Comparison of SARS-CoV-2 test performance by sample type and modality in close contacts of SARS-CoV-2 cases

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis is important for patients and public health to assess the levels of virus and infection risk. Due to the high need for SARS-CoV-2 testing, numerous rival testing technologies, sample types, and techniques have been developed and deployed. Compared to nucleic acid tests (NAT), rapid diagnostic procedures that use a lateral flow assay (LFA) to identify SARS-CoV-2 antigen offer scalability, convenience, and the possibility for home usage, but they have lower sensitivity.

Study: Limitations of molecular and antigen test performance for SARS-CoV-2 in symptomatic and asymptomatic COVID-19 contacts. Image Credit: anyaivanova/Shutterstock

In early symptomatic disease (within five days of symptom onset), infected individuals have a high probability of having significant viral loads, making antigen and molecular tests reliable. The viral burden of the index case has been linked to the risk of transmission for individuals who are close contacts. False-negative antigen testing can occur in the pre-symptomatic phase when viral loads are still modest. Only 64% of SARS-CoV-2 molecular test positive close contacts were identified by antigen testing, according to a recent study in the Netherlands; antigen test sensitivity was as low as 58.7% and 84.2% in symptomatic individuals.

In this study, researchers looked at how well molecular and antigen testing performed in symptomatic and asymptomatic close contacts of SARS-CoV-2 positive people. The scientists also used the VeroE6TMPRS2 cell model to examine the sensitivity of molecular and antigen testing in nasal swabs, as well as molecular tests in saliva, to diagnose close contact with infectious virus in NP swab viral transport media (VTM).

A preprint version of this study, which is yet to undergo peer review, is available on the medRxiv* server.

The study

For 22.6% of subjects who came into close contact with someone infected with SARS-CoV-2, the NP swab reference NAT was positive. Twenty-five of the 53 reference positive samples that were cultured were culture positive. PerkinElmer RT-PCR analyzed remnant frozen NP swab VTM for 158 of the 182 SARS-CoV-2 close contacts who tested negative by the reference test and found 13 samples positive with a median cycle threshold (Ct) of 36.8. Saliva testing was performed on 186 close contacts using PerkinElmer RT-PCR, including 143 of 182 reference test negative subjects.

Saliva was positive in 37 of 43 participants with a positive reference and 17 of 143 people who had a negative reference. SARS-CoV-2 was found by PerkinElmer RT-PCR of NP and saliva samples in an added 21 asymptomatic close contacts and seven symptomatic close contacts not identified by the NP reference test. In both NP and saliva samples, the median Ct value of symptomatic close contacts was lower than that of asymptomatic close contacts.

The sensitivity of saliva NAT was 80.6%, and NP was 77.6% among the 67 participants who tested positive for any NAT and had a saliva NAT result. Patients with systemic symptoms such as fever and muscle discomfort were more likely to test positive by both NP and saliva samples, while those with a runny nose were more likely to test positive by NP only.

The first 126 participants, of which 99 were close contacts, received antigen testing of a mid-turbinate swab utilizing the BD Veritor lateral flow assay from November 17, 2020, to March 11, 2021. Fifty-five people were asymptomatic, 35 were symptomatic within the first five days of symptom onset, and nine were symptomatic but past the first five days of symptom onset among close contacts who had antigen testing.

Compared to the molecular reference test, positive percent agreement (PPA) was 83.3%, and negative percent agreement was 95.7% among symptomatic close contacts in the first five days of symptom onset. The PPA was 18.2% for asymptomatic people or people who had symptoms after five days. Participants who tested positive by reference test but negative by BD Veritor had a median reference test Ct of 31.6 for asymptomatic patients, 30.8 for symptomatic in the first five days of symptom onset, and 30.3 for participants after five days of symptom onset. Eight of the eleven close contacts who were culture positive with BD Veritor results were also BD Veritor positive. Two of the three that were overlooked were asymptomatic.

Implications

Even as the pandemic enters its third year, ongoing SARS-CoV-2 transmission with increasingly contagious variations underlines the significance of extensive and reliable testing. These results in a wide group of close contacts show the limitations of cross-sectional antigen testing to rule out transmissibility and routine NAT to diagnose coronavirus disease 2019 (COVID-19).

Close contacts of people who have COVID-19 should be isolated and tested multiple times, particularly those with the highest risk exposures, such as home connections. Improvements in test performance features or the implementation of serial testing to detect patients with SARS-CoV-2 when they are most likely to develop transmissible disease are needed in the future.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.