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2.
J Biomol Struct Dyn ; : 1-22, 2022 May 13.
Article in English | MEDLINE | ID: covidwho-20235354

ABSTRACT

The genome feature of SARS-CoV-2 leads the virus to mutate and creates new variants of concern. Tackling viral mutations is also an important challenge for the development of a new vaccine. Accordingly, in the present study, we undertook to identify B- and T-cell epitopes with immunogenic potential for eliciting responses to SARS-CoV-2, using computational approaches and its tailoring to coronavirus variants. A total of 47 novel epitopes were identified as immunogenic triggering immune responses and no toxic after investigation with in silico tools. Furthermore, we found these peptide vaccine candidates showed a significant binding affinity for MHC I and MHC II alleles in molecular docking investigations. We consider them to be promising targets for developing peptide-based vaccines against SARS-CoV-2. Subsequently, we designed two efficient multi-epitopes vaccines against the SARS-CoV-2, the first one based on potent MHC class I and class II T-cell epitopes of S (FPNITNLCPF-NYNYLYRLFR-MFVFLVLLPLVSSQC), M (MWLSYFIASF-GLMWLSYFIASFRLF), E (LTALRLCAY-LLFLAFVVFLLVTLA), and N (SPRWYFYYL-AQFAPSASAFFGMSR). The second candidate is the result of the tailoring of the first designed vaccine according to three classes of SARS-CoV-2 variants. Molecular docking showed that the protein-protein binding interactions between the vaccines construct and TLR2-TLR4 immune receptors are stable complexes. These findings confirmed that the final multi-epitope vaccine could be easily adapted to new viral variants. Our study offers a shortlist of promising epitopes that can accelerate the development of an effective and safe vaccine against the virus and its adaptation to new variants.Communicated by Ramaswamy H. Sarma.

3.
China Tropical Medicine ; 23(4):338-341, 2023.
Article in Chinese | GIM | ID: covidwho-20245452

ABSTRACT

Objective: To analyze the vaccination status of SARS-CoV-2 in children, and explore the relationship between SARS-CoV-2 vaccination and COVID-19 in children. Methods: A retrospective study was conducted to analyze the clinical data of 335 cases of SARS-CoV-2 Omicron variant infection from February 15, 2022 to March 18, 2022 in Shenzhen Third People's Hospital. Results: Among 335 children with SARS-CoV-2 infection, 174(51.9%) cases were vaccinated with the SARS-CoV-2 vaccine;33(31.4%) cases were vaccinated in the 3-<6 years old group;141(61.3%) cases were vaccinated in the 6-<14 years old group. There was a statistically significant difference in the proportion of SARS-CoV-2 vaccination between the 6-<14 years old group and the 3-<6 years old group (X2=26.1, P < 0.05). In the study cohort, 3-<6 years old group and 6-<14 years old group, there was no significant difference in the incidence of COVID-19 in the vaccinated group compared with the unvaccinated group (P > 0.05). In the study cohort, the proportion of confirmed cases of 1 dose of SARS-CoV-2 vaccine and 2 doses or more of SARS-CoV-2 vaccine was 89.5% (68 cases) and 77.6% (76 cases), respectively;in the 6~<14 years old group, the proportion of confirmed cases of 1 dose of SARS-CoV-2 vaccine and 2 doses or more of SARS-CoV-2 vaccine was 90.0% (54 cases) and 76.5% (62 cases), respectively;the differences were statistically significant (X2=4.264, P < 0.05;X2=4.279, P < 0.05). The IgG levels of 18.28 (6.61, 55.2) AU/mL and 58.3 (25.85, 131.41) AU/mL in the study cohort who were vaccinated for 1 dose, 2 doses and more, respectively;the IgG levels of 20.13 (8.33, 44.33) AU/mL and 56.57 (25.85, 150.07) AU/mL in the 6~<14 years old group who were vaccinated for 1 dose, 2 doses and more, respectively;and the differences were statistically significant (Z=-4.37, P < 0.05;Z=-3.96, P < 0.05). Conclusions: Children who received 2 doses of SARS-CoV-2 vaccine have a lower incidence of COVID-19 and higher levels of SARS-CoV-2 antibodies compared with who received 1 dose. It is recommended that children are advised to be vaccinated against the COVID-19.

