Article
Medicine, General & Internal
Daxi Wang, Yanqun Wang, Wanying Sun, Lu Zhang, Jingkai Ji, Zhaoyong Zhang, Xinyi Cheng, Yimin Li, Fei Xiao, Airu Zhu, Bei Zhong, Shicong Ruan, Jiandong Li, Peidi Ren, Zhihua Ou, Minfeng Xiao, Min Li, Ziqing Deng, Huanzi Zhong, Fuqiang Li, Wen-jing Wang, Yongwei Zhang, Weijun Chen, Shida Zhu, Xun Xu, Xin Jin, Jingxian Zhao, Nanshan Zhong, Wenwei Zhang, Jincun Zhao, Junhua Li, Yonghao Xu
Summary: The study found active viral replication in the respiratory tract of COVID-19 patients and genetically distinct viruses within the same host. Comparisons between viral populations among patients revealed a narrow transmission bottleneck within the same households, indicating a dominant role of stochastic dynamics in both inter-host and intra-host evolutions.
FRONTIERS IN MEDICINE
(2021)
Review
Microbiology
Scott C. Weaver, Naomi L. Forrester, Jianying Liu, Nikos Vasilakis
Summary: Transmission of arthropod-borne viruses involves infection and replication in both arthropod vectors and vertebrate hosts, with population bottlenecks and founder effects playing important roles in arboviral evolution and spread, as well as the emergence of human disease.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Michael Orsted, Erika Yashiro, Ary A. Hoffmann, Torsten Nygaard Kristensen
Summary: It is increasingly clear that microbial symbionts have a significant impact on the health and adaptability of their hosts, and vice versa. This study explores how reductions in population size can affect microbiome diversity and the fitness of the host. The findings suggest that population bottlenecks not only lead to a loss of genetic variation, but also result in a constriction of microbiome richness and diversity, which in turn influences the overall fitness of the host in stressful environments.
Article
Microbiology
Katarina M. Braun, Gage K. Moreno, Cassia Wagner, Molly A. Accola, William M. Rehrauer, David A. Baker, Katia Koelle, David H. O'Connor, Trevor Bedford, Thomas C. Friedrich, Louise H. Moncla
Summary: The study shows that within-host diversity of SARS-CoV-2 is low and transmission bottlenecks are narrow, with most infections founded by very few viruses. Within-host variants are rarely transmitted, even within the same household, and are seldom detected along phylogenetically linked infections within the broader community. This suggests that most variation generated within-host is lost during transmission.
Article
Multidisciplinary Sciences
Jeremy Di Mattia, Babil Torralba, Michel Yvon, Jean-Louis Zeddam, Stephane Blanc, Yannis Michalakis
Summary: Multipartite viruses can reduce the cost of genome integrity by transmitting and complementing different genome segments between hosts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Virology
William W. Hannon, Pavitra Roychoudhury, Hong Xie, Lasata Shrestha, Amin Addetia, Keith R. Jerome, Alexander L. Greninger, Jesse D. Bloom
Summary: Using deep sequencing, researchers investigated the transmission of viral genetic variation among infected crew members during a SARS-CoV-2 outbreak. They found that the within-host viral diversity was low and occasional fixation of low-frequency mutations during transmission dominated viral evolution.
Article
Multidisciplinary Sciences
Katrina A. Lythgoe, Matthew Hall, Luca Ferretti, Mariateresa de Cesare, George MacIntyre-Cockett, Amy Trebes, Monique Andersson, Newton Otecko, Emma L. Wise, Nathan Moore, Jessica Lynch, Stephen Kidd, Nicholas Cortes, Matilde Mori, Rebecca Williams, Gabrielle Vernet, Anita Justice, Angie Green, Samuel M. Nicholls, M. Azim Ansari, Lucie Abeler-Dorner, Catrin E. Moore, Timothy E. A. Peto, David W. Eyre, Robert Shaw, Peter Simmonds, David Buck, John A. Todd, Thomas R. Connor, Shirin Ashraf, Ana da Silva Filipe, James Shepherd, Emma C. Thomson, David Bonsall, Christophe Fraser, Tanya Golubchik
Summary: The study found that SARS-CoV-2 infections in clinical samples in the UK are characterized by low levels of within-host diversity and a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with shared diversity not persisting.
