Prevalence of SARS-CoV-2 Antibodies after First 6 Months of COVID-19 Pandemic, Portugal.
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ABSTRACT:
SUBMITTER: Canto E Castro L
PROVIDER: S-EPMC8544986 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Proteomic Ig-SEQ identification of SARS-COV-2 specific antibodies from serum of two convalescent patients during the first wave of the COVID-19 pandemic. Total IgG was isolated from serum, digested with IdeS protease to generate F(ab)2 fragments, and subjected to antigen affinity chromatography using agarose beads coupled with SARS-COV-2 spike protein. Purified F(ab)2 fragments were reduced, alkylated, and digested with trypsin prior to LC-MSMS analysis on an Orbitrap Fusion Lumos mass spectrometer. Resulting peptide IDs were used to identify IgG clonotypes in antigen-specific and flow-through fractions.
2024-01-26 | PXD046829 | Pride
Project description:In comparison to other European countries, during the first months of the COVID-19 pandemic, Poland reported a relatively low number of confirmed cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. To estimate the scale of the pandemic in Poland, a serosurvey of antibodies against SARS-CoV-2 was performed after the first wave of COVID-19 in Europe (March-May 2020). Within this study, we collected samples from 28 July to 24 September 2020 and, based on the ELISA results, we found that 1.67% (25/1500, 95% CI 1.13-2.45) of the Poznan (Poland) metropolitan area's population had antibodies against SARS-CoV-2 after the first wave of COVID-19. However, the presence of anti-SARS-CoV-2 IgG antibodies was confirmed with immunoblotting in 56% (14/25) samples, which finally resulted in a decrease in seroprevalence, i.e., 0.93% (14/1500, 95% CI 0.56-1.56). The positive anti-SARS-CoV-2 IgG results were associated with age, occupation involving constant contact with people, travelling abroad, non-compliance with epidemiological recommendations and direct contact with the novel coronavirus. Our findings confirm the low SARS-CoV-2 incidence in Poland and imply that the population had little herd immunity heading into the second and third wave of the pandemic, and therefore, that herd immunity contributed little to preventing the high numbers of SARS-CoV-2 infections and COVID-19-related deaths in Poland during these subsequent waves.
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Project description:ObjectivesStudies that measure the prevalence of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ('seroprevalence') are essential to understand population exposure to SARS-CoV-2 among symptomatic and asymptomatic individuals. We aimed to measure seroprevalence in the Scottish population over the course of the COVID-19 pandemic - from before the first recorded case in Scotland through to the second pandemic wave.Study designThe study design of this study is serial cross sectional.MethodsWe tested 41,477 residual samples retrieved from primary and antenatal care settings across Scotland for SARS-CoV-2 antibodies over a 12-month period from December 2019-December 2020 (before rollout of COVID-19 vaccination). Five-weekly rolling seroprevalence estimates were adjusted for the sensitivity and specificity of the assays and weighted to reference populations. Temporal trends in seroprevalence estimates and weekly SARS-CoV-2 notifications were compared.ResultsFive-weekly rolling seroprevalence rates were 0% until the end of March, when they increased contemporaneously with the first pandemic wave. Seroprevalence rates remained stable through the summer (range: 3%-5%) during a period of social restrictions, after which they increased concurrently with the second wave, reaching 9.6% (95% confidence interval [CI]: 8.4%-10.8%) in the week beginning 28th December in 2020. Seroprevalence rates were lower in rural vs. urban areas (adjusted odds ratio [AOR]: 0.70, 95% CI: 0.61-0.79) and among individuals aged 20-39 years and 60 years and older (AOR: 0.74, 95% CI: 0.64-0.86; AOR: 0.80, 95% CI: 0.69-0.91, respectively) relative to those aged 0-19 years.ConclusionsAfter two waves of the COVID-19 pandemic, less than one in ten individuals in the Scottish population had antibodies to SARS-CoV-2. Seroprevalence may underestimate the true population exposure as a result of waning antibodies among individuals who were infected early in the first wave.
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Project description:Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates in the United States and elsewhere. To address this, we analyzed seropositivity in 9089 adults in the United States who had not been diagnosed previously with COVID-19. Individuals with characteristics that reflected the U.S. population (n = 27,716) were selected by quota sampling from 462,949 volunteers. Enrolled participants (n = 11,382) provided medical, geographic, demographic, and socioeconomic information and dried blood samples. Survey questions coincident with the Behavioral Risk Factor Surveillance System survey, a large probability-based national survey, were used to adjust for selection bias. Most blood samples (88.7%) were collected between 10 May and 31 July 2020 and were processed using ELISA to measure seropositivity (IgG and IgM antibodies against SARS-CoV-2 spike protein and the spike protein receptor binding domain). The overall weighted undiagnosed seropositivity estimate was 4.6% (95% CI, 2.6 to 6.5%), with race, age, sex, ethnicity, and urban/rural subgroup estimates ranging from 1.1% to 14.2%. The highest seropositivity estimates were in African American participants; younger, female, and Hispanic participants; and residents of urban centers. These data indicate that there were 4.8 undiagnosed SARS-CoV-2 infections for every diagnosed case of COVID-19, and an estimated 16.8 million infections were undiagnosed by mid-July 2020 in the United States.
