There is a reason some melodies linger long after the performance has ended. Not because they are triumphant, but because they carry memory gently. They remind us that meaning is often found not in fanfare, but in persistence, in the patient work of returning, rebuilding, and remaining.

This issue of the Philippine Journal of Pathology comes at the end of a season of milestones for the journal, and perhaps also a season of reflection.

The emergence of novel pathogens poses significant challenges to public health systems worldwide, demanding rapid and coordinated outbreak response mechanisms. The case of “Pathogen X,” a hypothetical novel pathogen, highlights the complexity of such efforts, which require rapid identification, diagnostic readiness, and effective containment strategies. Leveraging recent advances in ultrastructural pathology and genomics is essential to ensure a timely and robust response. Within this diagnostic framework, transmission electron microscopy (TEM) serves as a powerful imaging modality at high magnification that enables direct visualization of pathogen particles and infection-induced ultrastructural cellular changes. Unlike molecular techniques that infer presence through nucleic acids, TEM offers same-day morphological triage, confirmation of pathogen presence, and identification of co-infections. Through techniques such as negative staining and ultrathin sectioning, TEM reveals hallmark structural features that not only support provisional taxonomic classification and biosafety risk assessment but also inform the design and quality control of downstream assays such as metagenomic next-generation sequencing (mNGS) and targeted PCR. As such, TEM significantly accelerates and reinforces the overall outbreak investigation workflow. Its high-resolution imaging capabilities make it particularly valuable in situations where speed, morphological clarity, and pathogen diversity necessitate a direct visualization approach.

BACKGROUND

The COVID-19 pandemic caused by SARS-CoV-2 significantly strained healthcare systems in the Philippines, highlighting the critical importance of reliable molecular diagnostics and genomic surveillance. Although vaccination efforts and public health measures mitigated disease impact, the continued emergence of viral variants underscores the need for sustainable local surveillance strategies. Strengthening in-country capacity through the development of in silico–designed primers and cost-effective sequencing approaches can enhance rapid variant detection and improve preparedness for future emerging infectious diseases.

This paper offers a method in detecting the SARS-CoV-2 virus and its variants. A direct PCR product sequencing surveillance or DPPSS offers a new possibility of detecting emerging disease by using PCR products and using it as templates in determining the base sequence.

A total of 20 random positive samples for SARS-COV-2 from March 2022 sample pool in Metro Manila, Philippines was used in this study. The RNA was extracted using Purelink™ RNA Mini Kit, quantified with NanoDrop, and subjected to one-step RT-PCR. An in-house designed in silico primers were used in this study by using thermodynamic parameters to optimize specificity and amplification efficiency, considering GC contents, balanced Tm, minimal secondary structures and cross-dimers and in silico validation via Basic Local Alignment Search Tool (BLAST) against reference databases.

Amplicons were analyzed through gel electrophoresis, sequenced, and analyzed using BioEdit software. A nucleotide BLAST search identified COVID-19 variants, confirmed using Cov-Lineages website.

In silico designed primers (S1, S2, E/M, Orf1ab) collectively exhibited 100% sensitivity in detecting SARS-CoV2 in nasopharyngeal swab samples. Individual primer sensitivities varied, with Orf1ab at 58.82% and E/M at 90.91%. Our analysis revealed the prevalence of Omicron sublineage BA.2 in the Philippines, aligning with local data showing more BA.2 cases than the global predominance of BA.1.

Combined in silico primers (S1, S2, E/M, ORF1ab) accurately detect SARS-COV-2 and its variants. This method provides a valuable diagnostic and surveillance tool for public health management.

BACKGROUND

Breast cancer remains a leading malignancy among women globally. In addition to established factors like histopathology, hormone receptor status, and lymph node involvement, tools such as immunohistochemistry and molecular tests have been developed to assess tumor behavior and recurrence risk.

This study investigates the concordance between the Ki-67 proliferation index measured by immunohistochemistry and the recurrence risk scores obtained from molecular genomic testing in patients with invasive breast cancer.

This cross-sectional study included patients with invasive breast carcinoma at St. Luke’s Medical Center from 2019 to 2024, who underwent biopsy or mastectomy, with hormone status and Ki-67 index assessed by immunohistochemistry. All patients also had molecular genomic testing using either MammaPrint or OncotypeDX. Concordance between Ki-67 and the genomic recurrence risk score was evaluated using Kappa statistics, and results were further analyzed according to clinical risk and hormone receptor status.

Fifty-eight (58) patients met the study criteria. Most had grade 2, hormone receptor-positive, HER2-negative, and node-negative tumors, with high clinical risk based on Adjuvant! Online criteria (adapted from the MINDACT trial). The agreement between categorical Ki-67 and molecular recurrence risk was only fair: 66.7% for MammaPrint (kappa=0.35) and 60% for OncotypeDX (kappa = 0.29) using a 30% Ki-67 cutoff.

