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  1. Article ; Online: Immune imprinting as a barrier to effective COVID-19 vaccines.

    Faraone, Julia N / Liu, Shan-Lu

    Cell reports. Medicine

    2023  Volume 4, Issue 11, Page(s) 101291

    Abstract: Wang and colleagues show that immune imprinting impairs neutralizing antibody titers for bivalent mRNA vaccination against SARS-CoV-2 Omicron subvariants. Imprinting from three doses of monovalent vaccine can be alleviated by BA.5 or BQ-lineage ... ...

    Abstract Wang and colleagues show that immune imprinting impairs neutralizing antibody titers for bivalent mRNA vaccination against SARS-CoV-2 Omicron subvariants. Imprinting from three doses of monovalent vaccine can be alleviated by BA.5 or BQ-lineage breakthrough infection but not by a bivalent booster.
    MeSH term(s) Humans ; COVID-19 Vaccines ; COVID-19/prevention & control ; SARS-CoV-2/genetics ; Breakthrough Infections ; RNA, Messenger
    Chemical Substances COVID-19 Vaccines ; RNA, Messenger
    Language English
    Publishing date 2023-11-21
    Publishing country United States
    Document type Journal Article ; Comment
    ISSN 2666-3791
    ISSN (online) 2666-3791
    DOI 10.1016/j.xcrm.2023.101291
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Neutralizing antibody response to SARS-CoV-2 bivalent mRNA vaccine in SIV-infected rhesus macaques: Enhanced immunity to XBB subvariants by two-dose vaccination.

    Faraone, Julia N / Wang, Xiaolwei / Qu, Panke / Zheng, Yi-Min / Vincent, Eunice / Xu, Huanbin / Liu, Shan-Lu

    Journal of medical virology

    2024  Volume 96, Issue 3, Page(s) e29520

    Abstract: The evolution of SARS-CoV-2 paired with immune imprinting by prototype messenger RNA (mRNA) vaccine has challenged the current vaccination efficacy against newly emerged Omicron subvariants. In our study, we investigated a cohort of macaques infected by ... ...

    Abstract The evolution of SARS-CoV-2 paired with immune imprinting by prototype messenger RNA (mRNA) vaccine has challenged the current vaccination efficacy against newly emerged Omicron subvariants. In our study, we investigated a cohort of macaques infected by SIV and vaccinated with two doses of bivalent Pfizer mRNA vaccine containing wildtype and BA.5 spikes. Using a pseudotyped lentivirus neutralization assay, we determined neutralizing antibody (nAb) titers against new XBB variants, i.e., XBB.1.5, XBB.1.16, and XBB.2.3, alongside D614G and BA.4/5. We found that compared to humans vaccinated with three doses of monovalent mRNA vaccine plus a bivalent booster, the monkeys vaccinated with two doses of bivalent mRNA vaccines exhibited relatively increased titers against XBB subvariants. Of note, SIV-positive dam macaques had reduced nAb titers relative to SIV-negative dams. Additionally, SIV positive dams that received antiretroviral therapy had lower nAb titers than untreated dams. Our study underscores the importance of reformulating the COVID-19 vaccine to better protect against newly emerged XBB subvariants as well as the need for further investigation of vaccine efficacy in individuals living with HIV-1.
    MeSH term(s) Humans ; Animals ; Macaca mulatta ; Vaccines, Combined ; mRNA Vaccines ; SARS-CoV-2/genetics ; COVID-19 Vaccines ; COVID-19/prevention & control ; Vaccination ; Antibodies, Neutralizing ; RNA, Messenger ; Antibodies, Viral
    Chemical Substances Vaccines, Combined ; mRNA Vaccines ; COVID-19 Vaccines ; Antibodies, Neutralizing ; RNA, Messenger ; Antibodies, Viral
    Language English
    Publishing date 2024-03-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.29520
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: SARS-CoV-2 and Emerging Foodborne Pathogens: Intriguing Commonalities and Obvious Differences.