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Project description:To evaluate the gene expression profiling of peripheral leukocytes in different outcomes of SARS-CoV-2 infections, whole blood samples were collected from individuals with positive SARS-CoV-2 nasopharyngeal swab by RT-PCR (54 patients) and healthy uninfected individuals (12 volunteers). Infected patients were classified into mild, moderate, severe and critical groups according to a modified statement in the Novel Coronavirus Pneumonia Diagnosis and Treatment Guideline. Blood were collected into EDTA tubes and the buffy coat samples were stored in TRIzol reagent at -80 °C until use for RNA extraction. Affymetrix Clariom S array was used to perform the high-throughput gene expression profiling. Microarray analyses were performed using APT Affymetrix software, R packages and Bioconductor libraries. This systemic view of SARS-CoV-2 infections through blood transcriptomics will foster the understanding about molecular mechanisms and immunopathological processes involved in COVID-19 disease and its different outcomes.
2022-04-29 | E-MTAB-11240 | biostudies-arrayexpress
Project description:A cluster of pneumonia (COVID-19) cases have been found in Wuhan China in late December, 2019, and subsequently, a novel coronavirus with a positive stranded RNA was identified to be the aetiological virus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2), which has a phylogenetic similarity to severe acute respiratory syndrome coronavirus (SARS-CoV). SARS-CoV-2 transmits mainly through droplets and close contact and the elder or people with chronic diseases are high-risk population. People affected by SARS-CoV-2 can be asymptomatic, which brings about more difficulties to control the transmission. COVID-19 has become pandemic rapidly after onset, and so far the infected people have been above 2 000 000 and more than 130 000 died worldwide according to COVID-19 situation dashboard of World Health Organization (https://covid19.who.int). Here, we summarized the current known knowledge regarding epidemiological, pathogenesis, pathology, clinical features, comorbidities and treatment of COVID-19/ SARS-CoV-2 as reference for the prevention and control COVID-19.
| S-EPMC7264656 | biostudies-literature
Project description:Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein-protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein-protein and protein-nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
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Project description:BackgroundCare facilities are particularly challenged by the COVID-19 pandemic. Besides others this includes human and structural resources.ObjectiveThis cross-sectional study evaluated the occurrence of infections, psychosocial stress and the different strategies to handle the COVID-19 pandemic in care facilities.Material and methodsData collection took place in 7 care facilities in Baden-Württemberg, Germany between 17 July and 25 August 2020. This included a SARS-CoV‑2 PCR and antibody testing and a questionnaire for residents and staff. Care facilities were questioned on interventions and preventive measures taken.ResultsOut of 829 SARS-CoV‑2 PCR tests all remained negative. Only 2 asymptomatic subjects had detectable SARS-CoV‑2 antibodies. All subjects (n = 6) with a history of positive PCR had no detectable antibodies. Healthcare workers were mainly worried about infecting family, friends and especially residents (54.4%) with less fear to infect themselves (27.2%). Individual stress caused by the COVID-19 pandemic: 17.1% exhaustion, 16% financial burden and 13.1% sleeping disorders. Coping strategies included a moderate increase of harmful behavior (+3.3% alcohol, +4.3% nicotine). This was relevantly more important in staff aged under 35 years (+13% alcohol, +12.7% nicotine). Women reported a 2.4% increased use of medication, 49.8% of respondents reduced their social contacts, 76.8% changed their individual hygiene behavior. Care facilities felt prepared to a limited extent for the challenges faced by the pandemic.ConclusionEven with a low prevalence of infections at the time of the survey the COVID-19 pandemic challenged care facilities at multiple levels. This should result in better preventive management and coping strategies.
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Project description:SARS-CoV-2, the causal agent of COVID 19, is a new human pathogen that appeared in Wuhan, late December 2019. SARS-CoV-2 is a positive sense RNA virus, having four structural and six accessory proteins including that encoded by ORF8 gene known to be one of the most hypervariable and rapidly evolving genes. Thus, global characterization of mutations in this gene is important for pathogenicity and diagnostics. 240 different nonsynonymous mutations and 2 deletions were identified in 45,400 ORF8 nucleotide sequences during six months pandemic with about half of these variants were deleterious for ORF8, and the quarter of them were located in conserved amino acids. Genetic diversity analysis showed two main regions that harbor L84S and S24L. L84S is by far the most predominant mutation, followed by S24L that appeared first in USA. Phylogenetic analysis of ORF8 variants revealed the appearance of small clades with that of L84S being closer to bats. This is the first study that revealed the global nonsynonymous mutations in ORF8 from January to June 2020.
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