Article
Biology
Maija Jokinen, Suvi Sallinen, Mirkka M. Jones, Jukka Siren, Emy Guilbault, Hanna Susi, Anna-Liisa Laine
Summary: The assembly of viral communities is influenced by priority effects, where early viral infections can have positive or negative effects on subsequent colonization patterns. The direction of the effect depends on both the host genotype and the type of virus colonizing the host early in the season.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Ian W. Campbell, Karthik Hullahalli, Jerrold R. Turner, Matthew K. Waldor
Summary: In this study, the authors investigated the effect of pathogen dose on the initiation of infection in the mouse gut using Citrobacter rodentium as a model. They found that host bottlenecks prevent infections by eliminating invading pathogens, and the size of the pathogen's founding population in female mice is controlled by a severe bottleneck. The disruption of the microbiota was found to be the dominant bottleneck, while the loss of the critical virulence island led to a contraction in the diversity of the pathogen population.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Benjamin Wong Wei Xiang, Wilfried A. A. Saron, James C. Stewart, Arthur Hain, Varsha Walvekar, Dorothee Misse, Frederic Thomas, R. Manjunatha Kini, Benjamin Roche, Adam Claridge-Chang, Ashley L. St. John, Julien Pompon
Summary: A study found that DENV infection increases mosquito attraction to hosts and hinders their biting efficiency, resulting in infected mosquitoes needing more bites to reach similar blood repletion. By establishing transmission models and mathematical models, the study also revealed that the number of infected hosts per infected mosquito tripled when mosquito behavior was influenced by DENV infection.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
J. Walker Gussler, David S. Campo, Zoya Dimitrova, Pavel Skums, Yury Khudyakov
Summary: Background investigation of outbreaks is crucial for interrupting and preventing the transmission of infectious diseases. This study presents a new computational framework, PYCIVO, which can infer the primary case in viral outbreaks. By simulating the evolution of hepatitis C virus (HCV) variants between cases involved in direct transmission, PYCIVO constructs a probabilistic disease transmission tree. It improves upon previous work by implementing a custom heterogeneity index and identifying scenarios where the primary case may not have been sampled.
BMC BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Julie Perreau, Bo Zhang, Gerald P. Maeda, Mark Kirkpatrick, Nancy A. Moran
Summary: Many animal lineages have maternally inherited symbionts, but they also pose risks to hosts due to genetic drift or selfish mutations. Research has shown that closely related haplotypes are subject to strong within-host selection, resulting in rapid mutation fixation with little impact on host fitness.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Editorial Material
Public, Environmental & Occupational Health
Beatriz Salvesen von Essen, Denise D'Angelo, Holly B. Shulman, Wanda Hernandez Virella, Katherine Kortsmit, Beatriz Rios Herrera, Patricia Garcia Diaz, Aspy Taraporewalla, Leslie Harrison, Lee Warner, Manuel Vargas Bernal
Summary: The Pregnancy Risk Assessment Monitoring System-Zika Postpartum Emergency Response study collected pregnancy-related data using postpartum hospital-based surveys and telephone follow-up surveys during the Zika virus outbreak and hurricanes in Puerto Rico. It informed programs, increased the capacity of the Puerto Rico Department of Health to conduct maternal-infant health surveillance, and demonstrated the effectiveness of this methodology for collecting data during public health emergencies.
AMERICAN JOURNAL OF PUBLIC HEALTH
(2022)
Article
Mathematics
Lemesa Bedjisa Dano, Koya Purnachandra Rao, Temesgen Duressa Keno
Summary: This paper investigates the combined effect of hepatitis B virus (HBV) infection and heavy alcohol consumption on the progression of liver cirrhosis. By analyzing a deterministic model and a logistic function, it is shown that heavy alcohol consumption significantly accelerates the progression of liver cirrhosis in individuals with chronic hepatitis B infection.
