Community-acquired infectious meningoencephalitis is associated with high rates of mortality and morbidity, compounded by limited access to diagnostic resources. The current study assessed acute central nervous system (CNS) infections in patients with meningoencephalitis enrolled in a hospital-based diagnostic surveillance study in São Paulo, Brazil. Cerebrospinal fluid (CSF) was collected from 600 patients between March 2018 and November 2019 and initially screened for a broad range of pathogens according to a local diagnostic algorithm. Standard microbiological and molecular diagnostic methods were applied. Metagenomic sequencing was used as a complementary approach to investigating etiology in instances where no pathogen was initially identified. Standard testing identified infectious etiologies in 292 patients (48.6%), with 227 (77.7%) confirmed as viral infections, predominantly caused by enteroviruses ( n = 144) and herpesviruses ( n = 40). Nonviral agents were identified in 65 patients (22.3%). Metagenomic sequencing (mNGS) of 277 of 308 undiagnosed patients revealed several additional potential etiologies, including Parvovirus B19 , Toxoplasma gondii , Picobirnavirus , other enterovirus species and Vesivirus , the latter being associated with CNS infection for the first time. These findings underscore the complexity of CNS infections and highlight the potential of metagenomics to improve diagnostic accuracy, inform treatment strategies, and support efforts to address future pandemics.

Introduction—The dynamics of SARS-CoV-2 shedding and replication in humans remain incompletely understood. Methods—We analyzed SARS-CoV-2 shedding from multiple sites in individuals with an acute COVID-19 infection by weekly sampling for five weeks in 98 immunocompetent and 25 immunosuppressed individuals. Samples and culture supernatants were tested via RT-PCR for SARS-CoV-2 to determine viral clearance rates and in vitro replication. Results—A total of 2447 clinical specimens were evaluated, including 557 nasopharyngeal swabs, 527 saliva samples, 464 urine specimens, 437 anal swabs and 462 blood samples. The SARS-CoV-2 genome sequences at each site were classified as belonging to the B.1.128 (ancestral strain) or Gamma lineage. SARS-CoV-2 detection was highest in nasopharyngeal swabs regardless of the virus strain involved or the immune status of infected individuals. The duration of viral shedding varied between clinical specimens and individual patients. Prolonged shedding of potentially infectious virus varied from 10 days up to 191 days, and primarily occurred in immunosuppressed individuals. Virus was isolated in culture from 18 nasal swab or saliva samples collected 10 or more days after onset of disease. Conclusions—Our findings indicate that persistent SARS-CoV-2 shedding may occur in both competent or immunosuppressed individuals, at multiple clinical sites and in a minority of subjects is capable of in vitro replication.

Background: There is scarce information on Varicella–Zoster virus genetic variability in individuals with acute central nervous system infection in Brazil. The objective of this study was the molecular characterization of Varicella–Zoster virus isolates in cerebrospinal fluid from individuals with acute central nervous system infection. Methods: Cerebrospinal fluid samples were collected from individuals evaluated in emergency and community healthcare services in São Paulo, Brazil. Varicella–Zoster virus identification was performed using commercial platforms Biofire-FilmArray Meningitis/Encephalitis (BioMérieux, Craponne, France) and XGEN-UMLTI-N9^® (Mobius Life, Pinhais, Brazil). Positive samples were further characterized as wild-type or vaccine-strain by a real-time polymerase chain reaction assay that targeted a single nucleotide polymorphism in open reading frame 62. We also estimated the mean genetic distance and phylogenetic reconstruction based on open reading frames 22, 38, 54, and 62 in relation to sequences of intercontinentally circulating Varicella–Zoster virus isolates. Results: Among the 600 cerebrospinal fluid samples, we identified Varicella–Zoster virus in 30 (5%) samples. None were positive for the vaccine-strain. Twelve samples were sequenced and phylogenetically classified into Clades 1 (41.7%), 2 (25%), 3 (8.3%), 5 (16.7%), or 6 (8%). Conclusion: Enhanced characterization of circulating Varicella–Zoster virus Clades in Brazil identified previously unreported Clades 2 and 6 as well as three other Clades disseminated intercontinentally. These findings reinforce the importance of Varicella–Zoster virus molecular surveillance in cerebrospinal fluid.

Aerosolization may occur during reprocessing of medical devices. With the current coronavirus disease 2019 pandemic, it is important to understand the necessity of using respirators in the cleaning area of the sterile processing department. To evaluate the presence of severe acute respiratory syndrome coronavirus (SARS-CoV-2) in the air of the sterile processing department during the reprocessing of contaminated medical devices. Air and surface samples were collected from the sterile processing department of two teaching tertiary hospitals during the reprocessing of respiratory equipment used in patients diagnosed with coronavirus disease 2019 and from intensive care units during treatment of these patients. SARS-CoV-2 was detected only in 1 air sample before the beginning of decontamination process. Viable severe acute respiratory syndrome coronavirus 2 RNA was not detected in any sample collected from around symptomatic patients or in sterile processing department samples. The cleaning of respiratory equipment does not cause aerosolization of SARS-CoV-2. We believe that the use of medical masks is sufficient while reprocessing medical devices during the coronavirus disease 2019 pandemic.

Viral metagenomics has fundamentally transformed how we investigate the virosphere

In this study, viral metagenomics was applied to identify viruses related to the Dicistroviridae family in freshwater samples collected from urban reservoirs of the state of São Paulo, Brazil. Through next-generation sequencing, five complete RNA genomes similar to Dicistroviridae were detected. These genomes range from 8.032 to 9.425 nucleotides in length, and each contains two open reading frames (ORFs) with conserved protein domains and internal ribosome entry sites (IRES) characteristic of Dicistroviridae. Phylogenetic and genetic identity analyses based on the amino acid sequences of the nonstructural (ORF1) and structural (ORF2) polyproteins suggest that these five genomes represent four putative novel species provisionally named Hydro virus 1 to Hydro virus 4. These findings enhance our understanding of the diversity and distribution of Dicistroviridae in aquatic environments.