Analysis of SARS-CoV-2 RT-PCR Testing and Pooling Strategies for Screening of Asymptomatic Individuals - The Philippine Children's Medical Center Experience
Background. The availability of reverse transcription-polymerase chain reaction (RT-PCR) in detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is limited by the scarcity of resources prompting the use of pooling strategies. Evaluated in this study is the Philippine Children’s Medical Center’s (PCMC) experience in pooled testing done in asymptomatic population.
Objectives. Review the pooled SARS-CoV-2 RT-PCR results and case investigation forms (CIF) in asymptomatic population. Determine the incidence of SARS-CoV-2 in asymptomatic population and compare all the individual and pooled tests results. Determine the number of saved test kits and identify clustering in the community.
Methodology. This is a retrospective study that reviewed the pooled and individual SARS-CoV-2 RT-PCR results using Allsheng Auto-Pure 32a extraction kit, Sansure Biotech PCR machine and Maccura Sars-CoV-2 test kits. The pooling protocol used by the institution followed the recommendation by Lo et al in the study entitled “An Evaluation of Pooling Strategies for RT-qPCR testing for SARS-CoV-2 infection.”
Results. There are 1828 samples which resulted to 165 negative, 68 indeterminate, and 137 positive pools. There are 157, 135, and 68 pools containing 5 individual samples that were classified as negative, positive and indeterminate pools, respectively. Additionally, the negative pools contained 8 pools with 3 individual samples and the positive pools contained 2 pools with 2 individual samples. Deconvolution of the positive and indeterminate pools resulted to 227 and 74 positive individuals, respectively. In this review, the laboratory saved 24% of the test kits and shorten the overall turnaround time by 23 hours.
Conclusions and Recommendations. The incidence of SARS-CoV-2 in the population is higher compared to the prevalence of infection in the country. Pooled testing conserved test kits and congruence of pooled and individual ORF Ct-values was observed. An in-depth study including other genes is recommended and assessment of pooling in other population may be pursued.
Valencia DN. Brief Review on COVID-19: the 2020 pandemic caused by SARS-CoV-2. Cureus. 2020;12(3):e7386. https://pubmed.ncbi.nlm.nih.gov/32337113. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7179986. https://doi.org/10.7759/cureus.7386.
Department Memorandum No. 2020-0258. Updated Interim Guidelines on Expanded Testing for COVD-19. Department of Health, Republic of the Philippines. https://doh.gov.ph/node/24149.
Lo R, Barrientos A, Espiritu B, Santiago FK, Tandoc A, Velasco J, Yanez S. An Evaluation of pooling strategies for RT-qPCR testing for SARS-CoV-2 infection: a pragmatic multi-site parallel operational study. Philipp J Pathol. 2020;5(2):12-33. https://doi.org/10.21141/pjp.2020.12.
Department Memorandum No. 2020-0539. Interim Guidelines on the Conduct of COVID-19 Pooled Testing. Department of Health, Republic of the Philippines. https://doh.gov.ph/sites/default/files/health-update/dm2020-0539.pdf.
Interim Guidance for Use of Pooling Procedures in SARS-CoV-2 Diagnostic, Screening, and Surveillance Testing. (n.d.). Retrieved September 15, 2020, from https://www.cdc.gov/coronavirus/2019-ncov/lab/pooling-procedures.html.
Coronavirus disease 2019 (COVID-19) - WHO. (n.d.). Retrieved September 13, 2020. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200323-sitrep-63-covid-19.pdf?sfvrsn=b617302d_4.
Guo Y, Cao Q, Hong Z, et al. The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak – an update on the status. Mil Med Res. 2020;7(1):11. https://pubmed.ncbi.nlm.nih.gov/32169119. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068984. https://doi.org/10.1186/s40779-020-00240-0.
Wiersinga WJ, Rhodes A, Cheng AC, Peacock SJ, Prescott HC. Pathophysiology, transmission, diagnosis, and treatment of coronavirus disease 2019 (COVID-19). JAMA. 2020;324(8):782-93. https://pubmed.ncbi.nlm.nih.gov/32648899. https://doi.org/10.1001/jama.2020.12839.
