1.The acceptance of stroke telerehabilitation among rehabilitation providers and consumers in two tertiary hospitals in the Philippines.
Francis Exequiel M. Laxamana ; Marvin Louie S. Ignacio ; Reynaldo R. Rey-Matias ; Carl Froilan D. Leochico
Acta Medica Philippina 2026;60(8):37-50
BACKGROUND AND OBJECTIVES
Telerehabilitation is the remote delivery of rehabilitation services using telecommunication technologies. Its local adoption was catalyzed by the COVID-19 pandemic, prompting the need to assess user acceptance. This study aimed to determine the acceptance of stroke telerehabilitation among patients, carers, and rehabilitation providers in the Department of Physical Medicine and Rehabilitation at St. Luke’s Medical Center – Global City and Quezon City.
METHODSThis descriptive cross-sectional study used purposive sampling to recruit 73 rehabilitation providers and 10 consumers. Data were collected using a self-administered survey based on the Technology Acceptance Model, covering perceived ease of use, usefulness, and behavioral intent. Descriptive and inferential statistics were used for analysis.
RESULTSMost providers (94.4%) were familiar with telerehabilitation, while only half of the consumers were aware of it. Acceptance was moderate among providers (mean score: 35.75 ± 8.67) and high among consumers (mean score: 31.6 ± 7.52). Female providers were less likely to accept telerehabilitation (p=0.049). Consumers identified financial constraints and lack of a companion as key barriers, while providers cited internet issues and technology use. Both groups viewed telerehabilitation positively for teleconsultation, teletherapy, and telemonitoring. Smartphones were the preferred device; Viber and Facebook Messenger were the most commonly chosen platforms.
CONCLUSIONStroke telerehabilitation was moderately to highly accepted by rehabilitation stakeholders in two tertiary private hospitals in Manila. Findings may guide institutional planning for telerehabilitation services. Training, infrastructure support, and awareness campaigns can help address implementation barriers.
Human ; Male ; Female ; Adult: 25-44 Yrs Old ; Middle Aged: 45-64 Yrs Old ; Remote Consultation ; Physical And Rehabilitation Medicine ; Tertiary Care Centers ; Telecommunications ; Telerehabilitation ; Cross-sectional Studies ; Technology ; Stroke ; Covid-19
2.The value of convalescent plasma therapy as a strategy to decrease hospitalization in COVID-19 patients: A randomized clinical trial.
Theresia Monica Rahardjo ; Hendra Subroto ; Christian Adiutama ; Aloysius Suryawan
Acta Medica Philippina 2026;60(8):51-58
BACKGROUND
Convalescent plasma therapy (CPT) has been utilized as an emergency and last-resort treatment for viral infections, particularly in the absence of vaccine. During the COVID-19 pandemic, CPT was implemented worldwide based on its potential to provide passive immunity through SARS-CoV-2 antibodies. While numerous studies explored the effectiveness of CPT to cure COVID-19 patients, there has no research specifically focused on superiority of CPT impact on the length of hospitalization.
OBJECTIVEThis study aimed to evaluate the effect of CPT on the length of hospital stay among patients with moderate COVID-19.
METHODSThis is a single blind randomized controlled trial (RCT) study involved 30 moderate-grade COVID-19 patients age 18-75 years with positive PCR result treated at Unggul Karsa Medika Hospital Bandung from February 2 to May 31, 2022. Moderate-grade COVID-19 defined by clinical pneumonia symptoms based on World Health Organization (WHO) criteria. Eligible patients were randomly assigned (1:1 ratio) and outcome assessors were blinded, while care providers and patients were not due to the intervention nature. The intervention arm (n=15) received 200 ml of high-titer CPT within 24 hours of admission with standard care and the control arm (n=15) received standard care only. The primary outcome measured was the length of stay (LOS) in both the Emergency Room (ER) and COVID-19 High Care Unit (HCU). Data were analyzed using independent T-tests.
RESULTSThirty (30) eligible patients (mean age 40 years; 53% female) were analyzed for the primary outcome and all completed follow-ups. The CPT group had significantly shorter LOS than controls (mean difference for ER:-32.7 hours [95% CI:-45.0,-20.4]; HCU:-33.3 hours [95% CI:- 45.8,-20.8]; p
CONCLUSIONThe administration of CPT may reduce the LOS in moderate COVID-19 patients. However, the small sample size can limit the generalizability of this result and larger sample studies are needed to strengthen this finding. Early CPT implementation may improve patient management and optimize healthcare resource utilization during the pandemic.
