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. 2022 Sep:154:105247.
doi: 10.1016/j.jcv.2022.105247. Epub 2022 Jul 22.

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

Inger Heimdal  1 , Hilde Lysvand  2 , Sidsel Krokstad  3 , Andreas Christensen  4 , Henrik Døllner  5 , Svein Arne Nordbø  4
Affiliations

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

Inger Heimdal et al. J Clin Virol. 2022 Sep.

Abstract

Background: The importance of endemic human coronavirus (HCoV) in children has been insufficiently elucidated upon. Our aims were to develop subgenomic (sg) mRNA tests for HCoV species OC43 and NL63, and to evaluate the relationships to HCoV genomic loads, single HCoV detections and clinical manifestations.

Methods: We have used an 11-yearlong cohort study of children admitted with respiratory tract infection (RTI) and hospital controls. Nasopharyngeal aspirates were analyzed for HCoV subtypes OC43 and NL63 with in-house diagnostic PCR. Positive samples were tested with newly developed real-time PCRs targeting sg mRNA coding for the nucleocapsid protein.

Results: OC43 sg mRNA was detected in 86% (105/122) of available OC43-positive samples in the RTI group, and in 63% (12/19) of control samples. NL63 sg mRNA was detected in 72% (71/98) and 71% (12/17) of available NL63-positive patient and control samples, respectively. In RTI samples, sg mRNA detection was strongly associated with a Ct value <32 in both diagnostic PCR tests (OC43: OR = 54, 95% CI [6.8-428]; NL63: OR = 42, 95% CI [9.0-198]) and single NL63 detections (OR = 6.9, 95% CI [1.5-32]). Comparing RTI and controls, only OC43 was associated with RTI when adjusted for age (aOR = 3.2, 95% CI [1.1-9.4]).

Conclusion: We found strong associations between OC43 and NL63 sg mRNA and high viral genomic loads. sg mRNA for OC43 was associated with RTI. The association between sg mRNA and clinical manifestations needs further evaluation.

Keywords: Endemic human coronavirus; Hospital medicine; Pediatric infections; Subgenomic mRNA; Viral infections.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig 1
Fig. 1
Flowchart of HCoV OC43 and NL63-positive samples analyzed for sg mRNA In total, 58 samples were not available for testing for sg mRNA. Definitions: RTI group, Children <16 years of age hospitalized with respiratory tract infections; Control group, children undergoing elective day surgery.
Fig 2
Fig. 2
Gel electrophoresis of sg mRNA N OC43 and NL63. Lane A-D, OC43 sg mRNA positive samples; lane E, negative control (water); lane F, 1 kb Plus DNA ladder; lane G, NL63 sg mRNA positive sample; lane H, negative control (water).
Fig 3
Fig. 3
sg mRNA results for OC43 and NL63 compared to diagnostic PCR Ct values Each dot indicates one sample. Definitions: RTI group, Children <16 years of age hospitalized with respiratory tract infections; Control group, children undergoing elective day surgery. Abbreviations: Ct; Cyclic threshold.
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