    Abdelhamid, Ahmed G / Faraone, Julia N / Evans, John P / Liu, Shan-Lu / Yousef, Ahmed E

    Pathogens (Basel, Switzerland)

    2022  Volume 11, Issue 8

    Abstract: The coronavirus disease 2019 (COVID-19) has resulted in tremendous human and economic losses around the globe. The pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus that is closely related to SARS-CoV and ... ...

    Abstract The coronavirus disease 2019 (COVID-19) has resulted in tremendous human and economic losses around the globe. The pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus that is closely related to SARS-CoV and other human and animal coronaviruses. Although foodborne diseases are rarely of pandemic proportions, some of the causative agents emerge in a manner remarkably similar to what was observed recently with SARS-CoV-2. For example, Shiga toxin-producing
    Language English
    Publishing date 2022-07-27
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2695572-6
    ISSN 2076-0817
    ISSN 2076-0817
    DOI 10.3390/pathogens11080837
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: SARS-CoV-2 and Emerging Foodborne Pathogens: Intriguing Commonalities and Obvious Differences

    Abdelhamid, Ahmed G. / Faraone, Julia N. / Evans, John P. / Liu, Shan-Lu / Yousef, Ahmed E.

    Pathogens. 2022 July 27, v. 11, no. 8

    2022  

    Abstract: The coronavirus disease 2019 (COVID-19) has resulted in tremendous human and economic losses around the globe. The pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus that is closely related to SARS-CoV and ... ...

    Abstract The coronavirus disease 2019 (COVID-19) has resulted in tremendous human and economic losses around the globe. The pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus that is closely related to SARS-CoV and other human and animal coronaviruses. Although foodborne diseases are rarely of pandemic proportions, some of the causative agents emerge in a manner remarkably similar to what was observed recently with SARS-CoV-2. For example, Shiga toxin-producing Escherichia coli (STEC), the most common cause of hemolytic uremic syndrome, shares evolution, pathogenesis, and immune evasion similarities with SARS-CoV-2. Both agents evolved over time in animal hosts, and during infection, they bind to specific receptors on the host cell’s membrane and develop host adaptation mechanisms. Mechanisms such as point mutations and gene loss/genetic acquisition are the main driving forces for the evolution of SARS-CoV-2 and STEC. Both pathogens affect multiple body organs, and the resulting diseases are not completely cured with non-vaccine therapeutics. However, SARS-CoV-2 and STEC obviously differ in the nature of the infectious agent (i.e., virus vs. bacterium), disease epidemiological details (e.g., transmission vehicle and symptoms onset time), and disease severity. SARS-CoV-2 triggered a global pandemic while STEC led to limited, but sometimes serious, disease outbreaks. The current review compares several key aspects of these two pathogenic agents, including the underlying mechanisms of emergence, the driving forces for evolution, pathogenic mechanisms, and the host immune responses. We ask what can be learned from the emergence of both infectious agents in order to alleviate future outbreaks or pandemics.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; Severe acute respiratory syndrome-related coronavirus ; Shiga toxin-producing Escherichia coli ; bacteria ; disease severity ; evolution ; gene deletion ; hemolytic uremic syndrome ; humans ; immune evasion ; pandemic ; pathogenesis ; pathogens ; therapeutics ; viruses
    Language English
    Dates of publication 2022-0727
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2695572-6
    ISSN 2076-0817
    ISSN 2076-0817
    DOI 10.3390/pathogens11080837
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants.

    Qu, Panke / Xu, Kai / Faraone, Julia N / Goodarzi, Negin / Zheng, Yi-Min / Carlin, Claire / Bednash, Joseph S / Horowitz, Jeffrey C / Mallampalli, Rama K / Saif, Linda J / Oltz, Eugene M / Jones, Daniel / Gumina, Richard J / Liu, Shan-Lu

    Cell

    2024  Volume 187, Issue 3, Page(s) 585–595.e6

    Abstract: Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and XBB-derived variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose- ... ...

