Metagenomic next-generation sequencing of cell-free DNA for the identification of viruses causing central nervous system infections

Metagenomic next-generation sequencing (mNGS) can be used to detect pathogens, but there are limited data on its role in detecting viral central nervous system (CNS) infections. This was a multi-center retrospective study of patients clinically diagnosed with suspected viral CNS infection in Hunan between January 2018 and July 2021. mNGS detection was performed on cerebrospinal fluid (CSF) cell-free DNA (cfDNA) and whole-cell DNA (wcDNA) for diagnostic comparison. A total of 195 patients with suspected viral CNS infection underwent mNGS of CSF samples, and 175 of them received a final clinical diagnosis of CNS viral infection. A total of 100 (57.1%) cases were found to be virus-positive by mNGS, including 49 VZV, 32 HSV-1, 13 EBV, 5 HSV-2, and 1 porcine HSV. Compared with wcDNA, cfDNA mNGS showed a significantly lower proportion of human DNA (n = 26 patients; 0.91 +/- 0.1 vs 0.96 +/- 0.08, P < 0.01). Of these 26 patients, 24 were finally diagnosed with viral infections. The sensitivity of mNGS for detecting viruses using cfDNA and wcDNA was 66.7% (16/24) and 33.3% (8/24) (P < 0.01), respectively. Herpesviruses dominated the spectrum of DNA viruses in patients with viral CNS infections in Hunan, China, with VZV being the most common. mNGS, especially using cfDNA, is a promising complementary diagnostic method in detecting viral CNS infections.