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1.
Front Public Health ; 10: 974848, 2022.
Article in English | MEDLINE | ID: covidwho-2099265

ABSTRACT

Background: The coronavirus disease (COVID-19) pandemic, which has been ongoing for more than 2 years, has become one of the largest public health issues. Vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is one of the most important interventions to mitigate the COVID-19 pandemic. Our objective is to investigate the relationship between vaccination status and time to seroconversion. Methods: We conducted a cross-sectional observational study during the SARS-CoV-2 B.1.617.2 outbreak in Jiangsu, China. Participants who infected with the B.1.617.2 variant were enrolled. Cognitive performance, quality of life, emotional state, chest computed tomography (CT) score and seroconversion time were evaluated for each participant. Statistical analyses were performed using one-way ANOVA, univariate and multivariate regression analyses, Pearson correlation, and mediation analysis. Results: A total of 91 patients were included in the analysis, of whom 37.3, 25.3, and 37.3% were unvaccinated, partially vaccinated, and fully vaccinated, respectively. Quality of life was impaired in 30.7% of patients, especially for mental component summary (MCS) score. Vaccination status, subjective cognitive decline, and depression were risk factors for quality-of-life impairment. The chest CT score mediated the relationship of vaccination status with the MCS score, and the MCS score mediated the relationship of the chest CT score with time to seroconversion. Conclusion: Full immunization course with an inactivated vaccine effectively lowered the chest CT score and improved quality of life in hospitalized patients. Vaccination status could influence time to seroconversion by affecting CT score and MCS score indirectly. Our study emphasizes the importance of continuous efforts in encouraging a full vaccination course.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Pandemics , COVID-19 Vaccines , Seroconversion , COVID-19/prevention & control , Mental Health , Cross-Sectional Studies , Quality of Life , Tomography, X-Ray Computed , Vaccination
2.
Cureus ; 14(9): e29544, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2072222

ABSTRACT

BACKGROUND AND OBJECTIVES: India had faced a devastating second outbreak of COVID-19 infection, in which a majority of the viral sequences were found to be of the B.1.617.2 lineage (Delta-variant). While India and the world focused on vaccination, reports of vaccine-immunity evasion by the virus, termed "breakthrough cases", emerged worldwide. Our study was focused on the primary objective to identify the mutations associated with breakthrough infections SARS-CoV-2. METHODS: In our study, we extracted the SARS-CoV-2 RNA (ribonucleic acid) from reverse transcription-polymerase chain reaction (RT-PCR) positive COVID-19 patients, and 150 random samples were sent for sequencing to the Centre for Cellular & Molecular Biology, Hyderabad. Whole genome sequences of 150 SARS-CoV-2 viral samples were analyzed thoroughly. We mostly found B.1.617 and its sub-lineages in the genomic sequencing results. RESULTS AND INTERPRETATION: On further analysis of patient data, it was seen that nine patients had been vaccinated against the SARS-CoV-2 previously. These nine patients had B.1.617/B.1 or A strains, and all of them had similar genomic variations in spike proteins as well as non-structural proteins (NSPs). The mutations seen in these sequences in the Spike (S), NSPs, and open reading frame (ORF) regions would have produced amino acid changes known to improve viral replication, confer drug resistance, influence host-cell interaction, and lead to antigenic drift. CONCLUSIONS: Increased virulence culminating in vaccine immunity evasion may be inferred from these specific mutations. Our study adds to the growing body of evidence linking rapidly emerging mutations in the S (Spike) and ORF genes of the SARS-CoV-2 genome to immune evasion.

