for example.

“In fact, we’re working now on enhancing genomic surveillance around immunosuppressed patients because that’s exactly one of the concerns many have,” del Rio said.

Don’t Discount Delta

While what is known and unknown about Omicron continues to dominate the headlines and the attention of many health officials, “let’s not forget Delta, our current problem,” del Rio said.

Close to 100,000 people are newly diagnosed daily with COVID-19 in the United States, about 5000 people are hospitalized, “and we’re running about a thousand people dying from COVID, still, in our country each day,” he said.

Vaccination remains the number one priority. “With Delta circulating right now, I tell people you’re going to encounter Delta at some point in time,” del Rio said. “When you do, you’re much better off vaccinated than not vaccinated.”

“It’s no different than saying you’re going to encounter a traffic accident at some point in time, and you’re much better off wearing your seatbelt than not wearing one,” he said.

“We still have a major problem with Delta,” del Rio added. “Having said that, you know, Omicron is coming.”

Based on a December 2 media briefing on the SARS-CoV-2 Omicron variant by IDSA.

Damian McNamara is a staff journalist based in Miami. He covers a wide range of medical specialties, including infectious diseases, gastroenterology, and critical care. Follow Damian on Twitter: @MedReporter.

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