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1.
Commun Biol ; 5(1): 766, 2022 Jul 29.
Article in English | MEDLINE | ID: covidwho-1967631

ABSTRACT

Studying the antibody response to SARS-CoV-2 informs on how the human immune system can respond to antigenic variants as well as other SARS-related viruses. Here, we structurally identified a YYDRxG motif encoded by IGHD3-22 in CDR H3 that facilitates antibody targeting to a functionally conserved epitope on the SARS-CoV-2 receptor binding domain. A computational search for a YYDRxG pattern in publicly available sequences uncovered 100 such antibodies, many of which can neutralize SARS-CoV-2 variants and SARS-CoV. Thus, the YYDRxG motif represents a common convergent solution for the human humoral immune system to target sarbecoviruses including the Omicron variant. These findings suggest an epitope-targeting strategy to identify potent and broadly neutralizing antibodies for design of pan-sarbecovirus vaccines and antibody therapeutics.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , Epitopes/genetics , Humans , Membrane Glycoproteins/metabolism , Neutralization Tests , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Viral Envelope Proteins/metabolism
2.
Proc Natl Acad Sci U S A ; 119(29): e2205784119, 2022 Jul 19.
Article in English | MEDLINE | ID: covidwho-1908386

ABSTRACT

Many neutralizing antibodies (nAbs) elicited to ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through natural infection and vaccination have reduced effectiveness to SARS-CoV-2 variants. Here, we show that therapeutic antibody ADG20 is able to neutralize SARS-CoV-2 variants of concern (VOCs) including Omicron (B.1.1.529) as well as other SARS-related coronaviruses. We delineate the structural basis of this relatively escape-resistant epitope that extends from one end of the receptor binding site (RBS) into the highly conserved CR3022 site. ADG20 can then benefit from high potency through direct competition with ACE2 in the more variable RBS and interaction with the more highly conserved CR3022 site. Importantly, antibodies that are able to target this site generally neutralize a broad range of VOCs, albeit with reduced potency against Omicron. Thus, this conserved and vulnerable site can be exploited for the design of universal vaccines and therapeutic antibodies.


Subject(s)
Antibodies, Monoclonal , Antibodies, Neutralizing , Antibodies, Viral , COVID-19 , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Antibodies, Monoclonal/immunology , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , COVID-19/virology , Epitopes/immunology , Humans , Neutralization Tests , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology
3.
Nat Immunol ; 23(6): 960-970, 2022 06.
Article in English | MEDLINE | ID: covidwho-1873528

ABSTRACT

The emergence of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) and potential future spillovers of SARS-like coronaviruses into humans pose a major threat to human health and the global economy. Development of broadly effective coronavirus vaccines that can mitigate these threats is needed. Here, we utilized a targeted donor selection strategy to isolate a large panel of human broadly neutralizing antibodies (bnAbs) to sarbecoviruses. Many of these bnAbs are remarkably effective in neutralizing a diversity of sarbecoviruses and against most SARS-CoV-2 VOCs, including the Omicron variant. Neutralization breadth is achieved by bnAb binding to epitopes on a relatively conserved face of the receptor-binding domain (RBD). Consistent with targeting of conserved sites, select RBD bnAbs exhibited protective efficacy against diverse SARS-like coronaviruses in a prophylaxis challenge model in vivo. These bnAbs provide new opportunities and choices for next-generation antibody prophylactic and therapeutic applications and provide a molecular basis for effective design of pan-sarbecovirus vaccines.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Neutralizing , Antibodies, Viral , Broadly Neutralizing Antibodies , COVID-19/prevention & control , Humans , Spike Glycoprotein, Coronavirus
5.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-330381

ABSTRACT

Many neutralizing antibodies (nAbs) elicited to ancestral SARS-CoV-2 through natural infection and vaccination generally have reduced effectiveness to SARS-CoV-2 variants. Here we show therapeutic antibody ADG20 is able to neutralize all SARS-CoV-2 variants of concern (VOCs) including Omicron (B.1.1.529) as well as other SARS-related coronaviruses. We delineate the structural basis of this relatively escape-resistant epitope that extends from one end of the receptor binding site (RBS) into the highly conserved CR3022 site. ADG20 can then benefit from high potency through direct competition with ACE2 in the more variable RBS and interaction with the more highly conserved CR3022 site. Importantly, antibodies that are able to target this site generally neutralize all VOCs, albeit with reduced potency against Omicron. Thus, this highly conserved and vulnerable site can be exploited for design of universal vaccines and therapeutic antibodies.