3.
J Infect Dis ; 226(8): 1418-1427, 2022 Oct 17.
Article in English | MEDLINE | ID: covidwho-2070119

ABSTRACT

This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive correlation between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA in wastewater samples and clinical cases (r = 0.7749, P < .0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven third wave, was significantly higher than during the Omicron-driven fourth wave. Whole-genome sequencing confirmed presence of Omicron lineage defining mutations in wastewater with the first occurrence reported 23 November 2021 (BA.1 predominant). The variant spread rapidly, with prevalence of Omicron-positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sublineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. These findings demonstrate the value of wastewater-based epidemiology to monitor the spatiotemporal spread and potential origin of new Omicron sublineages.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Humans , Prevalence , RNA, Viral/genetics , SARS-CoV-2/genetics , South Africa/epidemiology , Waste Water
4.
American Journal of Translational Research ; 14(9):6375-6381, 2022.
Article in English | EMBASE | ID: covidwho-2058689

ABSTRACT

From the start of the coronavirus disease 2019 (COVID-19) pandemic in 2020, COVID-19 infection in the pediatric population has aroused great attention. This article presents dynamic epidemiological characteristics of COVID-19 infection in pediatric patients from January 2020 to March 2022 in China. These data contributed essential insights and shared experience on the management of COVID-19 in children. To date, the unvaccinated population and events with children need more attention. Copyright © 2022 E-Century Publishing Corporation. All rights reserved.

5.
Clin Infect Dis ; 75(Supplement_2): S298-S302, 2022 Oct 03.
Article in English | MEDLINE | ID: covidwho-2051358

ABSTRACT

We compared the mortality risk in Alaska among persons with symptomatic coronavirus disease 2019 (COVID-19) during the period the Delta variant was predominant to the risk among those with symptomatic COVID-19 before Delta predominance. The Delta period was associated with 2.43-fold higher odds of death. Unvaccinated persons were 4.49 times more likely to die than fully vaccinated persons.


Subject(s)
COVID-19 , SARS-CoV-2 , Alaska/epidemiology , Humans
6.
Virol Sin ; 2022 Sep 28.
Article in English | MEDLINE | ID: covidwho-2050059

ABSTRACT

During the two-year pandemic of coronavirus disease 2019 (COVID-19), its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been evolving. SARS-CoV-2 Delta, a variant of concern, has become the dominant circulating strain worldwide within just a few months. Here, we performed a comprehensive analysis of a new B.1.617.2 Delta strain (Delta630) compared with the early WIV04 strain (WIV04) in vitro and in vivo, in terms of replication, infectivity, pathogenicity, and transmission in hamsters. When inoculated intranasally, Delta630 led to more pronounced weight loss and more severe disease in hamsters. Moreover, 40% mortality occurred about one week after infection with 104 PFU of Delta630, whereas no deaths occurred even after infection with 105 PFU of WIV04 or other strains belonging to the Delta variant. Moreover, Delta630 outgrew over WIV04 in the competitive aerosol transmission experiment. Taken together, the Delta630 strain showed increased replication ability, pathogenicity, and transmissibility over WIV04 in hamsters. To our knowledge, this is the first SARS-CoV-2 strain that causes death in a hamster model, which could be an asset for the efficacy evaluation of vaccines and antivirals against infections of SARS-CoV-2 Delta strains. The underlying molecular mechanisms of increased virulence and transmission await further analysis.

7.
Public Health Rep ; : 333549221123584, 2022 Sep 21.
Article in English | MEDLINE | ID: covidwho-2038484

ABSTRACT

OBJECTIVES: In summer 2021, the number of COVID-19-associated hospitalizations in the United States increased with the surge of the SARS-CoV-2 Delta variant. We assessed how COVID-19 vaccine initiation and dose completion changed during the Delta variant surge, based on jurisdictional vaccination coverage before the surge. METHODS: We analyzed COVID-19 vaccination data reported to the Centers for Disease Control and Prevention. We classified jurisdictions (50 states and the District of Columbia) into quartiles ranging from high to low first-dose vaccination coverage among people aged ≥12 years as of June 30, 2021. We calculated first-dose vaccination coverage as of June 30 and October 31, 2021, and stratified coverage by quartile, age (12-17, 18-64, ≥65 years), and sex. We assessed dose completion among those who initiated a 2-dose vaccine series. RESULTS: Of 51 jurisdictions, 15 reached at least 70% vaccination coverage before the Delta variant surge (ie, as of June 30, 2021), while 35 reached that goal as of October 31, 2021. Jurisdictions in the lowest quartile of vaccination coverage (44.9%-54.9%) had the greatest absolute (9.7%-17.9%) and relative (18.1%-39.8%) percentage increase in vaccination coverage during July 1-October 31, 2021. Of those who received the first dose during this period across all jurisdictions, nearly 1 in 5 missed the second dose. CONCLUSIONS: Although COVID-19 vaccination initiation increased during July 1-October 31, 2021, in jurisdictions in the lowest quartile of vaccination coverage, coverage remained below that of jurisdictions in the highest quartile of vaccination coverage before the Delta variant surge. Efforts are needed to improve access to and increase confidence in COVID-19 vaccines, especially in low-coverage areas.

