Article
Biochemistry & Molecular Biology
Markus Hoffmann, Nadine Krueger, Sebastian Schulz, Anne Cossmann, Cheila Rocha, Amy Kempf, Inga Nehlmeier, Luise Graichen, Anna-Sophie Moldenhauer, Martin S. Winkler, Martin Lier, Alexandra Dopfer-Jablonka, Hans-Martin Jaeck, Georg M. N. Behrens, Stefan Poehlmann
Summary: The Omicron variant of SARS-CoV-2 is spreading rapidly and shows resistance to most therapeutic antibodies. It also evades neutralization by antibodies induced by infection or vaccination more efficiently than the Delta variant. This suggests that therapeutic antibodies may not be effective against the Omicron variant, and double vaccination with BNT162b2 may not provide adequate protection against severe disease caused by this variant.
Article
Biochemistry & Molecular Biology
Baoling Ying, Suzanne M. Scheaffer, Bradley Whitener, Chieh-Yu Liang, Oleksandr Dmytrenko, Samantha Mackin, Kai Wu, Diana Lee, Laura E. Avena, Zhenlu Chong, James Brett Case, LingZhi Ma, Thu T. M. Kim, Caralyn E. Sein, Angela Woods, Daniela Montes Berrueta, Gwo-Yu Chang, Guillaume Stewart-Jones, Isabella Renzi, Yen-Ting Lai, Agata Malinowski, Andrea Carfi, Sayda M. Elbashir, Darin K. Edwards, Larissa B. Thackray, Michael S. Diamond
Summary: The study showed that current vaccination can enhance protection against Omicron infections, but different vaccines have varying efficacy, which requires further investigation.
Article
Immunology
Masaud Shah, Hyun Goo Woo
Summary: The new SARS-CoV-2 variant Omicron has enhanced transmissibility and multiple mutations that may weaken the effectiveness of therapeutic antibodies. Computational studies have shown that Omicron binds to ACE2 with a higher strength and specific mutations contribute significantly to the binding energies. These mutations also result in a drop in the electrostatic potential between RBDOmic and monoclonal antibodies, particularly etesevimab, bamlanivimab, and CT-p59. Sotrovimab, which targets a conserved epitope on the Spike protein, could be used as a cocktail therapy for Omicron-driven COVID-19.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Brechje de Gier, Anne J. Huiberts, Christina E. Hoeve, Gerco den Hartog, Henri van Werkhoven, Rob van Binnendijk, Susan J. M. Hahne, Hester E. de Melker, Susan van den Hof, Mirjam J. Knol
Summary: The study shows that hybrid immunity (vaccination plus previous infection) provides the strongest protection against Omicron SARS-CoV-2 infection. The increasing proportion of individuals with hybrid immunity from COVID-19 vaccination and previous infection may affect the risk of new infection.
NATURE COMMUNICATIONS
(2023)
Article
Medicine, General & Internal
Stephanie J. Schrag, Jennifer R. Verani, Brian E. Dixon, Jessica M. Page, Kristen A. Butterfield, Manjusha Gaglani, Gabriela Vazquez-Benitez, Ousseny Zerbo, Karthik Natarajan, Toan C. Ong, Victoria Lazariu, Suchitra Rao, Ryan Beaver, Sascha R. Ellington, Nicola P. Klein, Stephanie A. Irving, Shaun J. Grannis, Salome Kiduko, Michelle A. Barron, John Midturi, Monica Dickerson, Ned Lewis, Melissa S. Stockwell, Edward Stenehjem, William F. Fadel, Ruth Link-Gelles, Kempapura Murthy, Kristin Goddard, Nancy Grisel, Nimish R. Valvi, Bruce Fireman, Julie Arndorfer, Deepika Konatham, Sarah Ball, Mark G. Thompson, Allison L. Naleway
Summary: This study found that maternal mRNA COVID-19 vaccination, including booster doses, provided protection against medically attended COVID-19. Vaccine effectiveness estimates were higher for COVID-19-associated hospitalizations compared to emergency department/urgent care visits, and lower for the Omicron variant than the Delta variant. Protection decreased over time, especially during the Omicron predominance.
Article
Medicine, General & Internal
Sandy Y. Joung, Joseph E. Ebinger, Nancy Sun, Yunxian Liu, Min Wu, Amber B. Tang, John C. Prostko, Edwin C. Frias, James L. Stewart, Kimia Sobhani, Susan Cheng
Summary: This study examined awareness of infectious status among individuals during the recent Omicron variant surge in Los Angeles County. The results showed that more than half of adults with recent Omicron variant infection were unaware of their infectious status, and awareness was higher among healthcare employees than non-employees.
