BACKGROUND: Improving the means to detect SARS-COV-2 infection is important in the ongoing battle against the COVID-19 pandemic. STANDARDTM Q COVID-19 Ag Test offers an easy to use, cheap and rapid way of testing that must be evaluated first to optimize its utility.

OBJECTIVES: This study aims to evaluate the diagnostic accuracy of this test kit compared with Reverse Transcription Polymerase Chain Reaction (RT-PCR) for SARS-COV-2 diagnosis.

METHODS: Using retrospective cross-sectional study, seventy seven (77) nasopharyngeal swabs in viral transport media were used to determine the sensitivity, specificity, positive predictive value and negative predictive value of STANDARDTM Q COVID-19 Ag Test compared with the reference method, RT-PCR.

RESULTS: Among all participants, the rapid antigen test has a sensitivity of 9.86%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 8.57%. The sensitivity increases among symptomatic participants and when Ct value is less than 20 to 25.00% and 31.58%, respectively.

CONCLUSION: Despite the low sensitivity, STANDARDTM Q COVID-19 Ag Test has a high specificity and positive predictive value and could be a cheap and efficient test in the proper clinical context. Its use in conjunction with RT-PCR for those who tested negative initially should be emphasized in the implementation of the existing policies.

Human

We have seen the events of the pandemic unfold from our unique perspective as pathologists. Early on, we stood helpless as the virus ravaged our cities and towns with ferocity while we could hardly do anything. We were woefully unprepared to cope with the testing. Very few labs were capable of doing RT-PCR testing, exposing our unpreparedness in molecular pathology.
COVID-19 ; Research ; Pandemics

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.

The X-linked dystonia-parkinsonism (XDP) is a severe progressive, adult-onset X-linked endemic disorder in Filipinos, which is characterized by dystonic movements that start in the third of fourth decade, and replaced by parkinsonism beyond the 10th year of illness. Understanding the pathophysiology of XDP and development of rational therapies will depend on observations from imaging pathological and genetic studies. In this paper we summarize the results of these studies on patients with XDP. The cranial magnetic resonance imaging shows hy-perintense putaminal rim in both dystonic and parkinsonian stages, and atrophy of the caudate head or putamen in the parkinsonian stage. Neuropathological findings show atrophy of the caudate nucleus and putamen, with mild to severe neuronal loss and gliosis. In the neostriatum, the dystonic phase of XDP shows the involvement of striosomes and matrix sparing, while the later, i.e., p[arkinsonian phase, shows matrix involvement as well. In the dystonic phase, the loss of striosomal inhibitory projections lead to disinhibition of nigral dopaminergic neurons, perhaps resulting in a hyperkinetic state; while in the parkinsonian phase, severe and critical reduction of matrix-based projection may result in extranigral parkinsonism. Genetic sequencing of the XDP critical region in Xq13.1 has revealed an SVA retronsposon insertion in an intron of TAF1. This may reduce neuron-specific expression of the TAF1 isoform in the caudade nucleus, and subsequently interfere with the transcription of many neuronal genes, including DRD2. Findings from imaging, pahtology, and genetics studies are gradually shedding light on the pathophysiology of XDP, which hopefully will lead to mare rational and directed therapies.

Human ; Adult ; Atrophy ; Caudate Nucleus ; Dopaminergic Neurons ; Dystonic Disorders ; Genetic Diseases, X-linked ; Gliosis ; Introns ; Parkinsonian Disorders ; Protein Isoforms ; Putamen

SARS-CoV-2 has infected more than 643 million individuals worldwide and accounts for close to 64,950 deaths in the Philippines. Due to COVID-19’s clinical overlap with other diseases and non-specific radiologic findings, its diagnosis rests primarily on laboratory methods, including reverse transcription polymerase chain reaction (RT-PCR) and multiplexed molecular platforms for rapid syndromic testing. Compared to RT-PCR which has a turnaround time of 24 to 72 hours, multiplexed molecular platforms can provide alternative diagnoses to COVID-19 in an average of one hour, providing meaningful data that can impact clinical and resource management when handling acute surge of patients with respiratory symptoms.
COVID-19 ; SARS-CoV-2

