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  1. Article ; Online: Establishing SARS-CoV-2 membrane protein-specific antibodies as a valuable serological target via high-content microscopy.

    Williams, Daniel M / Hornsby, Hailey R / Shehata, Ola M / Brown, Rebecca / Gallis, Marta / Meardon, Naomi / Newman, Thomas A H / Plowright, Megan / Zafred, Domen / Shun-Shion, Amber S M / Hodder, Anthony J / Bliss, Deepa / Metcalfe, Andrew / Edgar, James R / Gordon, David E / Sayers, Jon R / Nicklin, Martin J / Carroll, Miles / Collini, Paul J /
    Brown, Stephen / de Silva, Thushan I / Peden, Andrew A

    iScience

    2023  Volume 26, Issue 7, Page(s) 107056

    Abstract: The prevalence and strength of serological responses mounted toward SARS-CoV-2 proteins other than nucleocapsid (N) and spike (S), which may be of use as additional serological markers, remains underexplored. Using high-content microscopy to assess ... ...

    Abstract The prevalence and strength of serological responses mounted toward SARS-CoV-2 proteins other than nucleocapsid (N) and spike (S), which may be of use as additional serological markers, remains underexplored. Using high-content microscopy to assess antibody responses against full-length StrepTagged SARS-CoV-2 proteins, we found that 85% (166/196) of unvaccinated individuals with RT-PCR confirmed SARS-CoV-2 infections and 74% (31/42) of individuals infected after being vaccinated developed detectable IgG against the structural protein M, which is higher than previous estimates. Compared with N antibodies, M IgG displayed a shallower time-dependent decay and greater specificity. Sensitivity for SARS-CoV-2 seroprevalence was enhanced when N and M IgG detection was combined. These findings indicate that screening for M seroconversion may be a good approach for detecting additional vaccine breakthrough infections and highlight the potential to use HCM as a rapidly deployable method to identify the most immunogenic targets of newly emergent pathogens.
    Language English
    Publishing date 2023-06-07
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.107056
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A high content microscopy-based platform for detecting antibodies to the nucleocapsid, spike and membrane proteins of SARS-CoV-2

    Williams, Daniel M. / Hornsby, Hayley / Shehata, Ola M. / Brown, Rebecca / Zafred, Domen / Shun-Shion, Amber S.M. / Hodder, Anthony J. / Bliss, Deepa / Metcalfe, Andrew / Edgar, James / Gordon, David E. / Sayers, Jon R. / Nicklin, Martin J. / Collini, Paul J. / Brown, Steve / de Silva, Thushan I. / Peden, Andrew A.

    medRxiv

    Abstract: The strong humoral immune response produced against the SARS-CoV-2 nucleocapsid (N) and spike (S) proteins has underpinned serological testing but the prevalence of antibody responses to other SARS-CoV-2 proteins, which may be of use as further ... ...

    Abstract The strong humoral immune response produced against the SARS-CoV-2 nucleocapsid (N) and spike (S) proteins has underpinned serological testing but the prevalence of antibody responses to other SARS-CoV-2 proteins, which may be of use as further serological markers, is still unclear. Cell-based serological screening platforms can fulfil a crucial niche in the identification of antibodies which recognise more complex folded epitopes or those incorporating post-translation modifications which may be undetectable by other methods used to investigate the antigenicity of the SARS-CoV-2 proteome. Here, we employed automated high content immunofluorescence microscopy (AHCIM) to assess the viability of such an approach as a method capable of assaying humoral immune responses against full length SARS-CoV-2 proteins in their native cellular state. We first demonstrate that AHCIM provides high sensitivity and specificity in the detection of SARS-CoV-2 N and S IgG. Assessing the prevalence of antibody responses to the SARS-CoV-2 structural membrane protein (M), we further find that 85% of COVID-19 patients within our sample set developed detectable M IgG responses (M sensitivity 85%, N sensitivity 93%, combined N + M sensitivity 95%). The identification of M as a serological marker of high prevalence may be of value in detecting additional COVID-19 cases during the era of mass SARS-CoV-2 vaccinations, where serological screening for SARS CoV-2 infections in vaccinated individuals is dependent on detection of antibodies against N. These findings highlight the advantages of using cell-based systems as serological screening platforms and raise the possibility of using M as a widespread serological marker alongside N and S.
    Keywords covid19
    Language English
    Publishing date 2021-10-18
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.10.14.21264873
    Database COVID19

