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Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts Virus Evol. (IF 5.3) Pub Date : 2024-04-22 Sabrina Sadiq, Edward C Holmes, Jackie E Mahar
The RNA virus family Picobirnaviridae has traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family
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Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: implications for bird-mammal transmission in South America Virus Evol. (IF 5.3) Pub Date : 2024-04-15 Gonzalo Tomás, Ana Marandino, Yanina Panzera, Sirley Rodríguez, Gabriel Luz Wallau, Filipe Zimmer Dezordi, Ramiro Pérez, Lucía Bassetti, Raúl Negro, Joaquín Williman, Valeria Uriarte, Fabiana Grazioli, Carmen Leizagoyen, Sabrina Riverón, Jaime Coronel, Soledad Bello, Enrique Páez, Martín Lima, Virginia Méndez, Ruben Pérez
The highly pathogenic avian influenza viruses of the clade 2.3.4.4b have caused unprecedented deaths in South American wild birds, poultry, and marine mammals. In September 2023, pinnipeds and seabirds appeared dead on the Uruguayan Atlantic coast. Sixteen influenza virus strains were characterized by real-time reverse transcription PCR and genome sequencing in samples from sea lions (Otaria flavescens)
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High pathogenic avian influenza A(H5) viruses of clade 2.3.4.4b in Europe – why trends of virus evolution are more difficult to predict Virus Evol. (IF 5.3) Pub Date : 2024-04-06 Alice Fusaro, Bianca Zecchin, Edoardo Giussani, Elisa Palumbo, Montserrat Agüero-García, Claudia Bachofen, Ádám Bálint, Fereshteh Banihashem, Ashley C Banyard, Nancy Beerens, Manon Bourg, Francois-Xavier Briand, Caroline Bröjer, Ian H Brown, Brigitte Brugger, Alexander M P Byrne, Armend Cana, Vasiliki Christodoulou, Zuzana Dirbakova, Teresa Fagulha, Ron A M Fouchier, Laura Garza-Cuartero, George Georgiades
Since 2016, A(H5Nx) high pathogenic avian influenza (HPAI) virus of clade 2.3.4.4b has become one of the most serious global threats not only to wild and domestic birds, but also to public health. In recent years, important changes in the ecology, epidemiology and evolution of this virus have been reported, with an unprecedented global diffusion and variety of affected birds and mammalian species.
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Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies Virus Evol. (IF 5.3) Pub Date : 2024-04-04 Dylan H Westfall, Wenjie Deng, Alec Pankow, Lennie Chen, Hong Zhao, Carolyn Williamson, Morgane Rolland, Ben Murrell, James I Mullins
Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing, which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences
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Evolution of exploitation and replication of giant viruses and virophages Virus Evol. (IF 5.3) Pub Date : 2024-04-01 Ana del Arco, Matthias G Fischer, Lutz Becks
Tripartite biotic interactions are inherently complex, and the strong interdependence of species and often one-sided exploitation can make these systems vulnerable to extinction. The persistence of species depends then on the balance between exploitation and avoidance of exploitation beyond the point where sustainable resource use is no longer possible. We used this general prediction to test the potential
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Automated detection and classification of polioviruses from nanopore sequencing reads using piranha Virus Evol. (IF 5.3) Pub Date : 2024-03-27 Áine O’Toole, Rachel Colquhoun, Corey Ansley, Catherine Troman, Daniel Maloney, Zoe Vance, Joyce Akello, Erika Bujaki, Manasi Majumdar, Adnan Khurshid, Yasir Arshad, Muhammad Masroor Alam, Javier Martin, Alexander G Shaw, Nicholas C Grassly, Andrew Rambaut
Widespread surveillance, rapid detection, and appropriate intervention will be critical for successful eradication of poliovirus. Using deployable next-generation sequencing (NGS) approaches, such as Oxford Nanopore Technologies’ MinION, the time from sample to result can be significantly reduced compared to cell culture and Sanger sequencing. We developed piranha (poliovirus investigation resource
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VIPERA: Viral Intra-Patient Evolution Reporting and Analysis Virus Evol. (IF 5.3) Pub Date : 2024-03-20 Miguel Álvarez-Herrera, Jordi Sevilla, Paula Ruiz-Rodriguez, Andrea Vergara, Jordi Vila, Pablo Cano-Jiménez, Fernando González-Candelas, Iñaki Comas, Mireia Coscollá
Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA)
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Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages Virus Evol. (IF 5.3) Pub Date : 2024-03-12 Maxime Courcelle, Habib Salami, Kadidia Tounkara, Modou Moustapha Lo, Aminata Ba, Mariame Diop, Mamadou Niang, Cheick Abou Kounta Sidibe, Amadou Sery, Marthin Dakouo, Lanceï Kaba, Youssouf Sidime, Mohamed Keyra, Alpha Oumar Sily Diallo, Ahmed Bezeid El Mamy, Ahmed Salem El Arbi, Yahya Barry, Ekaterina Isselmou, Habiboullah Habiboullah, Baba Doumbia, Mohamed Baba Gueya, Joseph Awuni, Theophilus Odoom
Peste des petits ruminants virus (PPRV) causes a highly infectious disease affecting mainly goats and sheep in large parts of Africa, Asia, and the Middle East and has an important impact on the global economy and food security. Full genome sequencing of PPRV strains has proved to be critical to increasing our understanding of PPR epidemiology and to inform the ongoing global efforts for its eradication
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Swine influenza A virus infection dynamics and evolution in intensive pig production systems Virus Evol. (IF 5.3) Pub Date : 2024-03-12 Paula Lagan, Michael Hamil, Susan Cull, Anthony Hanrahan, Rosanna M Wregor, Ken Lemon
Swine influenza A virus (swIAV) is one of the main viral pathogens responsible for respiratory disease in farmed pigs. While outbreaks are often epidemic in nature, increasing reports suggest that continuous, endemic infection of herds is now common. The move towards larger herd sizes and increased intensification in the commercial pig industry may promote endemic infection; however, the impact that
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Virome release of an invasive exotic plant species in southern France Virus Evol. (IF 5.3) Pub Date : 2024-03-06 Oumaima Moubset, Denis Filloux, Hugo Fontes, Charlotte Julian, Emmanuel Fernandez, Serge Galzi, Laurence Blondin, Sélim Ben Chehida, Jean-Michel Lett, François Mesleard, Simona Kraberger, Joy M Custer, Andrew Salywon, Elizabeth Makings, Armelle Marais, Frédéric Chiroleu, Pierre Lefeuvre, Darren P Martin, Thierry Candresse, Arvind Varsani, Virginie Ravigné, Philippe Roumagnac
The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments
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Diverse RNA Viruses in the Venom-Related Microenvironment of Different Animal Phyla Virus Evol. (IF 5.3) Pub Date : 2024-03-05 Jingkai Ji, Cixiu Li, Tao Hu, Zhongshuai Tian, Juan Li, Lin Xu, Hong Zhou, Edward C Holmes, Weifeng Shi
Venom is known as the source of natural antimicrobial products. Previous studies have largely focused on the expression of venom-related genes and the biochemical components of venom. With the advent of metagenomic sequencing many more microorganisms, especially viruses, have been identified in highly diverse environments. Herein, we investigated the RNA virome in the venom-related microenvironment
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Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak. Virus Evol. (IF 5.3) Pub Date : 2024-03-05 Jia-Xin Lv, Xiang Liu, Yuan-Yuan Pei, Zhi-Gang Song, Xiao Chen, Shu-Jian Hu, Jia-Lei She, Yi Liu, Yan-Mei Chen, Yong-Zhen Zhang
Despite extensive scientific efforts directed toward the evolutionary trajectory of SARS-CoV-2 in humans at the beginning of the COVID-19 epidemic, it remains unclear how the virus jumped into and evolved in humans so far. Herein, we recruited almost all adult COVID-19 cases appeared locally or imported from abroad during the first eight months of the outbreak in Shanghai. From these patients, SARS-CoV-2
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Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections? Virus Evol. (IF 5.3) Pub Date : 2024-02-21 Chapin S Korosec, Lindi M Wahl, Jane M Heffernan
Despite a relatively low mutation rate, the large number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has allowed for substantial genetic change, leading to a multitude of emerging variants. Using a recently determined mutation rate (per site replication), as well as within-host parameter estimates for symptomatic SARS-CoV-2 infection, we apply a stochastic transmission-bottleneck
