The good and the bad of the national focal point to gather data on daily performance of PCR lab tests
BY Ruwan Laknath Jayakody
A recent article in the Sri Lankan Journal of Medical Administration has evaluated the benefits and weaknesses of the national focal point established under the direction of the Director General of Health Services (DGHS) as the competent authority, to gather data on the daily performance of polymerase chain reaction (PCR) tests at laboratories.
The article notes that it helps provide accurate and effective data dissemination, is a source of information for policy planners and decision makers, helps the maintaining of an appropriate logistics supply to labs in order to increase the PCR testing capacity and to project the disease trend, to improve patient care facilities, to identify the disease burden and for the evidence-based distribution of samples among labs that reduces overburdening.
However, limitations in the national focal point were that the computer literacy of the data entry operator and the supervision of the head of the relevant institution and the national focal point affected the accuracy of the data, the article added. Furthermore, strict discipline and responsibility should be maintained as individual users can enter the data for multiple laboratories. Moreover, although the system is compatible with mobile data entry, poor network connections still affect the entry of data. Also, the available data has limited value on epidemiological or demographic analysis.
The article was titled “Establishment of a national focal point to monitor the performance of PCR centres in Sri Lanka” and was authored by P. Athapattu, P.H. Wijenayake and P.K.G.P. Weediyawatta and published in the Sri Lankan Journal of Medical Administration (22) in December 2021.
The World Health Organisation declared the reverse transcription (RT)-PCR test as the confirmatory laboratory test for Covid-19 and with the gradual increase of cases and the need for accurate, reliable and real time data on laboratories performance, the information from the said test was used to understand the pandemic, determine which outcomes should be prioritised, plan resource allocation, decide on the intervention of health care delivery, and compare with other countries. Furthermore, due to the rapidly changing and uncertain context of the pandemic, it was essential to build up feedback loops and frequent pause points in order to revisit how things are taking place in the field. Per J. Ziegler and P. Mason’s “Adapting data collection and utilisation to a Covid-19 reality”, the data collection, storage, processing, and dissemination via online systems was deemed more beneficial as access to laboratories was limited during the pandemic.
The DGHS therefore ordered to establish a national focal point to gather data on the daily performance of PCR tests at laboratories and the Health Ministry’s Primary Care Services Directorate was assigned the task of collecting quality, accurate, real time data on the performance of PCR laboratories and to compile, analyse and disseminate information efficiently and effectively since the end of March 2020.
The general objective was to establish a national focal point to monitor the performance of PCR test centres while the specific objectives were to design a user friendly, comprehensive, online operational database, to identify and train a focal point from each functioning lab, to maintain timelines, the accuracy and the completeness of the data and to compile and disseminate a daily report for decision makers and planners.
A total of 10 data elements were defined – namely, 1. The name of the laboratory where the sample was tested, 2. The place from where the sample was sent to the lab, 3. The number of samples received from first time suspected Covid-19 patients, 4. The number of samples received from repeat patients who were already diagnosed as having Covid-19 and having received treatment for Covid-19, 5. The number of samples tested from among and out of the samples received from first time patients, 6. The number of samples tested from among and out of the samples received from repeat patients, 7. The number of positive samples received from and out of the samples tested of first time patients, 8. The number of positive samples received from and out of the samples tested of repeat patients, 9. The inconclusive samples or the number of samples that were tested and were unable to give results, and 10. Invalid samples or samples contaminated due to various reasons from the time of sample collection to sample testing – to monitor the performance of PCR laboratories by obtaining inputs from the relevant stakeholders.
The requirements for a digital solution were identified via key stakeholder interviews. A rapid literature review and market analysis were conducted to find a suitable product. The agile development method was used to develop the digital solution. It consisted of an online data entry module for collecting aggregated data, a central database, a real time data visualisation module, a data analytic module and a report module. The initial development and deployment was completed within two days with zero development cost. Online user training was given to the end users who were pre-identified officers at the laboratories, and a comprehensive, electronic user manual was provided. Also, round the clock user support was given in order to improve the data quality and to maintain the sustainability of the digital solution.
In terms of the process, the prescribed time for data entry with regard to the daily performance was before 10 p.m. daily, but data entered up to midnight was considered for the final report. Short message service reminders were sent to the laboratories to enter data by 10 p.m. The compiled daily performance report was disseminated to the heads of the laboratories and institutions daily at 7 a.m. the following day in order to get their feedback and to cross check the accuracy.
The PCR laboratories initiated entering the data into the system from 24 March 2020. The paper based data collected from 18 February 2020 were entered by the national focal point. Initially, there were six labs as of late March 2020 which by end September 2020 increased up to 25 laboratories and to 36 being identified by 28 February 2021.