Gao, Z, Xu Y, Sun C, et al. A systematic review of asymptomatic infections with COVID-19. J Microbiol Immunol Infect. 2021;54(1):12-6. https://pubmed.ncbi.nlm.nih.gov/32425996. https://www.ncbi.nlm.nih.gov/pmc/articles/ PMC7227597. https://doi.org/10.1016/j.jmii.2020.05.001.
Rao SN, Manissero D, Steele V, Pareja J. Correction to: A systematic clinical review of the utility of cycle threshold values in the context of COVID-19. Infect Dis Ther. 2020;9(3):587. https://pubmed.ncbi.nlm.nih.gov/ 32809140. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431897. https://doi.org/10.1007/s40121-020-00328-z.
Interim Guidance for Use of Pooling Procedures in SARS-CoV-2 Diagnostic, Screening, and Surveillance Testing (n.d.). Retrieved September 15, 2020. https://www.cdc.gov/coronavirus/2019-ncov/lab/pooling-procedures.html.
WHO Coronavirus Disease (COVID-19) Dashboard. (n.d.). Retrieved September 13, 2020, from https://covid19.who.int/.
Philippines: WHO Coronavirus Disease (COVID-19) Dashboard. (n.d.). Retrieved September 13, 2020, from https://covid19.who.int/region/wpro/country/ph.
Ben-Ami R, Klochendler A, Seidel M, et al. Large-scale implementation of pooled RNA-extraction and RT-PCR for SARS-CoV-2 detection. Clin Microbiol Infect. 2020;26(9):1248-53. https://pubmed.ncbi.nlm.nih.gov/32585353. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7308776. https://doi.org/10.1016/j.cmi.2020.06.009.
Das S, Lau AF, Youn J, Khil PP, Zelazny AM, Frank KM. Pooled testing for surveillance of SARS-CoV-2 in asymptomatic individuals. J Clin Virol. https://pubmed.ncbi.nlm.nih.gov/32920431. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7470739. https://doi.org/10.1016/j.jcv.2020.104619.
Lohse S, Pfuhl T, Berkó-Göttel B, et al. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people. Lancet Infect Dis. 2020;20(11):1231-2. https://pubmed.ncbi.nlm.nih.gov/32530425. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194818. https://doi.org/10.1016/S1473-3099(20)30362-5.
Agoti CN, Mutunga M, Lambisia AW, et al. Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast. Wellcome Open Res. 2021;5:186. https://pubmed.ncbi.nlm.nih.gov/33134555. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7590893. https://doi.org/10.12688/wellcomeopenres.16113.2.
Mastrianni D, Falivena R, Brooks T, et al. Pooled Testing for SARS-CoV-2 in Hospitalized Patients. J Hosp Med. 2020;15(9):538-9. https://pubmed.ncbi.nlm.nih.gov/32816669. :https://doi.org/10.12788/jhm.3501.
An overview of cycle threshold values and their role in SARS-CoV-2 real-time PCR test interpretation. Retrieved January 30, 2021. https://www.publichealthontario.ca/-/media/documents/ncov/main/2020/09/cycle-threshold- values-sars-cov2-pcr.pdf?la=en.
Abdulrahman A, Mallah S, AlAwadhi AI. Association between RT-PCR Ct values and COVID-19 new daily cases: a multicenter cross- sectional study. https://doi.org/10.1101/2020.12.07.20245233.
Faíco-Filho KS, Passarelli VC, Bellei N. Is higher viral load in SARS-CoV-2 associated with death? American J Trop Med Hyg. 2020;103(5):2019-21. https://pubmed.ncbi.nlm.nih.gov/32996443. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7646800. https://doi.org/10.4269/ajtmh.20-0954.
Denny TN, Andrews L, Bonsignori M, et al. Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections on a college campus — Duke University, Durham, North Carolina, August 2–October 11, 2020. MMWR Morb Mortal Wkly Rep. 2020;69(46):1743-7. https://pubmed.ncbi.nlm.nih.gov/33211678. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7676642. https://doi.org/10.15585/mmwr.mm6946e1.
Padua Jr R. The Philippine Society of Pathologists, Inc. Statement on the current pandemic situation strategic testing to assist in managing local COVID-19 outbreaks. 2021.
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