A research coordinated by the Carlos III Health Institute (ISCIII) highlights the added value of viral metagenomic sequencing as a diagnostic tool, allowing the localization of viruses in cerebrospinal fluid samples from adults suspected of central nervous system infection whose conventional analyses had been negative.
The work, made known in "Journal of General Virology," has been carried out by a team from the National Center for Microbiology (CNM) of the ISCIII along with the Puerta de Hierro University Hospital in Majadahonda, Madrid, and Reina Sofía in Córdoba, as well as various research groups both national and from other countries.
Viral infections affecting the central nervous system can cause meningitis, encephalitis, myelitis, and other neurological pathologies. Nevertheless, in a considerable percentage of patients, the responsible agent cannot be determined using standard diagnostic techniques.
As noted by the ISCIII, the enormous diversity of viruses capable of causing these infections, the possible presence of the virus in very low quantities, or the use of diagnostic panels that do not include all potential pathogens partly explain these difficulties in identification.
In this scenario, the research group has resorted to viral metagenomic sequencing techniques with enrichment by capture with probes, an approach that makes it possible to simultaneously track thousands of known viruses directly in clinical samples.
This approach has been applied to 40 cerebrospinal fluid samples from patients suspected of central nervous system infection in which previous tests had not detected any pathogen.
Detected viruses and the value of metagenomics
Thanks to this procedure, viral sequences have been identified in six of the cases. In detail, human pegivirus was found in three patients, Toscana virus in one, herpes simplex virus type 1 in another, and varicella-zoster virus in a sixth patient.
All these findings were subsequently verified using specific molecular techniques, and in several of the studied episodes, complete or nearly complete viral genomes were obtained, which has allowed for a deeper understanding of the genetic diversity of the involved viruses.
In relation to human pegivirus, relatively common and capable of persisting in the organism, the researcher from CNM-ISCIII María Dolores Fernández-García has recalled that it has not been conclusively linked to a specific disease. Its detection in cerebrospinal fluid represents a relevant clue for future work, but does not prove that it was the origin of the observed symptoms.
Regarding the Toscana virus identified in a patient with meningitis, the researcher raises the need to consider this virus in cases of meningitis of unknown cause that appear in the summer months, coinciding with the increased activity of phlebotomine sandflies, insects similar to mosquitoes that act as vectors.
In the case of herpes simplex virus type 1 and varicella-zoster virus found in two patients with negative results in the initial diagnostic panel, Fernández-García emphasizes that this data supports the importance of resorting to additional molecular tests when clinical suspicion remains.
"Finding a virus does not necessarily mean that it is the cause of the disease, but it can provide an important clue to guide the diagnosis and future investigations," Fernández-García has highlighted, who has pointed to metagenomic sequencing as "a complementary tool of great value" in cases like those studied.
The study is part of the doctoral thesis of the first author, Ana Donoso, who develops her work at CNM-ISCIII under the direction of María Dolores Fernández-García, head of the Viral Gastroenteritis group and researcher in the Area of Epidemiology and Public Health (CIBERESP) of the Biomedical Research Networking Center (CIBER-ISCIII), who has led the research.