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

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: Recombination events are common and serve as the primary driving force of diverse human adenovirus (HAdV), particularly in children with acute respiratory tract infections (ARIs). Therefore, continual monitoring of these events is essential for effective viral surveillance and control. METHODS: Respiratory specimens were collected from children with ARIs between January 2022 and December 2023. The penton base, hexon, and fiber genes were amplified from HAdV-positive specimens and sequenced to determine the virus type. In cases with inconsistent typing results, genes were cloned into the pGEM-T vector to detect recombination events. Metagenomic next-generation sequencing (mNGS) was performed to characterize the recombinant HAdV genomes. RESULTS: Among 6,771 specimens, 277 (4.09%, 277/6,771) were positvie for HAdV, of which 157 (56.68%, 157/277) were successfully typed, with HAdV-B3 being the dominant type (91.08%, 143/157), and 14 (5.05%, 14/277) exhibited inconsistent typing results, six of which belonged to species B. The penton base genes of these six specimens were classified as HAdV-B7, whereas their hexon and fiber genes were classified as HAdV-B3, resulting in a recombinant genotype designated P7H3F3, which closely resembled HAdV-B114. Additionally, a partial gene encoding L1 52/55 kD was identified, which originated from HAdV-B16. CONCLUSION A novel recombinant, P7H3F3, was identified, containing sequences derived from HAdV-B3 and HAdV-B7, which is similar to HAdV-B114, along with additional sequences from HAdV-B16.
Humans ; Adenoviruses, Human/isolation & purification* ; Respiratory Tract Infections/epidemiology* ; Child, Preschool ; Child ; Recombination, Genetic ; Male ; Beijing/epidemiology* ; Infant ; Female ; Phylogeny ; Adenovirus Infections, Human/epidemiology* ; Acute Disease ; Genome, Viral

BACKGROUND: An acute upper respiratory tract infection (URI) is the most common disease worldwide, irrespective of age or sex. This study aimed to evaluate the short-term effect of diurnal temperature range (DTR) on emergency room (ER) visits for URI in Seoul, Korea, between 2009 and 2013. METHODS: Daily ER visits for URI were selected from the National Emergency Department Information System, which is a nationwide daily reporting system for ER visits in Korea. URI cases were defined according to International Classification of Diseases, 10 RESULTS: There were 529,527 ER visits for URI during the study period, with a daily mean of 290 visits (range, 74-1942 visits). The mean daily DTR was 8.05 °C (range, 1.1-17.6 °C). The cumulative day (lag 02) effect of DTR above 6.57 °C per 1 °C increment was associated with a 1.42% (95% confidence interval [CI] 0.04-2.82) increase in total URI. Children (≤ 5 years of age) were affected by DTR above 6.57 °C per 1 °C, with 1.45% (95% CI 0.32-2.60) at lag 02, adults (19-64 years) with 2.77% (95% CI 0.39-5.20) at lag 07. When the DTR (lag02) was 6.57 °C to 11.03 °C, the relative risk was significant at 6.01% (95% CI 2.45-9.69) for every 1 °C increase in youth subjects aged for 6 to 18 years. CONCLUSIONS DTR was associated with a higher risk for ER visits for URI. In addition, the results suggested that the lag effects and relative risks of DTR on URI were quite different according to age.
Acute Disease/epidemiology* ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Cold Temperature/adverse effects* ; Emergency Service, Hospital/statistics & numerical data* ; Female ; Hot Temperature/adverse effects* ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Republic of Korea/epidemiology* ; Respiratory Tract Infections/etiology* ; Young Adult

As of February 2020, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak started in China in December 2019 has been spreading in many countries in the world. With the numbers of confirmed cases are increasing, information on the epidemiologic investigation and clinical manifestation have been accumulated. However, data on viral load kinetics in confirmed cases are lacking. Here, we present the viral load kinetics of the first two confirmed patients with mild to moderate illnesses in Korea in whom distinct viral load kinetics are shown. This report suggests that viral load kinetics of SARS-CoV-2 may be different from that of previously reported other coronavirus infections such as SARS-CoV.
China ; Coronavirus ; Coronavirus Infections ; Humans ; Kinetics ; Korea ; SARS Virus ; Severe Acute Respiratory Syndrome ; Viral Load

An epidemic of acute respiratory syndrome in humans, which appeared in Wuhan, China in December 2019, was caused by a novel coronavirus (SARS-CoV-2). This disease was named as "Coronavirus Disease 2019" (COVID-19). SARS-CoV-2 was first identified as an etiological pathogen of COVID-19, belonging to the species of severe acute respiratory syndrome-related coronaviruses (SARSr-CoV). The speed of both the geographical transmission and the sudden increase in numbers of cases is much faster than SARS and Middle East respiratory syndrome (MERS). COVID-19 is the first global pandemic caused by a coronavirus, which outbreaks in 211 countries/territories/areas. The vaccine against COVID-19, regarded as an effective prophylactic strategy for control and prevention, is being developed in about 90 institutions worldwide. The experiences and lessons encountered in the previous SARS and MERS vaccine research can be used for reference in the development of COVID-19 vaccine. The present paper hopes to provide some insights for COVID-19 vaccines researchers.
Betacoronavirus ; immunology ; Biomedical Research ; Coronavirus Infections ; epidemiology ; immunology ; prevention & control ; virology ; Humans ; Internationality ; Middle East Respiratory Syndrome Coronavirus ; immunology ; Pandemics ; prevention & control ; Pneumonia, Viral ; epidemiology ; immunology ; prevention & control ; virology ; SARS Virus ; immunology ; Severe Acute Respiratory Syndrome ; immunology ; Viral Vaccines ; immunology

