Article
Medicine, General & Internal
De-Ming Yang, Fan-Chi Lin, Pin-Hsing Tsai, Yueh Chien, Mong-Lien Wang, Yi-Ping Yang, Tai-Jay Chang
Summary: The study analyzed mutations in the Orf10 protein of SARS-CoV-2 patients, finding varying mutation rates in different regions, with higher rates in A8 and V30. The numbers of COVID-19 patients are correlated to the death numbers, but not with the death rates, and the A8, I13, and V30 sites in the Orf10 sequence show high mutation rates.
JOURNAL OF THE CHINESE MEDICAL ASSOCIATION
(2021)
Review
Plant Sciences
Yong Feng, Mengyun Jiang, Weichang Yu, Jiannan Zhou
Summary: The increasing recognition of the roles of short/small open reading frames (sORFs) in recent years is attributed to the development and application of the Ribo-Seq technique, which allows for the identification of sORFs in various organisms. However, caution should be exercised when using RPFs to identify sORFs in plants, particularly for polyploidy species, due to the small size and complexity of the plant genome. This study compares different approaches to the identification of plant sORFs, discusses their advantages and disadvantages, and provides a guide for researchers in choosing the appropriate method for plant sORF studies.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Aziza Kantri, Jihane Ziati, Mohamed Khalis, Amal Haoudar, Karim El Aidaoui, Youssef Daoudi, Inas Chikhaoui, Khalid El Yamani, Mohammed Mouhaoui, Jalila El Bakkouri, Nezha Dini, Mohammed Mahi, Abdelhamid Naitlho, Abdelkrim Bahlaoui, Ahmed Bennana, Mustapha Noussair, Lahcen Belyamani, Chafik El Kettani
Summary: This study critically analyzed the clinical and biological characteristics of 134 patients from the North African Mediterranean region with COVID-19, finding that factors such as age, comorbidities, gender, and infection type were associated with disease progression to a severe state. Abnormalities in certain parameters were closely linked to disease deterioration.
Article
Infectious Diseases
Sailen Barik
Summary: This study conducted a comparative analysis of ORF proteins in coronaviruses, revealing that even within the same genus, the gene order or naming of the ORFs were not fully conserved. Additionally, previously unrecognized ORFs in alternative translational frames were identified, leading to the proposal of systematic numbering for ORF genes in the viral genome to standardize names and orders.
INFECTION GENETICS AND EVOLUTION
(2021)
Review
Biochemistry & Molecular Biology
Yihan Liu, Shan Zeng, Minghua Wu
Summary: With the advancement of technology, the study of noncanonical open reading frames (nORFs) is gaining increasing attention. However, the translation potential of many putative nORFs remains unclear, and the functions of noncanonical peptides have not been systematically summarized. In this review, we highlight the recent technological advances that have facilitated the research on noncanonical peptides, such as ribosome profiling, bioinformatics approaches, and CRISPR/Cas9. We also summarize the diverse functions of noncanonical peptides in cancer and explore their potential in clinical applications.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2022)
Article
Hematology
Annabelle Dupont, Antoine Rauch, Senna Staessens, Mouhamed Moussa, Mickael Rosa, Delphine Corseaux, Emmanuelle Jeanpierre, Julien Goutay, Morgan Caplan, Pauline Varlet, Guillaume Lefevre, Fanny Lassalle, Anne Bauters, Karine Faure, Marc Lambert, Alain Duhamel, Julien Labreuche, Delphine Garrigue, Simon F. De Meyer, Bart Staels, Flavien Vincent, Natacha Rousse, Eric Kipnis, Peter Lenting, Julien Poissy, Sophie Susen
Summary: The study investigated the association between endothelial damage and immune dysregulation with organ failure, thrombus formation, and death in 82 patients with COVID-19, finding a direct role of endotheliopathy in organ failure and an association between dysregulated immune response and respiratory failure, liver injury, and death. Thrombi from COVID-19 patients on extracorporeal membrane oxygenation showed increased neutrophil accumulation and neutrophil extracellular traps compared to non-COVID-19 thrombi.
