Article
Computer Science, Artificial Intelligence
Ze Zhang, Woo Yong Chang, Kaiwen Wang, Yuqiu Yang, Xinlei Wang, Chen Yao, Tuoqi Wu, Li Wang, Tao Wang
Summary: This study investigates the relationship between B-cell receptors (BCRs) and B-cell gene expression in COVID-19. The researchers found a stronger coupling between BCRs and B-cell gene expression during COVID-19 infections. They developed the Benisse model, which revealed a gradient of B-cell activation along BCR trajectories.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Microbiology
Han Sun, Hu-Qin Yang, Kan Zhai, Zhao-Hui Tong
Summary: During Pneumocystis infection, plasma cells continuously increase, while naive B cells also increase but BCR diversity decreases. Biased usage of V(D)J genes is observed, and the frequency of IGHV9-3 rises.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Artem Mikelov, Evgeniia Alekseeva, Ekaterina A. Komech, Dmitry B. Staroverov, Maria A. Turchaninova, Mikhail Shugay, Dmitriy M. Chudakov, Georgii A. Bazykin, Ivan Zvyagin
Summary: The study analyzes the longitudinal dynamics of immune memory B cells and reveals a high degree of clonal persistence within memory B cell subsets. There is convergence between memory B cells and antibody-secreting cells (ASCs) among individuals. The study identifies two clusters of expanded clonal lineages with different prevalence and persistence, suggesting the reactivation of memory B cells during proliferation and differentiation into ASCs.
Article
Immunology
Hadas Neuman, Jessica Arrouasse, Meirav Kedmi, Andrea Cerutti, Giuliana Magri, Ramit Mehr
Summary: This article introduces a tool called IgTreeZ, which analyzes Ig gene lineage trees and their repertoires, and demonstrates its reliability in mutation and selection analysis through simulations. Researchers used IgTreeZ on empirical data and found different mutation patterns in different B cell subpopulations, as well as gained insights into antigen-driven selection in COVID-19 patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Kenneth B. Hoehn, Jackson S. Turner, Frederick Miller, Ruoyi Jiang, Oliver G. Pybus, Ali H. Ellebedy, Steven H. Kleinstein
Summary: The study found that after seasonal influenza vaccination, GC B cell lineages often exhibit measurable evolution, suggesting that the poor efficacy of seasonal influenza vaccines is not solely due to the inhibition of vaccine-specific B cell evolution.
Article
Oncology
Meng Wu, Jing Zhang, Yi Wang, Lan Mi, Xiaopei Wang, Weiping Liu, Jie Fu, Haifeng Song, Yuqin Song, Jun Zhu
Summary: This study provides evidence that the presence of residual malignant B cells is connected to the clonal diversity of the resulting BCR repertoire. The study suggests that the growth rate of a patient's peripheral B cell diversity after stem cell transplant can be used as a prognostic indicator for relapse. The study also highlights the impact of tumor cells on the replenishment of the peripheral BCR immune repertoire.
Article
Immunology
Modi Safra, Zvi Tamari, Pazit Polak, Shachaf Shiber, Moshe Matan, Hani Karameh, Yigal Helviz, Adva Levy-Barda, Vered Yahalom, Avi Peretz, Eli Ben-Chetrit, Baruch Brenner, Tamir Tuller, Meital Gal-Tanamy, Gur Yaari
Summary: In this study, a machine learning approach was applied to analyze B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV2 compared with uninfected controls, successfully differentiating infected from non-infected individuals and assessing disease severity. These findings have potential implications for the development of therapeutic strategies and quantitative assessment of diagnostic and therapeutic antibodies for COVID-19.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Kris Covens, Bert Verbinnen, Britt G. de Jong, Leen Moens, Greet Wuyts, Geert Verheyen, Kris Nys, Jonathan Cremer, Stijn Smulders, Rik Schrijvers, Andreas Weinhaeusel, Severine Vermeire, Patrick Verschueren, Ellen De Langhe, Jacques J. M. van Dongen, Menno C. van Zelm, Xavier Bossuyt
Summary: Antibody-secreting cells are present in the peripheral blood of healthy individuals, and a small population of CD19+CD43+ B cells lacking CD27 expression has been characterized. These CD27-CD43+ cells exhibit similar characteristics to conventional plasmablasts but have differences in function and homing potential.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Cell Biology
Carolina Monzo, Lisonia Gkioni, Andreas Beyer, Dario Riccardo Valenzano, Sebastian Gronke, Linda Partridge
Summary: Aging impairs immune function, but dietary restriction (DR) can attenuate this decline. In this study, it was shown that DR preserves B cell receptor (BCR) repertoire diversity and reduces clonal expansions during aging in mice. Remarkably, mice starting DR in mid-life have similar BCR diversity and clonal expansion rates as mice on chronic DR. These findings suggest a potential role of B cell repertoire dynamics in age-related health.