8.
Ann Med ; 54(1): 2391-2401, 2022 12.
Article in English | MEDLINE | ID: covidwho-2004870

ABSTRACT

PURPOSE: To analyse the clinical symptoms, laboratory examinations and chest CT findings of children infected by the B.1.617.2 variant of COVID-19 and to compare the differences between clinical subtypes. METHODS: Fifty-three children (28 males, 25 females; age ranging from 4 months to 17 years) were included with B.1.617.2 variant infection in Nanjing, China, from July 21 to August 12 2021. Clinical data from patients were collected and analysed in groups of mild and common types. Imaging data were divided into three stages for evaluation: early, intermediate and late stages. RESULTS: In our study, fever (53%), cough (34%) and pharyngeal discomfort (28%) were the main symptoms. There were no differences in clinical symptoms between the mild and common type. The most common laboratory test items outside the normal range were decreased mean corpuscular volume (68%), lymphocyte percentage (64% elevated and 2% decreased) and decreased serum alkaline phosphatase concentration (66%). The differences in haemoglobin and monocyte percentages between the mild and common types were statistically significant (p = .037 and .033, respectively). No influencing factor was statistically significant in the regression analysis of both symptoms and clinical subtypes. The main CT findings were ground-glass opacity and consolidation located in the periphery and bilateral multilobed involvement. The mean CT score was 1.6. CT score correlated with packet cell volume, haemoglobin, mean erythrocyte volume, mean platelet volume and platelet distribution width. CONCLUSION: The pathogenetic condition of children with B.1.617.2 variant infection is mild. Although there were intergroup differences in some blood cell analyses, T-lymphocyte counts, and comprehensive biochemical indicators, no factors had a significant effect on clinical typing and the presence or absence of symptoms. CT findings and CT scores reflect disease stage and pathological changes and correlate moderately with laboratory tests, making them of good value for disease diagnosis and monitoring.Key MessagesPaediatric patients infected with B.1.617.2 variant have a milder clinical and imaging presentation than adults and are similar to the prototype infection.CT findings and scores which reflect disease stages and pathological changes.There is a correlation between chest CT and laboratory tests, which can be useful for the diagnosis and follow-up of the disease.


Subject(s)
COVID-19 , Adult , COVID-19/diagnostic imaging , Child , Female , Fever , Humans , Lung/diagnostic imaging , Male , Retrospective Studies , SARS-CoV-2 , Tomography, X-Ray Computed
9.
Vaccines (Basel) ; 10(6)2022 Jun 17.
Article in English | MEDLINE | ID: covidwho-1988035

ABSTRACT

Background: The emergence of new SARS-CoV-2 variants, which evade immunity, has raised the urgent need for multiple vaccine booster doses for vulnerable populations. In this study, we aimed to estimate the BNT162b2 booster effectiveness against the spread of coronavirus variants in a hemodialysis population. Methods: We compared humoral and cell-mediated immunity in 100 dialysis patients and 66 age-matched volunteers, before and 2-3 weeks following the first booster vaccine dose. Participants were assessed for anti-spike (RBD) antibody titer, neutralizing antibodies against B.1.617.2 (Delta) and B.1.1.529 (Omicron) variants, spike-specific T-cell responses by FACS and infection outbreak after the first and second booster. Results: Anti-spike antibody titer was significantly increased following the booster, with reduced humoral and cellular response in the dialysis patients. Neutralizing antibody levels increased significantly after the booster dose, with an inferior effect (≤2 fold) against Omicron compared with the Delta variant. Furthermore, CD4+ and CD8+ T-cell activation by Delta spike protein was preserved in 70% of PBMCs from the dialysis patients. A second booster dose tended to reduce breakthrough infections in the dialysis patients. Conclusions: Until the release of an updated vaccine, BNT162b2 booster doses will improve the humoral and cell-mediated immunity against variants. These findings support the importance of repetitive booster doses for hemodialysis patients.

