Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Semen proteome analysis comparing the persistent effects of different SARS-COV-2 variants on male reproductive system in recovered men

ABSTRACT: After the initial COVID-19 wave, India experienced a second COVID-19 wave in March 2021, which was driven by the delta variant. By January 2021, India has also begun its vaccine campaign. Therefore, semen samples from recovered patients who were infected during the two waves of COVID-19 in India were obtained to study the impact of variants on the male reproductive system. We compared samples from the second wave with those of first wave in India. We also included control samples to the comparison.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Semen

SUBMITTER: Avinash singh

LAB HEAD: sanjeeva srivastava

PROVIDER: PXD041904 | Pride | 2024-01-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Semen proteomics reveals alterations in fertility-related proteins post-recovery from COVID-19.

Dash Ankita A Salkar Akanksha A Nissa Mehar Un MU Makwana Prashant P Athalye Arundhati A Parikh Swapneil S Srivastava Sanjeeva S Parikh Firuza F

Frontiers in physiology 20231109

<b>Introduction:</b> Changes to sperm quality and decline in reproductive function have been reported in COVID-19-recovered males. Further, the emergence of SARS-CoV-2 variants has caused the resurgences of COVID-19 cases globally during the last 2 years. These variants show increased infectivity and transmission along with immune escape mechanisms, which threaten the already burdened healthcare system. However, whether COVID-19 variants induce an effect on the male reproductive system even afte ...[more]

PMID: 38028760

Similar Datasets

Augmenting vaccine efficacy against delta variant with ‘Mycobacterium-w’ mediated modulation of NK-ADCC and TLR-MYD88 pathways

Project description:Fifty healthcare workers (HCW) who had received Mycobacterium-w (Mw) and at least one dose of ChAdOx1 nCoV-19 vaccine subsequently (Mw+ChAdOx1 group) were monitored for symptomatic COVID-19, during a major outbreak with the delta variant of SARS-CoV-2 (April-June, 2021) in India, along with 201 HCW receiving both doses of the vaccine without Mw (ChAdOx1 group). Bulk RNA-Seq analysis was carried out on 4 subjects enrolled from each group.

2023-02-28 | GSE216811 | GEO

Ghanbari2020 - forecasting the second wave of COVID-19 in Iran

Project description:One of the common misconceptions about COVID-19 disease is to assume that we will not see a recurrence after the first wave of the disease has subsided. This completely wrong perception causes people to disregard the necessary protocols and engage in some misbehavior, such as routine socializing or holiday travel. These conditions will put double pressure on the medical staff and endanger the lives of many people around the world. In this research, we are interested in analyzing the existing data to predict the number of infected people in the second wave of out-breaking COVID-19 in Iran. For this purpose, a model is proposed. The mathematical analysis corresponded to the model is also included in this paper. Based on proposed numerical simulations, several scenarios of progress of COVID-19 corresponding to the second wave of the disease in the coming months, will be discussed. We predict that the second wave of will be most severe than the first one. From the results, improving the recovery rate of people with weak immune systems via appropriate medical incentives is resulted as one of the most effective prescriptions to prevent the widespread unbridled outbreak of the second wave of COVID-19.

2022-10-17 | BIOMD0000000976 | BioModels

Project description:Evidence of vaccine escape by B1.351 during the second wave of COVID-19 in Bangladesh

| PRJNA728728 | ENA

Immune dysfunction in COVID-19 Associated Mucormycosis

Project description:The coronavirus pandemic (COVID-19) is associated with secondary bacterial and fungal infections globally. In India, inappropriate use of glucocorticoids, high prevalence of diabetes mellitus and a conducive environment for fungal growth are considered as the main factors for increased incidence of COVID-19 associated mucormycosis (CAM). Few cases of CAM without steroid abuse and normal blood glucose levels were also reported during the pandemic. This study was designed to explore whether altered immune responses due to severe COVID-19 infection predisposes towards development of mucormycosis. The global transcriptome profiling of monocytes and granulocytic cells derived from CAM, Mucormycosis, COVID-19 and healthy control groups were performed to identify the differentially expressed genes (DEGs) involved in dysregulated host immune response towards respective diseased and healthy conditions.

2024-02-09 | GSE226677 | GEO

Sarkar2020 - SAIR model of COVID-19 transmission with quarantine measures in India

Project description:In India, 100,340 confirmed cases and 3155 confirmed deaths due to COVID-19 were reported as of May 18, 2020. Due to absence of specific vaccine or therapy, non-pharmacological interventions including so- cial distancing, contact tracing are essential to end the worldwide COVID-19. We propose a mathematical model that predicts the dynamics of COVID-19 in 17 provinces of India and the overall India. A complete scenario is given to demonstrate the estimated pandemic life cycle along with the real data or history to date, which in turn divulges the predicted inflection point and ending phase of SARS-CoV-2. The proposed model monitors the dynamics of six compartments, namely susceptible (S), asymptomatic (A), recovered (R), infected (I), isolated infected ( I q ) and quarantined susceptible ( S q ), collectively expressed SARII q S q . A sensitivity analysis is conducted to determine the robustness of model predictions to parameter values and the sensitive parameters are estimated from the real data on the COVID-19 pandemic in India. Our re- sults reveal that achieving a reduction in the contact rate between uninfected and infected individuals by quarantined the susceptible individuals, can effectively reduce the basic reproduction number. Our model simulations demonstrate that the elimination of ongoing SARS-CoV-2 pandemic is possible by combining the restrictive social distancing and contact tracing. Our predictions are based on real data with reason- able assumptions, whereas the accurate course of epidemic heavily depends on how and when quaran- tine, isolation and precautionary measures are enforced.

