Coinfection of severe acute respiratory syndrome coronavirus 2 and polyomavirus in a patient with coronavirus disease 2019 detected by enrichment next-generation sequencing: a case report

Background: Severe acute respiratory syndrome coronavirus 2 was found first in Wuhan and declared a pandemic by the World Health Organization. Coinfection with other respiratory viruses may occur, complicating the diagnosis and treatment of coronavirus disease 2019. Herein, we identified a Karolinska Institute polyomavirus Stockholm 60 present in a nasopharyngeal swab of a patient with severe acute respiratory syndrome coronavirus 2 infection using next-generation sequencing with an enrichment method. Case presentation: A 24-year-old Indonesian woman was admitted to our institution due to a cough, cold, and sore throat. She had no family history of hypertension and diabetes mellitus, and she was well. Her vital signs were as follows: heart rate, 84 beats per minute; respiratory rate, 22 breaths per minute; temperature, 39 °C; and pulse oximetry, 96 on room air. She had runny nose and slightly inflamed pharynx. Her nasopharyngeal swab and real-time polymerase chain reaction were positive for the coronavirus disease 2019 nucleocapsid and open reading frame genes, with cycle threshold values of 32.33 and 33.74, respectively. Whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 was performed using the Nextera DNA Flex for Enrichment using the Respiratory Virus Oligos Panel, Illumina MiSeq instruments, and Illumina MiSeq reagent v3 150 cycles (2 × 75 cycles). The full genomes were aligned to the reference genome (NC045512.2) by the Burrow–Wheeler aligner algorithm. The whole-genome sequencing showed coinfection of Karolinska Institute polyomavirus Stockholm 60 (NC009238.1) with an overall coverage of 3561x. The patient was given acetaminophen, vitamin C, vitamin D, and zinc for the treatment and discharged uneventfully from the hospital 4 days after admission. Then, 2 weeks after discharge, she visited the outpatient clinic without any further concerns. Conclusion: This report presents a case of Karolinska Institute polyomavirus and severe acute respiratory syndrome coronavirus 2 coinfection in a patient with nonspecific clinical manifestation. Further studies with a larger sample size are mandatory to clarify the association between severe acute respiratory syndrome coronavirus 2 and Karolinska Institute polyomavirus coinfection, particularly on patient outcomes. Moreover, the results propose the usefulness of enrichment-based next-generation sequencing in detecting viral coinfection in patients with severe acute respiratory syndrome coronavirus 2. © The Author(s) 2024.