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Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa Virus Evol. (IF 5.3) Pub Date : 2024-02-19 Idrissa Nonmon Sanogo, Claire Guinat, Simon Dellicour, Mohamed Adama Diakité, Mamadou Niang, Ousmane A Koita, Christelle Camus, Mariette Ducatez
Avian influenza viruses (AIV) of the H9N2 subtype have become widespread in Western Africa since their first detection in 2017 in Burkina Faso. However, the genetic characteristics and diffusion patterns of the H9N2 virus remain poorly understood in Western Africa, mainly due to limited surveillance activities. In addition, Mali, a country considered to play an important role in the epidemiology of
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High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA Virus Evol. (IF 5.3) Pub Date : 2024-02-19 William M Switzer, Anupama Shankar, Hongwei Jia, Sergey Knyazev, Frank Ambrosio, Reagan Kelly, HaoQiang Zheng, Ellsworth M Campbell, Roxana Cintron, Yi Pan, Neeraja Saduvala, Nivedha Panneer, Rhiannon Richman, Manny B Singh, Douglas A Thoroughman, Erin F Blau, George M Khalil, Sheryl Lyss, Walid Heneine
We investigated transmission dynamics of a large HIV outbreak among persons who inject drugs (PWID) in Kentucky and Ohio during 2017–2020 by using detailed phylogenetic, network, recombination, and cluster dating analyses. Using polymerase (pol) sequences from 193 people associated with the investigation, we document high HIV-1 diversity, including subtype B (44.6 per cent); numerous circulating recombinant
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Genomic Epidemiology of Highly Pathogenic Avian Influenza A (H5N1) Virus in Wild Birds in South Korea during 2021–2022: Changes in Viral Epidemic Patterns Virus Evol. (IF 5.3) Pub Date : 2024-02-12 Ji-Yun Kim, Sol Jeong, Da-Won Kim, Dong-Wook Lee, Dong-Hun Lee, Daehun Kim, Jung-Hoon Kwon
Clade 2.3.4.4b highly pathogenic avian influenza A (HPAI) viruses have been detected in wild birds worldwide, causing recurrent outbreaks since 2016. During the winter of 2021–2022, we detected 1 H5N8 and 43 H5N1 clade 2.3.4.4b HPAI viruses from wild birds in South Korea. Phylogenetic analysis revealed that HA gene of H5N1 viruses was divided into two genetically distinct groups (N1.G1 and N1.G2).
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Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus Virus Evol. (IF 5.3) Pub Date : 2024-02-12 Sambit K Mishra, Chase W Nelson, Bin Zhu, Maisa Pinheiro, Hyo Jung Lee, Michael Dean, Laurie Burdett, Meredith Yeager, Lisa Mirabello
High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly
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Genomic Surveillance and Evolutionary Dynamics of Type-2 Porcine Reproductive and Respiratory Syndrome Virus in China Spanning the African Swine Fever Outbreak Virus Evol. (IF 5.3) Pub Date : 2024-02-09 Zhiyong Wu, Tong Chang, Decheng Wang, Hongliang Zhang, Haizhou Liu, Xinyi Huang, Zhijun Tian, Xiaoxiao Tian, Di Liu, Tongqing An, Yi Yan
Porcine reproductive and respiratory syndrome virus (PRRSV) poses a serious threat to the pig industry in China. Our previous study demonstrated that PRRSV persists with local circulations and overseas imports in China, and has formed a relatively stable epidemic pattern. However, the sudden African swine fever (ASF) outbreak in 2018 caused serious damage to China’s pig industry structure, which resulted
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Reassortments in Single-Stranded DNA Multipartite Viruses: Confronting Expectations Based on Molecular Constraints with Field Observations Virus Evol. (IF 5.3) Pub Date : 2024-02-02 Babil Torralba, Stéphane Blanc, Yannis Michalakis
Single-stranded DNA multipartite viruses, which mostly consist of members of the genus Begomovirus, family Geminiviridae and all members of the family Nanoviridae, partly resolve the cost of genomic integrity maintenance through two remarkable capacities. They are able to systemically infect a host even when their genomic segments are not together in the same host cell, and these segments can be separately
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Contemporary and historical human migration patterns shape hepatitis B virus diversity Virus Evol. (IF 5.3) Pub Date : 2024-02-01 Barney I Potter, Marijn Thijssen, Nídia Sequeira Trovão, Andrea Pineda-Peña, Marijke Reynders, Thomas Mina, Carolina Alvarez, Samad Amini-Bavil-Olyaee, Frederik Nevens, Piet Maes, Philippe Lemey, Marc Van Ranst, Guy Baele, Mahmoud Reza Pourkarim