Pandemics ; Polymerase Chain Reaction ; Randomized Controlled Trial ; Emergency Service, Hospital ; Hospitalization ; Emergencies ; Covid-19 ; Length Of Stay ; Antibodies
3.Mental health status and academic performance of graduating nursing students during COVID-19 pandemic in a government school in Leyte, mental health program model: A correlational study.
Maria Ivy Rochelle S. Tan ; Daisy Fangkingan-Faba-an
Acta Medica Philippina 2026;60(8):59-68
BACKGROUND
The COVID-19 pandemic disrupted education worldwide, prompting a rapid shift to emergency remote teaching that challenged students’ learning and mental health. Nursing students, in particular, faced heightened pressures due to the suspension or online adaptation of essential clinical experiences, alongside the need to master theoretical and practical competencies. Emerging evidence indicates that such stressors adversely affect students’ emotional and psychological well-being, potentially influencing academic outcomes. Understanding the relationship between mental health and academic performance among nursing students is crucial for developing targeted interventions that support their well-being and professional readiness.
OBJECTIVEThis study analyzed the mental health status and academic performance of graduating nursing students during the challenging period of remote learning amid the pandemic in a government school in Leyte.
METHODSThe study utilized a descriptive correlational design to explore the relationships between mental health status and academic performance among nursing students. A modified self-administered questionnaire was utilized to gather data. Ethical approval from Eastern Visayas Health Research and Development ConsortiumEthics Review with ERC number 2023-024 was secured, and data collection occurred through various methods. Data analysis used SPSS version 24, emphasizing the importance of understanding these relationships in educational settings.
RESULTSThe study assessed the demographic profile, online learning attributes, mental health status, and academic performance of 20 nursing students during the pandemic. All students passed their courses, despite reporting moderate emotional loneliness and irritability, but minimal fear of COVID-19. Significant correlations were found between demographic factors and mental health indicators. The null hypothesis, suggesting no relationship between demographic factors and mental health, is void, as significant associations were identified. Recommendations include enhancing mental health support in nursing education to address these challenges.
CONCLUSIONThis study highlights the experiences of 20 nursing students from a government college in Leyte during the COVID-19 pandemic. Predominantly young women from rural, low-income backgrounds, these students faced challenges like poor internet access but successfully completed their academic requirements, showcasing resilience. While they reported low fear of COVID-19, moderate emotional loneliness and irritability indicated underlying mental health issues. The findings stress the need for educational institutions to provide mental health support and address the digital divide to enhance student well-being and success.
Human ; Male ; Female ; Young Adult: 19-24 Yrs Old ; Adult: 25-44 Yrs Old ; Statistics As Topic ; Psychological Well-being ; Indicators And Reagents ; Students, Nursing ; Suspensions ; Academic Performance ; Learning ; Pandemics ; Nursing ; Education, Nursing ; Covid-19 ; Mental Health
4.A bibliometric analysis of research productivity on Kawasaki disease in Southeast Asia: Trend and socioeconomic drivers.
Maria Llaine J. Callanta ; Karol Ann T. Baldo
Acta Medica Philippina 2026;60(2):33-40
OBJECTIVES
The increasing prevalence of Kawasaki disease in Southeast Asia (SEA) and its potential relation with Coronavirus Disease 2019 (COVID-19) infection resulted in heightened interest in KD in the region, thus, this paper aimed to determine the trend and the socioeconomic facilitators of scientific productivity of KD research within the region. Specifically, this article determined the number of publication and citations related to KD per country, institution, and journal. We also explored the networks of countries within the region to the rest of the world and the keywords mostly associated with KD research in the region. Lastly, correlation of these bibliometric indices with socioeconomic factors in the region was analyzed.
METHODSA literature search of KD papers in SEA was performed using Scopus database. We obtained bibliographic data from the available literature and visualized network of existing collaborations and keywords using VOSviewer software.
RESULTSA total of 196 papers were included in the study. Bibliometric analysis showed a rising trend in publication within the region, most of which were from institutions in Singapore and Thailand. The most common topics on KD studies included clinical features, complications, treatment, and comorbidities.