Article
Microbiology
Mengjin Qu, Zhengmin Liang, Yulan Chen, Yuanzhi Wang, Haoran Wang, Ziyi Liu, Yiduo Liu, Yuhui Dong, Xin Ge, Hao Li, Xiangmei Zhou
Summary: Research shows that antibodies targeting the cell wall of M. bovis can protect against infection by promoting phagocytosis, inhibiting bacterial growth, and enhancing phagosome-lysosome fusion. This study highlights the importance of these antibodies in defense against tuberculosis.
MICROBIOLOGY SPECTRUM
(2023)
Article
Virology
Yudi Zhang, Qihong Yan, Kun Luo, Ping He, Ruitian Hou, Xinwei Zhao, Qian Wang, Haisu Yi, Huan Liang, Yijun Deng, Fengyu Hu, Feng Li, Xinglong Liu, Ying Feng, Pingchao Li, Linbing Qu, Zhaoming Chen, Qiang Pan-Hammarstrom, Liqiang Feng, Xuefeng Niu, Ling Chen
Summary: A comprehensive study of the B cell response against SARS-CoV-2 revealed significant clonal expansion of naive B cells with limited somatic hypermutation. The study also found a correlation between low-SHM IgG clones and spike-specific IgG antibody titers. Furthermore, the study identified a highly convergent antibody response to SARS-CoV-2, suggesting the presence of shared spike-specific IgH clusters.
JOURNAL OF VIROLOGY
(2022)
Article
Immunology
Doaa Waly, Aradana Muthupandian, Chia-Wei Fan, Harrison Anzinger, Brad G. G. Magor
Summary: This study reveals the existence of Aicda(+) cell clusters in fish that functionally resemble germinal centers in mammals. These clusters undergo B-cell clonal expansion and VDJ somatic hypermutation to achieve antibody affinity maturation. The study also provides evidence for positive selection for replacement mutations in regions encoding the antigen contact loops, leading to functional antibody modification. Additionally, melano-macrophages in the clusters trap antigens used for post-mutation B-cell selection, serving a role similar to follicular dendritic cells in mammalian germinal centers.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Xiyun Jin, Wenyang Zhou, Meng Luo, Pingping Wang, Zhaochun Xu, Kexin Ma, Huimin Cao, Chang Xu, Yan Huang, Rui Cheng, Lixing Xiao, Xiaoyu Lin, Fenglan Pang, Yiqun Li, Huan Nie, Qinghua Jiang
Summary: The study indicates that BCR diversity is significantly reduced in COVID-19 patients, with a skew towards different V gene segments. The heavy chain CDR3 sequences of clonal BCRs show increased convergence, and there is an increase in IgG and IgA isotypes in the disease. IgG isotypes exhibit the highest rate of class switch recombination events and somatic hypermutation in all clonal BCRs.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Kaixuan Wang, Xihao Hu, Jian Zhang
Summary: The researchers introduce a computational approach called fastBCR for inferring B cell clonal families from massive BCR heavy chain sequences. The results demonstrate that fastBCR reduces running time while ensuring high accuracy, and it can be applied to real BCR sequencing data to identify disease-associated antibodies and improve our understanding of the B cell immune response.
