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.

OBJECTIVE

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.

METHODOLOGY

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.

RESULTS

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.

CONCLUSION

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.

Covid-19 ; Polymerase Chain Reaction ; Molecular Diagnostic Techniques

OBJECTIVE: This study aimed to determine the accuracy of internal examination and ultrasound in early stage cervical cancer. Specific objectives were to determine the accuracy of internal examination and sonography in measuring tumor size and the accuracy of sonography in detecting vaginal involvement, stromal invasion, parametrial and lymph node involvement by comparing them with the surgicopathologic findings.
MATERIALS AND METHODS: 35 patients diagnosed with early stage cervical cancer for radical hysterectomy with bilateral salpingooophorectomy were recruited. Presence of poor prognostic factors was determined by internal examination and sonography and compared with the surgicopathologic result.
RESULTS: Ultrasound and internal examination have an accuracy of 74% and 68%, respectively. Ultrasound accuracy in detecting more than one third stromal invasion is 68%, vaginal involvement is 85%, parametrial involvement is 92% and lymph node involvement is 100%.
CONCLUSION: Ultrasound can be recommended as an adjunct to internal examination in the preoperative assessment of early stage cervical cancer.

Human ; Female ; Middle Aged ; Adult ; Uterine Cervical Neoplasms ; Prognosis ; Hysterectomy ; Ultrasonography ; Vagina ; Lymph Nodes