Guidance for converting academic research laboratory to
COVID-19 testing laboratory (operations, personnel, space organization and workflow)
Based on CCMB’s experience
Given its established research activities in viral pathogens and the availability of a BSL3 and BSL2+ facility, CCMB was the first academic laboratory to be designated as a testing centre for COVID-19, as well as the only non-ICMR lab to be designated as a validation centre for SARS-CoV-2 diagnostics. Following a thorough review of our readiness for performing these tasks safely and effectively, CCMB initiated testing on March 31, 2020. These SOPs incorporate WHO and ICMR best practices as outlined in the Handbook for COVID-19 testing issued by the PSA, Govt of India, and also provides additional details that might be of use to individual institutes. To date, CCMB has tested over 1000 samples.
Overall Operations: Coordinated by Director with a team of senior scientists and a larger advisory team
Personnel: Each step in the testing workflow has a designated coordinator. In addition to a designated team taking care of procurement, interactions with Govt hospitals, State Govt Health Department and CSIR HQ, there is a large group (30+) student volunteers who were trained in BSL3/2 operations.
Space organization: BSL3 and BSL2 facilities in Main Building for receiving samples, virus handling and sample aliquoting for RNA prep, additional BSL2 laboratory in iHUB where semiautomated RNA isolation and RT-PCR analysis are handled. Workflow: is an optimized format developed for safety and convenience in our laboratory space. CCMB scientists will be available to answer questions on any aspect of the operations and workflow for those laboratories that are planning these activities in the current pandemic.
Standard Operating Procedure for COVID-19 testing centre
April 15, 2020
These SOPs are governed by appropriate biosafety protocols and Personal Protection Equipment (PPE) at each stage.
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.||Connecting with state government|
|3.||BSL facility – oversee testing|
|4.||Reagent and machine management|
|5.||Data Analysis Team|
|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|
Instructions for sample collection centres
Protocol to be followed at testing centres
Samples will be received by the designated staff and parked in a designated place till processing for pooling starts.
The following description is for samples that are decided to be processed by pooling.
All individual samples that belonged to the negative pools will be reported as negative for SARS-CoV-2. The respective pool data (Ct value, etc.) will be associated with the five negative samples. Every single sample from the positive "pools" after re-testing individually will be reported as positive/negative, accordingly, with associated data (Ct value, etc.)