Overview
The Qiagen QIAamp DSP Viral RNA Mini Kit CDC COVID-19 RT-PCR is part of the CDC COVID-19 RT-PCR protocols that include the following functionality.
Preconfigured CDC COVID-19 RT-PCR protocols that support the preparation of upper and lower respiratory specimens for real-time RT-PCR qualitative detection of nucleic acid from the 2019-nCoV.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents at every step in the protocol.
Automatic step transition when required.
Automatic placement of samples when necessary.
Automated assignment of QC Pass/Fail, based on user-selected threshold values.
Protocol 1: Qiagen QIAamp DSP Viral RNA Mini Kit or QIAamp Viral RNA Mini Kit (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Step 1: Sample Concentration (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Sample Concentration (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Set Next Step - PurificationTrigger Location = Record Details
Trigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (output.::Purification Protocol:: == ::Spin::) {nextStep = ::Purification of Viral RNA - Spin Protocol (CDC COVID-19 RT-PCR v1.1)::} \
else {if (output.::Purification Protocol:: == ::Vacuum::) {nextStep = ::Purification of Viral RNA - Vacuum Protocol (CDC COVID-19 RT-PCR v1.1)::} }' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 2: Purification of Viral RNA - Spin Protocol (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Purification of Viral RNA - Spin Protocol (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Automations
Calculate Total Samples and Master MixTrigger Location = Record Details
Trigger Style = Automatic upon entry
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Buffer AVL Volume (ml):: = step.::Total Samples:: * 0.56 ; \
step.::Carrier RNA AVE Volume (uL):: = step.::Buffer AVL Volume (ml):: * 10 ' \
-log {compoundOutputFileLuid0}"
Set Next Step - SpinTrigger Location = Record Details
Trigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::REMOVE:: ; output.::Purification Protocol:: = input.::Purification Protocol::' \
-log {compoundOutputFileLuid0}"
Routing Script - SpinTrigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Purification Protocol' \
--FIELD_VALUE 'Spin' \
--WORKFLOW 'Qiagen QIAamp DSP Viral RNA Mini Kit CDC COVID-19 RT-PCR v1.1' \
--STEP 'Assay Set Up Sorting (CDC COVID-19 RT-PCR v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 3: Purification of Viral RNA - Vacuum Protocol (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Purification of Viral RNA - Vacuum Protocol (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
QIAvac 24 Plus vacuum manifold
Automations
Calculate Total Samples and Master MixTrigger Location = Record Details
Trigger Style = Automatic upon entry
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Buffer AVL Volume (ml):: = step.::Total Samples:: * 0.56 ; \
step.::Carrier RNA AVE Volume (uL):: = step.::Buffer AVL Volume (ml):: * 10 ' \
-log {compoundOutputFileLuid0}"
Set Next Step - AdvanceTrigger Location = Record Details
Trigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ADVANCE::' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Sample Table
Sample Display Default = Collapse
Table Columns - Global Fields
Protocol 2: Real-Time RT-PCR Prep (CDC COVID-19 RT-PCR v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Assay Set Up Sorting (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Assay Set Up Sorting (CDC COVID-19 RT-PCR v1.1)
Automations
Set Next Step - RT-qPCRTrigger Location = Record Details
Trigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (input.::RT-qPCR Assay:: == ::Thermofisher TaqPath 1-Step RT-qPCR::) {nextStep = ::Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)::} ; if (input.::RT-qPCR Assay:: == ::Promega GoTaq Probe 1-Step RT qPCR::) {nextStep = ::Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)::} ; if (input.::RT-qPCR Assay:: == ::Quantabio qScript XLT One-Step RT-qPCR Tough Mix::) {nextStep = ::Quantabio qScript XLT One-Step RT-qPCR Tough Mix (CDC COVID-19 RT-PCR v1.1)::} ; if (input.::RT-qPCR Assay:: == ::Quantabio UltraPlex 1-Step ToughMix (4X)::) {nextStep = ::Quantabio UltraPlex 1-Step ToughMix (4X) (CDC COVID-19 RT-PCR v1.1)::}' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 2: Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 3
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Thermofisher TaqPath 1-Step RT-qPCR Master Mix, CG
Catalog Number = A15299; A15300
Automations
auto placement for 7500 Covid-19 assayTrigger Location = Placement
Trigger Style = Automatic upon entry
Copy /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
Calculate Total Samples and Master MixTrigger Location = Record Details
Trigger Style = Automatic upon entry
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 8.5 ; \
step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \
