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| '''High- and moderate-complexity CLIA testing''' | | '''High- and moderate-complexity CLIA testing''' |
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| At various times during the pandemic, reagent shortages have hampered many efforts to expand testing in parts of the world, including the United States. For the attentive laboratory wanting to remain agile in its testing, the laboratory's reagent choices will likely be closely tied to both the assays it chooses to implement and how reliably the supplier can get them to the lab. This in turn is likely driven by whether the lab is using a lab-developed test or a test kit. In some cases, e.g., the Xiamen Zeesan Biotech SARS-CoV-2 Test Kit (Real-time PCR), all but the Virus RNA Extraction Kit is included.<ref name="FDAXiamenSARS20">{{cite web |url=https://www.fda.gov/media/140717/download |format=PDF |title=SARS-CoV-2 Test Kit (Real-time PCR) Instructions for Use |publisher=Xiamen Zeesan Biotech |date=July 2020 |accessdate=14 August 2020}}</ref> On the other hand, Biomeme's SARS-CoV-2 Real-Time RT-PCR Test requires the separate acquisition of PCR buffer and external controls other than the exogenous RNA Process Control that comes with the kit.<ref name="FDABiomemeSARS20">{{cite web |url=https://www.fda.gov/media/141052/download |format=PDF |title=Biomeme SARS-CoV-2 Real-Time RT-PCR Test Instructions for Use |publisher=Biomeme, Inc |date=2020 |accessdate=14 August 2020}}</ref> Yale's SalivaDirect is a more flexible test, validated for use with multiple instruments and reagents that are not proprietary to Yale.<ref name="GallagherFDA20">{{cite web |url=https://www.contagionlive.com/view/fda-grants-emergency-covid19-authorization-yale-open-source-method-saliva-testing |title=FDA Grants Emergency COVID-19 Authorization to Yale's Open Source Method of Saliva Testing |author=Gallagher, G.M. |work=ContagionLive |date=15 August 2020 |accessdate=16 August 2020}}</ref><ref name="ZillgittFDA20">{{cite web |url=https://www.usatoday.com/story/sports/nba/2020/08/15/fda-approves-covid-19-saliva-test-developed-yale-nba-nbpa-aid/5590452002/ |title=FDA approves COVID-19 saliva test developed at Yale in partnership with the NBA, NBPA |author=Zillgitt, J. |work=USA Today |date=15 August 2020 |accessdate=16 August 2020}}</ref> Pay close attention to what comes with the assay, typically by reviewing the instructions for use (IFU; found on the FDA's EUA page).
| | Non-reagent consumables for high- and moderate-complexity CLIA testing include PCR tubes and plates; pipettes and tips; films, foils, and sealing mats; swabs; and viral transport media, among others. Some like Kellner ''et al.'' have experimented with methods to make isothermal amplifications methods more approachable in resource-poor environments by, for example, developing a pipette-free version of LAMP.<ref name="KellnerARapid20">{{cite journal |title=A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing |journal=bioRxiv |author=Kellner, M.J.; Ross, J.J.; Schnabl, J. et al. |year=2020 |doi=10.1101/2020.06.23.166397}}</ref> |
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| For PCR, the five basic reagents are template DNA, PCR primers, nucleotides, PCR buffer, and thermostable DNA polymerase. Some of these components can be acquired pre-mixed as a "master mix." For example, Thermo Fisher's PCR Master Mix contains a thermostable DNA polymerase called ''Taq'', nucleotides called deoxynucleotide triphosphates (dNTPs), and a buffer, which "saves time and reduces contamination due to a reduced number of pipetting steps."<ref name="TFSPCRMaster">{{cite web |url=https://www.thermofisher.com/order/catalog/product/K0171#/K0171 |title=PCR Master Mix (2X) |publisher=Thermo Fisher Scientific |accessdate=16 August 2020}}</ref>
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| Reagent cost and usage for isothermal amplification methods such as LAMP are similar, though buffers and primers specific to the method are required.<ref name="DiegoProgress19">{{cite journal |title=Progress in loop-mediated isothermal amplification assay for detection of Schistosoma mansoni DNA: Towards a ready-to-use test |journal=Scientific Reports |author=Diego, J. G.-B.; Fernández-Soto, P.; Crego-Vicente, B. et al. |volume=9 |at=14744 |year=2019 |doi=10.1038/s41598-019-51342-2 |pmid=31611563 |pmc=PMC6791938}}</ref><ref name="NEBLoop14">{{cite web |url=https://www.neb.com/protocols/2014/06/17/loop-mediated-isothermal-amplification-lamp |title=Loop-mediated Isothermal Amplification (LAMP) |publisher=New England BioLabs |date=17 June 2014 |accessdate=14 August 2020}}</ref><ref name="OGIsoth">{{cite web |url=http://www.optigene.co.uk/isothermal-reaction-guide/ |title=Isothermal Reaction Guide |publisher=OptiGene Limited |accessdate=16 August 2020}}</ref><ref name="KashirLoop20">{{cite journal |title=Loop mediated isothermal amplification (LAMP) assays as a rapid diagnostic for COVID-19 |journal=Medical Hypotheses |author=Kashir, J.; Yaqinuddin, A. |volume=141 |at=109786 |year=2020 |doi=10.1016/j.mehy.2020.109786 |pmid=32361529 |pmc=PMC7182526 |quote=Reagent-wise, the costs would be similar to that of real time RT-PCR ...}}</ref>
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| '''CLIA-waived testing''' | | '''CLIA-waived testing''' |
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| The FDA EUA devices (Table 1 and 2) all come with the necessary reagents, with the exception of any controls or references you may require. Refer to the IFU for the waived test kit to determine what additional consumables you'll require. | | The FDA EUA devices (Table 1 and 2) may require a few extra consumables. For example, the Accula SARS-CoV-2 test kit comes with swabs<ref name="MBAccula20">{{cite web |url=https://www.fda.gov/media/136355/download |format=PDF |title=Accula Test |publisher=Mesa Biotech, Inc |date=April 2020 |accessdate=16 August 2020}}</ref> and the Xpert Xpress SARS-CoV-2 kit comes with disposable transfer pipettes.<ref name="CepheidXpert20">{{cite web |url=https://www.fda.gov/media/136315/download |format=PDF |title=Xpert Xpress SARS-CoV-2 |publisher=Cepheid |date=March 2020 |accessdate=16 August 2020}}</ref> Refer to the IFU for the waived test kit to determine what additional consumables you'll require. |
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| ==References== | | ==References== |
| {{Reflist|colwidth=30em}} | | {{Reflist|colwidth=30em}} |
High- and moderate-complexity CLIA testing
Non-reagent consumables for high- and moderate-complexity CLIA testing include PCR tubes and plates; pipettes and tips; films, foils, and sealing mats; swabs; and viral transport media, among others. Some like Kellner et al. have experimented with methods to make isothermal amplifications methods more approachable in resource-poor environments by, for example, developing a pipette-free version of LAMP.[1]
CLIA-waived testing
The FDA EUA devices (Table 1 and 2) may require a few extra consumables. For example, the Accula SARS-CoV-2 test kit comes with swabs[2] and the Xpert Xpress SARS-CoV-2 kit comes with disposable transfer pipettes.[3] Refer to the IFU for the waived test kit to determine what additional consumables you'll require.
References