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2021)
Article
Critical Care Medicine
Yaseen M. Arabi, Dunia Jawdat, Ali H. Hajeer, Musharaf Sadat, Jesna Jose, Ramesh K. Vishwakarma, Walid Almashaqbeh, Abdulaziz Al-Dawood
Summary: This study evaluated the inflammatory response in patients with severe acute respiratory infection due to the Middle East respiratory syndrome and non-Middle East respiratory syndrome, and identified two distinct inflammatory subtypes using latent class analysis. The findings showed that a subset of patients exhibited increased levels of interleukins, indicative of a cytokine storm. Further research is needed to explore the effects of immunomodulators on different inflammatory subtypes.
CRITICAL CARE MEDICINE
(2021)
Review
Cell Biology
Alyssa Zi-Xin Leong, Pey Yee Lee, M. Aiman Mohtar, Saiful Effendi Syafruddin, Yuh-Fen Pung, Teck Yew Low
Summary: This review discusses the history, development, and strategies used for identifying, validating, and characterizing sORFs and microproteins. Methods such as ribosome profiling, mass spectrometry-based proteomics, CRISPR/Cas9 screening, and protein-protein interaction studies are employed for detection and functional characterization. The review also highlights the challenges and potential solutions in identifying and validating these novel entities.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Article
Biochemical Research Methods
Mengyun Jiang, Weidong Ning, Shishi Wu, Xingwei Wang, Kun Zhu, Aomei Li, Yongyao Li, Shifeng Cheng, Bo Song
Summary: Accurate prediction of ORFs is essential for studying and utilizing genome sequences. This study introduces a novel approach utilizing nucleotide periodicity in populational genomic variants to predict ORFs and develops the OrfPP software package for validation. The method demonstrates high accuracy and reliability in various complex genomes.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Virology
Ana B. Gorini da Veiga, Leticia G. Martins, Irina Riediger, Alix Mazetto, Maria do Carmo Debur, Tatiana S. Gregianini
Summary: Respiratory viral infections can be severe, especially for children, elderly, and patients with comorbidities. In Brazil, the official surveillance system investigates various viruses, but some cases with no identified pathogens remain. This study analyzed viruses in patients without underlying diseases, revealing the potential for coronaviruses to cause severe disease in healthy adults.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Review
Infectious Diseases
Le-Le Wang, Jia-Wei Yang, Jin-Fu Xu
Summary: This article reviews the mechanisms of lung inflammation and injury caused by SARS-CoV-2 infection, including cellular inflammation, cytokine storm, and thrombotic inflammation.
CLINICAL MICROBIOLOGY AND INFECTION
(2022)
Review
Biochemistry & Molecular Biology
Xiaoping Dong, Kun Zhang, Chengfeng Xun, Tianqi Chu, Songping Liang, Yong Zeng, Zhonghua Liu
Summary: Small open reading frames (sORFs) have been previously overlooked as noncoding or transcriptional noise, but recent evidence suggests they may encode small polypeptides (SEPs) involved in various biological processes. Advances in computational algorithms, ribosome profiling, and peptidome have aided in the prediction and identification of new SEPs. This review discusses the history, development, and challenges in studying sORFs and SEPs, providing valuable insights and tools for future research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Zhiyong Li, Yajuan Fu, Jinyu Shen, Jiansheng Liang
Summary: WNK8 gene expression is post-transcriptionally regulated through an upstream open reading frame (uORF) in its 5' untranslated region, causing ribosome stalling. WNK8 and its downstream target RACK1 synergistically coordinate ABA signaling rather than antagonistically modulating glucose response and flowering.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Xiang Liu, Ali Zaid, Joseph R. Freitas, Nigel A. McMillan, Suresh Mahalingam, Adam Taylor
Summary: The study confirmed the value of the RG-rescued SARS-CoV-2 viruses in reproducing infection patterns and pathology typical of severe COVID-19 in a mouse model, providing important tools for advancing research on SARS-CoV-2 and COVID-19 therapeutics.