10.
Process Biochem ; 121: 656-660, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-1977736

ABSTRACT

The B.1.617.2 (Delta) variant of concern is causing a new wave of infections in many countries. In order to better understand the changes of the SARS-CoV-2 mutation at the genetic level, we selected six mutations in the S region of the Delta variant compared with the native SARS-CoV-2 and get the conductance information of these six short RNA oligonucleotides groups by construct RNA: DNA hybrids. The electronic characteristics are investigated by the combination of density functional theory and non-equilibrium Green's function formulation with decoherence. We found that conductance is very sensitive to small changes in virus sequence. Among the 6 mutations in the Delta S region, D950N shows the largest change in relative conductance, reaching a surprising 4104.75%. These results provide new insights into the Delta variant from the perspective of its electrical properties. This may be a new method to distinguish virus variation and possess great research prospects.

11.
IJID Reg ; 3: 106-113, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1899827

ABSTRACT

Background: : SARS-CoV-2 variants have been emerging and are shown to increase transmissibility, pathogenicity, and decreased vaccine efficacies. The objective of this study was to determine the distribution, prevalence, and dynamics of SARS-CoV-2 variants circulating in Brazzaville, the Republic of Congo (ROC). Methods: : Between December 2020 and July 2021, a total of n=600 oropharyngeal specimens collected in the community were tested for COVID-19. Of the samples tested, 317 (53%) were SARS-CoV-2 positive. All samples that had a threshold of Ct <30 (n=182) were sequenced by next-generation sequencing (NGS), and all complete sequenced genomes were submitted to GISAID; lineages were assigned using pangolin nomenclature and a phylogenetic tree was reconstructed. In addition, the global prevalence of the predominant lineages was analysed using data from GISAID and Outbreak databases. Results: : A total of 15 lineages circulated with B.1.214.2 (26%), B.1.214.1 (19%) and B.1.620 (18%) being predominant. The variants of concern (VOC) alpha (B.1.1.7) (6%) and for the first time in June delta (B.1.617.2) (4%) were observed. In addition, the B.1.214.1 lineage first reported from ROC was observed to be spreading locally and regionally. Phylogenetic analysis suggests that the B.1.620 variant (VUM) under observation may have originated from either Cameroon or the Central African Republic. SARS-CoV-2 lineages were heterogeneous, with the densely populated districts of Poto-Poto and Moungali likely the epicenter of spread. Conclusion: : Longitudinal monitoring and molecular surveillance across time and space are critical to understanding viral phylodynamics, which could have important implications for transmissibility and impact infection prevention and control measures.

12.
World J Pediatr ; 18(5): 343-349, 2022 05.
Article in English | MEDLINE | ID: covidwho-1739438

ABSTRACT

BACKGROUND: The aim of this study was to analyze the clinical characteristics of 66 pediatric patients with B.1.617.2 (Delta) variant of coronavirus disease 2019 (COVID-19). METHODS: Sixty-six pediatric patients with B.1.617.2 (Delta) variant of COVID-19 admitted to the hospital from July to August 2021 were classified into mild (n = 41) and moderate groups (n = 25). Clinical characteristics, laboratory data and dynamic trends in different time periods were analyzed retrospectively. RESULTS: There were no statistically significant differences in age, gender ratios and clinical symptoms between the mild group and the moderate group. All the patients in the moderate group had clusters of onsets, and the incubation period was shorter than that of the mild group. Within 24 hours of admission, the levels of erythrocyte sedimentation rate, cardiac troponin I, D-dimer in the moderate group were higher than that in the mild group (P < 0.05). The titers of immunoglobulin (Ig) G and IgM antibodies gradually increased after disease onset. Thirty-five (53.03%) children were tested positive for antibodies in 4-12 days. IgG increased gradually, while IgM decreased obviously in about 15 days after disease onset. The cycle threshold values of open reading frame 1ab and nucleocapsid protein gene in the severe acute respiratory syndrome coronavirus 2 genomes increased gradually on the 3rd, 6th, 9th, and 12th days after disease onset, compared with those in day 0. CONCLUSIONS: The symptoms of children with B.1.617.2 (Delta) variant of COVID-19 were mild. The description and analysis of the clinical characteristics and laboratory data can help medical staff to evaluate the condition of children with COVID-19 and to accumulate more clinical experience.