There is a fair agreement between Ki-67 and the molecular genomic tests. These findings are consistent with prior studies reporting weak to moderate association. Despite the limited sample size, Ki-67 remains a practical and accessible risk stratification tool, particularly where genomic assays are unavailable. The study supports integrating Ki-67 with clinicopathologic and genomic data to guide therapy, reflecting current best-practice recommendations.

BACKGROUND

Diabetes mellitus (DM) remains a major global health burden, with increasing prevalence in developing countries such as the Philippines. Accuracy of glucose measurement is vital for diagnosis and management; however, preanalytical variables, particularly glycolysis from varying collection tubes, temperature and time interval can significantly affect test results. Despite guideline recommendations favoring plasma, serum is still commonly used in local clinical practice.

This study evaluated the effectiveness of different commercially available blood collection tubes in preserving glucose stability by minimizing pre-analytical glycolysis.

A cross-sectional observational and quasi-experimental study was conducted among 40 healthy adult participants (18–59 years) from a tertiary institution in Quezon City, Philippines. A total of 160 samples were collected using four tube types (one plasma and three serum tubes). Samples were analyzed at varying time intervals (0–180 minutes) and storage conditions (room temperature and 4°C). Glucose levels were measured using the glucose oxidase method. Statistical analysis included Shapiro–Wilk, Kruskal–Wallis H-test, Welch’s t-test, and Dwass–Steel–Critchlow–Fligner post hoc comparisons at a 1% significance level.

Glucose concentrations differed significantly across tube types (pCONCLUSION

Blood collection tube type and delayed processing significantly influence glucose measurements. While acceptable within analytical limits, systematic biases may affect clinical interpretation. Standardization of blood collection practices and stricter pre-analytical protocols are essential to improve diagnostic accuracy for diabetes in the Philippines.

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide, requiring timely and accurate diagnosis to guide appropriate therapy and reduce antimicrobial resistance. Although urine culture remains the diagnostic gold standard, its prolonged turnaround time and susceptibility to pre-analytical variability limit its clinical efficiency. Recent advances in artificial intelligence (AI) have positioned urinalysis as a promising alternative diagnostic approach, utilizing machine learning and deep learning algorithms for automated analysis and prediction. This review synthesizes current evidence on AI applications in urinalysis for UTI diagnosis, examining computational techniques, diagnostic performance, clinical integration, limitations, and future directions. The literature demonstrates that AI-powered urinalysis can achieve diagnostic accuracy comparable to urine culture, with high sensitivity and specificity while reducing diagnostic time. Integration of AI into clinical workflows has the potential to enhance decision-making, streamline laboratory processes, and support antimicrobial stewardship. However, challenges related to data heterogeneity, algorithm interpretability, validation, and regulatory requirements remain significant barriers to widespread adoption. Overall, AI-driven urinalysis represents a transformative opportunity to complement the existing diagnostic standard and advance more rapid, efficient, and personalized approaches to UTI management.

Angiomyolipoma with epithelial cysts (AMLEC) is a rare subtype of angiomyolipoma that may closely mimic both malignant and benign neoplasms. We report a case of AMLEC in an 18-year-old female presenting with acute flank pain and radiologic suspicion for malignancy. This case highlights the diagnostic challenges posed by AMLEC, emphasizes its characteristic histopathologic and immunohistochemical features, and reviews current concepts regarding its pathogenesis. This case represents the first documented case of AMLEC in the Philippines.

This is a case of monomorphic epitheliotropic intestinal T cell lymphoma presenting as ruptured viscous in a 64-year-old male. Monotonous cells were seen to infiltrate the full thickness of the bowel with immunoreactivity for CD3, CD8, CD56, CD68 and Granzyme B. The patient subsequently presented with maxillary and alveolar mass with similar immunohistomorphologic findings, suggesting metastasis. This rare disease has poor prognosis thus further reports should be conducted to profile this type of tumor.

An elderly Filipino female presented with a 5-year enlarging left nasolacrimal mass initially diagnosed as Inverted Papilloma of the Lacrimal Sac. Repeat biopsy revealed a papillomatous neoplasm with thick and thin papillae, solid invaginating lobules, and anastomosing trabeculae of monomorphic squamotransitional cells, briskly infiltrated by neutrophils. Mucocytes, respiratory epithelium, and microcysts, typical of Inverting Sinonasal Papilloma, are absent. Immunohistochemistry, including a validated AFF2 IHC, confirmed the diagnosis of DEK::AFF2 sinonasal carcinoma. Awareness of this emerging entity is essential to prevent misdiagnosis and prompt surgical management.

Parathyroid carcinoma is a rare endocrine malignancy with an indolent course but a high risk of recurrence. Diagnosis remains challenging, requiring integration of clinical, biochemical, radiologic, and histopathologic findings. We report a young patient presenting with primary hyperparathyroidism complicated by multiple pathologic fractures and chronic renal failure. Despite initial surgical and medical management, late aggressive recurrence occurred, resulting in significant systemic complications. This case highlights the need for vigilant long-term surveillance and improved diagnostic and therapeutic strategies.