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1.
Cell Mol Immunol ; 19(5): 577-587, 2022 May.
Article in English | MEDLINE | ID: covidwho-1830043

ABSTRACT

Neutrophil extracellular traps (NETs) can capture and kill viruses, such as influenza viruses, human immunodeficiency virus (HIV), and respiratory syncytial virus (RSV), thus contributing to host defense. Contrary to our expectation, we show here that the histones released by NETosis enhance the infectivity of SARS-CoV-2, as found by using live SARS-CoV-2 and two pseudovirus systems as well as a mouse model. The histone H3 or H4 selectively binds to subunit 2 of the spike (S) protein, as shown by a biochemical binding assay, surface plasmon resonance and binding energy calculation as well as the construction of a mutant S protein by replacing four acidic amino acids. Sialic acid on the host cell surface is the key molecule to which histones bridge subunit 2 of the S protein. Moreover, histones enhance cell-cell fusion. Finally, treatment with an inhibitor of NETosis, histone H3 or H4, or sialic acid notably affected the levels of sgRNA copies and the number of apoptotic cells in a mouse model. These findings suggest that SARS-CoV-2 could hijack histones from neutrophil NETosis to promote its host cell attachment and entry process and may be important in exploring pathogenesis and possible strategies to develop new effective therapies for COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , Animals , Histones , Mice , N-Acetylneuraminic Acid , Protein Subunits/metabolism , Spike Glycoprotein, Coronavirus/chemistry , Virus Internalization
2.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-328537

ABSTRACT

Background: The unprecedented COVID-19 pandemic has been spreading for more than one and a half years. However, it is unclear whether the pandemic influenced admission in pediatric intensive care units (PICUs) that never received COVID-19 patients during the early major outbreak in China . Methods: A retrospective study was conducted in a PICU in a tertiary hospital in Chengdu, southwestern China. We sought to describe the trend of admission number from pre-epidemic years (2018 and 2019) to 2021. We explored the impact of the COVID-19 outbreak on PICU admission characteristics by including all patients younger than 18 years admitted to the PICU between January 23 and April 8 in 2020 and those admitted in the same time periods in pre-epidemic years and in 2021. Results: The percentage of patients admitted to the PICU from the Chengdu region increased from 34.2 percent in 2019 to 40.4 percent in 2020, whereas that from other provinces decreased from 11.7 percent in 2019 to 5.8 percent in 2020 ( P = 0.012). The median length of stay (LOS) in the PICU was significantly longer in the 2020 cohort (4.0 days) than in the 2019 cohort (2.0 days) ( P <0.001);the median hospital LOS was also significantly longer in the former (12.0 days) than in the latter (8.0 days) ( P < 0.001). Both hospital outcomes ( P = 0.005) and primary diagnosis distributions ( P = 0.025) between the 2020 and 2019 cohorts were significant. Conclusions: In a PICU that never received COVID-19 patients, the onset of the 2020 major outbreak was accompanied by changes in the composition of regions of patients, longer PICU and hospital stays, an increased proportion of unauthorized discharge and death, and a larger proportion of neoplasms, nervous system diseases and injury.

3.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-327445

ABSTRACT

Replicons are synthetic viral RNA molecules that recapitulate the self-replicating activities of the virus but are missing its infectivity potential. Here, we report on a scalable pipeline to generate a replicon of any SARS-CoV-2 strain using de-novo synthesis. Our pipeline relies only on publicly available sequencing data without requiring access to any material, simplifying logistical and bureaucratic issues of sample acquisition. In addition, our system retains the nucleotide sequence of most of the SARS-CoV-2 full genome and therefore better captures its underlying genomic and biological functions as compared to the popular pseudotypes or any replicon system published to-date. We utilized our system to synthesize a SARS-CoV-2 non-infectious version of the Beta strain. We then confirmed that the resulting RNA molecules are non-infectious and safe to handle in a BSL2/CL2 facility. Finally, we show that our replicon can be specifically inhibited by molnupiravir and RNAi treatments, demonstrating its utility for drug research and development.