2020-11-30 | BIOMD0000000977 | BioModels

SARS-CoV-2 spike P681R mutation, a hallmark of the Delta variant, enhances viral fusogenicity and pathogenicity

Project description:During the current SARS-CoV-2 pandemic, a variety of mutations have been accumulated in the viral genome, and currently, four variants of concerns (VOCs) are considered as the hazardous SARS-CoV-2 variants to the human society. The newly emerging VOC, the B.1.617.2/Delta variant, closely associates with a huge COVID-19 surge in India in Spring 2021. However, its virological property remains unclear. Here, we show that the B.1.617.2/Delta variant is highly fusogenic, and notably, more pathogenic than prototypic SARS-CoV-2 in infected hamsters. The P681R mutation in the spike protein, which is highly conserved in this lineage, facilitates the spike protein cleavage and enhances viral fusogenicity. Moreover, we demonstrate that the P681R-bearing virus exhibits higher pathogenicity than the parental virus. Our data suggest that the P681R mutation is a hallmark that characterizes the virological phenotype of the B.1.617.2/Delta variant and is closely associated with enhanced pathogenicity.

2021-09-30 | GSE182738 | GEO

Neutrophil and monocyte dysfunctional effector response towards bacterial challenge in critically ill COVID-19 patients

Project description:In this study, we aim to evaluate the relation between COVID-19 and bacterial secondary superinfections. We assessed the functional responses of neutrophils and monocytes isolated from acute and recovery COVID-19 patients upon bacterial infection using Flow-cytometry and proteomics based assays. Both neutrophils and monocytes showed impared intracellular microbicidal capacity along with a decreased functional response. Determination of plasma cytokines levels showed a significant association of certain cytokines towards secondary bacterial infection.

2021-12-10 | PXD029547 | Pride

c1406575-58ea-4744-86b7-78c168b658e0 - samples

Project description:This dataset contains paired RNA sequencing data for end-stage kidney disease (ESKD) patients on dialysis. There are two cohorts. The first includes 179 samples from 51 COVID-19 patients recruited during the initial phase of the COVID-19 pandemic (April-May 2020) and 55 non-infected ESKD patients as controls. 17 patients initially recruited as controls as part of the Wave 1 cohort were later infected with COVID-19 in January-March 2021. We acquired a total of 90 samples during the acute infection and convalescent samples for 12 of the 17 patients following the acute COVID-19 episode. RNA-seq counts and full clinical metadata for these cohorts are available without restriction from Zenodo (https://doi.org/10.5281/zenodo.6497251).

| EGAD00001009752 | EGA

High titers and low fucosylation of early anti-SARS-CoV-2 IgG promote hyper-inflammation by anti-inflammatory macrophages (MIL10)

Project description:Patients diagnosed with coronavirus disease 2019 (COVID-19) mostly become critically ill around the time of activation of the adaptive immune response. Here, we provide evidence that antibodies play a role in the worsening of disease at the time of seroconversion. We show that early phase severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) spike protein-specific IgG in serum of critically ill COVID-19 patients induces hyper-inflammatory responses by human alveolar macrophages. We identified that this excessive inflammatory response is dependent on two antibody features that are specific for patients with severe COVID-19. First, inflammation is driven by high titers of anti-spike IgG, a hallmark of severe disease. Second, we found that anti-spike IgG from patients with severe COVID-19 is intrinsically more pro-inflammatory because of different glycosylation, particularly low fucosylation, of the Fc tail. Notably, low anti-spike IgG fucosylation normalized in a few weeks after initial infection with SARS-CoV-2, indicating that the increased antibody-dependent inflammation mainly occurs at the time of seroconversion. We identified Fcγ Receptor (FcγR) IIa and FcγRIII as the two primary IgG receptors that are responsible for the induction of key COVID-19-associated cytokines such as interleukin-6 and tumor necrosis factor. In addition, we show that anti-spike IgG-activated macrophages can subsequently break pulmonary endothelial barrier integrity and induce microvascular thrombosis in vitro. Finally, we demonstrate that the hyper-inflammatory response induced by anti-spike IgG can be specifically counteracted by fostamatinib, an FDA- and EMA-approved therapeutic small molecule inhibitor of the kinase, Syk.

2021-04-30 | E-MTAB-10431 | biostudies-arrayexpress

The human host response to monkeypox infection: a proteomic case series study

Project description:The rapid rise of Monkeypox (MPX) cases outside previously endemic areas prompt for a better understanding of the disease. We studied the plasma proteome of a group of MPX patients with a similar infection history and clinical manifestation typical for the current outbreak. We report that MPX is associated with a strong plasma proteomic response among nutritional and acute phase response proteins. Moreover, we report a correlation between plasma proteins and disease severity. Contrasting the MPX host response with that of COVID-19, we find a range of similarities, but also important differences. For instance, CFHR1 is induced in COVID-19, but suppressed in MPX, reflecting the different role of the complement system in the two infectious diseases. The partial overlap in response proteins, however, allowed us to explore repurposing of a COVID-19 biomarker panel assay, which resulted in successful patient classification. Hence, our results provide a first proteomic characterization of the MPX human host response, and we reveal a thus far untapped potential for accelerating the response to disease outbreaks through the repurposing of biomarker assays.

2022-09-22 | PXD036074 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data