Letter
Immunology
Nadine Muller, Mareike Kunze, Fabienne Steitz, Neil J. Saad, Barbara Muehlemann, Joern I. Beheim-Schwarzbach, Julia Schneider, Christian Drosten, Lukas Murajda, Sandra Kochs, Claudia Ruscher, Jan Walter, Nadine Zeitlmann, Victor M. Corman
Summary: An outbreak of coronavirus disease with 74 cases related to a nightclub in Germany in March 2020 highlighted the potential for superspreader events, with staff members being particularly affected (56% attack rate) and likely causing sustained viral transmission after an event at the club. This event supports the current club closures as a precautionary measure to prevent further spread of the virus.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Microbiology
Chang Liu, Daming Zhou, Rungtiwa Nutalai, Helen M. E. Duyvesteyn, Aekkachai Tuekprakhon, Helen M. Ginn, Wanwisa Dejnirattisai, Piyada Supasa, Alexander J. Mentzer, Beibei Wang, James Brett Case, Yuguang Zhao, Donal T. Skelly, Rita E. Chen, Sile Ann Johnson, Thomas G. Ritter, Chris Mason, Tariq Malik, Nigel Temperton, Neil G. Paterson, Mark A. Williams, David R. Hall, Daniel K. Clare, Andrew Howe, Philip J. R. Goulder, Elizabeth E. Fry, Michael S. Diamond, Juthathip Mongkolsapaya, Jingshan Ren, David Stuart, Gavin R. Screaton
Summary: This study investigated several variants of SARS-CoV-2 and found that the Beta variant has the largest antigenic difference compared to other variants, such as Delta, and is poorly neutralized by serum from early pandemic and Delta viruses. The study also revealed that certain antibodies can recognize conserved neutralizing epitopes, while others target specific mutated residues in the Beta variant.
CELL HOST & MICROBE
(2022)
Letter
Medicine, General & Internal
Wanwisa Dejnirattisai, Robert H. Shaw, Piyada Supasa, Chang Liu, Arabella S. V. Stuart, Andrew J. Pollard, Xinxue Liu, Teresa Lambe, Derrick Crook, Dave I. Stuart, Juthathip Mongkolsapaya, Jonathan S. Nguyen-Van-Tam, Matthew D. Snape, Gavin R. Screaton
Article
Medicine, General & Internal
Sue Ann Costa Clemens, Lily Weckx, Ralf Clemens, Ana Verena Almeida Mendes, Alessandra Ramos Souza, Mariana B. Silveira, Suzete Nascimento Farias da Guarda, Maristela Miyamoto de Nobrega, Maria Isabel de Moraes Pinto, Isabela G. S. Gonzalez, Natalia Salvador, Marilia Miranda Franco, Renata Navis de Avila Mendonca, Isabelle Silva Queiroz Oliveira, Bruno Solano de Freitas Souza, Mayara Fraga, Parvinder Aley, Sagida Bibi, Liberty Cantrell, Wanwisa Dejnirattisai, Xinxue Liu, Juthathip Mongkolsapaya, Piyada Supasa, Gavin R. Screaton, Teresa Lambe, Merryn Voysey, Andrew J. Pollard
Summary: A study was conducted to evaluate the safety and immunogenicity of a third dose of heterologous or homologous vaccines in Brazilian adults who had previously received two doses of CoronaVac. The results showed that a third dose of heterologous vaccines (recombinant adenoviral vectored vaccine or mRNA vaccine) significantly increased immune responses and could improve protection against infection.
Article
Medicine, General & Internal
Arabella S. Stuart, Robert H. Shaw, Xinxue Liu, Melanie Greenland, Parvinder K. Aley, Nick J. Andrews, J. C. Cameron, Sue Charlton, Elizabeth A. Clutterbuck, Andrea M. Collins, Tom Darton, Tanya Dinesh, Christopher J. A. Duncan, Anna England, Saul N. Faust, Daniela M. Ferreira, Adam Finn, Anna L. Goodman, Christopher A. Green, Bassam Hallis, Paul T. Heath, Helen Hill, Bryn M. Horsington, Teresa Lambe, Rajeka Lazarus, Vincenzo Libri, Patrick J. Lillie, Yama F. Mujadidi, Ruth Payne, Emma L. Plested, Samuel Provstgaard-Morys, Maheshi N. Ramasamy, Mary Ramsay, Robert C. Read, Hannah Robinson, Gavin R. Screaton, Nisha Singh, David P. J. Turner, Paul J. Turner, Iason Vichos, Rachel White, Jonathan S. Nguyen-Van-Tam, Matthew D. Snape
Summary: The study investigated the mixed use of different COVID-19 vaccines within the same schedule, showing that in certain conditions, heterologous vaccination can achieve similar immunogenicity to homologous vaccination, facilitating rapid global vaccine deployment.