4.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-324909

ABSTRACT

Background: Widespread viral and serological testing for SARS-CoV-2 may present a unique opportunity to also test for HIV infection. We estimated the potential impact of adding linked, opt-out HIV testing alongside SARS-CoV-2 testing on HIV incidence and the cost-effectiveness of this strategy in six US cities.Methods: We calibrated a dynamic compartmental HIV transmission model to match the epidemiological characteristics of six US cities (Atlanta, Baltimore, Los Angeles, Miami, New York City, Seattle). For each city, we constructed three sets of scenarios: (1) sustained current levels of HIV-related treatment and prevention services (status quo);(2) temporary disruptions in health services and changes in sexual and injection risk behaviours at discrete levels between 0%-50%;and (3) linked HIV and SARS-CoV-2 testing offered to 10%-90% of the adult population in addition to scenario (2). We estimated cumulative HIV infections between 2020-2025, as well as incremental costs, quality-adjusted life years, and incremental cost-effectiveness ratios of linked HIV testing over 20 years.Findings: In the absence of linked, opt-out HIV testing, we estimated a best-case scenario (50% reduction in risk behaviours and no service disruptions) of 6,733 fewer HIV infections between 2020-2025 (16.5% decrease), and a worst-case scenario (no behavioural change and 50% reduction in service access) of 3,669 additional HIV infections (9.0% increase) across cities. If HIV testing could be offered to 10%-90% of the adult population, we estimated that a total of 576-7,225 (1.6%-17.2%) new infections could be averted. The intervention would require an initial investment of $20M-$218M across cities;however, the intervention would ultimately result in savings in health care costs in each city.Interpretation: Although COVID-19-related disruptions in HIV-related services may increase or decrease HIV incidence, a campaign in which HIV testing is linked with SARS-CoV-2 testing could substantially reduce HIV incidence and reduce direct and indirect health care costs attributable to HIV.Funding Statement: US NIH-NIDA Grant No. R01-DA041747Declaration of Interests: XZ, EK, SC, MP, WSA, CNB, CDR, DJF, BDLM, SHM, JM, LRM, BRS, SAS and BN declare no competing interests.

5.
Anal Chem ; 94(4): 2244-2254, 2022 02 01.
Article in English | MEDLINE | ID: covidwho-1625849

ABSTRACT

The cleavage-site specificities for many proteases are not well understood, restricting the utility of supervised classification methods. We present an algorithm and web interface to overcome this limitation through the unsupervised detection of overrepresented patterns in protein sequence data, providing insight into the mixture of protease activities contributing to a complex system. Here, we apply the RObust LInear Motif Deconvolution (RoLiM) algorithm to confidently detect substrate cleavage patterns for SARS-CoV-2 MPro protease in the N-terminome data of an infected human cell line. Using mass spectrometry-based peptide data from a case-control comparison of 341 primary urothelial bladder cancer cases and 110 controls, we identified distinct sequence motifs indicative of increased matrix metallopeptidase activity in urine from cancer patients. The evaluation of N-terminal peptides from patient plasma post-chemotherapy detected novel granzyme B/corin activity. RoLiM will enhance the unbiased investigation of peptide sequences to establish the composition of known and uncharacterized protease activities in biological systems. RoLiM is available at http://langelab.org/rolim/.


Subject(s)
Coronavirus 3C Proteases/metabolism , SARS-CoV-2/enzymology , Amino Acid Sequence , COVID-19 , Humans , Proteolysis , Substrate Specificity
6.
2021.
Preprint in English | Other preprints | ID: ppcovidwho-294887

ABSTRACT

Single-cell RNA-sequencing (scRNA-seq) has become a powerful tool to reveal the complex biological diversity and heterogeneity among cell populations. However, the technical noise and bias of the technology still have negative impacts on the downstream analysis. Here, we present a self-supervised Contrastive LEArning framework for scRNA-seq (CLEAR) profile representation and the downstream analysis. CLEAR overcomes the heterogeneity of the experimental data with a specifically designed representation learning task and thus can handle batch effects and dropout events. In the task, the deep learning model learns to pull together the representations of similar cells while pushing apart distinct cells, without manual labeling. It achieves superior performance on a broad range of fundamental tasks, including clustering, visualization, dropout correction, batch effect removal, and pseudo-time inference. The proposed method successfully identifies and illustrates inflammatory-related mechanisms in a COVID-19 disease study with 43,695 single cells from peripheral blood mononuclear cells. Further experiments to process a million-scale single-cell dataset demonstrate the scalability of CLEAR. This scalable method generates effective scRNA-seq data representation while eliminating technical noise, and it will serve as a general computational framework for single-cell data analysis.

7.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-293150

ABSTRACT

The cleavage-site specificities for many proteases are not well-understood, restricting the utility of supervised classification methods. We present an algorithm and web interface to overcome this limitation through the unsupervised detection of overrepresented patterns in protein sequence data, providing insight into the mixture of protease activities contributing to a complex system. Here, we apply the RObust LInear Motif Deconvolution (RoLiM) algorithm to confidently detect substrate cleavage patterns for SARS-CoV-2 Mpro protease in N terminome data of an infected human cell line. Using mass spectrometry-based peptide data from a case-control comparison of 341 primary urothelial bladder cancer cases and 110 controls, we identified distinct sequence motifs indicative of increased MMP activity in urine from cancer patients. Evaluation of N terminal peptides from patient plasma post-chemotherapy detected novel Granzyme B/Corin activity. RoLiM will enhance unbiased investigation of peptide sequences to establish the composition of known and uncharacterized protease activities in biological systems.

