BACKGROUND AND OBJECTIVE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent of COVID-19 has significantly challenged the public health landscape in late 2019. After almost 3 years of the first ever SARS-CoV-2 case, the World Health Organization (WHO) declared the end of this global health emergency in May 2023. Although, despite the subsequent drop of COVID-19 cases, the SARS-CoV-2 infection still exhibited multiple waves of infection, primarily attributed to the appearance of new variants. Five of these variants have been classified as Variants of Concern (VOC): Alpha, Beta, Gamma, Delta, and the most recent, Omicron. Therefore, the development of methods for the timely and accurate detection of viral variants remains fundamental, ensuring an ongoing and effective response to the disease. This study aims to evaluate the feasibility of the application of an in-house approach in genomic surveillance for the detection of SARS-CoV-2 variants using in silico designed primers.

METHODS

The primers used for the study were particularly designed based on conserved regions of certain genes in the virus, targeting distinct mutations found in known variants of SARS-CoV-2. Viral RNA extracts from nasopharyngeal samples (n=14) were subjected to quantitative and qualitative tests (Nanodrop and AGE). Selected samples were then analyzed by RT-PCR and amplicons were submitted for sequencing. Sequence alignment analysis was carried out to identify the prevailing COVID-19 variant present in the sample population.

RESULTS

The study findings demonstrated that the in-house method was able to successfully amplify conserved sequences (spike, envelope, membrane, ORF1ab) and enabled identification of the circulating SARS-CoV-2 variant among the samples. Majority of the samples were identified as Omicron variant. Three out of four designed primers effectively bound into the conserved sequence of target genes present in the sample, revealing the specific SARSCoV-2 variant. The detected mutations characterized for Omicron found in the identified lineages included K417N, S477N, and P681H which were also identified as mutations of interest. Furthermore, identification of the B.1.448 lineage which was not classified in any known variant also provided the potential of the developed in-house method in detecting unknown variants of COVID-19.

CONCLUSION

Among the five VOCs, Omicron is the most prevalent and dominant variant. The in-house direct PCR product sequencing surveillance (DPPSS) method provided an alternative platform for SAR-CoV-2 variant analysis which is accessible and affordable than the conventional diagnostic surveillance methods and the whole genome sequencing. Further evaluation and improvements on the oligonucleotide primers may offer significant contribution to the development of a specific and direct PCRbased detection of new emerging COVID-19 variants.

Sars-cov-2 ; Polymerase Chain Reaction ; Dna Primers ; Oligonucleotide Primers

OBJECTIVE

This study aimed to evaluate the nutritional adequacy and compliance with cardiovascular disease (CVD) guidelines in therapeutic diets implemented in four hospitals in General Santos City, Philippines.

METHODS

The study employed a cross-sectional study and analyzed the one-day therapeutic menus of four hospitals using the Philippine Food Composition Table and the United States Department of Agriculture nutrient database. The nutrient contents calculated in this study were compared among hospitals and benchmarked against the Philippine Dietary Reference Intakes (PDRI) and CVD-specific guidelines, the Dietary Approaches to Stop Hypertension (DASH), and Therapeutic Lifestyle Changes (TLC). The nutrient adequacy ratios (NARs) and the corresponding mean (SD) values were used to interpret the data.

RESULTS

Based on the PDRI, the mean (SD) NARs for proteins, simple sugars, vitamin B6, folate, and vitamin B12 were 116% (11%), 72% (16%), 139% (34%), 115% (7%), and 324% (156%), respectively, which were all interpreted as adequate. However, the mean (SD) NARs for energy, 88% (7%), and dietary fiber, 53% (33%), indicate non-compliance with the requirements for these components. As for the DASH guidelines, the hospitals failed to meet the recommendations for calcium, magnesium, and potassium, with mean (SD) NARs of 45% (14%), 49% (10%), and 51% (7%), respectively. The levels of saturated fatty acids, 195% (53%), and dietary cholesterol, 363% (177%), exceeded the limits set by the guidelines. For the TLC guidelines, the mean (SD) NARs of 70% (24%) and 40% (10%) for monounsaturated fatty acids and polyunsaturated fatty acids, respectively, were interpreted as suboptimal. Conclusive interpretations cannot be drawn for sodium, total carbohydrates, total fats due to large variations in their compositions among the hospitals.

CONCLUSION

At the menu analysis level, while the therapeutic diets adhered to the recommendations for proteins, simple sugars, and the vitamins, they fell short in their provision for energy, unsaturated fats, dietary fiber, and most minerals. They also exceeded the limits for most dietary lipid parameters set by DASH and TLC. The findings of this study highlight the need for improvements in nutritional adequacy and adherence to CVD guidelines in hospital therapeutic diets. Due to the limited number of observations, future research should aim to confirm and clarify these findings.

Cardiovascular Diseases ; Nutrients