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

Abstract

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. IMPORTANCE This study provides significant new data on the application of metagenomic next-generation sequencing (mNGS) to clinical diagnostics of central nervous system (CNS) viral infections, which can have high mortality rates and severe sequelae. Conventional diagnostic procedures for identifying viruses can be inefficient and rely on preconceived assumptions about the pathogen, making mNGS an appealing alternative. However, the effectiveness of mNGS is affected by the presence of human DNA contamination, which can be minimized by using cell-free DNA (cfDNA) instead of whole-cell DNA (wcDNA). This multi-center retrospective study of patients with suspected viral CNS infection found that mNGS using cfDNA had a significantly lower proportion of human DNA and higher sensitivity for detecting viruses than mNGS using wcDNA. Herpesviruses, particularly VZV, were found to be the most common DNA viruses in these patients. Overall, mNGS using cfDNA is a promising complementary diagnostic method for detecting CNS viral infections.