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  3. Article ; Online: Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

    Gordon, David E / Hiatt, Joseph / Bouhaddou, Mehdi / Rezelj, Veronica V / Ulferts, Svenja / Braberg, Hannes / Jureka, Alexander S / Obernier, Kirsten / Guo, Jeffrey Z / Batra, Jyoti / Kaake, Robyn M / Weckstein, Andrew R / Owens, Tristan W / Gupta, Meghna / Pourmal, Sergei / Titus, Erron W / Cakir, Merve / Soucheray, Margaret / McGregor, Michael /
    Cakir, Zeynep / Jang, Gwendolyn / O'Meara, Matthew J / Tummino, Tia A / Zhang, Ziyang / Foussard, Helene / Rojc, Ajda / Zhou, Yuan / Kuchenov, Dmitry / Hüttenhain, Ruth / Xu, Jiewei / Eckhardt, Manon / Swaney, Danielle L / Fabius, Jacqueline M / Ummadi, Manisha / Tutuncuoglu, Beril / Rathore, Ujjwal / Modak, Maya / Haas, Paige / Haas, Kelsey M / Naing, Zun Zar Chi / Pulido, Ernst H / Shi, Ying / Barrio-Hernandez, Inigo / Memon, Danish / Petsalaki, Eirini / Dunham, Alistair / Marrero, Miguel Correa / Burke, David / Koh, Cassandra / Vallet, Thomas / Silvas, Jesus A / Azumaya, Caleigh M / Billesbølle, Christian / Brilot, Axel F / Campbell, Melody G / Diallo, Amy / Dickinson, Miles Sasha / Diwanji, Devan / Herrera, Nadia / Hoppe, Nick / Kratochvil, Huong T / Liu, Yanxin / Merz, Gregory E / Moritz, Michelle / Nguyen, Henry C / Nowotny, Carlos / Puchades, Cristina / Rizo, Alexandrea N / Schulze-Gahmen, Ursula / Smith, Amber M / Sun, Ming / Young, Iris D / Zhao, Jianhua / Asarnow, Daniel / Biel, Justin / Bowen, Alisa / Braxton, Julian R / Chen, Jen / Chio, Cynthia M / Chio, Un Seng / Deshpande, Ishan / Doan, Loan / Faust, Bryan / Flores, Sebastian / Jin, Mingliang / Kim, Kate / Lam, Victor L / Li, Fei / Li, Junrui / Li, Yen-Li / Li, Yang / Liu, Xi / Lo, Megan / Lopez, Kyle E / Melo, Arthur A / Moss, Frank R / Nguyen, Phuong / Paulino, Joana / Pawar, Komal Ishwar / Peters, Jessica K / Pospiech, Thomas H / Safari, Maliheh / Sangwan, Smriti / Schaefer, Kaitlin / Thomas, Paul V / Thwin, Aye C / Trenker, Raphael / Tse, Eric / Tsui, Tsz Kin Martin / Wang, Feng / Whitis, Natalie / Yu, Zanlin / Zhang, Kaihua / Zhang, Yang / Zhou, Fengbo / Saltzberg, Daniel / Hodder, Anthony J / Shun-Shion, Amber S / Williams, Daniel M / White, Kris M / Rosales, Romel / Kehrer, Thomas / Miorin, Lisa / Moreno, Elena / Patel, Arvind H / Rihn, Suzannah / Khalid, Mir M / Vallejo-Gracia, Albert / Fozouni, Parinaz / Simoneau, Camille R / Roth, Theodore L / Wu, David / Karim, Mohd Anisul / Ghoussaini, Maya / Dunham, Ian / Berardi, Francesco / Weigang, Sebastian / Chazal, Maxime / Park, Jisoo / Logue, James / McGrath, Marisa / Weston, Stuart / Haupt, Robert / Hastie, C James / Elliott, Matthew / Brown, Fiona / Burness, Kerry A / Reid, Elaine / Dorward, Mark / Johnson, Clare / Wilkinson, Stuart G / Geyer, Anna / Giesel, Daniel M / Baillie, Carla / Raggett, Samantha / Leech, Hannah / Toth, Rachel / Goodman, Nicola / Keough, Kathleen C / Lind, Abigail L / Klesh, Reyna J / Hemphill, Kafi R / Carlson-Stevermer, Jared / Oki, Jennifer / Holden, Kevin / Maures, Travis / Pollard, Katherine S / Sali, Andrej / Agard, David A / Cheng, Yifan / Fraser, James S / Frost, Adam / Jura, Natalia / Kortemme, Tanja / Manglik, Aashish / Southworth, Daniel R / Stroud, Robert M / Alessi, Dario R / Davies, Paul / Frieman, Matthew B / Ideker, Trey / Abate, Carmen / Jouvenet, Nolwenn / Kochs, Georg / Shoichet, Brian / Ott, Melanie / Palmarini, Massimo / Shokat, Kevan M / García-Sastre, Adolfo / Rassen, Jeremy A / Grosse, Robert / Rosenberg, Oren S / Verba, Kliment A / Basler, Christopher F / Vignuzzi, Marco / Peden, Andrew A / Beltrao, Pedro / Krogan, Nevan J