    Abstract Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and XBB-derived variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose-vaccinated and bivalent-vaccinated healthcare workers, XBB.1.5-wave-infected first responders, and monoclonal antibody (mAb) S309. We assessed the biology of the variant spikes by measuring viral infectivity and membrane fusogenicity. BA.2.86 is less immune evasive compared to FLip and other XBB variants, consistent with antigenic distances. Importantly, distinct from XBB variants, mAb S309 was unable to neutralize BA.2.86, likely due to a D339H mutation based on modeling. BA.2.86 had relatively high fusogenicity and infectivity in CaLu-3 cells but low fusion and infectivity in 293T-ACE2 cells compared to some XBB variants, suggesting a potentially different conformational stability of BA.2.86 spike. Overall, our study underscores the importance of SARS-CoV-2 variant surveillance and the need for updated COVID-19 vaccines.
    MeSH term(s) Humans ; Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19/immunology ; COVID-19 Vaccines ; Immune Evasion ; SARS-CoV-2/classification ; SARS-CoV-2/physiology
    Chemical Substances Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines
    Language English
    Publishing date 2024-01-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2023.12.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Distinct patterns of SARS-CoV-2 BA.2.87.1 and JN.1 variants in immune evasion, antigenicity, and cell-cell fusion.

    Li, Pei / Liu, Yajie / Faraone, Julia N / Hsu, Cheng Chih / Chamblee, Michelle / Zheng, Yi-Min / Carlin, Claire / Bednash, Joseph S / Horowitz, Jeffrey C / Mallampalli, Rama K / Saif, Linda J / Oltz, Eugene M / Jones, Daniel / Li, Jianrong / Gumina, Richard J / Liu, Shan-Lu

    mBio

    2024  , Page(s) e0075124

    Abstract: The rapid evolution of SARS-CoV-2 variants presents a constant challenge to the global vaccination effort. In this study, we conducted a comprehensive investigation into two newly emerged variants, BA.2.87.1 and JN.1, focusing on their neutralization ... ...

    Abstract The rapid evolution of SARS-CoV-2 variants presents a constant challenge to the global vaccination effort. In this study, we conducted a comprehensive investigation into two newly emerged variants, BA.2.87.1 and JN.1, focusing on their neutralization resistance, infectivity, antigenicity, cell-cell fusion, and spike processing. Neutralizing antibody (nAb) titers were assessed in diverse cohorts, including individuals who received a bivalent mRNA vaccine booster, patients infected during the BA.2.86/JN.1-wave, and hamsters vaccinated with XBB.1.5-monovalent vaccine. We found that BA.2.87.1 shows much less nAb escape from WT-BA.4/5 bivalent mRNA vaccination and JN.1-wave breakthrough infection sera compared to JN.1 and XBB.1.5. Interestingly, BA.2.87.1 is more resistant to neutralization by XBB.1.5-monovalent-vaccinated hamster sera than BA.2.86/JN.1 and XBB.1.5, but efficiently neutralized by a class III monoclonal antibody S309, which largely fails to neutralize BA.2.86/JN.1. Importantly, BA.2.87.1 exhibits higher levels of infectivity, cell-cell fusion activity, and furin cleavage efficiency than BA.2.86/JN.1. Antigenically, we found that BA.2.87.1 is closer to the ancestral BA.2 compared to other recently emerged Omicron subvariants including BA.2.86/JN.1 and XBB.1.5. Altogether, these results highlight immune escape properties as well as biology of new variants and underscore the importance of continuous surveillance and informed decision-making in the development of effective vaccines.
    Importance: This study investigates the recently emerged SARS-CoV-2 variants, BA.2.87.1 and JN.1, in comparison to earlier variants and the parental D614G. Varied infectivity and cell-cell fusion activity among these variants suggest potential disparities in their ability to infect target cells and possibly pathogenesis. BA.2.87.1 exhibits lower nAb escape from bivalent mRNA vaccinee and BA.2.86/JN.1-infected sera than JN.1 but is relatively resistance to XBB.1.5-vaccinated hamster sera, revealing distinct properties in immune reason and underscoring the significance of continuing surveillance of variants and reformulation of vaccines. Antigenic differences between BA.2.87.1 and other earlier variants yield critical information not only for antibody evasion but also for viral evolution. In conclusion, this study furnishes timely insights into the spike biology and immune escape of the emerging variants BA.2.87.1 and JN.1, thus guiding effective vaccine development and informing public health interventions.
    Language English
    Publishing date 2024-04-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.00751-24
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Immune evasion and membrane fusion of SARS-CoV-2 XBB subvariants EG.5.1 and XBB.2.3.