Review
Virology
Yousra Kherabi, Odile Launay, Liem Binh Luong Nguyen
Summary: This review presents the principles and methods of vaccine effectiveness studies and summarizes the main available results on the efficacy of COVID-19 vaccines, particularly during the Omicron variant circulation. The results show that the efficacy of COVID-19 vaccines has been globally confirmed in real-world studies, and highlight the importance of booster doses in maintaining a high level of protection against severe forms. However, there are still challenges regarding booster doses and the duration of immunity, especially in specific subpopulations, as well as the need for adapted vaccines.
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: Early studies indicate that the BA.2 lineage may contribute to the prolongation of the Omicron wave.
Article
Public, Environmental & Occupational Health
Brief Report Haemin Kim, Hyo-Shin Kim, Hyun Mi Kim, Mi Ju Kim, Ki Tae Kwon, Hyun-Hwa Cha, Won Joon Seong
Summary: This study compared the clinical course of pregnant women with COVID-19 before and after the emergence of the omicron variant, taking into account vaccination status. A retrospective review of medical records revealed a decrease in disease severity and morbidity during the omicron era. Vaccination rates among patients were higher after the emergence of the variant. Overall, patients had a more favorable clinical course during the omicron era, and vaccinated individuals were better protected, highlighting the importance of vaccination against COVID-19.
AMERICAN JOURNAL OF INFECTION CONTROL
(2023)
Article
Immunology
Rapeepong Suphanchaimat, Pard Teekasap, Natthaprang Nittayasoot, Mathudara Phaiyarom, Nisachol Cetthakrikul
Summary: This study aimed to forecast the trends in COVID-19 cases and deaths from the Omicron variant in Thailand using different scenarios. The most pessimistic scenario predicted a peak in cases and deaths, while the most optimistic scenario showed a lower peak in cases. Thailand may face a new wave of the COVID-19 epidemic due to the Omicron variant, but the death toll is expected to be proportionately lower. Vaccination campaigns for booster doses should be expedited to prevent severe illnesses and deaths.
Review
Medicine, General & Internal
Zeinab Mohseni Afshar, Ali Tavakoli Pirzaman, Bardia Karim, Shiva Rahimipour Anaraki, Rezvan Hosseinzadeh, Elaheh Sanjari Pireivatlou, Arefeh Babazadeh, Dariush Hosseinzadeh, Seyed Rouhollah Miri, Terence T. Sio, Mark J. M. Sullman, Mohammad Barary, Soheil Ebrahimpour
Summary: Since the COVID-19 pandemic began, new variants of the SARS-CoV-2 virus have emerged with different sets of mutations, resulting in changes in pathogenicity, transmissibility, and morbidity. The most recent variant of concern is the Omicron variant, which is distinct from earlier variants. Diagnosis of the Omicron variant can be made using RT-PCR tests, rapid antigen assays, and chest CT scans, and therapeutic options include various drugs and treatments. The Omicron variant poses a threat to unvaccinated individuals due to its high transmissibility, pathogenicity, and infectivity, despite being milder than previous variants.
Review
Virology
Chao Wang, Bei Liu, Sihui Zhang, Ninghua Huang, Tianshuo Zhao, Qing-Bin Lu, Fuqiang Cui
Summary: This study aims to evaluate the evolution differences in the incidence and case fatality rate of SARS-CoV-2 Delta and Omicron variants. The findings suggest that the Omicron variant has a higher incidence but a lower case fatality rate worldwide, mainly due to the decreased pathogenicity caused by the mutation of the virus, while vaccination still plays a valuable role in preventing death.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Medicine, General & Internal
Irit Ayalon-Dangur, Adi Turjeman, Bar Basharim, Noa Bigman-Peer, Einat Magid, Hefziba Green, Tzippy Shochat, Alon Grossman, Jihad Bishara, Noa Eliakim-Raz
Summary: This study aimed to describe the rates and risk factors of hospital re-admissions two months following discharge during the fifth wave of the COVID-19 pandemic caused by the Omicron variant. The findings revealed higher re-admission rates compared to previous waves, with elevated creatinine being associated with a higher risk. Therefore, developing a discharge plan for surveillance and treatment is crucial in the management of pandemics.