6.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-329705

ABSTRACT

Pan-betacoronavirus neutralizing antibodies may hold the key to developing broadly protective vaccines against coronaviruses that cause severe disease, for anticipating novel pandemic-causing viruses, and to respond more effectively to SARS-CoV-2 variants. The emergence of the Omicron variant of SARS-CoV-2 has illustrated the limitations of solely targeting the receptor binding domain (RBD) of the envelope Spike (S)-protein. Here, we isolated a large panel of broadly neutralizing antibodies (bnAbs) from SARS-CoV-2 recovered-vaccinated donors that target a conserved S2 region in the fusion machinery on betacoronavirus spikes. Select bnAbs show broad in vivo protection against all three pathogenic betacoronaviruses, SARS-CoV-1, SARS-CoV-2 and MERS-CoV, that have spilled over into humans in the past 20 years to cause severe disease. The bnAbs provide new opportunities for antibody-based interventions and key insights for developing pan-betacoronavirus vaccines.

7.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-329430

ABSTRACT

Mucoralean fungi offer various pathogens to cause mucormycosis, especially in immunodeficient patients. Over the past decades, both the morbidity and mortality of mucormycosis have increased rapidly, particularly in developing countries. Nowadays, mucormycosis more often happens in India for the COVID-19 pandemic and its backward diagnostic techniques. Our epidemiologic outcomes show several identifications of Mucoralean fungi are limited to genus, while Rhizopus species, Mucor species and Lichtheimia species have high proportions. To find more molecular targets to make rapid and accurate identifications of Mucorales genus and species, Pan-genome analysis and Phylogenetic tree are conducted with four Mucorales isolates we sequenced and 43 fungi from NCBI. A few Mucorales- specific genes have been found such as STE/STE20 protein kinase, GH36 and sel1 repeat protein. Mucorales genus-specific genes are also found in Lichtheimia species and Cunninghamella species, which covered cellular structure, biochemistry metabolism, molecular processing, and signal transduction. Reported proteins related to the virulence of Mucorales species were run with Orthofinder and 112092 , cotH3 , gcn4 and igp1 have shown the potential to be the direct identification as well as the virulence detection of Mucorales species. The molecular biological techniques need to be promoted, for which our study provide hypothesis and feasibility analysis.

8.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-327570

ABSTRACT

The SARS-CoV-2 Omicron (B.1.1.529) variant possesses numerous spike (S) mutations that enhance transmissibility and evasion of neutralizing antibodies, making it a serious threat to existing COVID-19 vaccines and therapies. Accurately distinguishing emerging S variants and revealing their post-translational glycosylation changes can provide new insights for rational design and development of vaccines and therapeutics. Here we report the first comprehensive elucidation of the molecular variations and O-glycoform changes of the Omicron, Delta (B.1.617.2), and wild-type (WA1/2020) S receptor-binding domains (S-RBDs) using high-resolution top-down mass spectrometry (MS). A novel O-glycosite (Thr376) unique to the Omicron variant is identified. Moreover, we have directly quantified the Core 1 and Core 2 O-glycan structures and characterized the O-glycoform structural heterogeneity of the three variants. Our findings provide high resolution detail of Omicron O-glycoform and utilization, providing new insights into how this variant escapes immunological protection and informing strategies for developing Omicron-directed vaccines, diagnostics, and therapeutics.

9.
Sci Transl Med ; 14(637): eabi9215, 2022 03 23.
Article in English | MEDLINE | ID: covidwho-1673344

ABSTRACT

Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a CoV disease 2019 (COVID-19) convalescent donor that exhibits broad reactivity with human ß-CoVs. Here, we showed that CC40.8 targets the conserved S2 stem helix region of the CoV spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem peptide at 1.6-Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in ß-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted that CC40.8-like bnAbs are relatively rare in human COVID-19 infection, and therefore, their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on ß-CoV spike proteins for protective antibodies that may facilitate the development of pan-ß-CoV vaccines.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Animals , Antibodies, Neutralizing/metabolism , Antibodies, Viral , COVID-19/immunology , Humans , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology
10.
Front Environ Sci Eng ; 16(6): 70, 2022.
Article in English | MEDLINE | ID: covidwho-1446217