step.::TaqPath 1-Step RT-qPCR Master Mix (4x) (uL):: = step.::Total Samples:: * 5 ; \
step.::Total Volume (uL):: = step.::Total Samples:: * 15' \
-log {compoundOutputFileLuid0}"
Set Next Step - RT-qPCR AssayTrigger Location = Record Details
Trigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
copy PCR Product LIMSID to SampleTrigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 3: Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 3
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Promega GoTaq Probe 1- Step RT-qPCR System
Catalog Number = A6120; A6121
Automations
auto placement for 7500 Covid-19 assayTrigger Location = Placement
Trigger Style = Automatic upon entry
Copy /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
Calculate Total Samples and Master MixTrigger Location = Record Details
Trigger Style = Automatic upon entry
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 3.1 ; \
step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \
step.::GoTaq Probe qPCR Master Mix with dUTP (uL):: = step.::Total Samples:: * 10 ; \
step.::Go Script RT Mix for 1-Step RT-qPCR (uL):: = step.::Total Samples:: * 0.4 ; \
step.::Total Volume (uL):: = step.::Total Samples:: * 15' \
-log {compoundOutputFileLuid0}"
Set Next Step - RT-qPCR AssayTrigger Location = Record Details
Trigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
copy PCR Product LIMSID to SampleTrigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 4: Quantabio qScript XLT One-Step RT-qPCR Tough Mix (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Quantabio qScript XLT One-Step RT-qPCR Tough Mix (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 3
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Quantabio qScript XLT One-Step RT-qPCR ToughMix
Catalog Number = 95132-100; 95132-02K; 95132-500
Automations
auto placement for 7500 Covid-19 assayTrigger Location = Placement
Trigger Style = Automatic upon entry
Copy /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
Calculate Total Samples and Master MixTrigger Location = Record Details
Trigger Style = Automatic upon entry
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 3.5 ; \
step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \
step.::qScript XLT One-Step RT-qPCR Tough Mix (uL):: = step.::Total Samples:: * 10 ; \
step.::Total Volume (uL):: = step.::Total Samples:: * 15' \
-log {compoundOutputFileLuid0}"
Set Next Step - RT-qPCR AssayTrigger Location = Record Details
Trigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
copy PCR Product LIMSID to SampleTrigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Record Details
Step Data (Master Step Fields)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 5: Quantabio UltraPlex 1-Step ToughMix (4X) (CDC COVID-19 RT-PCR v1.1)
Master Step Name = Quantabio UltraPlex 1-Step ToughMix (4X) (CDC COVID-19 RT-PCR v1.1)
Derived Sample Generation = Fixed, 3
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
Quantabio UltraPlex 1-Step ToughMix (4X)
Catalog Number = 95166-100; 95166-500; 95166-01K
Automations
auto placement for 7500 Covid-19 assayTrigger Location = Placement
Trigger Style = Automatic upon entry
Copy /usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
Calculate Total Samples and Master MixTrigger Location = Record Details
Trigger Style = Automatic upon entry
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 8.5 ; \
step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \
step.::UltraPlex 1-Step ToughMix (4x) (uL):: = step.::Total Samples:: * 5 ; \
step.::Total Volume (uL):: = step.::Total Samples:: * 15' \
-log {compoundOutputFileLuid0}"
Set Next Step - RT-qPCR AssayTrigger Location = Record Details
Trigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"
copy PCR Product LIMSID to SampleTrigger Style = Automatic upon exit
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Record Details
Step Data (Master Step Fields)
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Step 6: ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)
Master Step Name = ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)
Automations
Generate ABI Instrument FileTrigger Location = Record Details
Trigger Style = Manual button
Copy bash -l -c "/opt/gls/clarity/bin/java -cp /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar driver_file_generator -i {processURI} -u {username} -p {password} -t /opt/gls/clarity/extensions/conf/covid/7900sds_container_setup_template.txt -o {compoundOutputFileLuid1}.txt -l {compoundOutputFileLuid0}.html && /opt/gls/clarity/bin/java -cp /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar addBlankLines -i {stepURI} -u {username} -p {password} -f {compoundOutputFileLuid1}.txt -l {compoundOutputFileLuid0}.html -sep TAB -b '0' -h 7 -c PLACEMENT"
PLACEHOLDER - Parse ABI FileTrigger Location = Record Details
Trigger Style = Manual button