4.
China Tropical Medicine ; 23(4):388-391, 2023.
Article in Chinese | GIM | ID: covidwho-20245139

ABSTRACT

Objective: To analyze and compare the effects of different clinical characteristics on the negative conversion time of nucleic acid detection after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant infection, and to provide a scientific basis for the isolation and treatment of coronavirus disease 2019 (COVID-19). Methods: The epidemiological and clinical data of 228 mild SARS-CoV-2 Omicron variant infected patients diagnosed in Shanghai were retrospectively collected from April 27, 2022 to June 8, 2022 in Wujiaochang designated Hospital, Yangpu District, Shanghai. The negative conversion time of nucleic acid detection was used as the outcome variable, and the patients were divided into A (18 days) and B (>18 days). Univariate and multivariate logistic regression analysis were used to analyze the influencing factors of the negative conversion time of nucleic acid detection. Results: The mean nucleic acid conversion time of 228 patients was (18.7+or-12.1) d, with the median time of 18 (2-46) d. Among them, 120 patients in group A had an average nucleic acid conversion time of (13.2+or-2.0) d, and 108 cases in group B had an average nucleic acid conversion time of (20.8+or-1.3) d. Univariate analysis showed that there were no statistically significant differences in the effects of hypertension, coronary heart disease, diabetes, hypokalemia, malignant tumors, neuropsychiatric diseases, chronic digestive diseases on the negative nucleic acid conversion time (P > 0.05);however, there were significant differences in the effects of combined cerebrovascular disease, leukopenia, chronic respiratory system diseases and vaccination on the negative nucleic acid conversion time (P < 0.05). Further multivariate logistic regression analysis revealed that the combination of chronic respiratory diseases and non-vaccination were significant risk factors for prolongation of negative nucleic acid conversion time (P < 0.05). Conclusions: The results of this study show that gender, age and whether hypertension, coronary heart disease, diabetes mellitus, hypokalemia, malignant tumor, neuropsychiatric disease and chronic digestive disease have no significant effect on the nucleic acid conversion time, whereas chronic respiratory disease and no vaccination are significantly correlated with the prolongation of nucleic acid conversion time in SARS-CoV-2 Omicron-infected patients.

5.
Microbes and Infectious Diseases ; 4(2):335-342, 2023.
Article in English | Scopus | ID: covidwho-20235811

ABSTRACT

Background: Evidence suggests that vaccines efficacy lies on the prevention of severe symptomatic disease. We aim to describe the clinical characteristics of COVID-19 infection among healthcare professionals (HCPs) after vaccination, during periods of transmission of SARS CoV-2 variants in a COVID-19 dedicated facility. Methods: A retrospective observational study of HCPs confirmed with COVID-19 during the period March 2021 to Jan 2022 was conducted. Delta period (March-August 2021), and Omicron period (Dec 2021-Jan 2022) were defined. Clinical, laboratory, radiology and vaccination history was collected from electronic medical records. Results: COVID-19 infection was reported in 16 and 138 HCPs during the Delta and Omicron period respectively. By category the nurses predominate, and a significant contribution of the healthcare related transmission against the community-related one. Higher frequency of loss of taste (37.5% vs 4.3%), and loss of smell (43.8% vs 3.6%) was observed during Delta period. Myalgia (12.5% vs 37.7%), and sore throat (6.3% vs 55.8%) predominated in Omicron period. Bilateral ground-glass appearance of the lung was observed in 28.6% and 7.1% in the Delta and Omicron period, respectively. Higher cycle threshold values of the polymerase chain reaction test during Omicron period, in comparison with Delta period, was observed (22.98 vs 25.98). Time from previous vaccine dose to positive laboratory test was longer during the Delta period (131 vs 98.26 days). Conclusion: SARS CoV-2 viral variants infections in HCPs were associated to selected clinical and epidemiological characteristics, with less severe disease for Omicron variant, and potential shorter duration of the immune response to vaccination. © 2020 The author (s)..