ABSTRACT

The rapid global spread of coronavirus disease 2019 (COVID-19) has promoted concern over human pathogens and their significant threats to public health security. The monitoring and control of human pathogens in public sanitation and health facilities are of great importance. Excessive sludge is an inevitable byproduct of sewage that contains human and animal feces in wastewater treatment plants (WWTPs). It is an important sink of different pollutants and pathogens, and the proper treatment and disposal of sludge are important to minimize potential risks to the environment and public health. However, there is a lack of comprehensive analysis of the diversity, exposure risks, assessment methods and inactivation techniques of pathogenic microorganisms in sludge. Based on this consideration, this review summarizes the control performance of pathogenic microorganisms such as enterovirus, Salmonella spp., and Escherichia coli by different sludge treatment technologies, including composting, anaerobic digestion, aerobic digestion, and microwave irradiation, and the mechanisms of pathogenic microorganism inactivation in sludge treatment processes are discussed. Additionally, this study reviews the diversity, detection methods, and exposure risks of pathogenic microorganisms in sludge. This review advances the quantitative assessment of pathogenic microorganism risks involved in sludge reuse and is practically valuable to optimize the treatment and disposal of sludge for pathogenic microorganism control.

11.
Biochemistry ; 60(27): 2153-2169, 2021 07 13.
Article in English | MEDLINE | ID: covidwho-1387101

ABSTRACT

A central tenet in the design of vaccines is the display of native-like antigens in the elicitation of protective immunity. The abundance of N-linked glycans across the SARS-CoV-2 spike protein is a potential source of heterogeneity among the many different vaccine candidates under investigation. Here, we investigate the glycosylation of recombinant SARS-CoV-2 spike proteins from five different laboratories and compare them against S protein from infectious virus, cultured in Vero cells. We find patterns that are conserved across all samples, and this can be associated with site-specific stalling of glycan maturation that acts as a highly sensitive reporter of protein structure. Molecular dynamics simulations of a fully glycosylated spike support a model of steric restrictions that shape enzymatic processing of the glycans. These results suggest that recombinant spike-based SARS-CoV-2 immunogen glycosylation reproducibly recapitulates signatures of viral glycosylation.


Subject(s)
COVID-19/genetics , Protein Conformation , SARS-CoV-2/ultrastructure , Spike Glycoprotein, Coronavirus/ultrastructure , Animals , COVID-19/immunology , COVID-19/virology , COVID-19 Vaccines/genetics , COVID-19 Vaccines/immunology , Chlorocebus aethiops , Glycosylation , Humans , Molecular Dynamics Simulation , Protein Binding/genetics , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , Vero Cells
12.
Sci Adv ; 7(31)2021 07.
Article in English | MEDLINE | ID: covidwho-1388435

ABSTRACT

Rationally designed protein subunit vaccines are being developed for a variety of viruses including influenza, RSV, SARS-CoV-2, and HIV. These vaccines are based on stabilized versions of the primary targets of neutralizing antibodies on the viral surface, namely, viral fusion glycoproteins. While these immunogens display the epitopes of potent neutralizing antibodies, they also present epitopes recognized by non-neutralizing or weakly neutralizing ("off-target") antibodies. Using our recently developed electron microscopy polyclonal epitope mapping approach, we have uncovered a phenomenon wherein off-target antibodies elicited by HIV trimer subunit vaccines cause the otherwise highly stabilized trimeric proteins to degrade into cognate protomers. Further, we show that these protomers expose an expanded suite of off-target epitopes, normally occluded inside the prefusion conformation of trimer, that subsequently elicit further off-target antibody responses. Our study provides critical insights for further improvement of HIV subunit trimer vaccines for future rounds of the iterative vaccine design process.


Subject(s)
AIDS Vaccines/immunology , HIV Antibodies/chemistry , HIV Infections/immunology , HIV-1/chemistry , env Gene Products, Human Immunodeficiency Virus/chemistry , AIDS Vaccines/chemistry , Animals , COVID-19/immunology , Female , HIV Antibodies/immunology , HIV-1/immunology , Humans , Macaca mulatta , Rabbits , SARS-CoV-2/chemistry , SARS-CoV-2/immunology , env Gene Products, Human Immunodeficiency Virus/immunology
13.
Economic Research-Ekonomska Istraživanja ; : 1-17, 2021.
Article in English | Taylor & Francis | ID: covidwho-1347972
14.
Biochemistry ; 60(27): 2153-2169, 2021 07 13.
Article in English | MEDLINE | ID: covidwho-1294429

ABSTRACT

A central tenet in the design of vaccines is the display of native-like antigens in the elicitation of protective immunity. The abundance of N-linked glycans across the SARS-CoV-2 spike protein is a potential source of heterogeneity among the many different vaccine candidates under investigation. Here, we investigate the glycosylation of recombinant SARS-CoV-2 spike proteins from five different laboratories and compare them against S protein from infectious virus, cultured in Vero cells. We find patterns that are conserved across all samples, and this can be associated with site-specific stalling of glycan maturation that acts as a highly sensitive reporter of protein structure. Molecular dynamics simulations of a fully glycosylated spike support a model of steric restrictions that shape enzymatic processing of the glycans. These results suggest that recombinant spike-based SARS-CoV-2 immunogen glycosylation reproducibly recapitulates signatures of viral glycosylation.


