Application of Pathogen Discovery/Metagenomic Sequencing in CNS HIV
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CENTRAL NERVOUS SYSTEM AND COGNITION (SS SPUDICH, SECTION EDITOR)
Application of Pathogen Discovery/Metagenomic Sequencing in CNS HIV Kiran T. Thakur 1,2
# Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Purpose of Review Neurological conditions associated with HIV/AIDS including central nervous system (CNS), opportunistic infections (OI), chronic conditions including HIV-associated neurocognitive disorder, and cerebrospinal fluid (CSF) viral escape remain major contributors to morbidity and mortality worldwide. CNS infections in HIV-infected patients are often challenging to diagnose by traditional microbiological testing, impacting treatment and outcome. Recent Findings Recent advances in diagnostic techniques, including metagenomic next-generation sequencing (mNGS), are changing the landscape of microbiological testing, mainly in resource-rich settings. Pathogen discovery techniques offer a hypothesis-free approach to diagnostic testing, yielding comprehensive analysis of microbial genetic material. Given the extent of genetic material produced, deep sequencing tools not only hold promise in the diagnosis of CNS infections but also in defining key pathogenic steps which have previously been unanswered. Summary Significant challenges remain to implementing pathogen discovery techniques in routine clinical practice including cost, expertise and infrastructure needed including laboratory and bioinformatics support, and sample contamination risk. The use in resource-limited regions where the burden of CNS complications due to HIV/AIDS is highest remains poorly defined. Though, major opportunities utilizing pathogen discovery techniques exist to enhance surveillance and diagnosis and improve our understanding of mechanisms of neuroinvasion in CNS conditions associated with HIV. Keywords Pathogen discovery . Metagenomic deep sequencing . CNS opportunistic infections . CNS HIV viral escape . Novel diagnostics for CNS infections
Introduction Despite the significant progress made, the global fight against HIV is not near its end. There has been recent focus around ending the HIV epidemic by the end of the next decade, though significant barriers exist to doing so, due to viral persistence as well as significant public health obstacles. Globally, the progress in reducing new HIV infections and reducing deaths is tapering. In 2018, there were 1.7 million people newly infected with HIV, 37.9 million people living with HIV, and over This article is part of the Topical Collection on Central Nervous System and Cognition * Kiran T. Thakur [email protected] 1
Columbia University Irving Medical Center, New York, NY, USA
2
New York Presbyterian Hospital, New York, NY, USA
750,000 people dying of AIDS-related illnesses worldwide [1•]. In the USA, at least 15% of individuals with HIV are unaware that they are infected, and approximately 40,000 people in the USA were newly infected with HIV in 2016 [2]. HIV/ AIDS remains a significant global health threat requiring ongoing vigilance by heal
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