Developing Norms for the Provision of Biological Laboratories in Low-Resource Contexts Proceedings of a Workshop (2019) / Chapter Skim
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4 MOLECULAR DIAGNOSTICS: AN ALTERNATIVE TO HIGH CONTAINMENT?
4 MOLECULAR DIAGNOSTICS: AN ALTERNATIVE TO HIGH CONTAINMENT?
Pages 27-42
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From page 27... ...
, for example, clustered regularly interspersed short palindromic repeats (CRISPR) -Cas based assays Genotyping Sequencing, including nanopore sequencing Signal amplification Target amplification (polymerase chain reaction [PCR]
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From page 28... ...
Compliance with CLIA requires validation and quality assurance for all laboratory tests used in clinical care, including "laboratory-developed tests." The Clinical and Laboratory Standards Institute (CLSI) also issues "Guidelines -- CLSI Molecular Diagnostic Methods for Infectious Diseases" (CLSI, 2015)
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From page 29... ...
Dr. Chiu explained that direct detection methods, such as sequencing, cannot fully replace serology, the branch of laboratory medicine that investigates blood serum to detect antibodies and antigens.1 He views molecular testing as complementary to, but not a replacement for, classical testing methods.
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2. Cost and other practical considerations favor true point-of-care molecular diagnostics (e.g., lateral flow immunoassays, CRISPR Cas)
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gave a presentation on his field experiences during several hemorrhagic viral outbreaks, including the West African Ebola outbreak in 2014-2015.
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The scale of the response to the West African Ebola outbreak generated its own challenges. For example, many different real-time PCR assays were used in the large network of laboratories, creating a need for quality panels and attempts to standardize assays.
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Chiu said that the costs of the molecular technologies need to be reduced before they can be used in low-resource settings, one participant stated that acceptable cost may depend on the disease, the number of affected patients, the costs of care and treatment, and other factors. This translates into common diseases needing cheaper analytical capabilities.
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From page 34... ...
Multinational corporations, such as Coca Cola, and oil companies, for example, have provided some of these supplies. The African Union, the Economic Community of West African States, and the South African Development Community have developed ways to address some of these problems, A participant suggested that biobanks be sited in secure locations, such as military bases.
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They also posed the question of how to interest donors in enhancing what already exists instead of building new facilities. Finally, they wondered how donors could help with "leave behind" facilities after an outbreak, as was done in Sierra Leone after the 2014 Ebola outbreak.
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From page 36... ...
He began by explaining that in "probe hybridization" or non-amplified nucleic acid probes, strands of DNA or RNA of less than 50 base pairs from a sample are probed for specific nucleic acid sequence "targets" that indicate the presence of particular pathogenic organisms. The DNA or RNA strands are labeled with enzymes, antigenic substrates, chemiluminescent molecular subunits, or radioisotopes.
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From page 37... ...
The concentration of the probe or target does not change, but sensitivity increases with increased concentration of labeled molecules attached to the target nucleic acid. Its advantage over target amplification methods, such as PCR, is that the detection "signal" is directly proportional to the amount of the target in a specimen, allowing for easier quantification.
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From page 38... ...
Many devices and methods for DNA sequencing currently exist. For example, for bacteria, 16S RNA forms part of the bacterial ribosome.
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is generated for analytes in the sample. Microbes are identified by comparing the MS spectrum of an unknown microbial isolate to the spectra of known isolates in a reference database.
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It is portable using a pocket-sized device, does not require internet connectivity, and offers potentially fast turnaround times, which are key for infectious disease sequencing. Its disadvantages are that its use is costly ($500 per flow cell)
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From page 41... ...
Gardy and Loman also report that obtaining a sufficient amount of viral nucleic acid for genome sequencing beyond simple diagnostics may also require PCR and an amplicon sequencing approach. Other challenges may include "access to reliable Internet connections, the ability to collect sample metadata, and translating genomic findings into real time, actionable recommendations."
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