    Science (New York, N.Y.)

    2020  Volume 370, Issue 6521

    Abstract: The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and ...

    Abstract The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analyses for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 ORF9b, an interaction we structurally characterized using cryo-electron microscopy. Combining genetically validated host factors with both COVID-19 patient genetic data and medical billing records identified molecular mechanisms and potential drug treatments that merit further molecular and clinical study.
    MeSH term(s) COVID-19/metabolism ; Conserved Sequence ; Coronavirus Nucleocapsid Proteins/genetics ; Coronavirus Nucleocapsid Proteins/metabolism ; Cryoelectron Microscopy ; Host Microbial Interactions ; Humans ; Mitochondrial Membrane Transport Proteins/genetics ; Mitochondrial Membrane Transport Proteins/metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Phosphoproteins/genetics ; Phosphoproteins/metabolism ; Protein Conformation ; Protein Interaction Maps ; Severe acute respiratory syndrome-related coronavirus/metabolism ; SARS-CoV-2/metabolism ; Severe Acute Respiratory Syndrome/metabolism
    Chemical Substances Coronavirus Nucleocapsid Proteins ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Phosphoproteins ; TOMM70 protein, human ; nucleocapsid phosphoprotein, SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-10-15
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abe9403
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

    Gordon, David E. / Hiatt, Joseph / Bouhaddou, Mehdi / Rezelj, Veronica V. / Ulferts, Svenja / Braberg, Hannes / Jureka, Alexander S. / Obernier, Kirsten / Guo, Jeffrey Z. / Batra, Jyoti / Kaake, Robyn M. / Weckstein, Andrew R. / Owens, Tristan W. / Gupta, Meghna / Pourmal, Sergei / Titus, Erron W. / Cakir, Merve / Soucheray, Margaret / McGregor, Michael /
    Cakir, Zeynep / Jang, Gwendolyn / O’Meara, Matthew J. / Tummino, Tia A. / Zhang, Ziyang / Foussard, Helene / Rojc, Ajda / Zhou, Yuan / Kuchenov, Dmitry / Hüttenhain, Ruth / Xu, Jiewei / Eckhardt, Manon / Swaney, Danielle L. / Fabius, Jacqueline M. / Ummadi, Manisha / Tutuncuoglu, Beril / Rathore, Ujjwal / Modak, Maya / Haas, Paige / Haas, Kelsey M. / Naing, Zun Zar Chi / Pulido, Ernst H. / Shi, Ying / Barrio-Hernandez, Inigo / Memon, Danish / Petsalaki, Eirini / Dunham, Alistair / Marrero, Miguel Correa / Burke, David / Koh, Cassandra / Vallet, Thomas / Silvas, Jesus A. / Azumaya, Caleigh M. / Billesbølle, Christian / Brilot, Axel F. / Campbell, Melody G. / Diallo, Amy / Dickinson, Miles Sasha / Diwanji, Devan / Herrera, Nadia / Hoppe, Nick / Kratochvil, Huong T. / Liu, Yanxin / Merz, Gregory E. / Moritz, Michelle / Nguyen, Henry C. / Nowotny, Carlos / Puchades, Cristina / Rizo, Alexandrea N. / Schulze-Gahmen, Ursula / Smith, Amber M. / Sun, Ming / Young, Iris D. / Zhao, Jianhua / Asarnow, Daniel / Biel, Justin / Bowen, Alisa / Braxton, Julian R. / Chen, Jen / Chio, Cynthia M. / Chio, Un Seng / Deshpande, Ishan / Doan, Loan / Faust, Bryan / Flores, Sebastian / Jin, Mingliang / Kim, Kate / Lam, Victor L. / Li, Fei / Li, Junrui / Li, Yen-Li / Li, Yang / Liu, Xi / Lo, Megan / Lopez, Kyle E. / Melo, Arthur A. / Moss, Frank R. / Nguyen, Phuong / Paulino, Joana / Pawar, Komal Ishwar / Peters, Jessica K. / Pospiech, Thomas H. / Safari, Maliheh / Sangwan, Smriti / Schaefer, Kaitlin / Thomas, Paul V. / Thwin, Aye C. / Trenker, Raphael / Tse, Eric / Tsui, Tsz Kin Martin / Wang, Feng / Whitis, Natalie / Yu, Zanlin / Zhang, Kaihua / Zhang, Yang / Zhou, Fengbo / Saltzberg, Daniel / Hodder, Anthony J. / Shun-Shion, Amber S. / Williams, Daniel M. / White, Kris M. / Rosales, Romel / Kehrer, Thomas / Miorin, Lisa / Moreno, Elena / Patel, Arvind H. / Rihn, Suzannah / Khalid, Mir M. / Vallejo-Gracia, Albert / Fozouni, Parinaz / Simoneau, Camille R. / Roth, Theodore L. / Wu, David / Karim, Mohd Anisul / Ghoussaini, Maya / Dunham, Ian / Berardi, Francesco / Weigang, Sebastian / Chazal, Maxime / Park, Jisoo / Logue, James / McGrath, Marisa / Weston, Stuart / Haupt, Robert / Hastie, C. James / Elliott, Matthew / Brown, Fiona / Burness, Kerry A. / Reid, Elaine / Dorward, Mark / Johnson, Clare / Wilkinson, Stuart G. / Geyer, Anna / Giesel, Daniel M. / Baillie, Carla / Raggett, Samantha / Leech, Hannah / Toth, Rachel / Goodman, Nicola / Keough, Kathleen C. / Lind, Abigail L. / Klesh, Reyna J. / Hemphill, Kafi R. / Carlson-Stevermer, Jared / Oki, Jennifer / Holden, Kevin / Maures, Travis / Pollard, Katherine S. / Sali, Andrej / Agard, David A. / Cheng, Yifan / Fraser, James S. / Frost, Adam / Jura, Natalia / Kortemme, Tanja / Manglik, Aashish / Southworth, Daniel R. / Stroud, Robert M. / Alessi, Dario R. / Davies, Paul / Frieman, Matthew B. / Ideker, Trey / Abate, Carmen / Jouvenet, Nolwenn / Kochs, Georg / Shoichet, Brian / Ott, Melanie / Palmarini, Massimo / Shokat, Kevan M. / García-Sastre, Adolfo / Rassen, Jeremy A. / Grosse, Robert / Rosenberg, Oren S. / Verba, Kliment A. / Basler, Christopher F. / Vignuzzi, Marco / Peden, Andrew A. / Beltrao, Pedro / Krogan, Nevan J.

    Science

    2020  , Page(s) eabe9403

    Abstract: The COVID-19 (Coronavirus disease-2019) pandemic, caused by the SARS-CoV-2 coronavirus, is a significant threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and ... ...

    Abstract The COVID-19 (Coronavirus disease-2019) pandemic, caused by the SARS-CoV-2 coronavirus, is a significant threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and MERS-CoV. Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analysis for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 Orf9b, an interaction we structurally characterized using cryo-EM. Combining genetically-validated host factors with both COVID-19 patient genetic data and medical billing records identified important molecular mechanisms and potential drug treatments that merit further molecular and clinical study.
    Keywords Multidisciplinary ; covid19
    Language English
    Publisher American Association for the Advancement of Science (AAAS)
    Publishing country us
    Document type Article ; Online
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abe9403
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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