    Faraone, Julia N / Qu, Panke / Goodarzi, Negin / Zheng, Yi-Min / Carlin, Claire / Saif, Linda J / Oltz, Eugene M / Xu, Kai / Jones, Daniel / Gumina, Richard J / Liu, Shan-Lu

    Emerging microbes & infections

    2023  Volume 12, Issue 2, Page(s) 2270069

    Abstract: Immune evasion by SARS-CoV-2 paired with immune imprinting from monovalent mRNA vaccines has resulted in attenuated neutralizing antibody responses against Omicron subvariants. In this study, we characterized two new XBB variants rising in circulation - ... ...

    Abstract Immune evasion by SARS-CoV-2 paired with immune imprinting from monovalent mRNA vaccines has resulted in attenuated neutralizing antibody responses against Omicron subvariants. In this study, we characterized two new XBB variants rising in circulation - EG.5.1 and XBB.2.3, for their neutralization and syncytia formation. We determined the neutralizing antibody titers in sera of individuals that received a bivalent mRNA vaccine booster, BA.4/5-wave infection, or XBB.1.5-wave infection. Bivalent vaccination-induced antibodies neutralized ancestral D614G efficiently, but to a much less extent, two new EG.5.1 and XBB.2.3 variants. In fact, the enhanced neutralization escape of EG.5.1 appeared to be driven by its key defining mutation XBB.1.5-F456L. Notably, infection by BA.4/5 or XBB.1.5 afforded little, if any, neutralization against EG.5.1, XBB.2.3 and previous XBB variants - especially in unvaccinated individuals, with average neutralizing antibody titers near the limit of detection. Additionally, we investigated the infectivity, fusion activity, and processing of variant spikes for EG.5.1 and XBB.2.3 in HEK293T-ACE2 and CaLu-3 cells but found no significant differences compared to earlier XBB variants. Overall, our findings highlight the continued immune evasion of new Omicron subvariants and, more importantly, the need to reformulate mRNA vaccines to include XBB spikes for better protection.
    MeSH term(s) Humans ; Membrane Fusion ; COVID-19/prevention & control ; HEK293 Cells ; Immune Evasion ; SARS-CoV-2/genetics ; Antibodies, Neutralizing ; mRNA Vaccines ; Antibodies, Viral
    Chemical Substances Antibodies, Neutralizing ; mRNA Vaccines ; Antibodies, Viral
    Language English
    Publishing date 2023-10-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2681359-2
    ISSN 2222-1751 ; 2222-1751
    ISSN (online) 2222-1751
    ISSN 2222-1751
    DOI 10.1080/22221751.2023.2270069
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Continued evasion of neutralizing antibody response by Omicron XBB.1.16.

    Faraone, Julia N / Qu, Panke / Zheng, Yi-Min / Carlin, Claire / Jones, Daniel / Panchal, Ashish R / Saif, Linda J / Oltz, Eugene M / Gumina, Richard J / Liu, Shan-Lu

    Cell reports

    2023  Volume 42, Issue 10, Page(s) 113193

    Abstract: The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to challenge the efficacy of vaccination efforts against coronavirus disease 2019 (COVID-19). The Omicron XBB lineage of SARS-CoV-2 has presented dramatic evasion of ... ...