Subject(s)
COVID-19 , Child , Humans , Immunoglobulin G , Immunoglobulin M , Retrospective Studies , SARS-CoV-2
13.
Informatics in Medicine Unlocked ; : 100900, 2022.
Article in English | ScienceDirect | ID: covidwho-1712708

ABSTRACT

Background and objective The B.1.617.2 known as the Delta-variant harbors diverse Spike-mutations with developed transmissibility and immune-evasion more than wild/D614G/N501Y variants. The Delta-variant claimed comparatively a large number of lives globally. In the present study, the binding-affinities of these variants’ spikes to the human lung-ACE2 were investigated. Further, a certain portion of the spike-protein with a desired mutation was tested in-silico to block the ACE2. Methods Structure of spike-variants were retrieved from PDB/GISAID and used for homology-modeling (SWISS-MODEL). A different combination of spike-ACE2 binding 1:1 or competitive blind-docking was performed using the Haddock 2.4 web-server. Eventually, two cut-segments (84 amino-acid of wild-spike, 432–516 Cut1) and its mutant T500S;Cut 2 were screened (Swiss-model Expasy-server) as blocker/inhibitor of all spike-variants (PyMOL-V2.2.2). Results It is shown that the stability and energy of the Delta binding-affinity to ACE2 is far more than others. The number H-bonding (5), their lengths (1.7 Å-2.8 Å) and energy, Van-der-Walls energy, Haddock-score were highly favorable for more stable-binding of Delta-RBD to ACE2. The Ramachandran-plot (Zlab/UMassMed Bioinfo) data supports this. We observed the best Haddock score as −120.8±2.6 for Delta with Van-der-Walls and electrostatic-energy as −62.9 and −208.7, respectively. The highest binding-affinity (ΔG) was −10.7 kcal/mol. Its THR500 and GLN506 strongly bind with the LYS353 of ACE2. The Cut1 and its mutant T500S completely blocked Delta-spike binding to ACE2 with ΔG -8.4 and −10.6 kcal/mol, respectively. But during the comparison between 2 Cuts, Cut1 showed better results. Conclusions Fractioned spike-protein from the conserved Receptor-Binding-Domain (RBD) could universally block the virus at entry-level, thus completely protecting any intercellular metabolism. Bioinformatics is an emerging field for screening of some drug/therapeutic targets from numerous options, minimizing time and expenses.

14.
J Infect Dis ; 225(11): 1909-1914, 2022 06 01.
Article in English | MEDLINE | ID: covidwho-1606029

ABSTRACT

The wide spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with phenotypes impacting transmission and antibody sensitivity necessitates investigation of immune responses to different spike protein versions. Here, we compare neutralization of variants of concern, including B.1.617.2 (delta) and B.1.1.529 (omicron), in sera from individuals exposed to variant infection, vaccination, or both. We demonstrate that neutralizing antibody responses are strongest against variants sharing certain spike mutations with the immunizing exposure, and exposure to multiple spike variants increases breadth of variant cross-neutralization. These findings contribute to understanding relationships between exposures and antibody responses and may inform booster vaccination strategies.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Neutralizing , Antibodies, Viral , Antibody Formation , Humans , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
15.
One Health ; 13: 100352, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1531692

ABSTRACT

In the frames of a One Health strategy, i.e. a strategy should be able to predict susceptibility to infection in both humans and animals, developing a SARS-CoV-2 mutation tracking system is a goal. We observed that the phylogenetic proximity of vertebrate ACE2 receptors does not affect the binding energy for the viral spike protein. However, all viral variants seem to bind ACE2 better in many animals than in humans. Moreover, two observations highlight that the evolution of the virus started at the beginning of 2020 and culminated with the appearance of the variants. First, codon usage analysis shows that the B.1.1.7 (alpha), B.1.351 (beta) and B.1.617.2 (delta) variants, similar in the use of codons, are also similar to a virus sampled in January 2020. Second, the host-specific D614G mutation becomes prevalent starting from March 2020. Overall, we show that SARS-CoV-2 undergoes a process of molecular evolution that begins with the optimization of codons followed by the functional optimization of the spike protein.