Country characteristics such as gross domestic product (GDP) per capita, research and development (R&D) expenditure (% GDP), and number of physician and R&D researchers were positively correlated with bibliometric indices of KD research in SEA. Moreover, number of international linkages was significantly associated with KD research productivity in the region.
CONCLUSIONIn summary, we showed an increasing trend of KD research in SEA. Funding allocation and capacity building are necessary to strengthen research productivity within the region.
Asia ; Asia, Southeastern ; Bibliometrics ; Capacity Building ; Coronavirus ; Covid-19 ; Database ; Disease ; Efficiency ; Gross Domestic Product ; Guanosine Diphosphate ; Infection ; Infections ; Literature ; Mucocutaneous Lymph Node Syndrome ; Paper ; Physicians ; Prevalence ; Publications ; Research ; Research Personnel ; Rest ; Singapore ; Socioeconomic Factors ; Software ; Thailand ; Therapeutics
5.Electrocardiographic profile of adult patients with coronavirus disease (COVID-19) who were given remdesivir and admitted in the University of the Philippines - Philippine General Hospital (UP-PGH).
Kaye Eunice L. Lustestica ; Felix Eduardo R. Punzalan ; Paul Anthony O. Alad ; Tam Adrian P. Aya-ay ; Zane Oliver M. Nelson III, ; Bryan Paul G. Ramirez ; Nigel Jeronimo C. Santos ; Elmer Jasper B. Llanes
Acta Medica Philippina 2026;60(2):59-65
BACKGROUND AND OBJECTIVE.
Severe Acute Respiratory Syndrome - Coronavirus-2 (SARS-CoV-2) was initially known to affect the respiratory system and has been reported to also involve the cardiovascular system leading to myocardial damage. Remdesivir is one of the approved treatments for COVID-19, wherein viral replication is inhibited by terminating the RNA transcription prematurely. According to studies, the primary electrocardiographic effect of remdesivir in COVID-19 patients are sinus bradycardia and QT prolongation. The use of electrocardiogram (ECG) is an essential diagnostic tool in assessing the electrical conditions of the heart. The objective of this study is to describe the electrocardiographic profile of adult patients with COVID-19 who were given remdesivir and admitted in the University of the Philippines-Philippine General Hospital (UP-PGH). To this date, this is the only study done locally identifying the electrocardiographic profiles of adult patients with COVID-19 who were given remdesivir.
METHODSThis was a retrospective descriptive study involving adult patients with COVID-19 who were given remdesivir and admitted in UP-PGH from June 2021 to June 2022. Demographic profiles and 12-lead ECG done during the hospital admission were gathered. Descriptive statistics was used to summarize the clinical characteristics and the electrocardiographic findings of the patients.
RESULTSThere were 412 confirmed COVID-19 patients who were given remdesivir (mean age 56 years old; female 52%) included in this study. The most common comorbidities were hypertension, diabetes mellitus, and stroke. Majority of the patients had severe (58%) to critical (22%) COVID-19 infection. Most of the patients had sinus rhythm (94%), normal rate (72%), and normal axis (93%). The most common baseline ECG findings were non-specific ST-T wave changes (42%). Some patients had atrioventricular blocks (3.4%), bundle branch blocks (3.6%), prolonged QT interval (1.9%). Among those with repeat 12-L ECG (136 patients) during admission, ECG changes observed were sinus bradycardia (6%), prolonged QT interval (4%), and both (1.5%).
CONCLUSIONBased on this retrospective review, which to our knowledge is the only study done locally investigating the effects of remdesivir on ECG of adult Filipino patients with COVID-19 infection, majority of the patients had sinus rhythm, normal rate, and axis. The most common ECG finding was non-specific ST-T wave changes. This study demonstrated a low incidence of adverse ECG changes that would preclude the administration of remdesivir when indicated. These include sinus bradycardia and QT interval prolongation which did not require further interventions. ECG remains to be useful, low-cost noninvasive tool that can help monitor electrophysiologic adverse events of remdesivir.
Electrocardiography ; COVID-19 ;
6.Challenges and adaptations of TB-DOTS services during the COVID-19 pandemic in South Cotabato Province, Philippines: A mixed-methods study.