Article
Immunology
Yanchun Peng, Suet Ling Felce, Danning Dong, Frank Penkava, Alexander J. Mentzer, Xuan Yao, Guihai Liu, Zixi Yin, Ji-Li Chen, Yongxu Lu, Dannielle Wellington, Peter A. C. Wing, Delaney C. C. Dominey-Foy, Chen Jin, Wenbo Wang, Megat Abd Hamid, Ricardo A. Fernandes, Beibei Wang, Anastasia Fries, Xiaodong Zhuang, Neil Ashley, Timothy Rostron, Craig Waugh, Paul Sopp, Philip Hublitz, Ryan Beveridge, Tiong Kit Tan, Christina Dold, Andrew J. Kwok, Charlotte Rich-Griffin, Wanwisa Dejnirattisa, Chang Liu, Prathiba Kurupati, Isar Nassiri, Robert A. Watson, Orion Tong, Chelsea A. Taylor, Piyush Kumar Sharma, Bo Sun, Fabiola Curion, Santiago Revale, Lucy C. Garner, Kathrin Jansen, Ricardo C. Ferreira, Moustafa Attar, Jeremy W. Fry, Rebecca A. Russell, Hans J. Stauss, William James, Alain Townsend, Ling-Pei Ho, Paul Klenerman, Juthathip Mongkolsapaya, Gavin R. Screaton, Calliope Dendrou, Stephen N. Sansom, Rachael Bashford-Rogers, Benny Chain, Geoffrey L. Smith, Jane A. McKeating, Benjamin P. Fairfax, Paul Bowness, Andrew J. McMichael, Graham Ogg, Julian C. Knight, Tao Dong
Summary: Specific CD8(+) T cell responses targeting NP105-113-B*07:02 are associated with mild COVID-19 disease and high antiviral efficacy, providing potential targets for T cell vaccine design. These T cell responses show long-lasting preservation of antiviral functionality post-infection.
Editorial Material
Medicine, General & Internal
Kanta Subbarao
Summary: We have been fortunate to avoid the co-circulation of influenza and SARS-CoV-2 since 2020, but this situation is likely to change.
MEDICAL JOURNAL OF AUSTRALIA
(2022)
Article
Virology
Annette Fox, Louise Carolan, Vivian Leung, Hoang Vu Mai Phuong, Arseniy Khvorov, Maria Auladell, Yeu-Yang Tseng, Pham Quang Thai, Ian Barr, Kanta Subbarao, Le Thi Quynh Mai, H. Rogier van Doorn, Sheena G. Sullivan
Summary: Prior vaccination and infection have different effects on the immunogenicity and effectiveness of influenza vaccines. In this study, prior infection enhanced vaccine immunogenicity, while prior vaccination attenuated it. Comparing antibody responses to A(H3N2) viruses, it was found that prior infection increased antibody titers, while prior vaccination decreased them. This study highlights the importance of considering the immunological history when developing new vaccine strains.
Editorial Material
Biotechnology & Applied Microbiology
Brad Gilbertson, Kanta Subbarao
Summary: An influenza vaccine is created by attenuating the live virus through targeted proteolysis.