16.
World J Pediatr ; 18(1): 37-42, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1527517

ABSTRACT

BACKGROUND: This study aimed to explore the imaging characteristics, diversity and changing trend in CT scans of pediatric patients infected with Delta-variant strain by studying imaging features of children infected with Delta and comparing the results to those of children with original COVID-19. METHODS: A retrospective, comparative analysis of initial chest CT manifestations between 63 pediatric patients infected with Delta variant in 2021 and 23 pediatric patients with COVID-19 in 2020 was conducted. Corresponding imaging features were analyzed. In addition, the changing trend in imaging features of COVID-19 Delta-variant cases were explored by evaluating the initial and follow-up CT scans. RESULTS: Among 63 children with Delta-variant COVID-19 in 2021, 34 (53.9%) showed positive chest CT presentation; and their CT score (1.10 ± 1.41) was significantly lower than that in 2020 (2.56 ± 3.5) (P = 0.0073). Lesion distribution: lung lesions of Delta cases appear mainly in the lower lungs on both sides. Most children had single lobe involvement (18 cases, 52.9%), 14 (41.2%) in the right lung alone, and 14 (41.2%) in both lungs. A majority of Delta cases displayed initially ground glass (23 cases, 67.6%) and nodular shadows (13 cases, 38.2%) in the first CT scan, with few extrapulmonary manifestations. The 34 children with abnormal chest CT for the first time have a total of 92 chest CT examinations. These children showed a statistically significant difference between the 0-3 day group and the 4-7 day group (P = 0.0392) and a significant difference between the 4-7 day group and the more than 8 days group (P = 0.0003). CONCLUSIONS: The early manifestations of COVID-19 in children with abnormal imaging are mostly small subpleural nodular ground glass opacity. The changes on the Delta-variant COVID-19 chest CT were milder than the original strain. The lesions reached a peak on CT in 4-7 days and quickly improved and absorbed after a week. Dynamic CT re-examination can achieve a good prognosis.


Subject(s)
COVID-19 , Child , Humans , Lung/diagnostic imaging , Retrospective Studies , SARS-CoV-2 , Tomography, X-Ray Computed
17.
Viruses ; 13(10)2021 10 06.
Article in English | MEDLINE | ID: covidwho-1463833

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved rapidly, leading to viral lineages characterized by multiple mutations in the spike protein, which could potentially confer to the virus the ability to avoid the vaccine-induced immune response, making the vaccines less effective or ineffective. Here, we initially evaluated the neutralization capabilities in vitro by serum neutralization (SN) of six serum samples collected from recipients of the BNT162b2 vaccine against 11 SARS-CoV-2 isolates belonging to the major SARS-CoV-2 lineages that had been circulating in Italy. Then, we considered 30 additional serum samples by SN assay against the dominant B.1.617.2 (Delta) variant. A B.1 lineage isolate was used as a reference. In the first analysis, significant differences when compared with the reference strain (p > 0.05) were not evidenced; instead, when the panel of 30 sera was tested against the B.1.617.2 (Delta) variant, a significant (p = 0.0015) 2.38-fold reduction in neutralizing titres compared with the reference after the first vaccine dose was demonstrated. After the second vaccine dose, the reduction was not significant (p = 0.1835). This study highlights that the BNT162b2 vaccine stimulates a humoral response able to neutralize all tested SARS-CoV-2 variants, thus suggesting a prominent role in mitigating the impact of the SARS-CoV-2 pandemic in real-world conditions. Long-term follow-up is currently ongoing.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19 Vaccines/immunology , COVID-19/therapy , SARS-CoV-2/immunology , Animals , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , Cell Line , Chlorocebus aethiops , Humans , Immunization, Passive/methods , Italy , Neutralization Tests , SARS-CoV-2/isolation & purification , Vero Cells
18.
Microorganisms ; 9(9)2021 Sep 16.
Article in English | MEDLINE | ID: covidwho-1410330

