Sara Navin has gotten tested for COVID-19 three times now. And, each time, the process has been a surprisingly pleasant experience. “I just sign up on the city’s free website where you don’t need insurance or any symptoms to make an appointment,” she said. “It’s really easy.” Part of that ease, Navin said, was the painless sample collection process. She simply sat in her car, coughed three times, swabbed her mouth for 20 seconds and then sealed the swab in a vial. This was a relief since she’d heard horror stories from friends about invasive sample collections — called nasopharyngeal swabs — that involved getting long plastic sticks jammed up their nose. “Most of the other people I’ve talked to have gotten that [deep] nasal swab,” she said, “And so I was wondering why city of Chicago sites were doing the mouth swab and if there was any difference in the accuracy of those tests.” We’ve heard similar questions from other Chicagoans who wonder why they were subjected to the uncomfortable nasopharyngeal swab (NPS) — affectionately referred to as the “brain poke” — while their friends got to administer their own mouth or nasal swabs. Many assumed the less invasive collection methods must not be as good, and they wanted to know why there was such a wide variety of methods instead of one standard. We took these questions to doctors, researchers and health officials and learned that pandemic shortages have forced healthcare providers to use several collection methods in recent months. But we also discovered some good news for people like Sara: Emerging research suggests that self-collected mouth and shallow nose swabs can be nearly as good, or better, than nasopharyngeal samples at detecting COVID-19. In fact, in late April, federal health authorities officially removed their preference for the use of NPS in COVID testing. And, beyond accuracy, the non-NPS methods offer some important advantages when it comes to ramping up testing to fight the virus. The “brain poke” method has pros and cons Still, most microbiologists and pathologists we talked to maintain their preference for nasopharyngeal samples as a first choice. “The gold standard is the nasopharyngeal swab,” said Karen Kaulk, chair of the pathology and laboratory medicine at NorthShore University Health System. “The COVID virus, like other viruses including the flu, likes to live in the nasopharynx and so that is the best place to go.”  This is why you still primarily see NPS collection at big hospitals such as Northwestern Medicine, Loyola University Medical Center and NorthShore University HealthSystem. But Kaulk said they’re all looking into alternatives because NPS has some major drawbacks right now. "In order to collect [using NPS] you need an appropriate supply chain of swabs which is one of the problems we’ve been dealing with,” she said. “And it also requires a bit more training than other collection methods." An even bigger problem may be the danger to healthcare workers who have to wear PPE and change it often, because when you put a stick up people’s nose, they “sneeze and cough, [creating] a risk of exposure there,” Kaulk said. On top of that, some patients swing their arms, swat away the swab or even accidentally hit healthcare workers as they involuntarily react to the “brain poke.” So, in recent months, medical professionals have turned to alternate collection methods including throat swabs, shallower nasal swabs and mouth swabs. “At University of Chicago, we started collecting [samples] from the front of the nose rather than the back of the nose [using NPS],” said Dr. Kathleen Beavis, the medical director of Microbiology and Immunology Laboratories at UChicago Medicine. “We wanted to do that for a few reasons and one of them was comfort to the patient … so now most specimens are collected that way at University of Chicago.” Beavis said front-of-the-nose samples (also called anterior nasal sampling) are proving just as accurate for them and they will soon move