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 ; 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

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.

METHODS

A 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.

RESULTS

A 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. 

CONCLUSION

In 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

Since the beginning of the 21st century, the severe respiratory infectious diseases worldwide [such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), influenza A H1N1 and novel coronavirus infection have attracted wide attention from all walks of life due to their superior pathogenicity and transmissibility. Aerosols-carrying pathogens are the main transmission route of many severe respiratory infectious diseases, which can lead to severe respiratory failure and even acute respiratory distress syndrome (ARDS) in infected individuals. Mechanical ventilation is the primary treatment for ARDS, and the small tidal volume, appropriate level of positive end-expiratory pressure based lung protective ventilation strategy can effectively reduce the incidence of ventilator-induced lung injury (VILI). However, in the process of clinical treatment, it is sometimes necessary to briefly disconnect the connection between the artificial airway and the ventilator circuit, which will not only cause the residual aerosol in the respiratory system to spill out and pollute the surrounding environment, increase the risk of nosocomial infection including medical staff, but also interfere with the implementation of lung protective ventilation strategy and aggravate ventilator-induced lung injury. In addition, studies have shown that a lot of medical staff have nosocomial infections, especially staff involved in tracheal intubation, extubation and other airway related operations. In addition to enhancing personal protective measures, it is crucial to safeguard healthcare workers from aerosol contamination and minimize associated risks during airway management. At present, there are few researches on the temporary sealing of airway lines and ventilator system, and there is a lack of clear guidance. This review summarizes the research status in related fields to provide a reference for corresponding solutions and programs.
Humans ; Respiratory Distress Syndrome/etiology* ; Respiration, Artificial ; Ventilator-Induced Lung Injury/prevention & control* ; Severe Acute Respiratory Syndrome ; COVID-19 ; Clinical Relevance

Porcine epidemic diarrhea virus (PEDV) is an intestinal coronavirus that can cause porcine epidemic diarrhea, leading to diarrhea, vomiting, weight loss, and even death in piglets. Due to the diversity of PEDV strains, traditional vaccines are difficult to sustainably and effectively prevent and control PEDV. This article reviews the strategies and mechanisms of active substances in regulating intracellular signaling pathways, viral proteins, and microbial metabolites to enhance the host immune function against PEDV. It emphasizes the prevention of PEDV resistance and the potential harm of PEDV breaking through interspecies barriers to the human society, aiming to provide reliable theoretical support for the development of new antiviral drugs or vaccines.
Porcine epidemic diarrhea virus/immunology* ; Animals ; Swine ; Swine Diseases/prevention & control* ; Antiviral Agents/pharmacology* ; Coronavirus Infections/virology* ; Viral Vaccines/immunology* ; Humans ; Signal Transduction

This study aims to establish an antibody detection method for porcine deltacoronavirus (PDCoV). The recombinant proteins PDCoV-N1 and PDCoV-N2 were expressed via the prokaryotic plasmid pColdII harboring the N gene sequence of the PDCoV strain CH/XJYN/2016. The reactivity and specificity of PDCoV-N1 and PDCoV-N2 with anti-PEDV sera were analyzed after the recombinant proteins were analyzed by SDS-PAGE and purified by the Ni-NTA Superflow Cartridge. Meanwhile, Western blotting and indirect immunofluorescence assay were carried out separately to validate the recombinant proteins PDCoV-N1 and PDCoV-N2. Finally, we established an indirect ELISA method based on the recombinant protein PDCoV-N2 after optimizing the conditions and tested the sensitivity, specificity, and reproducibility of the method. Then, the established method was employed to examine 102 clinical serum samples. The recombinant protein PDCoV-N2 showed low cross-reactivity with anti-PEDV sera. The optimal conditions of the indirect ELISA method based on PDCoV-N2 were as follows: the antigen coating concentration of 1.25 μg/mL and coating at 37 ℃ for 1 h; blocking by BSA overnight at 4 ℃; serum sample dilution at 1:50 and incubation at 37 ℃ for 1 h; secondary antibody dilution at 1:80 000 and incubation at 37 ℃ for 1 h; color development with TMB chromogenic solution at 37 ℃ for 10 min. The S/P value ≥ 0.45, ≤0.38, and between 0.45 and 0.38 indicated that the test sample was positive, negative, and suspicious, respectively. The testing results of the antisera against porcine epidemic diarrhea virus (PEDV), porcine circovirus 2 (PCV2), transmissible gastroenteritis virus (TGEV), foot-and-mouth disease virus (FMDV), and African swine fever virus (ASFV) showed that the S/P values were all less than 0.38. The testing results of the 800-fold diluted anti-PDCoV sera were still positive. The results of the inter- and intra-batch tests showed that the coefficients of variation of this method were less than 10%. Clinical serum sample test results showed the coincidence rate between this method and neutralization test was 94.12%. In this study, an ELISA method for the detection of anti-PDCoV antibodies was successfully established based on the truncated N protein of PDCoV. This method is sensitive, specific, stable, and reproducible, serving as a new method for the clinical diagnosis of PDCoV.
Animals ; Enzyme-Linked Immunosorbent Assay/methods* ; Swine ; Antibodies, Viral/blood* ; Recombinant Proteins/genetics* ; Deltacoronavirus/isolation & purification* ; Coronavirus Infections/virology* ; Swine Diseases/diagnosis* ; Coronavirus Nucleocapsid Proteins ; Sensitivity and Specificity