6.
China Tropical Medicine ; 23(4):404-408, 2023.
Article in Chinese | GIM | ID: covidwho-20235483

ABSTRACT

Objective: To explore the clinical characteristics of nucleic acid negative newborns delivered by pregnant women infected with SARS-CoV-2 (Omicron variant BA. 5.1.3) in Sanya area, and to provide evidence for understanding its clinical characteristics. Methods: A retrospective analysis was performed on 14 neonates with negative nucleic acid delivered by pregnant women who tested positive for SARS-CoV-2 (Omicron variant BA.5.1.3) in Sanya Central Hospital (the Third People's Hospital of Hainan Province) from June 2022 to September 2022 (observation group, n=14). The corresponding nucleic acid-negative newborns delivered by pregnant women detected negative with SARS-CoV-2 (Omicronon variant strain BA.5.1.3) were set as the control group (n=56), and the general data and clinical characteristics of neonates in the two groups were compared. Results: There was no significant difference between the observation group and the control group in pregnancy diabetes, pregnancy induced hypertension, gestational pre-eclampsia, fetal intrauterine distress, premature rupture of membranes (P > 0.05);there was no significant difference between the observation group and the control group in terms of sex, gestational age, birth weight, age, mode of delivery, birth Apgar score, heart screening, pulmonary disease, glucose 6-phosphate dehydrogenase (G6PD) deficiency, thalassemia, breast milk jaundice, hemolytic jaundice (P > 0.05). The bilirubin level, blue light irradiation cases and the duration of blue light irradiation of the newborns in the observation group at 7 days after birth were higher than those in the control group (P < 0.05);the ratio of blood oxygen saturation 90% in the observation group was lower than that in the control group (21.43% vs 89.29%, P < 0.05), and the ratio of blood oxygen saturation occasionally<90% was higher than that in the control group (57.14% vs 10.71%, P < 0.05). The ratio of blood oxygen saturation<90% had no significant difference compared with that in the control group (7.14% vs 0, P > 0.05), and the ratio of blood oxygen saturation reduced to the required oxygen uptake was higher than that in the control group (14.29% vs 0, P < 0.05). Conclusions: The jaundice manifestation of the nucleic acid-negative newborns delivered by pregnant women infected with SARS-CoV-2 (Omicronon variant strain BA.5.1.3) in Sanya area is relatively obvious, with blood oxygen saturation easily lower than 90% and even requiring oxygen inhalation in severe cases.

7.
BMC Genomics ; 24(1): 312, 2023 Jun 10.
Article in English | MEDLINE | ID: covidwho-20240423

ABSTRACT

BACKGROUND: The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic. We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing. Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available metadata. RESULTS: In total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs, accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its descendants predominated the peak observed in July-October 2021. It replaced the previously predominant B.1.351 lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-detected cases were genetically closely related. CONCLUSION: The global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country. It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or introduction of new SARS-COV-2 VOCs in the country.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19 Vaccines , Cross-Sectional Studies , Pandemics , COVID-19/epidemiology , Genomics
8.
J Med Virol ; 95(6): e28831, 2023 06.
Article in English | MEDLINE | ID: covidwho-20239959

