New Techniques for Viral Detection: Potential for Meningoencephalitis Diagnosis

Currently, the majority of cases of viral meningoencephalitis go undiagnosed as to the viral agent responsible for the disease. Of the cases actually diagnosed, the majority are found in the herpes virus family, where we have several sensitive and specific PCR tests for these more common etiologies. But what of the other viral causes? How can we even be sure a virus is responsible? It would help if we could be more sure of that, since there are always causes other than viruses to think about.

The paper below describes a new generic platform for detection of viral nucleic acids that can capture the needed information. This test seems to me to have a high potential to improve and streamline viral meningitis and encephalitis testing greatly, assuming that it is commercially (for the makers) and economically (for the hospitals) feasible, and can be shown to be sensitive and specific enough for good utility when used on day-old CSF samples.

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ABSTRACT

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

Authors: Thomas Briesea, Amit Kapoora, Nischay Mishraa, Komal Jaina, Arvind Kumara, Omar J. Jabadoa, W. Ian Lipkina,

mbio, published online 22 September 2015

Insensitivity and technical complexity have impeded the implementation of high-throughput nucleic acid sequencing in differential diagnosis of viral infections in clinical laboratories. Here, we describe the development of a virome capture sequencing platform for vertebrate viruses (VirCapSeq-VERT) that increases the sensitivity of sequence-based virus detection and characterization. The system uses ~2 million probes that cover the genomes of members of the 207 viral taxa known to infect vertebrates, including humans. A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform and used for solution-based capture of viral nucleic acids present in complex samples containing variable proportions of viral and host nucleic acids. The use of VirCapSeq-VERT resulted in a 100- to 10,000-fold increase in viral reads from blood and tissue homogenates compared to conventional Illumina sequencing using established virus enrichment procedures, including filtration, nuclease treatments, and RiboZero rRNA subtraction.

VirCapSeq-VERT had a limit of detection comparable to that of agent-specific real-time PCR in serum, blood, and tissue extracts. Furthermore, the method identified novel viruses whose genomes were approximately 40% different from the known virus genomes used for designing the probe library. The VirCapSeq-VERT platform is ideally suited for analyses of virome composition and dynamics.

Importance: VirCapSeq-VERT enables detection of viral sequences in complex sample backgrounds, including those found in clinical specimens, such as serum, blood, and tissue. The highly multiplexed nature of the system allows both the simultaneous identification and the comprehensive genetic characterization of all known vertebrate viruses, their genetic variants, and novel viruses. The operational simplicity and efficiency of the VirCapSeq-VERT platform may facilitate transition of high-throughput sequencing to clinical diagnostic as well as research applications.

So, will the NSA and CIA be investing in covert air samplers and rRNA sequencers next year?

Here.

ABSTRACT

Humans differ in their personal microbial cloud

Authors: James F. Meadow​, Adam E. Altrichter, Ashley C. Bateman, Jason Stenson, GZ Brown, Jessica L. Green, Brendan J.M. Bohannan

PEERJ: Published online September 22, 2015

Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106 biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants.

We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants.

Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.

An alternative to Kim's physicalism

In his book Physicalism, or Something Near Enough , Jaegwon Kim says: The final picture that has emerged is this: P is a cause of P*, wi...