Infection by hepatitis B virus (HBV) is responsible for approximately 296 million chronic cases of hepatitis B, and roughly 880,000 deaths annually. The global burden of HBV is distributed unevenly, largely owing to the heterogeneous geographic distribution of its subtypes, each of which demonstrates different severity and responsiveness to antiviral therapy. It is therefore crucial to the global public
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The untapped potential of phage model systems as therapeutic agents Virus Evol. (IF 5.3) Pub Date : 2024-01-16 Jordan Romeyer Dherbey, Frederic Bertels
With the emergence of widespread antibiotic resistance, phages are an appealing alternative to antibiotics in the fight against multidrug-resistant bacteria. Over the past few years, many phages have been isolated from various environments to treat bacterial pathogens. While isolating novel phages for treatment has had some success for compassionate use, developing novel phages into a general therapeutic
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Conserved Untranslated Regions of Multipartite Viruses: Natural Markers of Novel Viral Genomic Components and Tags of Viral Evolution Virus Evol. (IF 5.3) Pub Date : 2024-01-13 Song Zhang, Caixia Yang, Yuanjian Qiu, Ruiling Liao, Zhiyou Xuan, Fang Ren, Yafeng Dong, Xiaoying Xie, Yanhong Han, Di Wu, Pedro Luis Ramos-González, Juliana Freitas-Astúa, Huadong Yang, Changyong Zhou, Mengji Cao
Viruses with split genomes are classified as being either segmented or multipartite based on whether their genomic segments occur within a single virion or across different virions. Despite variations in number and sequence during evolution, the genomic segments of many viruses are conserved within the untranslated regions (UTRs). In this study, we present a methodology that combines RNA sequencing
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Human immunodeficiency virus (HIV) dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte (CTL) escape mutants Virus Evol. (IF 5.3) Pub Date : 2024-01-13 Wen-Jian Chung, Elizabeth Connick, Dominik Wodarz
In the secondary lymphoid tissues, human immunodeficiency virus (HIV) can replicate both in the follicular and the extrafollicular compartments. Yet, virus is concentrated in the follicular compartment in the absence of antiretroviral therapy, in part due to the lack of cytotoxic T lymphocyte (CTL)-mediated activity there. CTL home to the extrafollicular compartment, where they can suppress virus load
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SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine learning method Virus Evol. (IF 5.3) Pub Date : 2024-01-13 Adriano de Bernardi Schneider, Michelle Su, Angie S Hinrichs, Jade Wang, Helly Amin, John Bell, Debra A Wadford, Áine O’Toole, Emily Scher, Marc D Perry, Yatish Turakhia, Nicola De Maio, Scott Hughes, Russ Corbett-Detig
With the rapid spread and evolution of SARS-CoV-2, the ability to monitor its transmission and distinguish among viral lineages is critical for pandemic response efforts. The most commonly used software for the lineage assignment of newly isolated SARS-CoV-2 genomes is pangolin, which offers two methods of assignment, pangoLEARN and pUShER. PangoLEARN rapidly assigns lineages using a machine learning
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Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago Virus Evol. (IF 5.3) Pub Date : 2024-01-11 Ophélie Lebrasseur, Kuldeep Dilip More, Ludovic Orlando
Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century, and continue to be of major concern to the horse industry today. With a seroprevalence of 60-80%, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here, we screen the sequenced data of 264 archaeological
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Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection Virus Evol. (IF 5.3) Pub Date : 2024-01-05 Christopher J. R Illingworth, Jose A Guerra-Assuncao, Samuel Gregg, Oscar Charles, Juanita Pang, Sunando Roy, Rana Abdelnabi, Johan Neyts, Judith Breuer
Mutagenic antiviral drugs have shown promise against multiple viruses, but concerns have been raised about whether their use might promote the emergence of new and harmful viral variants. Recently, genetic signatures associated with molnupiravir use have been identified in the global SARS-COV-2 population. Here, we examine the consequences of using favipiravir and molnupiravir to treat SARS-CoV-2 infection
