TITLE: SW-2 SWAB PROCESSING
AUTHORS: REDI-NET Consortium

[DESCRIPTION]
This protocol details procedures for total nucleic acid extraction from swab samples.

[BEFORE_START]
BEFORE START

Pre-cool the Bullet Blender by adding dry ice into the cooling compartment and running the cooling program. 
Clean the work surfaces with RNaseZap, then wipe the surfaces with 70% molecular biology grade ethanol to remove additional contaminants.
Pre-heat the heater mixer at 56 °C. 
Transfer 0.1 mm zirconium oxide beads (2 spoons, Appendix 1) to Thermo Scientific Screw Cap Micro 1.5ml Tubes.
Buffer ATL may form precipitates upon storage. If necessary, warm to 56 °C until the precipitates have fully dissolved. Prepare buffer ATL-DX: add 100 µL Reagent DX to 15 mL Buffer ATL. If smaller amounts are needed, transfer 1.5 mL of Buffer ATL into a sterile 2ml vial and add 10 µL Reagent DX. Mix well, after addition of Reagent DX. After preparation, the mixture is stable for 6 months at Room temperature (15-25°C).
For the first time use of IndiMag pathogen kit, add 100% ethanol to Buffer AW1 and AW2, and add 100% isopropanol to ACB as indicated on the bottles.
MagAttract Suspension G from IndiMag pathogen kit needs to be vortexed thoroughly for 3 min (before first use) or 1 minute (before subsequent uses) to ensure that the magnetic silica particles are fully resuspended. 
Aliquot nuclease-free water in big bottle into a few 15ml tubes for preparing TNA elution in KingFisher Flex or KingFisher Duo Prime to avoid cross-contamination.

[GUIDELINES]
OBJECTIVE

To outline procedures for total nucleic acid extraction from swab samples.

SUMMARY/SCOPE

The overarching aim of the REDI-NET is to develop a collaborative laboratory network between domestic and international partnering institutions to address disease surveillance needs in order to effectively detect, predict and contain potentially emergent zoonosis. This SOP provides guidance on procedures for total nucleic acid extraction from swab samples to provide materials for downstream library preparation and sequencing for pathogen detection. 

RESPONSIBLE PERSON

Principal Investigator, Study Coordinator, Entomology Component Lead, Managers
 

MAINTENANCE OF EQUIPMENT

Caution on RNA handling

RNases are very stable and difficult to inactivate, and only minute amounts are sufficient to destroy RNA. 
Care should be taken to avoid inadvertently introducing RNases into the samples during or after the purification procedure. 
Sample handling and extraction should be performed under an extraction hood and respecting Good Laboratory Practices. 
Use filter tips all the time.

Storage of the buffers from IndiMag Pathogen Kit

Proteinase K is stable for at least 1 year after delivery when stored at Room temperature (15-25°C). To store for more than 1 year or if ambient temperature often exceeds 25°C, storage at 2-8 °C is recommended. Do not add Proteinase K directly to the Buffer VXL mixture! This can cause clogs or precipitates.
Precipitation may form after storage at low temperature or prolonged storage. To dissolve precipitate, incubate Buffer VXL or ACB for 30 min at 37 °C, with occasional shaking.
Reconstituted Buffer AW1 can be stored at Room temperature (15-25°C) for up to 1 year. Mix well after adding Ethanol.
Buffer AVE is RNase-free upon delivery. It contains sodium azide, an antimicrobial agent that prevents growth of RNase-producing organisms. However, as this buffer does not contain any RNase degrading chemicals, it will not actively inhibit RNases introduced by inappropriate handling. When handling Buffer AVE, take extreme care to avoid contamination with RNases. Follow general precautions for working with RNA, such as frequent change of gloves and keeping tubes closed whenever possible.

QUALITY CONTROL 

This SOP is reviewed by the applicable supervisor annually or as required in order to maintain its relevance.

APPENDICES
 

APPENDIX 1. MEASURING SPOON FOR 0.1 MM BEATING BEADS

The spoon (Next Advance, MSP01-RNA) is used for 0.1 mm beating beads measurement. One scoop equals to 100 uL.
 
APPENDIX 3. Expected Outcomes

 
 
      SampleAmountSample conditionElution volumeDNA conc. (ng/ul)RNA conc.(ng/ul)Swab1 swab Frozen/Fresh750-200-15

 
 

[STEPS]
SECTION: 1. SAMPLE LYSIS
1. 
 