Lee Daniel E. Suelan ; Nemuel S. Fajutagana ; Katherine C. Ciñ ; o ; Joel E. Genzon ; Charmae B. Corvera ; Kristine Joy L. Tomanan ; Amebella G. Taruc
Acta Medica Philippina 2026;60(5):46-67
BACKGROUND AND OBJECTIVE
The COVID-19 pandemic has adversely affected various healthcare services worldwide, including tuberculosis (TB) control programs. This paper examines the impact of the COVID-19 pandemic on TB case notification rate (CNR) and treatment success rate (TSR), and the challenges and interventions in TB-DOTS (directly observed treatment short-course) services in the Province of South Cotabato, SOCCSKSARGEN Region, Philippines.
METHODSAn explanatory sequential mixed methods design was used to describe the experiences of South Cotabato in implementing TB-DOTS services during COVID-19 pandemic. Monthly data on CNR and TSR under TB-DOTS from March 2019 to February 2022 were retrieved from the Department of Health’s Integrated Tuberculosis Information System (ITIS) through records review. One-way analysis of variance (ANOVA) and Tukey’s test were used to analyze quantitative data. Focus group discussions (FGD) were conducted among four groups of program implementers (NTP coordinators, nurses, medical technologists, and barangay health workers) encompassing the challenges encountered in the implementation of TB-DOTS services as well as interventions done before and during the COVID-19 pandemic.
RESULTSDuring the pre-COVID-19 period (March 2019-February 2020), a CNR of 334 per 100,000 population was reported in the province. There is a 35.19% decrease in TB CNR during COVID-19 Year 1 (March 2020-February 2021) at 216 per 100,000 population, followed by a 37.63% increase in Year 2 at 298 per 100,000 population. The mean TSR covering the pre-COVID period was 96% (SD = 0.01) while the mean TSR in COVID-19 Year 1 was 93% (SD = 0.02), significantly lower than that of the pre-pandemic period, followed by monthly TSR ranging from 91% to 98% (SD = 0.02), an increase in Year 2. From the FGDs, six pre-existing barriers were identified such as patients’ f inancial constraints, hard-to-reach areas, poor health seeking behavior, persistence of TB stigma, medicine and supply shortages, and inadequate health workforce were experienced before and during the COVID-19 pandemic. On the other hand, six emerging challenges brought by the COVID-19 pandemic were reallocation of services, movement restriction, additional protocols, reporting delays, and fears among patients and health workers. The decrease in CNR and TSR during COVID-19 Year 1 aligned with the emergence of new challenges in TB-DOTS services brought by the pandemic. These aggravated pre-existing barriers which further caused delays in the diagnosis and treatment of TB patients. Nine interventions done to address these challenges were also described, the most critical being health education, strengthening community-based services, use of telecommunications, resource pooling for essential medicines, adjusting medication dispensing, and coordination with local government units and policy enhancements.
CONCLUSIONTB-DOTS services in South Cotabato experienced various difficulties during the COVID-19 pandemic which led to initial declines in CNR and TSR. Addressing barriers and challenges were vital in ensuring the continuity of TB services and mitigating the impact of COVID-19 crisis on CNR and TSR. This study demonstrates the adaptability and resilience of South Cotabato's TB-DOTS services in response to COVID-19 challenges and highlights the need for strategies ensuring continuity of TB services and healthcare system resilience in light of Universal Health Care. Recommendations are outlined to improve current policies and practices as well as lay future directions for research on health service delivery and program implementation in relation to pandemics and other types of disasters.
Human ; Tuberculosis ; Covid-19 ; Pandemics ; Philippines
7.Infection control practices of dentists in an urbanized city in the Philippines during the COVID-19 pandemic within the period of general community quarantine.
Ma. Bianca B. Barrameda ; Ma. Chrizel Iana A. Madlangbayan ; Joshua Marcel A. Sy ; Melanie Ruth M. Karganilla
Acta Medica Philippina 2026;60(9):80-90
BACKGROUND
The global impact of the COVID-19 pandemic has instigated a profound public health crisis, particularly affecting professionals like dentists who, due to their close interaction with saliva—a potential viral reservoir—and the aerosols generated during specific procedures, face elevated risks of infection. To mitigate this, the Centers for Disease Control and Prevention (CDC) and the Philippine Dental Association (PDA) have established guidelines for averting cross-infection in dental settings.