JOURNAL OF MATHEMATICS
(2022)
Article
Multidisciplinary Sciences
Minami Nagai, Miyu Moriyama, Chiharu Ishii, Hirotake Mori, Hikaru Watanabe, Taku Nakahara, Takuji Yamada, Dai Ishikawa, Takamasa Ishikawa, Akiyoshi Hirayama, Ikuo Kimura, Akihito Nagahara, Toshio Naito, Shinji Fukuda, Takeshi Ichinohe
Summary: The ambient environmental temperature plays a role in the severity of a virus infection. Research shows that infection with influenza and SARS-CoV-2 at higher temperatures promotes gut microbiota derived deoxycholic acid signaling, which increases the host's resistance to infection.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Philippe Perot, Franck Bielle, Thomas Bigot, Vincent Foulongne, Karine Bollore, Delphine Chretien, Patricia Gil, Serafin Gutierrez, Gregory L'Ambert, Karima Mokhtari, Jan Hellert, Marie Flamand, Carole Tamietti, Muriel Coulpier, Anne Huard de Verneuil, Sarah Temmam, Therese Couderc, Edouard De Sousa Cunha, Susana Boluda, Isabelle Plu, Marie Bernadette Delisle, Fabrice Bonneville, David Brassat, Claire Fieschi, Marion Malphettes, Charles Duyckaerts, Bertrand Mathon, Sophie Demeret, Danielle Seilhean, Marc Eloit
Summary: The study identified Umbre arbovirus in the brain tissue of two immunocompromised patients, representing a previously unidentified orthobunyavirus in humans. In addition, viral sequences related to the virus were found in mosquitoes in southern France, indicating the presence of similar arboviruses in Europe and their potential public health impact.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Virology
Yannis Moreau, Patricia Gil, Antoni Exbrayat, Ignace Rakotoarivony, Emmanuel Breard, Corinne Sailleau, Cyril Viarouge, Stephan Zientara, Giovanni Savini, Maria Goffredo, Giuseppe Mancini, Etienne Loire, Serafin Gutierrez
Summary: Genome segmentation in bluetongue virus (BTV) can result in differences in segment abundance in populations, leading to potential differences in evolution rates between segments. This phenomenon, observed in both ruminants and Culicoides biting midges, expands knowledge on gene frequency variation and highlights the need for further studies on its role beyond multipartite viruses.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Patricia Gil, Virginie Dupuy, Rachid Koual, Antoni Exbrayat, Etienne Loire, Assane G. Fall, Geoffrey Gimonneau, Biram Biteye, Momar Talla Seck, Ignace Rakotoarivony, Albane Marie, Benoit Frances, Gregory Lambert, Julie Reveillaud, Thomas Balenghien, Claire Garros, Emmanuel Albina, Marc Eloit, Serafin Gutierrez
Summary: Our current understanding of viral communities associated with animals lags behind that of bacteriomes, partly due to technical challenges and insufficient focus on key steps such as library preparation in viral metagenomics. By optimizing library preparation for insect vectors of viral diseases, our approach has shown increased virus-like sequences and potential for studying virome composition trends and sensitivity in community ecology of viruses.
MOLECULAR ECOLOGY RESOURCES
(2021)
Editorial Material
Anesthesiology
Mircea T. Sofonea, Corentin Boennec, Yannis Michalakis, Samuel Alizon
ANAESTHESIA CRITICAL CARE & PAIN MEDICINE
(2021)
Article
Infectious Diseases
Mircea T. Sofonea, Bastien Reyne, Baptiste Elie, Ramses Djidjou-Demasse, Christian Selinger, Yannis Michalakis, Samuel Alizon
Summary: The study developed a parsimonious discrete-time model to analyze the spread of COVID-19 in France, estimating key epidemiological parameters and the impact of lockdown implementation delay. By incorporating memory effects into the model, the accuracy of fitting epidemiological data was greatly improved.
Article
Infectious Diseases
Orianne Constant, Patricia Gil, Jonathan Barthelemy, Karine Bollore, Vincent Foulongne, Caroline Desmetz, Agnes Leblond, Isabelle Desjardins, Sophie Pradier, Aurelien Joulie, Alain Sandoz, Rayane Amaral, Michel Boisseau, Ignace Rakotoarivony, Thierry Baldet, Albane Marie, Benoit Frances, Florence Reboul Salze, Bachirou Tinto, Philippe Van de Perre, Sara Salinas, Cecile Beck, Sylvie Lecollinet, Serafin Gutierrez, Yannick Simonin
Summary: The study observed active transmission of WNV and USUV in Southern France, with higher USUV prevalence in humans, dogs, birds, and mosquitoes, and higher WNV prevalence in horses. Genetic data showed the presence of the same lineages in mosquitoes from 2015 to 2020. The findings support existing literature suggesting endemicity of WNV and USUV in the region.