Add 500 µL of ATL-DX buffer and 20 µL Proteinase K to the bead tubes prepared in Step 4 of Before Start section under the Guidelines & Warning tab.

SECTION: 1. SAMPLE LYSIS
2. Place the sample swab in the bead tube with ATL buffer and Proteinase K. Use sterile scissors to carefully cut off the swab heads or transfer the pre-cut swab head from the original container to the bead tube with forceps.
SECTION: 1. SAMPLE LYSIS
3. Include a positive control for each batch of samples: transfer 37.5 µL ZymoBIOMICS Microbial Community Standard Material, 100 µL EBV, and 100 µL ZIKV standard into a tube from Step 3 of Before Start section. Add 250 µL ATL-DX buffer and 20 µL proteinase K.

SECTION: 1. SAMPLE LYSIS
4. Include a negative control for each batch of samples: a bead tube from Step 3 of Before Start section with 500 µL ATL-DX buffer and 20 µL proteinase K.

SECTION: 1. SAMPLE LYSIS
5. Incubate samples in a thermomixer at  .

SECTION: 1. SAMPLE LYSIS
6. Refill the dry ice compartment of the Bullet Blender if necessary. After incubation, load all samples into the Bullet Blender.
SECTION: 1. SAMPLE LYSIS
7. Set the speed at 12 and the time at 3. Press Start.
SECTION: 1. SAMPLE LYSIS
8. Let the samples settle for 1 min in the Bullet Blender and then repeat Step 7. 
 


SECTION: 2. INSTRUMENT SET UP
9. 
 

Confirm 96 deep-well magnetic heads and 96 well deep-well heat blocks are being used.
SECTION: 2. INSTRUMENT SET UP
10. Ensure the program IndiMag_Pathogen_KF_Flex_4wash or the program has been downloaded and loaded onto the KingFisher Flex instrument.
SECTION: 2.1 SET UP THE PROCESSING PLATES
11. Set up the Tip Comb, Wash, and Elution Plates outside the instrument according to the following table. 
 
 
     Plate ID      Plate position      Plate type      Reagent      Volume per well        Tip   comb      7      Place   a 96 Deep-well Tip comb in a deep-well plate        Elution      6      Deep-Well      Nuclease-free   water      75   µL        Wash   4      5      Deep-Well      100   % ethanol      750   µL        Wash   3      4      Deep-Well      80%   ethanol      750   µL        Wash   2      3      Deep-Well      Buffer   AW2      700   µL        Wash   1      2      Deep-Well      Buffer   AW1      700   µL        Sample         1      Sample   Lysate      Lysate   and lysis buffer      985   µL   
 
SECTION: 2.2 EXTRACTION
12. Centrifuge the bead tubes with lysate from Step 8 for 12000 x g, 5 min.

SECTION: 2.2 EXTRACTION
13. Transfer 290 µL supernatant without any particle carryover to the wells of the Deep-well plate. This plate becomes the Sample Plate.

SECTION: 2.2 EXTRACTION
14. Add 135 µL Buffer VXL, 540 µL Buffer ACB, and 20 µL MagAttract Suspension G to each sample in the sample plate. For multiple samples, make a master mix with 10% overage. Invert slowly to mix the master mix; avoid foaming (it can be mixed on a Hula mixer for 2 min). Add 695 µL mixture to each sample. Each well including sample lysate should be 985 µL.

SECTION: 2.2 EXTRACTION
15. Select the program IndiMag_Pathogen_KF_Flex_4wash on the instrument.
SECTION: 2.2 EXTRACTION
16. Start the run, then load the prepared plates into position when prompted by the instrument.
SECTION: 2.3 QUANTIFICATION AND STORAGE
17. After the running protocol is completed (~35 minutes), immediately remove the elution plate from the instrument and cover the plate or transfer the eluate to the final tube or plate of choice for final storage. 
SECTION: 2.3 QUANTIFICATION AND STORAGE
18. In a 0.6mL microcentrifuge tube, use 3 µL total nucleic acid for DNA and RNA concentration measurement using Qubit 4 Fluorometer following manufacturer instructions (Kits needed: Qubit 1X dsDNA HS Assay Kit and Qubit RNA HS Assay Kit) (see Appendix 2 and Appendix 3).

SECTION: 2.3 QUANTIFICATION AND STORAGE
19. Proceed with sample testing following the REDI-NET SOP SW-4 Swab Testing or store at -20 °C for less than 2 weeks (for long-term storage the sample needs to be stored at -80 °C following the REDI-NET SOP SW-3 Swab Storage).

SECTION: 3. INSTRUMENT SET UP
20. 
 

