National strategy for SARS-CoV-2 testing.
The national COVID-19 testing strategy was implemented for SARS-CoV-2 testing at HTD . The real-time (RT)-PCR assay is considered as a confirmatory test. Two swabs are collected (one nasopharyngeal and one throat) from each patient and stored in viral transport media (VTM). Samples in VTM are stored at 4ºC and transported to the laboratory using triple layer packing. Chain of custody and sample information documents are packed separately and transported to the laboratory along with the samples .
Risk assessment and risk management
The risk assessment includes pre-analytic (sample handling after receiving, examining for acceptance criteria, and organizing for analytic process), analytic (sample inactivation, nucleic acid extraction and RT-PCR assay) and post-analytic (data retrieval, report generation, 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, logistics, and human resources and worked together to ensure the quality, safety and timely testing of the SARS-CoV-2 samples. This includes sharing infrastructure and facilities (e.g., specimen reception room, cold chain units (2-8 ºC and -86 ºC freezer), molecular diagnostic facility, BSL3 laboratory), instruments, manpower and safety system implementation.
Risk management includes the spraying of sample containers (outer containers) with freshly prepared disinfecting solution (chlorine 1000 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 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 (10 gm/L) sprayed with an ultra-low volume sprayer at a dose of 20 to 30 mL/m2. 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 (LIS) and evaluated for quality. The results were rejected if controls failed or if there were signs of carry-over contamination. The results were reviewed, transcribed to test report forms and 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 6-8 air changes per hour.
SOPs for SARS-CoV-2 testing processes, including sample reception, acceptance and rejection criteria, chain of custody, sample inactivation, TNA extraction, and sample retention/destruction, were developed. All SOPs and training presentations were bilingual (English and Vietnamese) and were posted in the OUCRU portal for easy access. A training programme was implemented for staff working with SARS-CoV-2 testing, including sample reception, testing, facility decontamination, waste management and janitors. The training included risk assessment, biosafety, PPE use (donning and doffing), and the assignment process (e.g., sample reception, sample inactivation, total nucleic acid (TNA) extraction, PT-PCR assay, facility decontamination, waste management and sample destruction). Overall, 14 clinical laboratory staff (4 staff for pre-analytic, 8 staff for analytic and 2 staff for post-analytic processes) were responsible for SARS-CoV-2 testing. In addition to this, 4 laboratory staff members from Children’s Hospital No. 1 and 8 research laboratory staff members were involved in SARS-CoV-2 testing during the high sample load periods. Additionally, 6 OUCRU laboratory management staff members were involved in safety process implementation. None of the staff involved in sample reception, testing, facility decontamination or cleaning reported any symptoms of COVID-19.
MDL was certified by the Department of Health (DoH), HCM on March 14, 2020 for SARS-CoV-2 testing. External audits were conducted by HCM city CDC in early September. An inter-laboratory comparison programme was implemented for the initial two months of testing, where all positive samples were retested at Pasteur institute in HCM city. No discrepancies were identified between the two laboratories. The OUCRU laboratory management team conducted daily inspections of the facilities. All instruments, including BSC, TNA extraction system, real-time PCR systems, freezers and refrigerators, were maintained and calibrated as per GCLP standards. All processes implemented are in compliance with the laboratory safety for SARS-CoV-2 testing from the Ministry of Health (MoH) of Vietnam.
A logistic management system for PPE and diagnostic reagents were implemented. A bulk procurement for 20,000 SARS-CoV-2 diagnostic tests was initiated in March 2020, and procurement was continued as per need. For PPE (surgical mask, N95 mask, disposable lab coat, nitrile gloves) disinfectants, and hand sanitizers, 3 months stock was considered sufficient.
Sample testing and reporting
SARS CoV-2 samples were collected in different locations, including i) designated infectious diseases hospitals for COVID-19; ii) makeshift hospitals for COVID-19 patients; iii) quarantine facilities; iv) local lockdown communities; and v) field investigation sites. Samples were collected for screening of patients, confirmation of COVID-19 diagnosis or confirmation of cure. All samples received for SARS-CoV-2 testing were registered in the clinical laboratory database. Respiratory and oropharyngeal samples for RT-PCR were tested in MDL, and blood samples for clinical haematology and biochemistry tests were processed in a routine clinical laboratory. Respiratory and oropharyngeal samples for microbiology culture were performed in the BSL3 microbiology laboratory.
During the reporting period, there were two local outbreaks that influenced the number of samples and tests. 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 Ho Chi Minh City 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) for SARS-CoV-2 testing in our hospital was 3.54 ± 2.97 days (1.30 ± 1.23 during the non-outbreak period and 4.55 ± 2.99 during the outbreak period) (Fig 1). 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 (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).