JOURNAL OF CLINICAL MEDICINE
(2022)
Review
Infectious Diseases
David S. Y. Ong, Paraskevi C. Fragkou, Valentijn A. Schweitzer, Roy F. Chemaly, Charalampos D. Moschopoulos, Chrysanthi Skevaki
Summary: Molecular tests are considered the gold standard for COVID-19 diagnostics, but serological and immunological tests can also be valuable in certain situations. The presence of antibodies against SARS-CoV-2 may indicate a recent or past COVID-19 infection, and tests like ELISA and CLIA have higher sensitivities. Cellular immunity is crucial in host defences against viruses, and T-cell responses against SARS-CoV-2 can provide important information on past infections.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Review
Biochemistry & Molecular Biology
Abdul Hawil Abas, Siti Marfuah, Rinaldi Idroes, Diah Kusumawaty, Fatimawali, Moon Nyeo Park, Abolghasem Siyadatpanah, Fahad A. Alhumaydhi, Shafi Mahmud, Trina Ekawati Tallei, Talha Bin Emran, Bonglee Kim
Summary: The COVID-19 pandemic caused by the SARS-CoV-2 virus is still ongoing, with the Omicron variant being the latest mutation. While Omicron shows increased transmissibility, it also appears to have milder symptoms and lower hospitalization rates, especially among vaccinated individuals. This has led to speculation that Omicron could provide a natural form of vaccination, potentially leading to the end of the pandemic. However, it is important to note that subsequent mutations may not necessarily result in less severe disease, highlighting the need for ongoing vaccinations to adapt to the evolving virus.
Article
Biochemical Research Methods
Rafael D. Melani, Benjamin J. Des Soye, Jared O. Kafader, Eleonora Forte, Michael Hollas, Voislav Blagojevic, Fernanda Negrao, John P. McGee, Bryon Drown, Cameron Lloyd-Jones, Henrique S. Seckler, Jeannie M. Camarillo, Philip D. Compton, Richard D. LeDuc, Bryan Early, Ryan T. Fellers, Byoung-Kyu Cho, Basil Baby Mattamana, Young Ah Goo, Paul M. Thomas, Michelle K. Ash, Pavan P. Bhimalli, Lena Al-Harthi, Beverly E. Sha, Jeffrey R. Schneider, Neil L. Kelleher
Summary: Ig-MS is a novel serological readout capturing the immunoglobulin repertoire at molecular resolution without sequencing of B cells. This method can be used to assess exposure or immunity to a pathogen.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Michael A. R. Hollas, Matthew T. Robey, Ryan T. Fellers, Richard D. LeDuc, Paul M. Thomas, Neil L. Kelleher
Summary: The Human Proteoform Atlas is an online repository storing experimentally verified human proteoforms, using a FAIR system to assign persistent identifiers and facilitate tracking and organization. Users can submit new proteoforms via email, and future iterations will help in studying and organizing these protein molecules further.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Hannah J. Barbian, Melanie S. Seaton, Srinivas D. Narasipura, Jennillee Wallace, Reshma Rajan, Beverly E. Sha, Lena Al-Harthi
Summary: Latency is the main obstacle towards an HIV cure, and targeting multiple latency maintenance pathways is essential. In this study, beta-catenin, a transcriptional co-activator and central mediator of Wnt signaling, is identified as a regulator of HIV latency. Inhibiting or activating the beta-catenin pathway can reactivate or repress HIV, and it also enhances or inhibits the activity of other HIV latency reversing agents.
Article
Biochemistry & Molecular Biology
Luis F. Schachner, Benjamin Des Soye, Soo Ro, Grace E. Kenney, Ashley N. Ives, Taojunfeng Su, Young Ah Goo, Michael C. Jewett, Amy C. Rosenzweig, Neil L. Kelleher
Summary: The phosphorylation of triosephosphate isomerase (TPI) enhances its activity and facilitates substrate binding to the active site. Hetero-dimerization and subunit asymmetry are key features of TPI, and tetramerization plays a crucial role in enzymatic regulation. This study highlights the importance of studying endogenous proteoforms for understanding the functional role of post-translational modifications (PTMs).
ACS CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Pei Su, John P. McGee, Kenneth R. Durbin, Michael A. R. Hollas, Manxi Yang, Elizabeth K. Neumann, Jamie L. Allen, Bryon S. Drown, Fatma Ayaloglu Butun, Joseph B. Greer, Bryan P. Early, Ryan T. Fellers, Jeffrey M. Spraggins, Julia Laskin, Jeannie M. Camarillo, Jared O. Kafader, Neil L. Kelleher
Summary: Imaging of proteoforms in human tissues is limited by low molecular specificity and proteome coverage. Proteoform imaging mass spectrometry (PiMS) overcomes these limitations by increasing the size limit for proteoform detection and identification, and revealing the spatial localization of proteoforms in tissues at high resolution.