The ongoing outbreak of the coronavirus disease 2019 (COVID-19) as named by the World Health Organization has millions of confirmed cases around the world and has claimed hundreds of thousands of lives. The virus was named SARS-CoV-2 in February by International Committee on Taxonomy of Viruses. COVID-19 presents as fever, dry cough, dyspnea, headache and pneumonia. In a small subset of severe cases, the disease quickly progresses to respiratory failure and even death. Since the 21st century, there have been three major outbreaks caused by human coronaviruses, including the severe acute respiratory syndrome (SARS) that broke out in 2003, the Middle East respiratory syndrome (MERS) in 2012, and the recent pandemic of COVID-19. Since 2003, significant progress has been made in the study of SARS-CoV and MERS-CoV concerning their natural origins, pathogenesis, antiviral development and vaccine design. Since SARS-CoV-2 and SARS-CoV are closely related, previous findings on SARS-CoV are highly relevant to a better understanding as well as diagnosis, treatment, prevention and control of SARS-CoV-2. In this review, we highlight recent progresses in the field; compare the biological characteristics of SARS-CoV and SARS-CoV-2; summarize the urgently-needed diagnostic, treatment, prevention and control options; and provide future perspectives for the outcome of the outbreak and research questions to be answered, including some of the difficulties in vaccine development. Hopefully, our comments and suggestions would prove useful for the control of the SARS-CoV-2 epidemic in China and the world.
Antiviral Agents ; pharmacology ; therapeutic use ; Betacoronavirus ; drug effects ; immunology ; pathogenicity ; Coronavirus Infections ; diagnosis ; prevention & control ; therapy ; virology ; Humans ; Middle East Respiratory Syndrome Coronavirus ; drug effects ; immunology ; pathogenicity ; Pandemics ; prevention & control ; Pneumonia, Viral ; diagnosis ; prevention & control ; therapy ; virology ; SARS Virus ; drug effects ; immunology ; pathogenicity ; Severe Acute Respiratory Syndrome ; diagnosis ; prevention & control ; therapy ; virology ; Viral Vaccines

Adenosine Monophosphate ; analogs & derivatives ; therapeutic use ; Adult ; Aged ; Alanine ; analogs & derivatives ; therapeutic use ; Anti-Arrhythmia Agents ; therapeutic use ; Arrhythmias, Cardiac ; diagnosis ; epidemiology ; Coronavirus Infections ; diagnosis ; drug therapy ; epidemiology ; Echocardiography ; Electrocardiography ; methods ; statistics & numerical data ; Female ; Follow-Up Studies ; Humans ; Male ; Pandemics ; statistics & numerical data ; Pneumonia, Viral ; diagnosis ; drug therapy ; epidemiology ; Sampling Studies ; Severe Acute Respiratory Syndrome ; diagnosis ; epidemiology ; Singapore ; Treatment Outcome

OBJECTIVES: To develop a new Chinese medicine (CM)-based drug and to evaluate its safety and effect for suppressing acute respiratory distress syndrome (ARDS) in COVID-19 patients. METHODS: A putative ARDS-suppressing drug Keguan-1 was first developed and then evaluated by a randomized, controlled two-arm trial. The two arms of the trial consist of a control therapy (alpha interferon inhalation, 50 µg twice daily; and lopinavir/ritonavir, 400 and 100 mg twice daily, respectively) and a testing therapy (control therapy plus Keguan-1 19.4 g twice daily) by random number table at 1:1 ratio with 24 cases each group. After 2-week treatment, adverse events, time to fever resolution, ARDS development, and lung injury on newly diagnosed COVID-19 patients were assessed. RESULTS: An analysis of the data from the first 30 participants showed that the control arm and the testing arm did not exhibit any significant differences in terms of adverse events. Based on this result, the study was expanded to include a total of 48 participants (24 cases each arm). The results show that compared with the control arm, the testing arm exhibited a significant improvement in time to fever resolution (P=0.035), and a significant reduction in the development of ARDS (P=0.048). CONCLUSIONS Keguan-1-based integrative therapy was safe and superior to the standard therapy in suppressing the development of ARDS in COVID-19 patients. (Trial registration No. NCT04251871 at www.clinicaltrials.gov ).
Administration, Inhalation ; Adult ; China ; Coronavirus Infections ; diagnosis ; drug therapy ; mortality ; Dose-Response Relationship, Drug ; Drug Administration Schedule ; Drugs, Chinese Herbal ; administration & dosage ; Female ; Follow-Up Studies ; Humans ; Integrative Medicine ; Interferon-alpha ; administration & dosage ; Lopinavir ; administration & dosage ; Male ; Middle Aged ; Pandemics ; Pneumonia, Viral ; diagnosis ; drug therapy ; mortality ; Risk Assessment ; Severe Acute Respiratory Syndrome ; diagnosis ; drug therapy ; mortality ; Severity of Illness Index ; Survival Rate

Betacoronavirus ; Coronavirus Infections ; epidemiology ; transmission ; Disease Outbreaks ; Humans ; Pandemics ; Pneumonia, Viral ; epidemiology ; transmission ; Severe Acute Respiratory Syndrome ; epidemiology