OBJECTIVEThis study, conducted in an urbanized Metro Manila City, delves into the infection control practices of dentists amid the pandemic.
METHODSDentists from a Metro Manila city dental chapter were invited to participate in an online survey (Google Forms) consisting of participants' demographics, patient triage, engineering, administrative controls, disinfection personal hygiene, personal protective equipment (PPE), and waste management practices. Descriptive statistics, employing frequency distributions and percentages, summarized the dentists' adherence to infection control protocols.
RESULTSOut of forty-nine respondents (49), the majority (92%) provided their teams' orientation on COVID-19 infection control protocols before reopening. Notably, 57% deferred elective procedures and 43% postponed aerosolgenerating procedures (AGPs). Only 39% utilized rubber dam isolation during AGPs. Most respondents reported full implementation of recommended administrative controls during the pandemic, with 92% isolating their treatment areas from other parts of the clinic. Most respondents adopted high-efficiency particulate air (HEPA) filtration units (82%) as one of their clinic’s engineering controls, and an extraoral vacuum machine, accounting for 71% of the respondents. The most common disinfection product used by the participants was alcohol, which was at 94%. Additionally, over 90% adhered to all recommended hand hygiene practices for both dental staff and patients. For the waste management protocols, only 55% of the respondents have their infectious waste collected by third-party Treatment Storage and Disposal (TSD) facilities.
CONCLUSIONThe data shows that with the guidelines posted by both the PDA and CDC, the city’s dental practitioners could still provide services to the community in the safest manner at the time by being updated and following the infection control practices suggested by both organizations. Although some areas could have been improved, such as third-party waste management and the utilization of RT-PCR testing, some of these problems could have been attributed to the lack of availability in their areas.
Human ; Male ; Female ; Adult: 25-44 Yrs Old ; Middle Aged: 45-64 Yrs Old ; Aged: 65-79 Yrs Old ; World Health Organization ; Residence Characteristics ; Quarantine ; Public Health ; Centers For Disease Control And Prevention (u.s.) ; Covid-19 ; Centers For Disease Control And Prevention, U.s.
8.Knowledge, Attitude, and Practices Assessment of Unvaccinated Adult In-patients Regarding COVID-19 Vaccination in a Tertiary Hospital in Nueva Vizcaya, Philippines: A Cross-sectional Study.
Charity May B. Pazziwagan ; Emmeline B. Borillo
Acta Medica Philippina 2026;60(3):78-87
OBJECTIVES
his quantitative cross-sectional study aimed to determine the level of knowledge, attitude, and practices
regarding COVID-19 vaccination of unvaccinated adult patients admitted at Region II Trauma and Medical Center
(R2TMC). This may help determine the knowledge gap regarding COVID-19 vaccination, address it, and to achieve
the goal to vaccinate all eligible Filipinos. Furthermore, this may also be a springboard for future researches and
management regarding novel infections needing new vaccinations.
Collected data from the sample size of 197 using the formula for finite population with 95% confidence
level, population proportion of 50%, population size of 400, allowing 5% margin of error were summarized in a
Microsoft excel database and tables, then were analyzed using Jamovi version 2.6.22 software. Frequency, mean,
and standard deviation were calculated to measure the knowledge, attitude, and practices; Pearson correlation and
Kendall’s Tau b correlation for its relationship.
There is moderate level of knowledge (MS: 9.80-11.8), a positive attitude (MR: 2.35-2.60), and good preventive
practices (MS: 12.00-13.00) regarding SARS-CoV-2 (COVID-19) vaccination among the unvaccinated adult in-patients
of R2TMC post-pandemic. Knowledge, attitudes, and practices statistically differed (pCONCLUSION
There is a significant correlation among the knowledge of the respondents about COVID-19 vaccination,
their attitude towards it, and their practices, implying that promoting preventive behaviors toward COVID-19 would
require promoting both knowledge and efficacy beliefs among the public.
Human ; Bacteria ; Male ; Female ; Adult: 25-44 Yrs Old ; Middle Aged: 45-64 Yrs Old ; Wounds And Injuries ; Population Density ; Cross-sectional Studies ; Forecasting ; Sars-cov-2 ; Sars Virus ; Covid-19
9.External ocular manifestations among patients diagnosed with Coronavirus disease 2019 in a referral center in the Philippines.
