Novel Assay Detects Subgenomic mRNA From Human Coronavirus Subtypes

Subgenomic mRNA from human coronavirus (HCoV) subtype OC43 was found to be commonly detected in children with respiratory tract infections (RTIs) OC43. These findings were published in the Journal of Clinical Virology.

This study was conducted between 2006 and 2017 at the Trondheim University Hospital in Norway. Researchers evaluated nasopharyngeal aspirate samples obtained from children aged younger than 16 years with community-acquired RTI and healthy children (controls) undergoing elective surgical procedures. The samples were analyzed for 17 respiratory viruses. Positive samples from children in the RTI (n=4312) and control (n=668) groups were tested using 2 novel real-time polymerase chain reaction (PCR) assays, targeting subgenomic mRNA coding for the nucleocapsid protein of HCoV subtypes OC43 and NL63. A PCR test result indicating a cycle threshold (Ct) value of greater than 40 was considered negative for the detection of both HCoV subtypes.

The product size for subgenomic mRNA from HCoV subtypes NL63 and OC43 was 170 and 128 base pairs, respectively.

Among children in the RTI and control groups, diagnostic PCR testing of nasopharyngeal samples was positive for HCoV subtype OC41 in 157 and 24 patients, respectively. For the NL63 subtype, PCR testing was positive in 113 samples obtained from children in the RTI group vs 19 samples obtained from those in the control group.

On analysis of 122 samples obtained from children in the RTI group and 19 from those in the control group, the positivity rates for subgenomic mRNA detection of OC43 were 86% and 63%, respectively. Additional PCR testing was performed on 97 samples obtained from children in the RTI group and 17 from those in the control group, resulting in positivity rates of 72% and 71% for the detection of subgenomic mRNA of subtype NL63, respectively.

Among patients in the RTI group, OC43 positivity was associated with a Ct value of less than 32 (odds ratio [OR], 54; 95% CI, 6.8-428). Further analysis showed that NL63 positivity was associated with a Ct value of less than 32 (OR, 42; 95% CI, 9.0-198), an age of less than 2 years (OR, 11.5; 95% CI, 4.0-32.9), single HCoV detection (OR, 6.9; 95% CI, 1.5-31.8), and hospitalization for more than 24 hours (OR, 2.5; 95% CI, 1.0-6.3).

Compared with children in the control group, the rate of positivity for the detection of subgenomic mRNA from HCoV subtype OC43 was significantly increased among those in the RTI group (OR, 3.6; 95% CI, 1.2-10.4), with similar results noted after adjustments were made on the basis of age (adjusted OR, 3.2; 95% CI, 1.1-9.4).

Limitations include the inability to culture HCoV subtypes OC43 and NL63 via conventional cell lines, the lack of longitudinal data, and the small sample size.

According to the researchers, “…the presence of [subgenomic] mRNA may reflect viral replication in both hospitalized children with RTI and in symptomatic controls with mild upper airway symptoms, as well as in asymptomatic controls in which the presence of [subgenomic] mRNA may reflect an asymptomatic HCoV infection.”

Reference

Heimdal I, Lysvand H, Krokstad S, Christensen A, Døllner H, Nordbø SA. Detection of subgenomic mRNA from endemic human coronavirus OC43 and NL63 compared to viral genomic loads, single virus detection and clinical manifestations in children with respiratory tract infections. J Clin Virol. 2022;154:105247. doi:10.1016/j.jcv.2022.105247