Complete Genome Analysis of Human Influenza C Virus Co-Infection with WU Polyomavirus in a Sri Lankan Child: A Brief Report

Background Influenza C virus (ICV) is a lesser-known member of the Orthomyxoviridae family, primarily causing respiratory tract infections in children. Co-infection with WU polyomavirus (WUPyV), a recently identified human polyomavirus, is rarely reported. This study presents the first laboratory-confirmed case of ICV infection in Sri Lanka and its co-infection with WUPyV. Methods Nasopharyngeal and oropharyngeal swabs were collected from children aged 3 months to 14 years with respiratory tract symptoms between November 2022 and February 2023. Samples were screened using multiplex real-time PCR and SARS-CoV-2 RT-PCR. A nasopharyngeal swab from a 14-month-old baby showing an insignificant curve in respiratory PCR was subjected to whole-genome sequencing using the Illumina platform. Data were analyzed for genomic characterization, and phylogenetic analysis was performed using the haemagglutinin-esterase (HE) gene of ICV. Results Full genome sequencing identified ICV and WUPyV in the sample. Phylogenetic analysis revealed that the ICV isolate belonged to the C/Sao Paulo lineage. The patient presented with mild symptoms, including fever, cough, and cold, with normal inflammatory markers, and recovered with supportive care. Discussion This case highlights the importance of considering ICV in pediatric respiratory illnesses, despite its under-diagnosis due to limited diagnostic tools. Unlike Influenza A and B, ICV lacks neuraminidase, rendering neuraminidase inhibitors ineffective. The absence of ICV in current influenza vaccines further complicates preventive strategies. Co-detection of WUPyV raises questions about its role as a co-pathogen, with its clinical significance requiring further investigation. Conclusion This report underscores the need for enhanced molecular diagnostic techniques and surveillance to better understand the epidemiology and clinical impact of ICV and its co-infections.