Background and Objectives: Sample pooling of COViD-19 PCR tests has been recently proposed as a low-cost alternative to individual tests. This multi-site, laboratory-based, proof-of-concept study explores the feasibility of pooled SARS-CoV-2 RT-qPCR testing, by demonstrating the effect of pooling on sensitivity, specificity, accuracy, number of tests saved, and turnaround time. Methodology: The research was conducted in two experiments. In Experiment 1, archival nasopharyngeal (NPS) and oropharyngeal (OPS) swab samples were diluted to simulate 5, 10, and 20 sized pools, and tested for SARS-CoV-2 RNA using RT-qPCR. In Experiment 2, actual nasopharyngeal and oropharyngeal swab samples were collected from asymptomatic low-risk volunteers. Aliquots of the samples were pooled following the 5, 10-5, and 20-10-5 multi-staged Dorfman pooling methods and tested. The sensitivity, specificity, accuracy, test savings, and turnaround time for each pooling method were documented. Results and Conclusions The study provided evidence that pooling of NP and OP samples for SARS-CoV-2 RNA detection using RT-qPCR is feasible and can be implemented in the Philippines. A 2-stage Dorfman 5 pooling strategy appears to be the best method, because it has the highest over-all accuracy, while still achieving acceptable test savings, and turnaround time. Pooling of nasopharyngeal and oropharyngeal swab samples prior to RT-qPCR testing may be considered by select molecular diagnostic laboratories to further increase testing capacity and at the same time reduce the cost of testing.
COVID-19 ; SARS-CoV-2

Background: Gastrointestinal stromal tumors (GIST) is defined as specific, typically kit (CD117)-positive and CKIT or platelet-derived growth factor receptor alpha (PDGFRA) mutation-driven mesenchymal tumors that can occur anywhere in the GI tract. GIST diagnosis relies heavily on immunohistomorphology. However, with the advent of molecular testing, the classification, diagnosis and targeted-therapy for gastrointestinal mesenchymal tumors have been greatly improved. In the Philippines, molecular testing is not yet readily available as in other countries. The local molecular profile of gastrointestinal stromal tumors is a point of investigation as treatment may be more tailored to the patients’ needs. Objective: This study aims to determine the prevalence of CKIT and PDGFRA mutations among formalin-fixed and paraffin embedded gastrointestinal stromal tumors and other gastrointestinal mesenchymal tumors in St. Luke’s Medical Center – Quezon City. Methods: A retrospective cross-sectional study of formalin fixed and paraffin embedded tumor samples diagnosed as Gastrointestinal Stromal Tumor from January 1, 2009 to December 31, 2017 will be analyzed for KIT and PDGFRA mutations. Result: The epidemiology of GIST remains constant in that mean age group is the 5th to 6th decade, with equal gender distribution, and stomach followed by small bowel are the most common sites. Mutational analysis of the GISTs showed predominantly KIT Exon 11 (47.83%) followed by CKIT Exon 9 (13.04%) and PDGFRA Exon 18 (10.87%). For KIT Exon 11, deletion is the most common mutations followed by point mutations. No mutation is detected in 47.83% of GISTs. Conclusion Mutational analysis for CKIT-PDGFRA is warranted among GIST patients, as it may significantly influence treatment protocol in our patients.
Gastrointestinal Stromal Tumors

Background: Nasopharyngeal swab/oropharyngeal swab (NPS/OPS) qRT-PCR is the gold standard for detecting SARS-CoV-2. However, it has its own limitations including cost and invasiveness. As an alternative, individual qRT-PCR testing of saliva samples was validated and shown to be comparable in sensitivity and specificity with NP-OP qRT-PCR. To further maximize its utility, the researchers wish to explore antigen and pooled testing methods. Objective: The study aimed to evaluate the diagnostic accuracy of detecting SARS-CoV-2 infection using saliva-based pooled qRT-PCR and rapid antigen test compared with individual saliva qRT-PCR. Methodology: In this retrospective cross-sectional study, saliva specimen from individuals aged 18 years old and above from the outpatient specimen collection station at the Philippine Children’s Medical Center were tested individually using qRT-PCR (Mag-bind RNA Extraction Kit/MACURA, Allsheng Extraction Machine, Sansure PCR kit, and MA-600 Sansure Biotech). Non-probability convenience sampling was utilized. Based on the individual results, pools of five (5) individual specimens, which includes one (1) positive sample were tested with qRT-PCR for sensitivity. DNK-2150-1S Dynamiker SARS-CoV-2 Ag Rapid Test (Dynamiker Biotechnology Co., Ltd., Tianjin, China) was also used to test individual saliva specimens. . Out of 196 individual saliva specimens, 73 were detected to have SARS-COV-2 by qRT-PCR, while the remaining 123 were negative. Compared with the individual saliva qRT-PCR, rapid antigen tests done showed sensitivity of 46.58% (95% CI 35.13%, 58.02%), specificity of 86.18% (95% CI 80.08%, 92.28%), positive and negative predictive value of 66.67% (95% CI 53.71%, 79.60%) and 73.10% (95% CI 65.89%, 80.32%) respectively. Based on the results of individual saliva-based qRT-PCR, 62 pools were tested and showed sensitivity of 98.39% (95% CI 91.34%, 99.96%). Conclusion and Recommendation Pooled saliva-based testing for SARS-CoV-2 is comparable with individual saliva-based rapid antigen testing. The use of rapid antigen testing is less sensitive and less specific compared with qRT-PCR consistent with prior reports. Additional studies are recommended to determine optimal conditions for testing.
SARS-CoV-2 ; COVID-19