Analysis of SARS-CoV-2 RT-PCR Testing and Pooling Strategies for Screening of Asymptomatic Individuals - The Philippine Children's Medical Center Experience

Abstract

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.

Spit or Swab? The Diagnostic Accuracy of Saliva-Based Testing as a Sars-Cov-2 Surveillance Tool

“…This yielded a sensitivity of 98.39%, and there were no statistical differences observed in the ORF and N-gene Ct-values of the individual and pooled saliva test results. 27 A study by Barat et al, which included 449 individuals showed that the positive and negative agreement of saliva samples compared to NP swabs were 81.1% and 99.8% respectively. Pooling of the saliva samples using pools of five (5) showed sensitivities of 94%, 90%, and 94% using easyMAG/ABI 7500, Hologic Panther Fusion, and Roche Cobas 6800, respectively.…”

“…Pooling using NP/OP samples was previously demonstrated to be cost-effective and efficient at PCMC with pools of five ( 5) having the highest sensitivity. 12,27 In this study, pooling of saliva was done using five (5) saliva samples comprising of one (1) aliquot of SARS-CoV-2 detected saliva mixed with four (4) aliquots of SARS-CoV-2 negative saliva. This yielded a sensitivity of 98.39%, and there were no statistical differences observed in the ORF and N-gene Ct-values of the individual and pooled saliva test results.…”