ABSTRACT

Despite the higher transmissibility of Omicron Variant of Concern (VOC), several reports have suggested lower risk for hospitalization and severe outcomes compared to previous variants of SARS-CoV-2. This study, enrolling all COVID-19 adults admitted to a reference hospital who underwent both the S-gene-target-failure test and VOC identification by Sanger sequencing, aimed to describe the evolving prevalence of Delta and Omicron variants and to compare the main in-hospital outcomes of severity, during a trimester (December 2021 to March 2022) of VOCs' cocirculation. Factors associated with clinical progression to noninvasive ventilation (NIV)/mechanical ventilation (MV)/death within 10 days and to MV/admission to intensive care unit (ICU)/death within 28 days, were investigated through multivariable logistic regressions. Overall, VOCs were: Delta n = 130/428, Omicron n = 298/428 (sublineages BA.1 n = 275 and BA.2 n = 23). Until mid-February, Delta predominance shifted to BA.1, which was gradually displaced by BA.2 until mid-March. Participants with Omicron VOC were more likely to be older, fully vaccinated, with multiple comorbidities and to have a shorter time from symptoms' onset, and less likely to have systemic symptoms and respiratory complications. Although the need of NIV within 10 days and MV within 28 days from hospitalization and the admission to ICU were less frequent for patients with Omicron compared to those with Delta infections, mortality was similar between the two VOCs. In the adjusted analysis, multiple comorbidities and a longer time from symptoms' onset predicted 10-day clinical progression, while complete vaccination halved the risk. Multimorbidity was the only risk factor associated with 28-day clinical progression. In our population, in the first trimester of 2022, Omicron rapidly displaced Delta in COVID-19 hospitalized adults. Clinical profile and presentation differed between the two VOCs and, although Omicron infections showed a less severe clinical picture, no substantial differences for clinical progression were found. This finding suggests that any hospitalization, especially in more vulnerable individuals, may be at risk for severe progression, which is more related to the underlying frailty of patients than to the intrinsic severity of the viral variant.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , Humans , SARS-CoV-2/genetics , COVID-19/epidemiology , Hospitals , Disease Progression
9.
Eur J Neurol ; 2023 Jun 13.
Article in English | MEDLINE | ID: covidwho-20238912

ABSTRACT

BACKGROUND AND PURPOSE: An enhanced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine regimen could improve humoral vaccine response in patients with multiple sclerosis (MS) treated by anti-CD20. The aim was to evaluate the serological response and the neutralizing activity after BNT162b2 primary and booster vaccination in MS patients, including patients on anti-CD20 receiving a primary vaccine regimen enhanced with three injections. METHODS: In this prospective longitudinal cohort study of 90 patients (47 on anti-CD20, 10 on fingolimod, 33 on natalizumab, dimethylfumarate or teriflunomide), anti-SARS-CoV-2 receptor binding domain (RBD) immunoglobulin G antibodies were quantified and their neutralization capacity was evaluated by enzyme-linked immunosorbent assay (GenScript) and a virus neutralization test against B.1 historical strain, Delta and Omicron variants, before and after three to four BNT162b2 injections. RESULTS: After the primary vaccination scheme, the anti-RBD positivity rate was strongly decreased in patients on anti-CD20 (28% [15%; 44%] after two shots, 45% [29%; 62%] after three shots) and fingolimod (50% [16%; 84%]) compared to other treatments (100% [90%; 100%]). Neutralization activity was also decreased in patients on anti-CD20 and fingolimod, and notably low for the Omicron variant in all patients (0%-22%). Delayed booster vaccination was performed in 54 patients, leading to a mild increase of anti-RBD seropositivity in patients on anti-CD20 although it was still lower compared to other treatments (65% [43%; 84%] vs. 100% [87%; 100%] respectively). After a booster, Omicron neutralization activity remained low on anti-CD20 and fingolimod treated patients but was strongly increased in patients on other treatments (91% [72%; 99%]). DISCUSSION: In MS patients on anti-CD20, an enhanced primary vaccination scheme moderately increased anti-RBD seropositivity and anti-RBD antibody titre, but neutralization activity remained modest even after a fourth booster injection. TRIAL REGISTRATION INFORMATION: COVIVAC-ID, NCT04844489, first patient included on 20 April 2021.

10.
11.
J Infect Dis ; 2023 Jun 06.
Article in English | MEDLINE | ID: covidwho-20244485

ABSTRACT

We compared neutralizing antibody responses to BA.4/5, BQ.1.1, XBB, and XBB.1.5 Omicron SARS-CoV-2 variants after a bivalent or ancestral COVID-19 mRNA booster vaccine or post-vaccination infection. We found that the bivalent booster elicited moderately high antibody titers against BA.4/5 that were approximately two-fold higher against all Omicron variants than titers elicited by the monovalent booster. The bivalent booster elicited low but similar titers against both XBB and XBB.1.5 variants. These findings inform risk assessments for future COVID-19 vaccine recommendations and suggest that updated COVID-19 vaccines containing matched vaccine antigens to circulating divergent variants may be needed.

