Severe Acute Respiratory Syndrome Coronavirus 2 Detection and Variant Analysis in Respiratory Specimens from a...

The Korea Respiratory Virus Integrated Surveillance System (K-RISS) operates as a sentinel surveillance system. This study complements K-RISS by testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients who presented to healthcare facilities with respiratory symptoms but were not tested for coronavirus disease 2019 (COVID-19).

Among specimens collected from patients presenting to healthcare facilities with respiratory symptoms and submitted for multiplex testing for 19 respiratory viruses, specimens that tested negative for all respiratory viruses were additionally tested for SARS-CoV-2 using molecular assays. Whole-genome sequencing using next-generation sequencing was performed on SARS-CoV-2-positive specimens to characterize circulating sublineages.

Of the 5,400 total specimens, 591 were SARS-CoV-2-positive, resulting in an overall positivity rate of 10.9%. This positivity rate exhibited a seasonal pattern: it increased after July, peaked in August, and subsequently declined. This trend aligned with the annual SARS-CoV-2 detection rates observed by K-RISS. Moreover, changes in variant prevalence identified through whole-genome sequencing were comparable to those reported by K-RISS.

This study's approach of testing and analyzing respiratory virus-negative specimens after Korea transitioned to the current sentinel surveillance system identified additional SARS-CoV-2-positive specimens. This enabled a reliable assessment of domestic COVID-19 transmission and variant circulation occurring during the surveillance transition period. It also confirmed that the current K-RISS delivers representative insights into community-level epidemic trends.