CELL REPORTS METHODS
(2023)
Article
Virology
Sean T. Jones, Kejun Guo, Emily H. Cooper, Stephanie M. Dillon, Cheyret Wood, David H. Nguyen, Guannan Shen, Bradley S. Barrett, Daniel N. Frank, Miranda Kroehl, Edward N. Janoff, Katerina Kechris, Cara C. Wilson, Mario L. Santiago
Summary: Humoral immune perturbations contribute to pathogenic outcomes in persons with HIV-1 infection. Gut barrier dysfunction in PWH is associated with microbial translocation and dysbiosis. IgA, the most abundant immunoglobulin in the gut, plays a role in gut homeostasis by interacting with the microbiome. HIV-1 infection leads to decreased antibody repertoire diversity and somatic hypermutation in IgA, which is correlated with gut CD4(+) T cell loss, mucosal inflammation, and microbial translocation.
JOURNAL OF VIROLOGY
(2022)
Article
Multidisciplinary Sciences
Wooseob Kim, Julian Q. Zhou, Stephen C. Horvath, Aaron J. Schmitz, Alexandria J. Sturtz, Tingting Lei, Zhuoming Liu, Elizaveta Kalaidina, Mahima Thapa, Wafaa B. Alsoussi, Alem Haile, Michael K. Klebert, Teresa Suessen, Luis Parra-Rodriguez, Philip A. Mudd, Sean P. J. Whelan, William D. Middleton, Sharlene A. Teefey, Iskra Pusic, Jane A. O'Halloran, Rachel M. Presti, Jackson S. Turner, Ali H. Ellebedy
Summary: SARS-CoV-2 mRNA vaccination induces a persistent germinal center reaction in humans, resulting in affinity-matured long-term antibody responses that potently neutralize the virus.
Correction
Biochemistry & Molecular Biology
Moritz U. G. Kraemer, Oliver G. Pybus, Christophe Fraser, Simon Cauchemez, Andrew Rambaut, Benjamin J. Cowling
Article
Multidisciplinary Sciences
Dinesh Aggarwal, Ben Warne, Aminu S. Jahun, William L. Hamilton, Thomas Fieldman, Louis du Plessis, Verity Hill, Beth Blane, Emmeline Watkins, Elizabeth Wright, Grant Hall, Catherine Ludden, Richard Myers, Myra Hosmillo, Yasmin Chaudhry, Malte L. Pinckert, Iliana Georgana, Rhys Izuagbe, Danielle Leek, Olisaeloka Nsonwu, Gareth J. Hughes, Simon Packer, Andrew J. Page, Marina Metaxaki, Stewart Fuller, Gillian Weale, Jon Holgate, Christopher A. Brown, Rob Howes, Duncan McFarlane, Gordon Dougan, Oliver G. Pybus, Daniela De Angelis, Patrick H. Maxwell, Sharon J. Peacock, Michael P. Weekes, Chris Illingworth, Ewan M. Harrison, Nicholas J. Matheson, Ian G. Goodfellow
Summary: Understanding the transmission of SARS-CoV-2 in higher education settings is crucial in limiting spread among students and at-risk populations. A study conducted at the University of Cambridge analyzed viral isolates and found limited introductions of the virus into the university. Student cases were primarily linked to a single genetic cluster, likely originating from social gatherings outside of the university. Transmission was observed within student accommodations and courses but was effectively contained through local infection control measures and a national lockdown. The study highlights important factors in SARS-CoV-2 transmission and effective interventions in higher education settings.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Baisheng Li, Aiping Deng, Kuibiao Li, Yao Hu, Zhencui Li, Yaling Shi, Qianling Xiong, Zhe Liu, Qianfang Guo, Lirong Zou, Huan Zhang, Meng Zhang, Fangzhu Ouyang, Juan Su, Wenzhe Su, Jing Xu, Huifang Lin, Jing Sun, Jinju Peng, Huiming Jiang, Pingping Zhou, Ting Hu, Min Luo, Yingtao Zhang, Huanying Zheng, Jianpeng Xiao, Tao Liu, Mingkai Tan, Rongfei Che, Hanri Zeng, Zhonghua Zheng, Yushi Huang, Jianxiang Yu, Lina Yi, Jie Wu, Jingdiao Chen, Haojie Zhong, Xiaoling Deng, Min Kang, Oliver G. Pybus, Matthew Hall, Katrina A. Lythgoe, Yan Li, Jun Yuan, Jianfeng He, Jing Lu