12.
Monatsschr Kinderheilkd ; : 1-6, 2023 Jun 05.
Article in German | MEDLINE | ID: covidwho-20244351

ABSTRACT

Background: The COVID-19 pandemic posed special challenges for the existing structures for vaccination prevention in Germany with respect to 1) understanding the role and aims of those involved and the interests of the children and 2) the definition of adequate criteria and assessment of the risk of severe diseases in children. Objectives: Do the priorities of different groups of interest differ in the recommendations for COVID-19 vaccination? Which data on the pathogenicity of different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV­2) are necessary and how did they change during the pandemic? Methods: The tasks, objectives and perception of politics and the German national vaccination advisory committee regarding vaccination of children are discussed in the face of summarized recent data on clinical manifestations of pediatric SARS-CoV­2 infections among children and adolescents in Germany, which could be estimated by combining different German data sources. Results: The perspectives of politics and children differ but are legitimate when they are clearly stated. The decisive risk for a severe course or the pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV­2 (PIMS-TS) per 10,000 SARS-CoV­2 infections for the decision on vaccination from the perspective of children, decreased during the course of the pandemic with dominance of the omicron variant. Severe courses of COVID-19 still predominantly affect children with underlying diseases. The age-stratified analysis of vaccinated and nonvaccinated children showed that the alterations in the pathogenicity of the virus in the course of the pandemic is particularly reflected in the reduction in the risk of PIMS-TS. The general reduction of severe courses of COVID-19 again can be explained by the characteristics of variants of concern (VOC) as well as increasing vaccination rates and immunity following a SARS-CoV­2 infection. Conclusion: The primary goal of COVID-19 vaccination in children and adolescents is the prevention of severe courses of the disease. In pediatric risk groups the best possible immunity or immune protection by vaccination should be strived for. It is currently unclear whether catch-up vaccination in already infected or vaccinated children or whether forthcoming healthy children will need vaccination, aiming for hybrid immunity.

13.
J Med Virol ; 95(6): e28847, 2023 06.
Article in English | MEDLINE | ID: covidwho-20240737

ABSTRACT

Recently emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants are generally less pathogenic than previous strains. However, elucidating the molecular basis for pulmonary immune response alterations is challenging owing to the virus's heterogeneous distribution within complex tissue structure. Here, we revealed the spatial transcriptomic profiles of pulmonary microstructures at the SARS-CoV-2 infection site in the nine cynomolgus macaques upon inoculation with the Delta and Omicron variants. Delta- and Omicron-infected lungs had upregulation of genes involved in inflammation, cytokine response, complement, cell damage, proliferation, and differentiation pathways. Depending on the tissue microstructures (alveoli, bronchioles, and blood vessels), there were differences in the types of significantly upregulated genes in each pathway. Notably, a limited number of genes involved in cytokine and cell damage response were differentially expressed between bronchioles of the Delta- and Omicron-infection groups. These results indicated that despite a significant antigenic shift in SARS-CoV-2, the host immune response mechanisms induced by the variants were relatively consistent, with limited transcriptional alterations observed only in large airways. This study may aid in understanding the pathogenesis of SARS-CoV-2 and developing a clinical strategy for addressing immune dysregulation by identifying potential transcriptional biomarkers within pulmonary microstructures during infection with emerging variants.