ABSTRACT

Rapid antigen tests (RATs) are an integral part of SARS-CoV-2 containment strategies. As emerging variants of concern (VOCs) displace the initially circulating strains, it is crucial that RATs do not fail to detect these new variants. In this study, four RATs for nasal swab testing were investigated using cultured strains of B.1.1 (non-VOC), B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta). Based on dilution series in cell culture medium and pooled saliva, the limit of detection of these RATs was determined in a laboratory setting. Further investigations on cross-reactivity were conducted using recombinant N-protein from seasonal human coronaviruses (hCoVs). RATs evaluated showed an overall comparable performance with cultured strains of the non-VOC B.1.1 and the VOCs Alpha, Beta, Gamma, and Delta. No cross-reactivity was detected with recombinant N-protein of the hCoV strains HKU1, OC43, NL63, and 229E. A continuous evaluation of SARS-CoV-2 RAT performance is required, especially with regard to evolving mutations. Moreover, cross-reactivity and interference with pathogens and other substances on the test performance of RATs should be consistently investigated to ensure suitability in the context of SARS-CoV-2 containment.

19.
Virol J ; 18(1): 178, 2021 08 30.
Article in English | MEDLINE | ID: covidwho-1379795

ABSTRACT

BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 pandemic, has infected more than 179 million people worldwide. Testing of infected individuals is crucial for identification and isolation, thereby preventing further spread of the disease. Presently, Taqman™ Reverse Transcription Real Time PCR is considered gold standard, and is the most common technique used for molecular testing of COVID-19, though it requires sophisticated equipments, expertise and is also relatively expensive. OBJECTIVE: Development and optimization of an alternate molecular testing method for the diagnosis of COVID-19, through a two step Reverse Transcription Loop-mediated isothermal AMPlification (RT-LAMP). RESULTS: Primers for LAMP were carefully designed for discrimination from other closely related human pathogenic coronaviruses. Care was also taken that primer binding sites are present in conserved regions of SARS-CoV2. Our analysis shows that the primer binding sites are well conserved in all the variants of concern (VOC) and variants of interest (VOI), notified by World Health Organization (WHO). These lineages include B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427/B.1.429, P.2, B.1.525, P.3, B.1.526 and B.1.617.1. Various DNA polymerases with strand displacement activity were evaluated and conditions were optimized for LAMP amplification and visualization. Different LAMP primer sets were also evaluated using synthetic templates as well as patient samples. CONCLUSION: In a double blind study, the RT-LAMP assay was validated on more than 150 patient samples at two different sites. The RT-LAMP assay appeared to be 89.2% accurate when compared to the Taqman™ rt-RT-PCR assay.


Subject(s)
COVID-19 Testing/methods , COVID-19/virology , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , SARS-CoV-2/genetics , COVID-19/diagnosis , Humans , Reverse Transcription , SARS-CoV-2/isolation & purification , SARS-CoV-2/physiology , Sensitivity and Specificity
20.
Euro Surveill ; 26(26)2021 07.
Article in English | MEDLINE | ID: covidwho-1295604

ABSTRACT

SARS-CoV-2 Delta (B.1.617.2) variant of concern (VOC) and other VOCs are spreading in Europe. Micro-neutralisation assays with sera obtained after Comirnaty (BNT162b2, BioNTech/Pfizer) vaccination in 36 healthcare workers (31 female) demonstrated significant fold change reduction in neutralising titres compared with the original virus: Gamma (P.1) 2.3, Beta (B.1.351) 10.4, Delta 2.1 and 2.6. The reduction of the Alpha (B.1.1.7) variant was not significant. Despite being lower, remaining neutralisation capacity conferred by Comirnaty against Delta and other VOCs is probably protective.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Vaccines , Europe , Female , Health Personnel , Humans , Israel , Vaccination
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