Article
Multidisciplinary Sciences
Jeremy Di Mattia, Babil Torralba, Michel Yvon, Jean-Louis Zeddam, Stephane Blanc, Yannis Michalakis
Summary: Multipartite viruses can reduce the cost of genome integrity by transmitting and complementing different genome segments between hosts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Virology
Romain Gallet, Jeremy Di Mattia, Sebastien Ravel, Jean-Louis Zeddam, Renaud Vitalis, Yannis Michalakis, Stephane Blanc
Summary: Multipartite viruses have a segmented genome that allows for regulation of gene expression through changes in genome formula and gene copy number variations. The genome formula variations modulate gene expression and maintain a similar ratio between different viral mRNAs. The regulation of genome formula is independent of DNA segment sequence mutation.
Article
Microbiology
Bachirou Tinto, Didier Patinde Alexandre Kabore, Dramane Kania, Therese Samdapawinde Kagone, Alice Kiba-Koumare, Laura Pinceloup, Guillaume Thaurignac, Philippe Van de Perre, Roch Kounbobr Dabire, Thierry Baldet, Serafin Guitierrez, Patricia Gil, Ahidjo Ayouba, Sara Salinas, Yannick Simonin
Summary: Based on a study of blood donor samples in Burkina Faso, the seroprevalence of Zika virus and dengue virus is high in the region, especially for dengue virus. Although molecular evidence of Zika virus circulation could not be demonstrated, this research suggests the need to strengthen arbovirus surveillance in Burkina Faso and further investigate the epidemiology of these viruses.
Article
Microbiology
Bachirou Tinto, Didier Patinde Alexandre Kabore, Therese Samdapawinde Kagone, Orianne Constant, Jonathan Barthelemy, Alice Kiba-Koumare, Philippe Van de Perre, Roch Kounbobr Dabire, Thierry Baldet, Serafin Gutierrez, Patricia Gil, Dramane Kania, Yannick Simonin
Summary: Usutu virus (USUV) and West Nile virus (WNV) are closely related arboviruses that mainly spread through mosquitoes and birds, but can also infect humans and other mammals. A study conducted in Burkina Faso showed a high prevalence of both viruses in humans and horses, indicating active transmission. The study highlights the importance of surveillance programs to prevent, detect, and raise awareness about USUV and WNV circulation.
Article
Biochemistry & Molecular Biology
Maeelle Deshoux, Baptiste Monsion, Elodie Pichon, Jaime Jimenez, Aranzazu Moreno, Bastien Cayrol, Gael Thebaud, Sam T. Mugford, Saskia A. Hogenhout, Stephane Blanc, Alberto Fereres, Marilyne Uzest
Summary: To ensure sustained feeding, aphids deliver effectors into plant cells using their mouthparts, avoiding the activation of plant defenses. Recent research has shown that the distribution of effectors near feeding sites in plant tissues is uneven. However, the specific process of delivering effectors into specific plant compartments is still unknown. This study demonstrates that the acrostyle, a cuticular organ located at the tip of maxillary stylets, binds with a saliva effector called Mp10 during aphid probing. The acrostyle's capacity to bind with effectors supports its role in delivering aphid effectors into plant cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Microbiology
Melia Bonnamy, Stephane Blanc, Yannis Michalakis
Summary: The replication of plant-infecting single-stranded DNA viruses, Geminiviridae and Nanoviridae, involves rolling-circle replication (RCR) and recombination-dependent replication (RDR) mechanisms. RCR relies on a virus-encoded Replication-associated protein (Rep) and specific sequences called iterons, while RDR is also observed in some double-stranded DNA viruses. This article provides a synthesis of the current understanding of these replication modes and discusses the potential role of gene copy number regulation in viral gene expression.
Article
Virology
Mahsa Mansourpour, Romain Gallet, Alireza Abbasi, Stephane Blanc, Akbar Dizadji, Jean-Louis Zeddam
Summary: This study investigates the impact of SCSA 1 on various traits of FBNYV in its host plant and aphid vector. The results show that SCSA 1 changes the relative amounts of virus genomic segments and increases the rate of plant-to-plant transmission.
JOURNAL OF VIROLOGY
(2022)
