1. The State Government informs a designated person in the testing centre the number of samples they are sending.
2. Samples arrive at CCMB in thermocol boxes brought by hospital ambulances. Sample boxes are not to be removed from the ambulance at security office.
3. The designated person at security confirms with the designated person who has been in touch with the State Government,if the samples are to be accepted or not.
4. The designated person at the security checks the shipment papers, records (in a specific register for COVID-19 samples) the details of the samples (hospital that is sending the samples, when (date and time) it reaches the testing centre, and their number (number of boxes per case sheet, and number of case sheets). The sample boxes are not taken out of the ambulance.
5. Based on the availability of volunteers in BSL facility the samples are to be taken directly to theBSL facility for testing or stored ina cold room at 4-6?C. The designated security person accompanies the hospital personnel from security office to the appropriate location.
6. The hospital personnel place the samples in the cold room or hand them to the volunteers at BSL facility along with their respective case sheets.

1. If there is more than one box per shipment from a particular hospital, the security officer accompanying the hospital personnel ensures the boxes are numbered with marker so that the case sheets can be linked to all boxes from that hospital.
2. Thestored samples are matched with the intimation received from the State Government by the designated person at the testing centre.
3. The samples are then taken for documentation and testing in BSL facility.

1. The test samples are taken into the BSL-3 lab inside the BSL facility, and the case sheets go to the COVID19 Documentation Room in the BSL facility.
2. Every case sheet is allotted a unique code by the testing centre. This information is printed out on label stickers, and passed onto the volunteers in the BSL-3 lab who catalogue the samples received. They also receive a printout for records in a register in the BSL-3 lab.
3. The name and age written on the sample tubes is visible to volunteers but not the area of its origin.

1. The sample code number with its case sheet are cross-checked, and entered in a register in the BSL-3 lab.
2. The sample packaging integrity (for tube leakage, labelling, cold chain) is checked, the sample tube surfaceis cleaned with alcohol (70% isopropanol), and are stored in -80?C, in numbered racks until they need to be processed for testing.The rack number is also noted in the register along with other sample details.
3. Upon their turn for testing, the samples are thawed and aliquoted. One of the aliquots is lysed, and set aside for viral RNA analysis. The code number of the sample aliquot is recorded in the register in the BSL-3 lab. The other aliquots of the same sample are stored in their designated locations in -80?Cfor future usage.
4. The aliquots of each sample designated for testing, along with associated case sheets are taken to BSL-2 lab for testing.

1. The sample lysates are received, verified and registered by the team in the COVID-19 BSL-2 testing facility.
2. RNA is isolated from the samples in the RNA preparation room.
3. The RNA is taken to the RT-PCR room for analysis.
4. The RT-PCR pre-mix is prepared and distributed into 96-well plates in Hood #1. The plate is then shifted to Hood #2 where RNA template is added. The plate containing the complete reaction mix is then loaded into the RT-PCR machine. Readings are digitally recorded in realtime by the software in the associated computer. The file for each is named with catalogue number and date. These files are stored on the computer in datewise folders for collection by documentation team.
5. After the reaction is complete the plate is discarded in a biohazard bag.
6. Biohazard bags are autoclaved and disposed every day. The designated lab personnel for handling the biohazard bagswear the entire PPE kit, and move the biohazard bags into the Autoclave Room. After autoclaving at 121?C for 20 min at a pressure of 15psa, these bags are sealed in cardboard boxes, and stored for being picked up by an external agency.

1. Results from the computer attached to RT-PCR machine are downloaded in the pdf format onto pen drives, and pendrives carried to the documentation room by RT-PCR volunteers. The files are labelled with the date, batch and sample numbers, and arranged in a folder, date wise.
2. The Data Analysis Team analyse the results. A sample is considered positive if the Ct value for a gene is determined to be<36. If a given sample tests positive for 2 out of 3 genes (genes E/N, ORF1b, RdRp), the case is considered to be COVID-19 positiveas per ICMRguidelines.
3. The Analysis Team also decode the samples -thesample code allottedby the testing centre is matched with the case sheet of the patient received from the hospital.
4. Entire patient details are filled in the testing centre's portal.
5. The test results are uploaded to the State Government portal, and emailed to pertinent State Government Officials, and also the respective hospitals where the samples originated from.
6. The reports are also uploaded on the ICMR portal(https://cvstatus.icmr.gov.in).
7. TheState Government is updated by the designated person at the testing centretwice a day by WhatsApp, at 7 am and 5 pm.

The case sheets are stored securely in the documentation room in the testing centre. All data is backed up on an external storage device. The data can only be accessed by authorized personnel.

1. Biosafety protocols governing each location in sample receiving and handling workflow are as per guidelines.
   1. All personnel at each location have been trained to handle the samples according to the safety level required.
   2. Tables and floor of all labs are cleaned with 1% sodium hypochlorite.
   3. The sample boxes from the hospitals are cleaned with 1% sodium hypochlorite, followed by water and 70% isopropanol before opening them in BSL-3.
   4. Laminar hood areas are disinfected with UV exposure of 15 min daily, and cleaned with 70% ethanol/isopropanol.
   5. Testing and cleaning personnel clean their hands with Sterilium (45% isopropanol and 30% propanol).
   6. Entire PPE kits are worn during sample lysis, RNA isolation and RT-PCR in BSL-3 and BSL-2 labs.
2. Below are the main roles which should have a primary person as well as a back up person.

   No	Role
   1.	Connecting with state government
   2.	Pre-test documentation
   3.	BSL facility - oversee testing
   4.	Reagent and machine management
   5.	Data Analysis Team
   5.	Report generation

3. Roster for testingvolunteers

   No.	Sample entry	Batch 1	Batch 2	Frequency of turn of each batch
   A	Documentation	A1, A2	A3, A4	Every day for half a day
   B	Sample storage and lysis	B1, B2, B3	B4, B5, B6	Every day for half a day
   C	RNA isolation	C1, C2	C5, C6	Every alternate day for half a day
   		C3, C4	C7, C8
   D	RT-PCR	D1, D2	D7, D8	Every alternate day for one third of a day
   		D3, D4	D9, D10
   		D5, D6	D11, D12
   E	Report generation	E1, E2, E3	E4, E5, E6	Every day for half a day