    Abstract The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to challenge the efficacy of vaccination efforts against coronavirus disease 2019 (COVID-19). The Omicron XBB lineage of SARS-CoV-2 has presented dramatic evasion of neutralizing antibodies stimulated by mRNA vaccination and COVID-19 convalescence. XBB.1.16, characterized by two mutations relative to the dominating variant XBB.1.5, i.e., E180V and K478R, has been on the rise globally. In this study, we compare the immune escape of XBB.1.16 with XBB.1.5, alongside ancestral variants D614G, BA.2, and BA.4/5. We demonstrate that XBB.1.16 is strongly immune evasive, with extent comparable to XBB.1.5 in bivalent-vaccinated healthcare worker sera, 3-dose-vaccinated healthcare worker sera, and BA.4/5-wave convalescent sera. Interestingly, the XBB.1.16 spike is less fusogenic than that of XBB.1.5, and this phenotype requires both E180V and K478R mutations to manifest. Overall, our findings emphasize the importance of the continued surveillance of variants and the need for updated mRNA vaccine formulations.
    MeSH term(s) Humans ; Antibodies, Neutralizing ; Antibody Formation ; COVID-19 ; Convalescence ; Immune Evasion ; SARS-CoV-2 ; Antibodies, Viral
    Chemical Substances Antibodies, Neutralizing ; Antibodies, Viral
    Language English
    Publishing date 2023-09-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2023.113193
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Mass Spectral Analyses of

    Scheuch, Aaron / Moran, Sara A M / Faraone, Julia N / Unwin, Sophia R / Vu, Gialinh / Benítez, Andrea Denisse / Mohd Redzuan, Nurul Humaira / Molleur, Dana / Pardo, Sammy / Weintraub, Susan T / Thomas, Julie A

    Viruses

    2023  Volume 15, Issue 3

    Abstract: ... ...

    Abstract Salmonella
    MeSH term(s) Capsid/metabolism ; Proteolysis ; Peptide Hydrolases/metabolism ; Capsid Proteins/chemistry ; Salmonella ; Endopeptidases/genetics ; Endopeptidases/metabolism
    Chemical Substances Peptide Hydrolases (EC 3.4.-) ; Capsid Proteins ; Endopeptidases (EC 3.4.-)
    Language English
    Publishing date 2023-03-10
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15030723
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: SARS-CoV-2 Serological Investigation of White-Tailed Deer in Northeastern Ohio.

    Boley, Patricia A / Dennis, Patricia M / Faraone, Julia N / Xu, Jiayu / Liu, Mingde / Niu, Xiaoyu / Gibson, Stormy / Hale, Vanessa / Wang, Qiuhong / Liu, Shan-Lu / Saif, Linda J / Kenney, Scott P

    Viruses

    2023  Volume 15, Issue 7

    Abstract: Coronaviruses are known to cross species barriers, and spill over among animals, from animals to humans, and vice versa. SARS-CoV-2 emerged in humans in late 2019. It is now known to infect numerous animal species, including companion animals and captive ...

    Abstract Coronaviruses are known to cross species barriers, and spill over among animals, from animals to humans, and vice versa. SARS-CoV-2 emerged in humans in late 2019. It is now known to infect numerous animal species, including companion animals and captive wildlife species. Experimental infections in other animals have established that many species are susceptible to infection, with new ones still being identified. We have developed an enzyme-linked immunosorbent assay (ELISA) for detecting antibodies to SARS-CoV-2 nucleocapsid (N) and spike (S) proteins, that is both sensitive and specific. It can detect S antibodies in sera at dilutions greater than 1:10,000, and does not cross-react with antibodies to the other coronaviruses tested. We used the S antibody ELISA to test serum samples collected from 472 deer from ten sites in northeastern Ohio between November 2020 and March 2021, when the SARS-CoV-2 pandemic was first peaking in humans in Ohio, USA. Antibodies to SARS-CoV-2 were found in serum samples from every site, with an overall positivity rate of 17.2%; we further compared the viral neutralizing antibody titers to our ELISA results. These findings demonstrate the need to establish surveillance programs to monitor deer and other susceptible wildlife species globally.
    MeSH term(s) Humans ; Animals ; SARS-CoV-2 ; COVID-19/epidemiology ; COVID-19/veterinary ; Deer ; Ohio/epidemiology ; Antibodies, Viral ; Enzyme-Linked Immunosorbent Assay/methods ; Animals, Wild ; Spike Glycoprotein, Coronavirus
    Chemical Substances Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2023-07-22
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15071603
    Database MEDical Literature Analysis and Retrieval System OnLINE

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