Study shows the QuickNavi-COVID19 Ag test has a high diagnostic performance for SARS-CoV-2 Omicron sublineages BA.1 and BA.2 in nasopharyngeal samples

In a recent study published in the medRxiv* preprint server, researchers evaluated the diagnostic performance of a coronavirus disease 2019 (COVID-19) antigen test during the recent surge caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron variant.

Background

With the emergence of SARS-CoV-2 Omicron, global COVID-19 cases have soared to new record highs, and the BA.1 and BA.2 sub-lineages have become predominant by early 2022. Antigen tests are valuable diagnostic tools to detect infectious diseases because they are affordable, simple, and offer faster results.

SARS-CoV-2 antigen tests have been recommended for asymptomatic and symptomatic individuals, particularly if the nucleic acid amplification testing is limited or the viral prevalence exceeds 5%. Although it is believed that diagnostic performance of antigen tests is presumably preserved for SARS-CoV-2 Omicron, the sensitivity to the variant has been reportedly impaired for nine different tests.

About the study

In the present study, researchers prospectively examined the diagnostic performance of the QuickNavi-COVID-19 antigen test, comparing it to the reverse-transcription polymerase chain reaction (RT-PCR) test results. The study was conducted from December 28, 2021, to February 16, 2022, and samples were collected at a drive-through site at Tsukuba Medical Center Hospital (TMCH).

Two samples were collected from each individual for antigen and RT-PCR tests. Antigen testing was performed immediately at the site. RT-PCR was performed using an in-house method and another method by the National Institute of Infectious Diseases (NIID) in the TMCH microbiology department. To account for the discrepancy between results from in-house RT-PCR and NIID methods, additional analyses were carried out using Xpert Xpress SARS-CoV-2 and GeneXpert system.

Moreover, positive samples were subject to genome sequencing and SARS-CoV-2 variant analysis. In addition, a supplemental evaluation of eight different lots of QuickNavi-COVID-19 antigen and QuickNavi-Flu + COVID-19 antigen test was conducted during a non-surge period (November 2021 – January 2022). This was carried out to estimate false positivity for SARS-CoV-2 detection.

Findings

Nasopharyngeal swab samples were obtained from 1073 individuals, of which 154 were asymptomatic, and the remaining were symptomatic. The median time from symptom onset to sampling was two days. Overall, 411 samples were positive for SARS-CoV-2 using the NIID-developed method, and six discordant results were observed between in-house and NIID methods. When tested with GeneXpert System, these six were found SARS-CoV-2-positive; therefore, the total number of positive samples was 417.

The QuickNavi antigen test was 94.2% sensitive and 99.5% specific, with positive and negative predictive values of 99.2% and 96.5%, respectively. The sensitivity and specificity for symptomatic individuals were 94.3% and 99.8%, respectively, whereas, for asymptomatic individuals, it was 93.1% (sensitivity) and 98.4% (specificity). The lowest sensitivity (47.4%) was noted for PCR-positive samples with cycle threshold (Ct) values of 30 or above.

During the non-surge period, no sample tested positive for SARS-CoV-2 with RT-PCR testing in the supplemental analysis. The researchers performed 1200 tests (QuickNavi COVID-19 and Flu + COVID-19 antigen tests) with 400 swab samples and found zero false positives. Genome analysis of 185 samples revealed that 140 samples had BA.1.1.2 variant, 21 samples contained BA.2.3 variant, and two each were BA.2 and BA.1.1.1 variants. Overall, more than 85.9% of samples were of Omicron BA.1 sub-lineage, 12.4% of BA.2 sub-lineage, and 1.6% were of B.1.617.2 (Delta) variant.

Conclusions

The researchers noted that more than 90% of PCR-positive samples were positive with QuickNavi antigen testing. These findings indicated that the antigen test was sensitive enough to detect BA.1 and BA.2 variants, the two major sub-lineages of SARS-CoV-2 Omicron. Previously, the authors evaluated the same during the SARS-CoV-2 Delta wave and found 88.3% sensitivity for symptomatic individuals and 69.4% for asymptomatic subjects.

The diagnostic performance was slightly better during the Omicron wave, plausibly due to the higher proportion of symptomatic subjects or high viral load among the infected individuals. Despite the encouraging results, some study limitations include the small sample size of asymptomatic individuals and all samples collected at one center. For PCR testing, samples were frozen and transported later, affecting the results.

Further, only nasopharyngeal swab samples were analyzed but not anterior nasal samples. In conclusion, the study demonstrated that the QuickNavi antigen test had sufficient diagnostic performance to detect SARS-CoV-2 Omicron BA.1 and BA.2 sub-variants from nasopharyngeal swabs.

 
*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.

Written by

Tarun Sai Lomte

Tarun is a writer based in Hyderabad, India. He has a Master’s degree in Biotechnology from the University of Hyderabad and is enthusiastic about scientific research. He enjoys reading research papers and literature reviews and is passionate about writing.