Subject(s)
COVID-19/genetics , Protein Conformation , SARS-CoV-2/ultrastructure , Spike Glycoprotein, Coronavirus/ultrastructure , Animals , COVID-19/immunology , COVID-19/virology , COVID-19 Vaccines/genetics , COVID-19 Vaccines/immunology , Chlorocebus aethiops , Glycosylation , Humans , Molecular Dynamics Simulation , Protein Binding/genetics , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , Vero Cells
15.
J Immunol ; 207(1): 344-351, 2021 07 01.
Article in English | MEDLINE | ID: covidwho-1286955

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike pseudotyped virus (PSV) assays are widely used to measure neutralization titers of sera and of isolated neutralizing Abs (nAbs). PSV neutralization assays are safer than live virus neutralization assays and do not require access to biosafety level 3 laboratories. However, many PSV assays are nevertheless somewhat challenging and require at least 2 d to carry out. In this study, we report a rapid (<30 min), sensitive, cell-free, off-the-shelf, and accurate assay for receptor binding domain nAb detection. Our proximity-based luciferase assay takes advantage of the fact that the most potent SARS-CoV-2 nAbs function by blocking the binding between SARS-CoV-2 and angiotensin-converting enzyme 2. The method was validated using isolated nAbs and sera from spike-immunized animals and patients with coronavirus disease 2019. The method was particularly useful in patients with HIV taking antiretroviral therapies that interfere with the conventional PSV assay. The method provides a cost-effective and point-of-care alternative to evaluate the potency and breadth of the predominant SARS-CoV-2 nAbs elicited by infection or vaccines.


Subject(s)
Antibodies, Neutralizing/analysis , Neutralization Tests , SARS-CoV-2/isolation & purification , Angiotensin-Converting Enzyme 2/immunology , Antibodies, Neutralizing/immunology , Cohort Studies , Humans , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology
16.
Nat Commun ; 12(1): 2938, 2021 05 19.
Article in English | MEDLINE | ID: covidwho-1236086

ABSTRACT

Pre-existing immunity to seasonal endemic coronaviruses could have profound consequences for antibody responses to SARS-CoV-2, induced from natural infection or vaccination. A first step to establish whether pre-existing responses can impact SARS-CoV-2 infection is to understand the nature and extent of cross-reactivity in humans to coronaviruses. Here we compare serum antibody and memory B cell responses to coronavirus spike proteins from pre-pandemic and SARS-CoV-2 convalescent donors using binding and functional assays. We show weak evidence of pre-existing SARS-CoV-2 cross-reactive serum antibodies in pre-pandemic donors. However, we find evidence of pre-existing cross-reactive memory B cells that are activated during SARS-CoV-2 infection. Monoclonal antibodies show varying degrees of cross-reactivity with betacoronaviruses, including SARS-CoV-1 and endemic coronaviruses. We identify one cross-reactive neutralizing antibody specific to the S2 subunit of the S protein. Our results suggest that pre-existing immunity to endemic coronaviruses should be considered in evaluating antibody responses to SARS-CoV-2.


Subject(s)
Antibodies, Viral/blood , COVID-19/immunology , Cross Protection/immunology , SARS Virus/immunology , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , B-Lymphocytes/immunology , Cross Reactions/immunology , Female , Humans , Immunologic Memory/immunology , Male
17.
Aging (Albany NY) ; 12(24): 24570-24578, 2020 11 24.
Article in English | MEDLINE | ID: covidwho-1011832

ABSTRACT

As of May 5, 2020, the number of confirmed coronavirus disease (COVID-19) cases has been more than 3.5 million with 243,540 deaths. We aimed to determine the associations between ageing population, median age, life expectancy at birth and COVID-19 mortality. The numbers of COVID-19 cases and deaths in the European region were obtained from the World Health Organization database. The data on percentage of the population aged 65 and over, median age and life expectancy at birth were extracted from the World Factbook of Central Intelligence Agency. A total of 56 countries/areas in the Europe reported COVID-19 cases and deaths (1,121,853 cases and 100,938 deaths) on April 20, 2020. The results showed significant positive associations between COVID-19 mortality and ageing population (r =0.274; P =0.021), median age (r =0.255; P=0.029), male median age (r =0.284; P =0.017), female median age (r =0.224; P=0.049), life expectancy at birth (r =0.336; P=0.006), male life expectancy at birth (r =0.342; P=0.005), female life expectancy at birth (r =0.312; P=0.01) in the 56 European countries/areas. This study illustrated that COVID-19 mortality was positively associated with ageing population, median age, and life expectancy at birth.