Subject(s)
COVID-19 , SARS-CoV-2 , Animals , SARS-CoV-2/genetics , Transcriptome , COVID-19/genetics , Pulmonary Alveoli , Cytokines/genetics , Macaca
14.
J Environ Chem Eng ; 11(3): 110289, 2023 Jun.
Article in English | MEDLINE | ID: covidwho-20230859

ABSTRACT

With the global COVID-19 pandemic, wastewater surveillance has received a considerable attention as a method for the early identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater treatment plant (WWTP) and sewer systems. For the first time in Korea, this study utilized the wastewater surveillance technique to monitor the COVID-19 outbreak. Sampling efforts were carried out at the WWTPs in the capital city of Korea, Seoul, and Daegu the place where the first severe outbreak was reported. The RNA of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been extracted from the collected wastewater influent and primary sewage sludge samples. The outcomes were contrasted with the COVID-19 cases in the WWTPs served area. Additionally, whole transcriptome sequencing was used to compare the microbial community alterations before and after the COVID-19 outbreak and SARS-CoV-2 variations. The results demonstrated that the changes in SARS-CoV-2 RNA concentrations in the influent and sludge matched the trends of reported COVID-19 cases, especially sludge showed high-resolution data, which is well-matched when fewer COVID-19 cases (0-250) are reported. Interestingly, one month before the clinical report, we found that the SARS-CoV-2 Beta variant (South Africa, B.1.351) in the wastewater. In addition, the Aeromonas bacterial species was dominated (21.2%) among other bacterial species in wastewater after the COVID-19 outbreak, suggesting a potential indirect microbial indicator of the COVID-19 outbreak.

15.
J Virol Methods ; 319: 114759, 2023 May 29.
Article in English | MEDLINE | ID: covidwho-2327796

ABSTRACT

The circulation of certain SARS-CoV-2 variants may have a great impact on the epidemiological status of a geographical area; therefore, it is important that their presence is monitored. Currently, the gold standard method used to identify newly emerged variants is sequencing of either genes or whole genomes. However, since this method is relatively expensive and has a long turnaround time, other rapid strategies should also be employed. The current study aimed to evaluate the performance of the Simplexa® SARS-CoV-2 Variants Direct assay, which is a RT-PCR that determines the variant present in a nasopharyngeal swab sample in approximately two hours. Totally, 527 positive samples for SARS-CoV-2 were analyzed from January until December 2022 and next-generation sequencing (NGS) was used as the reference method. The assay showed high sensitivity, ranging from 94.12 % to 100 %, depending on the variant. The assay also showed high specificity, reaching 100 % for Delta and BA.1 variants, and 99.74 % and 98.67 % for BA.2 and BA.4/BA.5 variants, respectively. Moreover, the assay was able to identify the correct variant category in the presence of any subvariant in the sample. We conclude that the assay can be used to facilitate faster monitoring of circulating SARS-CoV-2 variants, however sequencing cannot be completely replaced, since new variants always emerge, and constant updates are needed, so that the user is able to interpret the melting curve patterns.

16.
China Tropical Medicine ; 23(3):272-276, 2023.
Article in Chinese | GIM | ID: covidwho-2322742

ABSTRACT

Objective: To investigate the chest computed tomography (CT) manifestations and dynamic changes of coronavirus disease 2019 (COVID-19) in the patients younger than 18 years old infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, and to provide a basis for determining the chest CT changes and efficacy of COVID-19 caused by Omicron virus variant in patients younger than 18 years old. Methods The clinical and imaging data of 30 cases of patients younger than 18 years old infected with COVID-19 Omicron variant, who admitted to the Third People's Hospital of Shenzhen from February 11 to March 26, 2022 were collected and retrospectively analyzed. The clinical manifestations, imaging features and dynamic changes of lesions were summarized. Results A total of 41 intrapulmonary lesions in 30 patients with COVID-19 caused by SARS-CoV-2 Omicron variant. The main manifestations were patchy or nodular ground-glass opacities and/or consolidation, with focal subpleural distribution, lesions mainly occur in the right lung (70.73%, 29/41). There were 42 lesion morphologies, with 22 (52.38%) striped shadows and 16 (38.10%) nodular shadows, with small lamellar and patchy shadows predominating. There were 36 lesion density variations, with ground glass shadows being the most common, with a total of 24 ground glass shadows (66.66%) in each lobe of the lung, and also 6 consolidation lesions (16.67%) and 6 mixed ground glass opacity and consolidation lesions (16.67%). With the progression of the disease, lesions gradually enlarged, appeared on the 2nd day (312.93 mm3), peaked on the 9th day (1 837.18 mm3). The average absorption time of the lesions was (16+or-3) days, and there was no significant difference between the absorption time of patchy and nodular lesions (ground glass and/or consolidation) (t=0.853, P > 0.05). The lesions showed focal ground-glass opacity in the early stage, 77.78% lesions were absorbed after treatment in the late stage. Inflammatory nodules were absorbed slowly (9-19 days), without residual fibrotic changes. Conclusions The imaging manifestations of COVID-19 in patients younger than 18 years old infected with SARS-CoV-2 Omicron variant have certain characteristics, showed patchy or nodular ground glass opacities and/or consolidation, mainly distributed in the subpleural area, with small and few lesions and slow change, didn't remain fibrosis. Being familiar with its clinical and imaging manifestations can assist in early diagnosis, but confirming the diagnosis requires a combination of epidemiological history, clinical symptoms, SARS-CoV-2 nucleic acid and radiological manifestations.