INTRODUCTION: Health literacy plays an essential role in one's ability to acquire and understand critical medical information in the coronavirus disease 2019 (COVID-19) infodemic and in other pandemics. We aimed to summarise the assessment, levels and determinants of pandemic-related health literacy and its associated clinical outcomes. METHODS: A systematic review was performed in Medline ® , Embase ® , PsycINFO ® , CINAHL ® and four major preprint servers. Observational and interventional studies that evaluated health literacy related to the novel COVID-19, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) were included. Items used in health literacy instruments were grouped under the themes of knowledge, attitudes and practices. Determinants of health literacy were grouped into five domains: sociodemographic, medical, psychological/psychiatric, health systems-related and others. RESULTS: Of the 2,065 articles screened, 70 articles were included. Of these, 21, 17 and 32 studies evaluated health literacy related to COVID-19, SARS and MERS, respectively. The rates of low pandemic health literacy ranged from 4.3% to 57.9% among medical-related populations and from 4.0% to 82.5% among nonmedical populations. Knowledge about the symptoms and transmission of infection, worry about infection, and practices related to mask usage and hand hygiene were most frequently evaluated. Sociodemographic determinants of health literacy were most frequently studied, among which higher education level, older age and female gender were found to be associated with better health literacy. No studies evaluated the outcomes associated with health literacy. CONCLUSION The level of pandemic-related health literacy is suboptimal. Healthcare administrators need to be aware of health literacy determinants when formulating policies in pandemics.
Humans ; Health Literacy ; COVID-19/epidemiology* ; Severe Acute Respiratory Syndrome/epidemiology* ; Health Knowledge, Attitudes, Practice ; Pandemics ; SARS-CoV-2 ; Coronavirus Infections/epidemiology* ; Middle East Respiratory Syndrome Coronavirus ; Female ; Male

OBJECTIVE: Vaccine hesitancy has been a public health issue for some time now, but gained more attention during COVID-19 pandemic. This systematic review aimed to estimate the prevalence of COVID-19 vaccination hesitancy and identify factors affecting it among adolescents. MATERIALS AND METHODS: The preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P 2020) was used. A search was performed in PubMed/ MEDLINE, EMBASE, Google Scholar, Herdin, and Cochrane databases on September 2023 using the key words: (COVID-19 OR SARS-COV OR corona virus) AND (Vaccination OR immunization) AND (adolescence OR teenagers OR youth) AND (hesitancy OR acceptance). Observational studies which determined the prevalence or risk factors for COVID-19 vaccine hesitancy among adolescents aged 10-19 years old were included. RESULTS: There were 5 good quality cross-sectional studies included. The prevalence of adolescents who did not want to be vaccinated ranged between 8.4% and 61.0%; while the prevalence of being unsure if they want to be vaccinated was between 31.6% and 88.0%. Factors associated with vaccine hesitancy included being economically disadvantaged, not having influenza vaccination, worrying about its effectiveness and safety, and low perceived necessity. CONCLUSION There is good quality evidence that COVID-19 vaccine hesitancy exists among adolescents. It is recommended that health workers should conduct information and education campaigns to iterate the effectiveness, safety, and misconceptions about of COVID-19 vaccination. Vaccination programs should also reach out to economically disadvantaged adolescents, and tapping parents and social media may be an effective strategy to improve vaccination acceptance among adolescents.
COVID-19 ; SARS-COV ; Severe acute respiratory syndrome-related coronavirus ; Vaccination ; Immunization ; Adolescent ; Adolescence ; Teenagers ; Youth