Subject(s)
COVID-19/epidemiology , Life Expectancy , SARS-CoV-2 , Adult , Age Factors , Aged , Aged, 80 and over , COVID-19/mortality , COVID-19/virology , Europe/epidemiology , Female , Humans , Male , Middle Aged , Mortality , Population Surveillance
18.
bioRxiv ; 2020 Sep 23.
Article in English | MEDLINE | ID: covidwho-807603

ABSTRACT

Pre-existing immune responses to seasonal endemic coronaviruses could have profound consequences for antibody responses to SARS-CoV-2, either induced in natural infection or through vaccination. Such consequences are well established in the influenza and flavivirus fields. A first step to establish whether pre-existing responses can impact SARS-CoV-2 infection is to understand the nature and extent of cross-reactivity in humans to coronaviruses. We compared serum antibody and memory B cell responses to coronavirus spike (S) proteins from pre-pandemic and SARS-CoV-2 convalescent donors using a series of binding and functional assays. We found weak evidence of pre-existing SARS-CoV-2 cross-reactive serum antibodies in pre-pandemic donors. However, we found stronger evidence of pre-existing cross-reactive memory B cells that were activated on SARS-CoV-2 infection. Monoclonal antibodies (mAbs) isolated from the donors showed varying degrees of cross-reactivity with betacoronaviruses, including SARS and endemic coronaviruses. None of the cross-reactive mAbs were neutralizing except for one that targeted the S2 subunit of the S protein. The results suggest that pre-existing immunity to endemic coronaviruses should be considered in evaluating antibody responses to SARS-CoV-2.

19.
Mycopathologia ; 185(4): 599-606, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-691142

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been sweeping across the globe. Based on a retrospective analysis of SARS and influenza data from China and worldwide, we surmise that the fungal co-infections associated with global COVID-19 might be missed or misdiagnosed. Although there are few publications, COVID-19 patients, especially severely ill or immunocompromised, have a higher probability of suffering from invasive mycoses. Aspergillus and Candida infections in COVID-19 patients will require early detection by a comprehensive diagnostic intervention (histopathology, direct microscopic examination, culture, (1,3)-ß-D-glucan, galactomannan, and PCR-based assays) to ensure effective treatments. We suggest it is prudent to assess the risk factors, the types of invasive mycosis, the strengths and limitations of diagnostic methods, clinical settings, and the need for standard or individualized treatment in COVID-19 patients. We provide a clinical flow diagram to assist the clinicians and laboratory experts in the management of aspergillosis, candidiasis, mucormycosis, or cryptococcosis as co-morbidities in COVID-19 patients.


Subject(s)
Coronavirus Infections/complications , Mycoses/complications , Pneumonia, Viral/complications , COVID-19 , Candidiasis, Invasive/complications , Candidiasis, Invasive/diagnosis , Candidiasis, Invasive/therapy , China , Coronavirus Infections/diagnosis , Cryptococcosis/complications , Cryptococcosis/diagnosis , Cryptococcosis/therapy , Humans , Invasive Pulmonary Aspergillosis/complications , Invasive Pulmonary Aspergillosis/diagnosis , Invasive Pulmonary Aspergillosis/therapy , Mucormycosis/complications , Mucormycosis/diagnosis , Mucormycosis/therapy , Mycoses/diagnosis , Mycoses/therapy , Pandemics , Pneumonia, Viral/diagnosis
20.
Biocell ; 2(44): 127-135, 2020.
Article in English | WHO COVID, ELSEVIER | ID: covidwho-599888

ABSTRACT

From late December 2019 a new human-adapted coronavirus, SARS-CoV-2, was observed and isolated in clustered patients in Wuhan, China. It has been proved to be able to transmit human-to-human and cause pneumonia, leading to about 2% fatality. Its genome characteristics, immune responses and related potential treatments, such as chemical drugs, serum transfusion and vaccines including DNA vaccines, are discussed in this review for a brief summary.

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