Nasopharyngeal swabs unrivaled for detection of early-stage COVID-19

Nasopharyngeal and throat swabs have the best clinical sensitivity for the molecular detection of the novel coronavirus disease (COVID-19), especially in its early stages, according to a recent Singapore study. However, the performance of these upper respiratory specimens deteriorates beyond the first week of the disease, or when pneumonic symptoms start to manifest.

“Given the limited comparative data on simultaneously obtained clinical specimens, we sought to assess the clinical sensitivity of various specimen types for the diagnosis of SARS-CoV-2 in relation to duration of onset of illness and the presence of pneumonia,” the researchers said.

Of the 105 enrolled patients, only 73 tested positive for COVID-19 and were deemed to have an active infection; the remaining 32 had either recovered from the disease or had other diagnoses. The following samples were collected for molecular testing: unilateral nasopharyngeal, nasal midturbinate, throat swabs, and saliva.

The researchers saw that nasopharyngeal specimens offered the highest clinical sensitivity, with a value of 85 percent. This means that tests performed on nasopharyngeal samples would correctly identify SARS-CoV-2-infected patients 85 percent of the time. Throat swabs were a close second place, providing an 80-percent clinical sensitivity. [Open Forum Infect Dis 2020;doi:10.1093/ofid/ofaa335]

Midturbinate and saliva samples had sensitivity values of 62 percent and 38–52 percent, respectively. The combination of throat swabs with either nasopharyngeal or midturbinate samples yielded the best overall sensitivities, at 91.7 percent and 89.0 percent, respectively.

Notably, the performance of the tests appears to decline as COVID-19 progresses. For example, in patients who have had symptoms ≤7 days, unilateral nasopharyngeal swabs could correctly detect SARS-CoV-2 around 95 percent of the time. In those who had been tested >7 days after symptom onset, the corresponding clinical sensitivity dropped to 70.0 percent.

This trend was true for all the other upper respiratory sampling sites. In addition, patients with radiographic evidence of pneumonia also derived diminishing value from the diagnostic tests. Nasopharyngeal swabs, for instance, only had a 70-percent clinical sensitivity in these patients. In comparison, its sensitivity in those with normal radiological findings was 92 percent.

“In the pneumonic stage or later disease (>7 days), upper respiratory specimens perform poorly, and clinicians should be aware and seek alternate specimen types and other adjuncts to support a diagnosis of COVID-19,” the researchers said.

In the present study, patients were enrolled from a convenience sample of suspected COVID-19 patients admitted to the National Centre for Infectious Diseases in Singapore. Those who were positive for SARS-CoV-2 were tested daily until clinical and molecular recovery. All nasal and nasopharyngeal samples were collected unilaterally.

Important limitations of the study were failure to include lower respiratory tract and nonrespiratory samples for diagnosis and unilateral sampling, which also precluded the comparative analysis of the sensitivity of unilateral vs bilateral samples. The extrapolation of data from individual sampling sites to assess their combined effects was also a shortcoming.