8.
Microbiol Spectr ; 9(2): e0019721, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1381169

ABSTRACT

The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic variants of the entire SARS-CoV-2 genome, we developed and clinically validated a hybridization capture SARS-CoV-2 NGS assay, integrating novel methods for panel design using double-stranded DNA (dsDNA) biotin-labeled probes, and built accompanying software. This test is the first hybrid capture-based NGS assay given Food and Drug Administration (FDA) emergency use authorization for detection of the SARS-CoV-2 virus. The positive and negative percent agreement (PPA and NPA, respectively) were defined in comparison to the results for an orthogonal real-time reverse transcription polymerase chain reaction (RT-PCR) assay (PPA and NPA, 96.7 and 100%, respectively). The limit of detection was established to be 800 copies/ml with an average fold enrichment of 46,791. Furthermore, utilizing the research-use-only analysis to profile the variants, we identified 55 novel mutations, including 11 in the functionally important spike protein. Finally, we profiled the full nasopharyngeal microbiome using metagenomics and found overrepresentation of 7 taxa and evidence of macrolide resistance in SARS-CoV-2-positive patients. This hybrid capture NGS assay, coupled with optimized software, is a powerful approach to detect and comprehensively map SARS-CoV-2 genetic variants for tracking viral evolution and guiding vaccine updates. IMPORTANCE This is the first FDA emergency-use-authorized hybridization capture-based next-generation sequencing (NGS) assay to detect the SARS-CoV-2 genome. Viral metagenomics and the novel hybrid capture NGS-based assay, along with its research-use-only analysis, can provide important genetic insights into SARS-CoV-2 and other emerging pathogens and improve surveillance and early detection, potentially preventing or mitigating new outbreaks. Better understanding of the continuously evolving SARS-CoV-2 viral genome and the impact of genetic variants may provide individual risk stratification, precision therapeutic options, improved molecular diagnostics, and population-based therapeutic solutions.


Subject(s)
Genetic Variation/genetics , Genome, Viral/genetics , Microbiota/genetics , Nasopharynx/microbiology , SARS-CoV-2/genetics , Anti-Bacterial Agents/pharmacology , COVID-19/pathology , Drug Resistance, Bacterial/genetics , High-Throughput Nucleotide Sequencing , Humans , Limit of Detection , Macrolides/pharmacology , Metagenomics/methods , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/isolation & purification
9.
Clin Infect Dis ; 72(11): e828-e834, 2021 06 01.
Article in English | MEDLINE | ID: covidwho-1249293

ABSTRACT

BACKGROUND: Widespread viral and serological testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may present a unique opportunity to also test for human immunodeficiency virus (HIV) infection. We estimated the potential impact of adding linked, opt-out HIV testing alongside SARS-CoV-2 testing on the HIV incidence and the cost-effectiveness of this strategy in 6 US cities. METHODS: Using a previously calibrated dynamic HIV transmission model, we constructed 3 sets of scenarios for each city: (1) sustained current levels of HIV-related treatment and prevention services (status quo); (2) temporary disruptions in health services and changes in sexual and injection risk behaviors at discrete levels between 0%-50%; and (3) linked HIV and SARS-CoV-2 testing offered to 10%-90% of the adult population in addition to Scenario 2. We estimated the cumulative number of HIV infections between 2020-2025 and the incremental cost-effectiveness ratios of linked HIV testing over 20 years. RESULTS: In the absence of linked, opt-out HIV testing, we estimated a total of a 16.5% decrease in HIV infections between 2020-2025 in the best-case scenario (50% reduction in risk behaviors and no service disruptions), and a 9.0% increase in the worst-case scenario (no behavioral change and 50% reduction in service access). We estimated that HIV testing (offered at 10%-90% levels) could avert a total of 576-7225 (1.6%-17.2%) new infections. The intervention would require an initial investment of $20.6M-$220.7M across cities; however, the intervention would ultimately result in savings in health-care costs in each city. CONCLUSIONS: A campaign in which HIV testing is linked with SARS-CoV-2 testing could substantially reduce the HIV incidence and reduce direct and indirect health care costs attributable to HIV.


Subject(s)
COVID-19 , Epidemics , HIV Infections , Adult , COVID-19 Testing , Cities , Cost-Benefit Analysis , HIV , HIV Infections/diagnosis , HIV Infections/epidemiology , Humans , SARS-CoV-2
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