17.
GeroScience ; 44(5):2337-2572, 2022.
Article in English | GIM | ID: covidwho-2321196

ABSTRACT

This journal issue includes 15 articles that discuss continent-wide evolutionary trends of emerging SARS-CoV-2 variants;use of convalescent plasma therapy in hospitalised adult patients with non-critical COVID-19;evidence for preserved insulin responsiveness in the aging rat brain;SARS-CoV-2 infection in HIV-infected patients;different patterns of excess all-cause mortality by age and sex in Hungary during the 2nd and 3rd waves of the COVID-19 pandemic;mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs.

18.
Razi Journal of Medical Sciences ; 29(9), 2022.
Article in Persian | GIM | ID: covidwho-2325313

ABSTRACT

Background & Aims: Epidemics of human viruses began during the period of Neolithic around 12,000 years ago. Humans developed more densely population which allowed viruses to spread rapidly among communities. Also, plant and livestock viruses increased along with human viruses (2). At the January 2020, the coronavirus disease (COVID-19 7th human coronavirus) was discovered in Wuhan, Hubei province of China. COVID-19 virus caused six million deads in the world to date and cussed infection of more than seven million of cases in Iran (1). This infectious disease caused by the SARS-CoV-2 virus. This virus was contagious and fast-spread. Despite the aquarantine politics, SARS-CoV-2 virus caused many permanent economic and health damages in most countries. Coronaviruses are positive-sense, single- stranded enveloped RNA viruses with helical capsids that infect a wide range of hosts including humans, bats, other mammals, and birds (2). Coronaviruses are belonging to Nidovirales order, Coronaviridae family, Coronovirinae subfamily and four genera of alpha, beta, delta, and gamma. Alpha and beta coronaviruses are known as human infection agents. SARS-COV-2 virus abilities are including: high mortality number, short period of incubation, widespread transmission protocols, asymptomatic infection and affecting on most vital organs (heart, brain, lungs and ...) which have attracted the health system attention and caused neglect to the other chronic and non-communicable diseases (4). Therefore, the disease incidence, prevalence and prioritization around the world may change in the future. From the beginning of COVID-19 pandemic, some symptoms and risk-factors have been introduced to the world as the increase elements of morbidity and mortality. Studies have shown that having any kind of underlying diseases and risk factors will be effective in the COVID-19 disease severity and mortality (6). Some of these important risk factors are including of chronic kidney disease, hypertension, age, gender, obesity, obstructive pulmonary diseases, diabetes, lung diseases, cardiovascular diseases, cancer, and liver disease. Also, each risk factors have different impact in different geographic areas (7). Some factors, such as different viral load kinetics in each individual person, epidemiological history, therapeutic or pharmacological effects and immune response have some major impacts on the laboratory diagnostic results. Due to the successive mutations of the SARS-CoV-2 virus and the high incidence disease, it seems that the vaccination alone cannot prevent the COVID-19 (9). On the other hand, the World Health Organization has warned about the vaccination as the only pandemic control protocol. Therefore, the prevalence of morbidity and mortality have become the public health concerns in the world since the beginning of the COVID-19 epidemic and the vaccination. Recognizing of the risk-factors and symptoms on COVID-19 in different geographic areas can be a helpful source to prevent the mortality. Understanding risk factors can help the world to control of the coronaviruses pandemic period and similar situations in the future. Therefore, the aim of this study was to determine the risk-factors of mortality of COVID-19 patients in three cities of Khuzestan province, Iran. Methods: This research was an analytical cross-sectional study. Some details of 27963 COVID-19 patients such as clinical symptoms, individual characteristics and underlying diseases were gathered from hospitals in Abadan, Shadegan and Khorramshahr cities in Khuzestan province, Iran, from 20 February 2020 to November 2020. All the under-study population was previously investigated in terms of COVID-19 infection by the medical examinations and laboratory methods. This under-study population was categorized into three different groups such as hospitalized, outpatients and dead patients. Hospitalized patients have admitted in general or ICU (Intensive Care Unit) sector. Obtained database of COVID-19 patients was analyzed by IBM SPSS version 22.0 under regression, logistic model (u

