Detection of SARS-CoV-2 in two cats during the second wave of the COVID-19 pandemic in France.
Ontology highlight
ABSTRACT:
SUBMITTER: Fritz M
PROVIDER: S-EPMC8661769 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Against the backdrop of the second wave of COVID-19 pandemic in India that started in March 2021, we have monitored the spike (S) protein mutations in all the reported (GISAID portal) whole-genome sequences of SARS-CoV-2 circulating in India from 1 January 2021 to 31 August 2021. In the 43,102 SARS-CoV-2 genomic sequences analysed, we have identified 24,260 amino acid mutations in the S protein, based on which 265 Pango lineages could be categorized. The dominant lineage in most of the 28 states of India and its 8 union territories was B.1.617.2 (the delta variant). However, the states Madhya Pradesh, Jammu & Kashmir, and Punjab had B.1.1.7 (alpha variant) as the major lineage, while the Himachal Pradesh state reported B.1.36 as the dominating lineage. A detailed analysis of various domains of S protein was carried out for detecting mutations having a prevalence of >1%; 70, 18, 7, 3, 9, 4, and 1 (N = 112) such mutations were observed in the N-terminal domain, receptor binding domain, C -terminal domain, fusion peptide region, heptapeptide repeat (HR)-1 domains, signal peptide domain, and transmembrane region, respectively. However, no mutations were recorded in the HR-2 and cytoplasmic domains of the S protein. Interestingly, 13.39% (N = 15) of these mutations were reported to increase the infectivity and pathogenicity of the virus; 2% (N = 3) were known to be vaccine breakthrough mutations, and 0.89% (N = 1) were known to escape neutralizing antibodies. The biological significance of 82% (N = 92) of the reported mutations is yet unknown. As SARS-CoV-2 variants are emerging rapidly, it is critical to continuously monitor local viral mutations to understand national trends of virus circulation. This can tremendously help in designing better preventive regimens in the country, and avoid vaccine breakthrough infections.
| S-EPMC9115369 | biostudies-literature
Project description:BackgroundThe interplay between age and symptoms intensity on antibody response to SARS-CoV-2 infection has not been studied in a general population setting.MethodsWe explored the serologic profile of anti-SARS-CoV-2 antibodies after the first wave of the pandemic, by assessing IgG against the spike protein (ELISA-S), IgG against the nucleocapsid protein (ELISA-NP) and neutralizing antibodies (SN) in 82,126 adults from a French population-based multi-cohort study.ResultsELISA-S positivity was increased in 30- to 49-year-old adults (8.5%) compared to other age groups (5.6% in 20- to 29-year-olds, 2.8% in ≥ 50-year-olds). In the 3681 ELISA-S positive participants, ELISA-NP and SN positivity exhibited a U-shaped relationship with age, with a lower rate in 30- to 49-year-old adults, and was strongly associated with COVID-19-like symptoms.ConclusionOur study confirms the independent role of age and symptoms on the serologic profile of anti-SARS-CoV-2 antibodies, but the non-linear relationship with age deserves further investigation.
| S-EPMC8614216 | biostudies-literature
Project description:We conducted a severe acute respiratory syndrome coronavirus 2 antibody seroprevalence study among >2,000 domestic cats from 4 countries during the first coronavirus disease wave in Europe. We found 4.4% seroprevalence using a virus neutralization test and 4.3% using a receptor-binding domain ELISA, demonstrating probable human-to-cat transmission.
| S-EPMC8632155 | biostudies-literature
Project description:ObjectivesStrasbourg University Hospital faced an important COVID-19 first wave from early March 2020. We performed a longitudinal prospective cohort study to describe clinical and virological data, exposure history to COVID-19, and adherence to strict hygiene standards during the first pandemic wave in 1497 workers undergoing a SARS-CoV-2 serological test at our hospital, with a follow up of serology result three months later.Patients and methodsA total of 1497 patients were enrolled from April 6 to May 7, 2020. Antibody response to SARS-CoV-2 was measured, and COVID-19 exposure routes were analyzed according to SARS-CoV-2 serological status.ResultsA total of 515 patients (34.4%) were seropositive, mainly medical students (13.2%) and assistant nurses (12.0%). A history of COVID-19 exposure in a professional and/or private setting was mentioned by 83.1% of seropositive subjects (P<0.05; odds ratio [OR]: 2.5; 95% confidence interval [CI]: 1.8-3.4). COVID-19 exposure factors associated with seropositive status were non-professional exposure (OR: 1.9, 95% CI: 1.3-2.7), especially outside the immediate family circle (OR: 2.2, 95% CI: 1.2-3.9) and contact with a COVID-19 patient (OR: 1.6; 95% CI: 1.1-2.2). Among professionally exposed workers, systematic adherence to strict hygiene standards was well observed, except for the use of a surgical mask (P<0.05, OR: 1.9, 95% CI: 1.3-2.8). Of those who reported occasionally or never wearing a surgical mask, nurses (25.7%), assistant nurses (16.2%), and medical students (11.7%) were predominant.ConclusionInfection of staff members during the first pandemic wave in our hospital occurred after both professional and private COVID-19 exposure, underlining the importance of continuous training in strict hygiene standards.