Confirm 12-tip magnetic heads and 12 well deep-well heat blocks are being used.
SECTION: 3. INSTRUMENT SET UP
21. Ensure the program IndiMag_Pathogen_KF_Duo_4wash has been downloaded and loaded onto the KingFisher Duo Prime instrument.
SECTION: 3.1 SET UP THE SAMPLE PLATE AND ELUTION STRIP
22. Set up the Sample Plate according to the table below:
 
     Row ID      Plate Row      Reagent      Volume per well        Sample row      A      Lysate   and lysis buffer      985   µL        Wash 1      B      Buffer   AW1      700   µL        Wash 2      C      Buffer   AW2      700   µL        Wash 3      D      80   % ethanol      750   µL        Wash 4      E      100   % ethanol      750   µL        Tip Comb       F      Tip   comb                       G      Empty               H   
 
SECTION: 3.1 SET UP THE SAMPLE PLATE AND ELUTION STRIP
23. Set up the Elution Strip according to the table below:
 
 
     Strip ID      Row       Reagent      Volume per well        Elution         A      Nuclease-free   water      75   µL   
 
SECTION: 3.2 EXTRACTION
24. Centrifuge the bead tubes with lysate from Step 8 for 12000 x g, 5 min.

SECTION: 3.2 EXTRACTION
25. Transfer 290 µL supernatant without any particle carryover to the wells of the Deep-well Row A. This row becomes the Sample Row.

SECTION: 3.2 EXTRACTION
26. Add 135 µL Buffer VXL, 540 µL Buffer ACB, and 20 µL MagAttract Suspension G to each sample in the Sample Plate. For multiple samples, make a master mix with 10% overage. Invert slowly to mix the master mix and avoid foaming. Add 695 µL mixture to each sample. Each well including sample lysate should be 985 µL.

SECTION: 3.2 EXTRACTION
27. Select the program IndiMag_Pathogen_KF_Duo_4wash on the instrument.
SECTION: 3.2 EXTRACTION
28. Start the run, then load the prepared plate and Elution Strip into position when prompted by the instrument.

 

SECTION: 3.3 QUANTIFICATION AND STORAGE
29. After the running protocol is completed (~35 minutes), immediately remove the elution plate from the instrument and cover the plate or transfer the eluate to the final tube or plate of choice for final storage. 
SECTION: 3.3 QUANTIFICATION AND STORAGE
30. In a 0.6mL microcentrifuge tube, use 3 µL total nucleic acid for DNA and RNA concentration measurement using Qubit 4 Fluorometer following manufacturer instructions (Kits needed: Qubit 1X dsDNA HS Assay Kit and Qubit RNA HS Assay Kit) (see Appendix 2 and Appendix 3).

SECTION: 3.3 QUANTIFICATION AND STORAGE
31. Proceed with sample testing following the REDI-NET SOP SW-4 Swab Testing or store at -20 °C for less than 2 weeks (for long-term storage the sample needs to be stored at -80 °C following the REDI-NET SOP SW-3 Swab Storage).

SECTION: APPENDIX 2. DNA and RNA Measurement using QUBIT FLUOROMETER 4.0
32. DNA quantification: 
SECTION: APPENDIX 2. DNA and RNA Measurement using QUBIT FLUOROMETER 4.0
32.1. According to the volume of sample used, add the 1x HS dsDNA Qubit Assay for a final volume of 200 µL (i.e., if using 3 µL of sample, add 197 µL of 1x HS dsDNA Qubit Assay). Vortex for 5 - 10 seconds, then incubate for  2 min  at Room temperature 

SECTION: APPENDIX 2. DNA and RNA Measurement using QUBIT FLUOROMETER 4.0
33. RNA Quantification:
SECTION: APPENDIX 2. DNA and RNA Measurement using QUBIT FLUOROMETER 4.0
33.1. In a new microcentrifuge tube/falcon tube (depending on the number of samples processed), prepare a working solution of the Qubit HS RNA Assay:
 
     Reagents      Volume/sample      Volume   for n+1 sample        Qubit RNA HS Assay buffer      199   µL      ….   µL        Qubit RNA HS Assay Dye      1   µL      ….   µL   
 
SECTION: APPENDIX 2. DNA and RNA Measurement using QUBIT FLUOROMETER 4.0
33.2. In a new 0.6ml tube, mix 197 µL of Qubit HS RNA Assay working solution and 3 µL of the sample.  Vortex for 5 - 10 seconds, then incubate for 2 min at Room temperature before reading.