The compilation and data analysis were carried out at the national focal point, and the chief controlling officer sent an interim report to the intelligence services, namely the State Intelligence Service (SIS), and the now defunct National Operation Centre for the Prevention of the Covid-19 Outbreak (NOCPCO) every day at 10 p.m. The final report was prepared before 7 a.m. the following day and sent to the SIS, the NOCPCO, the Health Ministry officials, all consultants in charge of the laboratories and the heads of the relevant institutions to assess their own performances and for data validation with their feedback.
The samples were tested during the reporting period from 18 February 2020 to 28 February 2021.
During phase one, the total number of samples tested was 292,155, and out of them, 276,357/94.59% were suspected or first time patients and 15,798/5.41% tests were conducted on diagnosed or repeat patients who were at treatment centres. The positivity rate of first timers was 1.22% (3,377/276,357).
During phase two, the total number of samples tested was 1,832,355, and out of them, 1,821,972/99.43% samples were tested in first time patients, and 10,383/0.57% were tested on diagnosed patients who were at treatment centres. The positivity rate of first timers was 4.66% (850,571/832,355).
The total number of samples tested during the reporting period was 2,124,510, and out of them, 2,098,329/98.76% samples were tested in suspected patients and 26,181/1.24% tests were conducted in diagnosed patients. The positivity rate in the reporting period was 4.21% (88,434/2,098,329).
The daily and cumulative report was issued when required as per the details of the performance of individual laboratories. Also, the daily average, District wise community samples were tested, and the private sector performance reports were also issued as routine.
There were 21 Government sector laboratories, six university laboratories and nine private sector laboratories. The maximum number of tests was done by a private hospital (293,588). Out of the State sector institutions, the Medical Research Institute (MRI) and the Bandaranaike International Airport tested more than 200,000 samples during the referring period.
The average number of PCR tests conducted by labs was calculated weekly. In phase one (eight to 40 weeks of 2020), the maximum number was 2,723, which was during the 34th week of 2020. In phase two, the maximum daily average of 16,921 was achieved in the third week of 2021.
The total community samples tested in the reported period were 1,005,763/47.3%, and out of that, 51,923 were positive, with a rate of 5.16%. During phase one, 81,376/27.85% samples were tested, and 424/0.52% were positive. In phase two, 924,387/50.73% community samples were tested, and 51,499 (5.57%) were positive. In both phases, the Colombo, Kalutara and Gampaha Regional Director of Health Services areas reported the highest numbers for the community samples.
Four private laboratories conducted PCR tests in phase one and though it was expanded up to 10 laboratories in phase two, only nine laboratories entered data during the reporting period. Overall, the private sector contribution was 631,677/29.73%. The majority were performed by a particular private hospital during both the phases.
“As the pandemic progressed over time, large-scale testing and contact tracing were the central efforts made to understand the spread, and to respond appropriately. Based on the evidence, patient management criteria were advanced, and the testing of discharged patients was decided with reference to the initial viral load; thus, conducting two consecutive negative samples was omitted. Therefore, the number of tests performed on diagnosed patients was reduced. With the increased demand, accredited private sector labs were recruited to conduct PCR tests. A particular private hospital’s performance was higher than even the MRI, the reference lab that was initiated in January 2020. Convenience, the maintenance of privacy and the stigma attached to positivity may be the causes. Increasing the testing capacity reduced unnecessary self isolation, the depletion of the workforce, especially for essential services, and missing the potentiality of individual cases that would minimise the risk of transmission. Introducing mass testing for the community on both symptomatic and asymptomatic cases reduced the risk of nosocomial (originating in a hospital) transmission. Another key epidemiological parameter that could inform the intensity and range of social distancing strategies to combat Covid-19 is the asymptomatic proportion (per K. Mizumoto, K. Kagaya, A. Zarebski and G. Chowell’s “Estimating the asymptomatic proportion of Covid-19 cases onboard the Diamond Princess cruise ship, Yokohama, Japan, 2020”, it is a useful quantity to gauge the true burden of the Disease and to better interpret the estimates of the transmission potential). Remarkable improvement was achieved in this aspect in phase two than in phase one. Regular feedback sessions were conducted for updating knowledge and technical modifications. Issues and opposing events were discussed at review meetings, technical advisory meetings and lab meetings. Frequent feedback and daily performance reports helped to manage the continuous logistic supply. Cumulative reports were issued at different milestones. This daily performance report was validated with the comments of expert officials. In some labs, there was a difference noted between the sample tested, and the sample received, and the reasons were that the number of samples received was not compatible with the number of actual samples in the container, single samples were tested several times in the same laboratory (duplicate samples), invalid samples and data entry-related errors (duplicate values). A discrepancy was noted between figures of this system and the Epidemiology Unit, because the system reported a number of positive samples while the Epidemiology Unit reported positive patients during the reported period. Duplicate samples, several samples of one individual being sent to several labs, receiving multiple samples of a single individual to a laboratory, especially in post-mortem samples, were other reasons for the discrepancy. Also, data disseminated to the Health Promotion Bureau were used for the national dashboard, which were in turn used for country level comparison,” Athapattu et al. explained.