| S-EPMC8582228 | biostudies-literature
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:Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil that presented more than 21 million coronavirus disease 2019 cases and 590 000 deaths. The recent emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide. The present study describes the temporal spreading and evolution of SARS-CoV2 in the beginning of the second pandemic wave in Brazil, highlighting the fast dissemination of the two major concerning variants (P.1 and P.2). A total of 2507 SARS-CoV-2 whole-genome sequences (WGSs) with available information from the country (Brazil) and sampling date (July 2020-February 2021), were obtained and the frequencies of the lineages were evaluated in the period of the growing second pandemic wave. The results demonstrated the increasing prevalence of P.1 and P.2 lineages in the period evaluated. P.2 lineage was first detected in the middle of 2020, but a high increase occurred only in the last trimester of this same year and the spreading to all Brazilian regions. P.1 lineage emerged even later, first in the North region in December 2020 and really fast dissemination to all other Brazilian regions in January and February 2021. All SARS-CoV-2 WGSs of P.1 and P.2 were further separately evaluated with a Bayesian approach. The rates of nucleotide and amino acid substitutions were statistically higher in P.1 than P.2 (p < 0.01). The phylodynamic analysis demonstrated that P.2 gradually spread in all the country from September 2020 to January 2021, while P.1 disseminated even faster from December 2020 to February 2021. Skyline plots of both lineages demonstrated a slight rise in the spreading for P.2 and exponential growth for P.1. In conclusion, these data demonstrated that the P.1 (recently renamed as Gamma) and P.2 lineages have predominated in the second pandemic wave due to the very high spreading across all geographic regions in Brazil at the end of 2020 and beginning of 2021.
| S-EPMC8661965 | biostudies-literature
Project description:Although SARS-CoV-2 surface contamination has been investigated in health care settings, little is known about the SARS-CoV-2 surface contamination in public urban areas, particularly in tropical countries. Here, we investigated the presence of SARS-CoV-2 on high-touch surfaces in a large city in Brazil, one of the most affected countries by the COVID-19 pandemic in the world. A total of 400 surface samples were collected in February 2021 in the City of Recife, Northeastern Brazil. A total of 97 samples (24.2%) tested positive for SARS-CoV-2 by RT-qPCR using the CDC-USA protocol. All the collection sites, except one (18/19, 94.7%) had at least one environmental surface sample contaminated. SARS-CoV-2 positivity was higher in public transport terminals (47/84, 55.9%), followed by health care units (26/84, 30.9%), beach areas (4/21, 19.0%), public parks (14/105, 13.3%), supply centre (2/21, 9.5%), and public markets (4/85, 4.7%). Toilets, ATMs, handrails, playgrounds and outdoor gyms were identified as fomites with the highest rates of SARS-CoV-2 detection. Taken together, our data provide a real-world picture of SARS-CoV-2 dispersion in highly populated tropical areas and identify critical control points that need to be targeted to break SARS-CoV-2 transmission chains.
| S-EPMC9303906 | biostudies-literature
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:Breakthrough infections following SARS-CoV-2 vaccination remain the global concern. The current study was conducted during the second wave of COVID-19 (1st March-7th July 2021) in Pune, India, at two tertiary care hospitals. Of the 6,159 patients diagnosed as COVID-19, 372/2,210 (16.8%) were breakthrough infections. Of these, 81.1 and 18.8% received one or two doses of Covishield or Covaxin, respectively. Of note, 30.7% patients were with comorbidities, hypertension being the commonest (12.44%). The majority of infections were mild (81.2%). Forty-three patients with breakthrough infections were hospitalized with severe (n = 27, 62.8%) or moderate (n = 16, 37.2%) disease. The receptor binding domain (RBD) sequences from vaccinated (n = 126) and non-vaccinated (n = 168) samples were used for variant analysis. The delta variant was predominant followed by kappa in both vaccinated and non-vaccinated groups. Viral load (qRT-PCR) was not different among these categories. Full-genome comparisons of sequences in relation to vaccination status did not identify any mutation characteristic of the vaccinated group. Irrespective of the number of doses, neutralizing antibody titers (PRNT50) during the first week of clinical disease were higher in the vaccinated patients than the unvaccinated category. In conclusion, though not completely, SARS-CoV-2 vaccines used for country-wide immunization did reduce disease severity among the individuals without any comorbidity by inducing rapid immune response against distinctly different delta and kappa variants. The utility against emerging variants with further mutations need to be carefully examined.
| S-EPMC9877521 | biostudies-literature
Project description:Background The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has led to a global health crisis, with various variants emerging over time. In India, particularly in Maharashtra, a resurgence of cases and distinct transmission patterns have been observed. This study aimed to identify and characterize the circulating SARS-CoV-2 variants during the early second wave in Maharashtra, India. Materials and methods Nasopharyngeal swabs were collected from 24 RT-PCR-positive coronavirus disease of 2019 (COVID-19) cases across four districts of Maharashtra. Whole genome sequencing (WGS) was performed using the ARTIC amplicon sequencing protocol, and the data were analyzed. Results A total of 189 amino-acid mutations were identified across the 24 samples. Compared to the Indian genomes, 44 amino-acid mutations were unique to 24 genomes. Clade 20A was the most prevalent (66.66%), followed by 20B and 21B. The lineage B.1.36 (45.83%) was the most common, followed by B.1.617.1 (16.67%). The D614G mutation was the most frequent spike mutation (95.83%). Four samples from the Amravati district clustered distinctly under Clade 21B with spike mutations E154K in the N-terminal domain (NTD), L452R and E484Q in the receptor-binding domain (RBD) and P681R in proximity to the furin cleavage site. The temporal distribution of samples revealed the presence of Clade 21B in Maharashtra since the 31st of January 2021. Conclusion The study provides valuable insights into the circulating SARS-CoV-2 variants during the early second wave in Maharashtra, highlighting specific clades and mutations. The unique clustering patterns and the high prevalence of immune-escape mutations emphasize the need for continuous monitoring and genomic surveillance.
| S-EPMC10711336 | biostudies-literature