Summary: This article reports the first local transmission of the Delta variant in mainland China. Compared to A/B lineage infections during the first wave in China in early 2020, Delta infections had viral loads that were on average about 1000 times greater when they first tested positive, suggesting potentially faster viral replication and greater infectiousness during early infection. The transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in most donor-recipient transmission pairs. However, transmission of minor intra-host variants resulted in at least 3 of the 34 substitutions identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Alexander Eugene Zarebski, Louis du Plessis, Kris Varun Parag, Oliver George Pybus
Summary: Inferring the dynamics of pathogen transmission is crucial in infectious disease epidemiology. The study proposes a novel method that combines epidemiological and phylodynamic data to estimate the transmission rate and unobserved prevalence. This method is applicable to large datasets.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Infectious Diseases
Sabrina L. Li, Andre L. Acosta, Sarah C. Hill, Oliver J. Brady, Marco A. B. de Almeida, Jader da C. Cardoso, Arran Hamlet, Luis F. Mucci, Juliana Telles de Deus, Felipe C. M. Iani, Neil S. Alexander, G. R. William Wint, Oliver G. Pybus, Moritz U. G. Kraemer, Nuno R. Faria, Jane P. Messina
Summary: This study predicts the environmental suitability of yellow fever's main vectors in Brazil and identifies locations prone to transmission and spillover risk by integrating data on human population and non-human primate host reservoirs. High-resolution mapping tools are provided to assist with mosquito and arbovirus surveillance, especially in low-resource settings.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Review
Genetics & Heredity
Stephen W. Attwood, Sarah C. Hill, David M. Aanensen, Thomas R. Connor, Oliver G. Pybus
Summary: This Review discusses the use of phylogenetic and phylodynamic methods in understanding viral evolution, specifically focusing on the SARS-CoV-2 pandemic. These approaches have provided insights into transmission routes, timings, and effectiveness of intervention measures. The study summarizes the contributions of these methods in tracking virus genetic changes, identifying emerging variants, and informing public health strategies.
NATURE REVIEWS GENETICS
(2022)
Article
Biochemical Research Methods
Kenneth B. Hoehn, Oliver G. Pybus, Steven H. Kleinstein
Summary: This study developed parsimony-based summary statistics to characterize migration, differentiation, and isotype switching along B cell phylogenetic trees, demonstrating their effectiveness through simulations and application in HIV and allergy patient datasets.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Infectious Diseases
Zoraima Neto, Pedro A. Martinez, Sarah C. Hill, Domingos Jandondo, Julien Theze, Marinela Mirandela, Renato Santana Aguiar, Joilson Xavier, Cruz dos Santos Sebastiao, Ana Luisa Micolo Candido, Filipa Vaz, Gisel Reyes Castro, Joana Paula Paixao, Nicholas J. Loman, Philippe Lemey, Oliver G. Pybus, Jocelyne Vasconcelos, Nuno Rodrigues Faria, Joana de Morais
Summary: The study in Angola revealed predominantly urban transmission of DENV2, as well as co-circulation of DENV2 with DENV1 and CHIKV. Several RT-PCR confirmed severe dengue cases were reported in the country.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Ecology
Sarah C. Hill, Sarah Francois, Julien Theze, Adrian L. Smith, Peter Simmonds, Christopher M. Perrins, Lia van der Hoek, Oliver G. Pybus
Summary: Wildlife carries pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. Changes in wildlife population age-structures and age-stratified behaviors can alter the level of pathogen detection within a species and the risk of spillover to other species. By using a metagenomic approach, this study characterized viral and prokaryotic carriage in a healthy wild bird population and identified novel virus species and the core prokaryotic microbiome. The findings suggest that perturbations in wildlife population age-structures could impact the circulation dynamics and spillover risk of microbes, potentially including pathogens.