Alyssa Louise B. Pejana-Paulino ; Aramis B. Torrefranca Jr. ; Nilo Vincent DG. Florcruz ; Ma. Dominga B. Padilla
Acta Medica Philippina 2026;60(1):69-77
BACKGROUND AND OBJECTIVES
The global pandemic caused by Coronavirus Disease 2019 (COVID-19) has affected millions, with growing evidence of the potential role of ocular tissues in viral transmission. At the time of writing, local data regarding the phenomenon was limited. This study investigated external ocular manifestations in patients with COVID-19 at a referral center in the Philippines, examined correlations between demographics, systemic manifestations, and laboratory results with ocular manifestations, and determined their timing relative to systemic symptoms.
METHODSThis single-center, descriptive cross-sectional study was carried out from December 8 to 18, 2020 at the adult COVID-19 wards of the Philippine General Hospital involving 72 participants. Data collection involved relevant clinical history taking and performing gross eye examination. The prevalence of ocular manifestations was described with 95% confidence intervals. Correlations between ocular manifestations and quantitative variables were analyzed with point-biserial correlation, and associations with qualitative variables were tested using chi-square or Fisher’s exact tests.
RESULTSAmong participants, 31.9% presented with ocular manifestations with foreign body sensation as the most prevalent ocular symptom (11.1%) and conjunctival hyperemia as the most prevalent ocular finding (19.4%). The median age of patients with ocular manifestations was 41 years old with a higher prevalence in the male population (73.9%, CI=95%, p=0.001). No significant correlation was observed between presence of external ocular manifestations and the different systemic and ocular co-morbidities as well as with COVID-19 clinical classification. Among those who experienced symptoms, majority (29.2%) of the patients experienced systemic symptoms prior to the onset of ocular symptoms. Ocular complaints may present as the sole manifestation (13.9%). Several laboratory parameters were measured and only temperature and AST levels showed a low positive correlation with the presence of ocular manifestations.
CONCLUSIONOcular manifestations occur in roughly one third of patients with COVID-19 based on this study population. With some individuals presenting with ocular signs or symptoms as the initial and sole manifestation, healthcare practitioners must exercise caution and remain vigilant in managing patients who present as such. At the time of writing, this is the first local study investigating the different external ocular manifestations in patients with COVID-19. There is a need to pursue more robust studies and conduct more local investigations which will guide both ophthalmologists and other practitioners in strengthening existing guidelines regarding precautionary practices, clinical diagnosis, and management of COVID-19 patients.
Human ; Sars-cov-2 ; Covid-19 ; Philippines ; Adult ; Association ; Classification ; Collection ; Confidence Intervals ; Coronavirus ; Cross-sectional Studies ; Data Collection ; Demography ; Diagnosis ; Disease ; Exercise ; Eye ; Foreign Bodies ; History ; Hospitals ; Hospitals, General ; Hyperemia ; Laboratories ; Male ; Morbidity ; Ophthalmologists ; Pandemics ; Patients ; Population ; Prevalence ; Referral And Consultation ; Role ; Sensation ; Temperature ; Time ; Tissues ; Volition ; World Health Organization ; Writing
10.Genomic variant surveillance of SARS-CoV-2 positive specimens using a direct PCR product sequencing surveillance (DPPSS) method.
Nicole Ann L. Tuberon ; Francisco M. Heralde III ; Catherine C. Reportoso ; Arturo L. Gaitano III ; Wilmar Jun O. Elopre ; Kim Claudette J. Fernandez
Acta Medica Philippina 2026;60(1):57-68
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.
METHODSThe 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.
RESULTSThe 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.
CONCLUSIONAmong 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 ; Computer Simulation ; Conserved Sequence ; Coronavirus ; Covid-19 ; Disease ; Emergencies ; Evaluation Studies As Topic ; Genes ; Genome ; Global Health ; Health ; Identification (psychology) ; Infection ; Infections ; Membranes ; Methods ; Mutation ; Oligonucleotides ; Organizations ; Population ; Public Health ; Rna ; Rna, Viral ; Sars Virus ; Sequence Alignment ; Severe Acute Respiratory Syndrome ; Syndrome ; Viruses ; Whole Genome Sequencing ; World Health Organization


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