19.
Immunol Lett ; 259: 21-23, 2023 07.
Article in English | MEDLINE | ID: covidwho-2323977

ABSTRACT

Inactivated vaccine is one of the platforms employed in COVID-19 vaccines. Inactivated vaccines have been associated with concerns of antibody-dependent enhancement (ADE) and original antigenic sin (OAS), which are related to non-neutralising or poorly neutralising antibodies against the pathogen. Since inactivated COVID-19 vaccines use whole-SARS-CoV-2 virus as the immunogen, they are expected to generate antibodies against non-spike structural proteins, which are highly conservative across variants of SARS-CoV-2. These antibodies against non-spike structural proteins have found to be largely non-neutralising or poorly neutralising in nature. Hence, inactivated COVID-19 vaccines could possibly be associated with ADE and OAS, especially as novel variants emerge. This article explores the potential concern of ADE and OAS in the context of inactivated COVID-19 vaccine, and outlines the future research directions.


Subject(s)
COVID-19 Vaccines , COVID-19 Vaccines/immunology , Antibodies, Viral/immunology , COVID-19/prevention & control , Humans
20.
J Theor Biol ; 570: 111522, 2023 08 07.
Article in English | MEDLINE | ID: covidwho-2323883

ABSTRACT

The successive emergence of SARS-CoV-2 mutations has led to an unprecedented increase in COVID-19 incidence worldwide. Currently, vaccination is considered to be the best available solution to control the ongoing COVID-19 pandemic. However, public opposition to vaccination persists in many countries, which can lead to increased COVID-19 caseloads and hence greater opportunities for vaccine-evasive mutant strains to arise. To determine the extent that public opinion regarding vaccination can induce or hamper the emergence of new variants, we develop a model that couples a compartmental disease transmission framework featuring two strains of SARS-CoV-2 with game theoretical dynamics on whether or not to vaccinate. We combine semi-stochastic and deterministic simulations to explore the effect of mutation probability, perceived cost of receiving vaccines, and perceived risks of infection on the emergence and spread of mutant SARS-CoV-2 strains. We find that decreasing the perceived costs of being vaccinated and increasing the perceived risks of infection (that is, decreasing vaccine hesitation) will decrease the possibility of vaccine-resistant mutant strains becoming established by about fourfold for intermediate mutation rates. Conversely, we find increasing vaccine hesitation to cause both higher probability of mutant strains emerging and more wild-type cases after the mutant strain has appeared. We also find that once a new variant has emerged, perceived risk of being infected by the original variant plays a much larger role than perceptions of the new variant in determining future outbreak characteristics. Furthermore, we find that rapid vaccination under non-pharmaceutical interventions is a highly effective strategy for preventing new variant emergence, due to interaction effects between non-pharmaceutical interventions and public support for vaccination. Our findings indicate that policies that combine combating vaccine-related misinformation with non-pharmaceutical interventions (such as reducing social contact) will be the most effective for avoiding the establishment of harmful new variants.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/prevention & control , Vaccination Hesitancy , Pandemics , Vaccination
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