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Analysis of SARS-CoV-2 variants by proteomics

ABSTRACT: Analysis fo SARS-CoV-2 proteins from variants delta, gamma and omicron from clinical respiratory tract samples.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: VALDEMIR CARVALHO

LAB HEAD: Valdemir Melechco Carvalho

PROVIDER: PXD034582 | Pride | 2022-10-26

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	DELTA1_DDA.pep.xml	Pepxml
	DELTA1_DDA.raw	Raw
	DELTA2_DDA.pep.xml	Pepxml
	DELTA2_DDA.raw	Raw
	DELTA3_DDA.pep.xml	Pepxml

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Publications

Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts.

Cardozo Karina Helena Morais KHM Lebkuchen Adriana A Okai Guilherme Gonçalves GG Schuch Rodrigo Andrade RA Viana Luciana Godoy LG Olive Aline Nogueira AN Lazari Carolina Dos Santos CDS Fraga Ana Maria AM Granato Celso Francisco Hernandes CFH Pintão Maria Carolina Tostes MCT Carvalho Valdemir Melechco VM

Nature communications 20201203 1

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 9 ...[more]

PMID: 33273458

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Total Proteomics of SARS-CoV-2 variants

Project description:The ancestral SARS-CoV-2 strain that initiated the Covid-19 pandemic at the end of 2019 has rapidly mutated into multiple variants of concern with variable pathogenicity and increasing immune escape strategies. However, differences in host cellular antiviral responses upon infection with SARS-CoV-2 variants remains elusive. Leveraging whole cell proteomics, we determined host signalling pathways that are differentially modulated upon infection with the clinical isolates of the ancestral SARS-CoV-2 B.1 and the variants of concern Delta and Omicron BA.1. Our findings illustrate alterations in the global host proteome landscape upon infection with SARS-CoV-2 variants and the resulting host immune responses. Additionally, viral proteome kinetics reveal declining levels of viral protein expression during Omicron BA.1 infection when compared to ancestral B.1 and Delta variants, consistent with its reduced replication rates. Moreover, molecular assays reveal deferral activation of specific host antiviral signalling upon Omicron BA.1 and BA.2 infection. Our study provides an overview of host proteome profile of multiple SARS-CoV-2 variants and brings forth a better understanding of the instigation of key immune signalling pathways causative for the differential pathogenicity of SARS-CoV-2 variants.

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SARS-CoV-2 variants evolve convergent strategies to remodel the host response: Infection proteomics

Project description:We sought to compare differences in the human cellular response to distinct SARS-CoV-2 variants of concern. Here, we infected Calu-3 lung epithelial cells with each of the SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, Delta, and Omicron) compared to two early-lineage controls (VIC and IC19). We performed global abundance proteomics and phosphoproteomics at 10, 24, and, for certain samples, 48 hours post infection to comprehensively characterize the host response to infection.

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Project description:To date five variants of concern (VOC) of SARS-CoV-2 have emerged that show increased immune evasion. While their evolving escape from humoral immune responses has been analyzed in detail, adaptation of SARS-CoV-2 to human innate immune processes like autophagy are less understood. Here we demonstrate that currently predominant mutation T9I in the structural envelope (E) protein conveys increased resistance against autophagy of recent Omicron VOCs (BA.1, BA5 and XBB.5) compared to earlier SARS-CoV-2 variants. Rare omicron isolates that do not carry E T9I are sensitive towards autophagy. Mechanistic analyses revealed that E I9 inhibits autophagic turnover more efficiently than E T9 due to increased recruitment to autophagosomes and enhanced interaction with early autophagosome markers. Using pseudotyping assays we revealed that mutation T9I in E reduces release efficiency, but protects incoming virion from autophagy. In line, introduction of E T9I into recombinant 2020 SARS-CoV-2 increases its resistance against autophagy, but also attenuates replication. Our data thus reveal autophagy as a fundamental driver of SARS-CoV-2 evolution and improved autophagy escape may have contributed to the success of the Omicron variant.

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Immunological and Metabolic Characteristics of the Omicron Variants Infection

Project description:The Omicron variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in November 2021 in South Africa, has initiated the 5th wave of global pandemics. Here, we systemically examined immunological and metabolic characteristics of Omicron variants infection. We found Omicron resisted to neutralizing antibody targeting receptor binding domain (RBD) of wild-type SARS-CoV-2. Omicron could not be neutralized by sera of Corona Virus Disease 2019 (COVID-19) convalescent individuals who were infected with the Delta variant. Through mass spectrometry on MHC-bound peptidomes, we found that the spike protein of the Omicron variants could generate additional CD8+ T cell epitopes, compared with Delta. These epitopes could induce robust CD8+ T cell responses. Moreover, we found booster vaccination increased the cross-memory CD8+ T cell responses against Omicron. Metabolic regulome analysis of Omicron-specific T cell showed a metabolic profile that promoted memory T cell responses. Consistently, a higher fraction of memory CD8+ T cells were found in Omicron stimulated peripheral blood mononuclear cells (PBMCs). In addition, CD147 was also a receptor for the Omicron variants, and CD147 antibody inhibited infection of Omicron. CD147-mediated Omicron infection in a human CD147 transgenic mouse model induced exudative alveolar pneumonia. Taken together, our data suggested that vaccination booster and receptor blocking antibody are two effective strategies against Omicron.

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