NATURE BIOTECHNOLOGY
(2022)
Article
Cell Biology
Emily Phung, Lauren A. Chang, Maryam Mukhamedova, Lijuan Yang, Deepika Nair, Scott A. Rush, Kaitlyn M. Morabito, Jason S. McLellan, Ursula J. Buchholz, John R. Mascola, Michelle C. Crank, Grace Chen, Barney S. Graham, Tracy J. Ruckwardt
Summary: RSV pre-F vaccination results in expansion and activation of RSV and HMPV F-specific B cells that contribute to long-term pneumovirus immunity.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Immunology
Hong-Su Park, Yumiko Matsuoka, Cindy Luongo, Lijuan Yang, Celia Santos, Xueqiao Liu, Laura R. H. Ahlers, Ian N. Moore, Sharmin Afroz, Reed F. Johnson, Bernard A. P. Lafont, David W. Dorward, Elizabeth R. Fischer, Craig Martens, Siba K. Samal, Shirin Munir, Ursula J. Buchholz, Cyril Le Nouen
Summary: This study used avian paramyxovirus type 3 (APMV3) as an intranasal vaccine vector to express the SARS-CoV-2 spike (S) protein. It was found that a single intranasal dose of APMV3/S-6P induced strong antibody responses and provided protection against SARS-CoV-2, demonstrating high immunogenicity and safety.
Editorial Material
Immunology
Brad Gilbertson, Kanta Subbarao
Summary: There is a widespread and unprecedented spread of highly pathogenic avian influenza A H5N1 viruses in bird species on five continents, with infections also reported in mammals, most likely caused by consuming infected birds. The increase in H5N1 virus infections in different species could lead to the emergence of new viral variants that may adapt to mammals and potentially humans. It is crucial to monitor and assess the presence of mutations in mammalian-origin H5N1 clade 2.3.4.4b viruses that could increase their risk for human pandemics. Although there have been a limited number of human cases so far, the infection of mammals provides opportunities for the virus to acquire mutations that enhance infection, replication, and spread in mammals, which were not observed in the past viruses.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
David S. Khoury, Steffen S. Docken, Kanta Subbarao, Stephen J. Kent, Miles P. Davenport, Deborah Cromer
Summary: Booster vaccination is necessary to combat waning immunity and variants of SARS-CoV-2. Data on neutralization titers from multiple sources suggest that using ancestral vaccines can enhance protection against symptomatic and severe disease caused by variant viruses. Variant-modified vaccines may provide additional benefits. This study provides evidence-based guidance for future COVID-19 vaccine regimens.
Article
Virology
Brad Gilbertson, Melanie Duncan, Kanta Subbarao
Summary: This review discusses the crucial role of viral polymerase in host adaptation of influenza A viruses (IAV), focusing on the interactions between viral polymerase genes and host factors. The known viral mutations and the adaptation of avian IAV to mammalian hosts are also highlighted.
CURRENT OPINION IN VIROLOGY
(2023)
Article
Microbiology
Marilou H. Barrios, Suellen Nicholson, Rowena A. Bull, Marianne Martinello, William Rawlinson, Michael Mina, Jeffrey J. Post, Bernard Hudson, Nicole Gilroy, Andrew R. Lloyd, Pamela Konecny, Francesca Mordant, Mike Catton, Kanta Subbarao, Leon Caly, Julian Druce, Hans J. Netter
Summary: Serological diagnostic assays are crucial for understanding an individual's immunity to SARS-CoV-2, tracking the virus spread, and evaluating population immunity. Through a dot blot assay, researchers compared the antibody profiles of individuals with different severities of COVID-19 and found patient-specific differences in the anti-SARS-CoV-2 antibody responses. These findings highlight the variability in the antibody response and the importance of considering individual differences when assessing protective antibody status.
Article
Immunology
Nicole L. Messina, Susie Germano, Rebecca McElroy, Rajeev Rudraraju, Rhian Bonnici, Laure F. Pittet, Melanie R. Neeland, Suellen Nicholson, Kanta Subbarao, Nigel Curtis
Summary: BCG vaccination has immunomodulatory effects on SARS-CoV-2 and reduces the secretion of cytokines associated with severe COVID-19. In addition, BCG vaccination promotes specific T cell immune responses and activates eosinophils.
CLINICAL & TRANSLATIONAL IMMUNOLOGY
(2022)