Qiagen QIAamp DSP Viral RNA Mini Kit v1.1

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)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}

Automations

Set Next Step - Purification

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Directions	Multiline Text		Default = Add up to 3.5 ml of sample to the microconcentrator Centrifuge to a final volume of 140 μl.
  Sample Volume (mL)	Numeric		Default = 3.5

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • Well Sort Order = Row
  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Purification Protocol	Text Dropdown	Required Field	Presets Spin Vacuum
    Derived Sample	Sample Name	Built-in

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)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • Buffer AW1

    • Catalog Number = 61904

Automations

Calculate Total Samples and Master Mix

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Set Next Step - Spin

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Routing Script - Spin

• Trigger Location = Step
• Trigger Style = Automatic upon exit

ℹ The version of the workflow and step name for the routing script may be different depending on the version of IPP installed.

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  96-100% EtOH Prep Date	Date
  Buffer AVL Volume (ml)	Numeric		Decimal Places Displayed = 2
  Carrier RNA AVE Volume (uL)	Numeric		Decimal Places Displayed = 2
  Incubation End Time:	Text
  Incubation Start Time:	Text
  Total Samples	Numeric		Default = 0

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • Well Sort Order = Row
  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • Buffer AW1

    • Catalog Number = 61904
  • QIAvac 24 Plus vacuum manifold

    • Catalog Number = 19413

Automations

Calculate Total Samples and Master Mix

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  96-100% EtOH Prep Date	Date
  Buffer AVL Volume (ml)	Numeric		Decimal Places Displayed = 2
  Carrier RNA AVE Volume (uL)	Numeric		Decimal Places Displayed = 2
  Incubation End Time:	Text
  Incubation Start Time:	Text
  Total Samples	Numeric		Default = 0

• Sample Table

  • Sample Display Default = Collapse
  • Well Sort Order = Row
  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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)
• Step Type = No Outputs

Automations

Set Next Step - RT-qPCR

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • Well Sort Order = Row
  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	RT-qPCR Assay	Text Dropdown	Required Field	Presets Thermofisher TaqPath 1-Step RT-qPCR Promega GoTaq Probe 1-Step RT qPCR Quantabio qScript XLT One-Step RT-qPCR Tough Mix Quantabio UltraPlex 1-Step ToughMix (4X)
    Derived Sample	Sample Name	Built-in

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)
• Step Type = Standard
• Derived Sample Generation = Fixed, 3
• Naming Convention = {InputItemName}-{LIST:N1,N2,P}
• Reagent Kits

  • Thermofisher TaqPath 1-Step RT-qPCR Master Mix, CG

    • Supplier = Thermofisher
    • Catalog Number = A15299; A15300
• Control Types

  • HSC
  • nCoVPC
  • NTC

Automations

auto placement for 7500 Covid-19 assay

• Trigger Location = Placement
• Trigger Style = Automatic upon entry

Calculate Total Samples and Master Mix

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Set Next Step - RT-qPCR Assay

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

copy PCR Product LIMSID to Sample

• Trigger Location = Step
• Trigger Style = Automatic upon exit

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
  • Placement Pattern = Row
• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Combined Primer/Probe Mix (uL)	Numeric		Decimal Places Displayed = 2
  Nuclease-free Water (uL)	Numeric		Decimal Places Displayed = 2
  TaqPath 1-Step RT-qPCR Master Mix (4x) (uL)	Numeric		Decimal Places Displayed = 2
  Total Samples	Numeric		Default = 0
  Total Volume (uL)	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • Well Sort Order = Row
  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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)
• Step Type = Standard
• 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
• Control Types

  • HSC
  • nCoVPC
  • NTC

Automations

auto placement for 7500 Covid-19 assay

• Trigger Location = Placement
• Trigger Style = Automatic upon entry

Calculate Total Samples and Master Mix

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Set Next Step - RT-qPCR Assay

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

copy PCR Product LIMSID to Sample

• Trigger Location = Step
• Trigger Style = Automatic upon exit

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
  • Placement Pattern = Row
• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Combined Primer/Probe Mix (uL)	Numeric		Decimal Places Displayed = 2
  Go Script RT Mix for 1-Step RT-qPCR (uL)	Numeric		Decimal Places Displayed = 2
  GoTaq Probe qPCR Master Mix with dUTP (uL)	Numeric		Decimal Places Displayed = 2
  Nuclease-free Water (uL)	Numeric		Decimal Places Displayed = 2
  Total Samples	Numeric		Default = 0
  Total Volume (uL)	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • Well Sort Order = Row
  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

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)
• Step Type = Standard
• 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
• Control Types

  • HSC
  • nCoVPC
  • NTC

Automations

auto placement for 7500 Covid-19 assay

• Trigger Location = Placement
• Trigger Style = Automatic upon entry

Calculate Total Samples and Master Mix

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Set Next Step - RT-qPCR Assay

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

copy PCR Product LIMSID to Sample

• Trigger Location = Step
• Trigger Style = Automatic upon exit

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
  • Placement Pattern = Row
• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Combined Primer/Probe Mix (uL)	Numeric		Decimal Places Displayed = 2
  Nuclease-free Water (uL)	Numeric		Decimal Places Displayed = 2
  qScript XLT One-Step RT-qPCR Tough Mix (uL)	Numeric		Decimal Places Displayed = 2
  Total Samples	Numeric		Default = 0
  Total Volume (uL)	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • Well Sort Order = Row
  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in