Article
Chemistry, Analytical
John P. McGee, Michael W. Senko, Kevin Jooss, Benjamin J. Des Soye, Philip D. Compton, Neil L. Kelleher, Jared O. Kafader
Summary: Charge detection mass spectrometry (CDMS) is a method for detecting mass spectra of large and highly heterogeneous analytes. CDMS has been multiplexed on Orbitrap instruments to achieve Individual Ion Mass Spectrometry (I2MS). In this study, an automated method called Automatic Ion Control (AIC) was developed to adjust ion injection times in I2MS for image current detectors like the Orbitrap. AIC utilizes signal density in the m/z domain to adjust ions in real-time for sample adaptability, online separations, and ease of use. The technique was successfully applied to denatured and native proteins, producing high quality data without human intervention directly in the mass domain.
ANALYTICAL CHEMISTRY
(2022)
Article
Microbiology
Elena Whitney, David Pitrak, Kathleen G. Beavis, Nicholas M. Moore, Shivanjali Shankaran, Ana Precy Abeleda, Jessica Schmitt, Beverly E. Sha
Summary: This study identifies the accuracy of using S/CO ratio and antigen index (Al) to improve the diagnosis accuracy of acute HIV infection (AHI). The results show that a threshold value of 3.78 for S/CO ratio and 2.83 for Al can provide high sensitivity and specificity in identifying AHI patients. However, there may still be false-positive results, indicating the possibility of biological false-positives.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Chemistry, Physical
Jarrett L. Mason, Caleb D. Huizenga, Manisha Ray, Jared O. Kafader, Caroline Chick Jarrold
Summary: The electronic structure of mixed Ce-Pt clusters has been studied experimentally and theoretically. The clusters exhibit unique magnetic and electron coupling properties, which have potential implications for the study of Ce-rich intermetallic materials.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Biochemical Research Methods
John P. McGee, Rafael D. Melani, Ben Des Soye, Derek Croote, Valerie Winton, Stephen R. Quake, Jared O. Kafader, Neil L. Kelleher
Summary: This study used native tandem mass spectrometry to probe antibody-antigen complexes and successfully characterized the molecular composition of protein antigens. The results demonstrated the potential of native top-down mass spectrometry as a platform for precise and thorough characterization of immunocomplexes, enabling the discovery of antigen proteoforms and their binding sites.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Mathematical & Computational Biology
Taojunfeng Su, Michael A. R. Hollas, Ryan T. Fellers, Neil L. Kelleher
Summary: Alternative splicing plays a crucial role in regulating gene expression and protein diversity in eukaryotic cells. Traditional short-read RNA sequencing has been widely used for studying alternative splicing, but the emergence of long-read RNA sequencing and top-down mass spectrometry offers new opportunities to identify alternative splicing events and protein isoforms with higher accuracy. This review summarizes the recent improvements in short-read RNA sequencing and computational methods for alternative splicing analysis, as well as the approaches used in top-down proteomics to identify protein isoforms. However, future efforts are needed to further enhance the effectiveness, integration, and proteome coverage of alternative splicing events.
ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE
(2023)
Article
Biochemical Research Methods
Nickolas P. Fisher, John P. McGee, Kyle P. Bowen, Michael Goodwin, Michael W. Senko, Neil L. Kelleher, Jared O. Kafader
Summary: Ion mobility spectrometry (IMS) measurements of collision cross section (CCS) provide valuable information about the structure of proteins in gas phase, which complements mass analysis. Methods for determining CCS without a dedicated IMS system have been developed for Fourier transform mass spectrometry (FT-MS) platforms. Individual ion mass spectrometry (IMS-M-2) allows charge detection and measures ion lifetimes throughout the detection event of FT-MS, enabling simultaneous determination of charge, mass, and CCS for proteins and complexes ranging in size from approximately 8 to approximately 232 kDa.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Meeting Abstract
Biochemical Research Methods
Pei Su, John P. McGee, Kenneth R. Durbin, Michael A. Hollas, Ryan T. Fellers, Jeannie M. Camarillo, Jared O. Kafader, Neil L. Kelleher
MOLECULAR & CELLULAR PROTEOMICS
(2022)
