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Volume 7, Issue 10

Complete genome analysis of human influenza C virus co-infection with WU polyomavirus in a Sri Lankan child: A brief report Open Access

Abstract

Influenza C virus (ICV) is a lesser known member of the family, primarily causing respiratory tract infections in children. Co-infection with WU polyomavirus (WUPyV), a recently identified human polyomavirus, has been rarely reported. This study presents the first laboratory-confirmed case of ICV infection in Sri Lanka and its co-infection with WUPyV.

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 (RT-PCR) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RT-PCR. A nasopharyngeal swab from a 14-month-old infant showing an insignificant curve in respiratory PCR was subjected to whole-genome sequencing using the Illumina platform. Data were analysed for genomic characterization, and phylogenetic analysis was performed using the haemagglutinin-esterase gene of ICV.

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.

This case highlights the importance of considering ICV in paediatric 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.

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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): influenza C , respiratory tract infection , Sri Lanka , whole-genome analysis and WU polyomavirus (WUPyV)
Funding
This study was supported by the:
  • University of Peradeniya, Sri Lanka
    • Principal Award Recipient: I.De Silva
  • Health System Enhancement Project
    • Principal Award Recipient: T.K.G.SSumathipala
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2025-10-29
2025-11-10

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Complete genome analysis of human influenza C virus co-infection with WU polyomavirus in a Sri Lankan child: A brief report
Access Microbiology 7, 000968.v3 (2025); https://doi.org/10.1099/acmi.0.000968.v3
/content/journal/acmi/10.1099/acmi.0.000968.v3
/content/journal/acmi/10.1099/acmi.0.000968.v3
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