Article
Biochemistry & Molecular Biology
Guogang Zhang, Bingying Li, Jayna Raghwani, Bram Vrancken, Ru Jia, Sarah C. Hill, Guillaume Fournie, Yanchao Cheng, Qiqi Yang, Yuxin Wang, Zengmiao Wang, Lu Dong, Oliver G. Pybus, Huaiyu Tian
Summary: Migratory birds have played a crucial role in the rapid dissemination of highly pathogenic avian influenza (HPAI) H5N8 virus clade 2.3.4.4 across Eurasia. This study investigated the seasonal transmission dynamics of HPAI H5N8 viruses using new genomic data obtained from surveying wild birds in China and tracking the migratory patterns of bird species across China since 2006. The findings reveal the association between the introductions of HPAI H5N8 viruses in different Eurasian regions and the seasonal migration of wild birds, and highlight Europe's role as both a source and a sink in the global HPAI virus transmission network.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Marina Escalera-Zamudio, Sergei L. Kosakovsky Pond, Natalia Martinez de la Vina, Bernardo Gutierrez, Rhys P. D. Inward, Julien Theze, Lucy van Dorp, Hugo G. Castelan-Sanchez, Thomas A. Bowden, Oliver G. Pybus, Ruben J. G. Hulswit
Summary: Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, although the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Wafaa B. Alsoussi, Sameer Kumar Malladi, Julian Q. Zhou, Zhuoming Liu, Baoling Ying, Wooseob Kim, Aaron J. Schmitz, Tingting Lei, Stephen C. Horvath, Alexandria J. Sturtz, Katherine M. McIntire, Birk Evavold, Fangjie Han, Suzanne M. Scheaffer, Isabella F. Fox, Senaa F. Mirza, Luis Parra-Rodriguez, Raffael Nachbagauer, Biliana Nestorova, Spyros Chalkias, Christopher W. Farnsworth, Michael K. Klebert, Iskra Pusic, Benjamin S. Strnad, William D. Middleton, Sharlene A. Teefey, Sean P. J. Whelan, Michael S. Diamond, Robert Paris, Jane A. O'Halloran, Rachel M. Presti, Jackson S. Turner, Ali H. Ellebedy
Summary: Boosting with COVID-19 vaccines induces robust immune responses and can generate new antibody responses targeting variant-specific epitopes. The B cells involved in the immune response can mature and produce antibodies that recognize the original virus as well as the variants.
Correction
Virology
Verity Hill, Louis Du Plessis, Thomas P. Peacock, Dinesh Aggarwal, Rachel Colquhoun, Alesandro M. Carabelli, Nicholas Ellaby, Eileen Gallagher, Natalie Groves, Ben Jackson, J. T. McCrone, Aline O'Toole, Anna Price, Theo Sanderson, Emily Scher, Joel Southgate, Erik Volz, Wendy S. Barclay, Jeffrey C. Barrett, Meera Chand, Thomas Connor, Ian Goodfellow, Ravindra K. Gupta, Ewan M. Harrison, Nicholas Loman, Richard Myers, David L. Robertson, Oliver G. Pybus, Andrew Rambaut
Article
Virology
Verity Hill, Louis Du Plessis, Thomas P. Peacock, Dinesh Aggarwal, Rachel Colquhoun, Alesandro M. Carabelli, Nicholas Ellaby, Eileen Gallagher, Natalie Groves, Ben Jackson, J. T. McCrone, Aine O'Toole, Anna Price, Theo Sanderson, Emily Scher, Joel Southgate, Erik Volz, Wendy S. Barclay, Jeffrey C. Barrett, Meera Chand, Thomas Connor, Ian Goodfellow, Ravindra K. Gupta, Ewan M. Harrison, Nicholas Loman, Richard Myers, David L. Robertson, Oliver G. Pybus, Andrew Rambaut
Summary: The text discusses the origin and characteristics of the first designated variant of concern (VOC) of SARS-CoV-2, Alpha, and its rapid global spread. It explores the sampled sequences ancestral to Alpha and proposes explanations for how Alpha acquired numerous mutations while remaining largely undetected in a region with high genomic surveillance. The study also compares the ancestral branches and mutation profiles of other VOCs, highlighting the distinctiveness of the Delta variant.