The SARS-CoV-2 focused risk assessment includes pre-analytic (sample handling after receiving, acceptance criteria assessment, and organizing samples for analytic process), analytic (sample inactivation, nucleic acid extraction and RT-PCR assay) and post-analytic (data retrieval, reporting, and storage or destruction of samples) processes. Risk management includes engineering (infrastructure, facility, workflow, primary and secondary containment), administrative (SOPs, PPE, and disinfectants), operational process controls (training, facility decontamination, waste management, LAI reporting, logistics, and safety compliance monitoring), and monitoring of the implementation (Table 1).
As a part of the risk management strategy, HTD and OUCRU shared the laboratory infrastructure and facilities (e.g., specimen reception room, cold chain units, MDF, BSL3 laboratory), instruments, logistics, human resource and safety system implementation. Risk management includes the spraying of sample containers (outer containers) with freshly prepared disinfecting solution (chlorine 5000 ppm) and opening secondary containers in biosafety cabinets (BSC) Class (Cl) I to examine acceptance criteria. PPE used for sample reception area includes reusable lab coats (equivalent to AAMI level 2), surgical face masks (equivalent to American Society for Testing and Materials (ASTM) level 2), nitrile gloves, goggles, hair caps, and shoe covers. The specimen reception facility is decontaminated 3 times daily (7:00 AM, 1:00 PM and 5:00 PM) with Virkon S (Peroxygen 49.8%, Sodium chloride 27.6%; 10 g/L) disinfectant (10 g/L) sprayed with an ultra-low volume sprayer at a dose of 20 to 30 mL/m2. Waste is stored in double bags and removed before each decontamination cycle. Samples are transported to MDL in batches in secondary container and inactivated in the BSL2 laboratory in BSC Cl I following BSL2+ laboratory practices. BSL2+ laboratory practice includes disposable PPE, including fit-tested particulate respirators (equivalent to an N95 mask), long-sleeved gowns (equivalent to AAMI level 3), goggles, round caps, latex gloves and shoe covers. All aerosol generating procedures are conducted in BSCs and centrifugation in sealed buckets. The MDL was decontaminated 5 times daily (7:00 AM, 11:00 AM, 3:00 PM, 6:00 PM and 11:00 PM) with Virkon S as mentioned above. In the laboratory, all BSCs are cleaned with Surfanios (DD BioLab, Barcelona, Spain) after use and irradiated with UV light once a day for 2 hours. Waste is stored in double bags and removed before each decontamination cycle. Test results were extracted from the instruments through a laboratory information system and test reports are delivered to the CDC, Ho Chi Minh City. Remaining SARS-CoV-2 positive or negative samples were stored in the BSL3 biorepository or destroyed, respectively. The heating, ventilation and air conditioning (HVAC) system of the facility was set at 26 ºC, with 8-10 air changes per hour.
SOPs for testing including sample reception, sample inactivation, TNA extraction, and sample retention/destruction, were developed. A task specific (e.g. sample reception, sample inactivation, total nucleic acid (TNA) extraction, PT-PCR assay, facility decontamination, waste management and sample destruction) training programme was implemented for staff. The training included SARS-CoV-2 focused risk assessment, biosafety, PPE use (donning and doffing), and the assigned task. Overall, 14 clinical laboratory staff (4 staff for pre-analytic, 8 staff for analytic and 2 staff for post-analytic processes) were responsible for routine SARS-CoV-2 testing. In addition to this, 4 laboratory staff members from another hospital and 8 research laboratory staff members were involved in testing during the high sample load periods. Additionally, 6 OUCRU laboratory management staff were involved in safety process implementation. All staff reported symptom daily and during the reported period none of the staff reported any symptoms of COVID-19 and a subsequent study excluded asymptomatic infection among laboratory staff .
The laboratory was certified by the Department of Health (DoH), HCMC on March 14, 2020 for SARS-CoV-2 testing and a safety audit were conducted by CDC, HCMC in early September. As a part of inter-laboratory comparison all positive samples were retested at Pasteur institute, HCMC and no discrepancies were identified between the two laboratories. The OUCRU laboratory management conducted daily inspections of safety system implementation. For logistic management a bulk procurement for 20,000 diagnostic tests was initiated in March 2020, and procurement was continued as per need. For PPE (surgical mask, N95 mask, lab coat, gloves) disinfectants, and hand sanitizers, 3 months stock was considered sufficient.
All samples received for SARS-CoV-2 testing were registered in the laboratory database. Respiratory and oropharyngeal samples for RT-PCR were tested in MDL, and samples for microbiology culture were performed in the BSL3 laboratory. During the reporting period, there were two local COVID-19 outbreaks. The first occurred from March 24 to April 13, 2020, mostly in Hanoi and around the north, and in Ho Chi Minh City in the south of the country. The second occurred from July 28 to August 8, 2020, mostly in and around Da Nang in the centre of the country (Fig 1). From February 1, 2020 to September 17, 2020, 38,377 samples were received for testing (Table 2), accounting for 18.6% (38,377/206,626) of all tests done in HCMC during the reporting period. Among these 38,377 samples, 301 (0.8%) were rejected as they did not fulfil the acceptance criteria. The mean number of samples received per day was 166, with a range of 3 to 2,377. The turnaround time (mean ± SD) was 3.54 ± 2.97 days (1.30 ± 1.23 during the non-outbreak period and 4.55 ± 2.99 during the outbreak period) (Table 2). During the first (March 24 to April 13) and second (July 28 to August 8) outbreaks, the numbers of samples received (mean and range) were 11,904 and 14,293, with daily numbers of 626 (106-2,061) and 1050 (34-2,377), respectively (Fig 1, Table 2). Overall, 4,924 (12.8%) samples were sent to other laboratories for testing during the outbreak periods (2,648 during the first and 2,276 during the second outbreak).