OBJECTIVE: To explore the quantitative analysis results of different patterns of chest computed tomography (CT) in patients with coronavirus infection and its relationship with viral load and pathophysiological status. METHODS: A retrospective clinical cohort study was conducted. Patients with coronavirus infection admitted to Qingdao Municipal Hospital from June 9 to 15, 2023 (all patients underwent chest CT examination within 24 hours after diagnosis) were enrolled. The patients were divided into coronavirus infection non-pneumonia group and coronavirus infection associated pneumonia group according to CT findings. Relevant baseline data, such as demographic characteristics, chest CT characteristics, and laboratory indicators within 12 hours before and after CT examination were collected from each group. Spearman correlation test was used to quantitatively analyze the correlation between CT features and laboratory indicators. The receiver operator characteristic curve (ROC curve) was drawn to evaluate the predictive value of each laboratory index for pneumonia in patients infected with coronavirus. Multiple linear regression analysis was used to explore the relationship between different CT patterns such as ground-glass opacity (GGO) and consolidation and ventilatory oxygenation status. RESULTS: A total of 171 patients were enrolled, including 44 patients in the coronavirus infection non-pneumonia group and 127 patients in the coronavirus infection associated pneumonia group (the incidence of pneumonia was 74.3%). Compared with patients with coronavirus infection alone, patients with coronavirus infection associated pneumonia had significantly lower lymphocyte count (LYM), oxygenation index (PaO₂/FiO₂), total lung capacity, GGO volume and GGO ratio, and significantly higher C-reactive protein (CRP), neutrophil/lymphocyte ratio (NLR), D-dimer, fraction of inspired oxygen (FiO₂) level, real volume variation and consolidation ratio, the differences were all statistically significant. There were no statistically significant differences in the nucleocapin protein (N) gene cycle threshold (Ct) value and open reading frame (ORF) gene Ct value between the two groups. ROC curve analysis showed that, after adjusting for age, gender, CRP level and other related factors, compared with N gene Ct value, ORF gene Ct value, N gene Ct value+LYM, ORF gene Ct value+LYM, the LYM had the most potential diagnosis power for coronavirus infection associated pneumonia. The area under the ROC curve (AUC) of LYM for predicting coronavirus infection was 0.703. When the cut-off value of LYM was 0.7×10⁹/L, the sensitivity was 55.5%, and the specificity was 79.5%, respectively. Multiple linear regression analysis showed that, when adjusted for consolidation ratio, age, gender, Hb and D-dimer levels, the GGO ratio in patients with coronavirus infection associated pneumonia was correlated with PaO₂/FiO₂ (β = -2.18, P < 0.001). When adjusted for GGO ratio, age, sex, Hb and D-dimer levels, the proportion of consolidation in patients with coronavirus infection associated pneumonia was correlated with PaCO₂ (β = 0.36, P = 0.004). When adjusted for GGO ratio, the proportion of consolidation in patients with coronavirus infection associated pneumonia was also associated with NLR (β = 0.79, P = 0.006). CONCLUSIONS LYM could be a potential marker for predicting coronavirus associated pneumonia, and the correlation seems to be independent of viral load. In addition, in the analysis of imaging features, GGO is associated with hypoxia, while consolidation is associated with PaCO₂ level and inflammation. The increased proportion of consolidation in the whole lung may be detrimental to lung ventilation.
Humans ; Tomography, X-Ray Computed/methods* ; Retrospective Studies ; COVID-19/diagnostic imaging* ; Viral Load ; Coronavirus Infections/diagnostic imaging* ; ROC Curve ; Male ; Lung/diagnostic imaging* ; Female ; Middle Aged ; C-Reactive Protein/analysis*

To screen and identify the key host proteins interacting with the non-structural protein 15 (Nsp15) of porcine epidemic diarrhea virus (PEDV). The IP/pull-down assay and mass spectrometry were employed to screen and identify the host proteins interacting with Nsp15. The interaction between the host protein and Nsp15 was studied by co-immunoprecipitation and laser scanning confocal microscopy. Finally, Western blotting and RT-qPCR were employed to examine the interaction between SLC25a3 and PEDV. The recombinant eukaryotic expression vector pcDNA3.1(+)-Flag-Nsp15 was successfully constructed, and the host protein SLC25a3 interacting with PEDV Nsp15 was screened out. An interaction existed between SLC25a3 and Nsp15, and SLC25a3 significantly inhibited PEDV replication in a dose-dependent manner. SLC25a3 inhibits PEDV replication. The results of this study provide a basis for deciphering the role and mechanism of SLC25a3 in the host immune response to PEDV infection.
Porcine epidemic diarrhea virus/genetics* ; Viral Nonstructural Proteins/metabolism* ; Animals ; Swine ; Virus Replication ; Coronavirus Infections/veterinary* ; Swine Diseases/metabolism*

Objective: To determine incidence, predictors, and impact of liver injury among hospitalized COVID-19 patients Methods: This is a retrospective cohort study of hospitalized COVID-19 patients at the University of the PhilippinesPhilippine General Hospital. Liver injury (LI) was defined as ALT elevation above institutional cut-off (>50 u/L) and was classified as mild (>1x to 3x ULN), moderate (>3x to 5x ULN), or severe (>5x ULN). Significant liver injury (SLI) was defined as moderate to severe LI. Univariate analysis of SLI predictors was performed. The impact of LI on clinical outcomes was determined and adjusted for known predictors -age, sex, and comorbidities. Results: Of the 1,131 patients, 565 (50.04%) developed LI. SLI was associated with male sex, alcohol use, chronic liver disease, increasing COVID-19 severity, high bilirubin, AST, LDH, CRP, and low lymphocyte count and albumin. An increasing degree of LI correlated with ICU admission. Only severe LI was associated with the risk of invasive ventilation (OR: 3.54, p=0.01) and mortality (OR: 2.76, p=0.01). Severe LI, male sex, cardiovascular disease, and malignancy were associated with longer hospital stay among survivors. Conclusion The liver injury occurred commonly among COVID-19 patients and was associated with important clinicodemographic characteristics. Severe liver injury increases the risk of adverse outcomes among hospitalized patients.
Liver injury ; Coronavirus disease-19 ; Severe Acute Respiratory Syndrome Coronavirus-2 ; Clinical outcomes