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Development of a rapid, cost-effective and sensitive metagenomics based test for the diagnosis and surveillance of viruses associated with Encephalitis/Meningitis

Grant number: 21/11827-0
Support Opportunities:Scholarships in Brazil - Post-Doctoral
Effective date (Start): December 01, 2021
Effective date (End): May 31, 2023
Field of knowledge:Biological Sciences - Microbiology - Applied Microbiology
Acordo de Cooperação: MRC, UKRI ; Newton Fund, with FAPESP as a partner institution in Brazil
Principal Investigator:Ester Cerdeira Sabino
Grantee:Mohd Jaseem Khan
Host Institution: Faculdade de Medicina (FM). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Associated research grant:18/14389-0 - Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE), AP.TEM


Viral infections of the brain tissue (Encephalitis) and inflammation of meninges (Meningitis) are processes of the Central Nervous System CNS) that can result in significant morbidity and mortality and several Viruses can be involved. Since, almost 70% of viral encephalitis cases are left without an etiologic agent identified. Arthropod-borne Viruses (ArboVirus) presents a serious challenge to public and animal health and one of the most important emerging and re-emerging agents nearly worldwide. Multiple factors, such as increased travel, trade,urbanization, climate change and deforestations are fueling local outbreaks and global spread.In Brazil, the threat of arboViruses associate with Encephalitis/congenital or intrauterine transmission within this environment continues to loom. Especially, Chikungunya Virus (CHIKV), Dengue Virus (DENV), West Nile Virus (WNV) and Zika Virus (ZIKAV). Some emergences of novel or unexpected pathogens not targeted by routine diagnostics [e.g; Ilheus Virus (ILHV), Oropouche Virus (OROV), Rocio Virus (ROCV), St. Louis Encephalitis Virus (SLEV), Tucunduba Virus (TUCV,) Venezuelan Equine Encephalitis Virus (VEEV)]. Other non-arboviral viruses cause Encephalitis are Herpes Simplex Virus (HSV-1, HSV-2, HSV-6), Varicella-Zoster (VZV), EnteroVirus (EV), Human ParechoVirus (HPeV) and CytomegaloVirus (CMV) in Brazil. These Viruses require special attention to confirm. A significant barrier for preventing local outbreaks from becoming epidemics is detecting cases early enough for effective interventions. The primary causes of prolonged surveillance gaps that allow local outbreaks to spread are related to challenges during primary clinical diagnoses. Currently, real-time PCR considered to be the gold standard test to confirm infection with viral agents. However, these devices are expensive to run, and require specialized personnel to detect virus at an outbreak site. Since 2014, due to the economic and political crises that began in Brazil, which is directly affect health systems by reducing funds for health services and increasing demand for social protection programs. To solve this, there is an urgent need to develop an alternative method to bring diagnostics test which will fully automates and able to discover silent multiple viral agents from a single clinical sample in less than hour. In this study, we will development of a rapid, cost-effective, and sensitive assay based on Oxford nanopore technology for the diagnosis of Encephalitis/Meningitis viruses from human Cerebrospinal Fluid (CSF) or other body fluid samples. (AU)

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