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New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes Virus Evol. (IF 5.3) Pub Date : 2024-01-04 Forgia Marco, Daghino Stefania, Chiapello Marco, Ciuffo Marina, Turina Massimo
Recent advances on NGS approaches allowed a broad exploration of viromes from different fungal hosts, unveiling a great diversity of mycoviruses with interesting evolutionary features. The word mycovirus historically applies also to viruses infecting oomycetes but most studies are on viruses infecting fungi, with less mycoviruses found and characterized in oomycetes, particularly in the obligatory
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Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage Virus Evol. (IF 5.3) Pub Date : 2024-01-04 Anton Labutin, Gerald Heckel
Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host-shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic
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Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market Virus Evol. (IF 5.3) Pub Date : 2023-12-30 Jesse D Bloom
In March 2023, the Chinese CDC publicly released raw metagenomic sequencing data for environmental samples collected in early 2020 from the Huanan Seafood Market. Prior to that data release, some scientists had suggested that these samples could be informative for establishing if animals such as raccoon dogs had been infected with SARS-CoV-2. However, no one had analyzed how much SARS-CoV-2 was actually
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Computational host range prediction – the good, the bad, and the ugly Virus Evol. (IF 5.3) Pub Date : 2023-12-21 Abigail A Howell, Cyril J Versoza, Susanne P Pfeifer
The rapid emergence and spread of antimicrobial resistance across the globe have prompted the usage of bacteriophages (i.e., viruses that infect bacteria) in a variety of applications ranging from agriculture to biotechnology and medicine. In order to effectively guide the application of bacteriophages in these multifaceted areas, information about their host ranges – that is the bacterial strains
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The coevolutionary mosaic of bat betacoronavirus emergence risk Virus Evol. (IF 5.3) Pub Date : 2023-12-21 Norma R Forero-Muñoz, Renata L Muylaert, Stephanie N Seifert, Gregory F Albery, Daniel J Becker, Colin J Carlson, Timothée Poisot
Pathogen evolution is one of the least predictable components of disease emergence, particularly in nature. Here, building on principles established by the geographic mosaic theory of coevolution, we develop a quantitative, spatially-explicit framework for mapping the evolutionary risk of viral emergence. Driven by interest in diseases like SARS, MERS, and COVID-19, we examine the global biogeography
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EvoLaps 2: Advanced Phylogeographic Visualization Virus Evol. (IF 5.3) Pub Date : 2023-12-19 F Chevenet, D Fargette, P Bastide, T Vitré, S Guindon
EvoLaps is a user-friendly web application designed to visualize the spatial and temporal spread of pathogens. It takes an annotated tree as entry, such as a maximum clade credibility tree obtained through continuous phylogeographic inference. By following a ‘Top-Down’ reading of a tree recursively, transitions (latitude/longitude changes from a node to its children) are represented on a cartographic
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Tracing the adaptive evolution of SARS-CoV-2 during vaccine roll-out in Norway Virus Evol. (IF 5.3) Pub Date : 2023-12-18 Ignacio Garcia, Yunsung Lee, Ola Brynildsrud, Vegard Eldholm, Per Magnus, Anita Blomfeldt, Truls M Leegaard, Fredrik Müller, Susanne Dudman, Dominique A Caugant
Vaccination against SARS-CoV-2 has greatly mitigated the impact of the COVID-19 pandemic. However, concerns have been raised about the degree to which vaccination might drive the emergence and selection of immune escape mutations that will hamper the efficacy of the vaccines. In this study we investigate whether vaccination impacted the micro-scale adaptive evolution of SARS-CoV-2 in the Oslo region
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Synergetic association between coxsackievirus A16 genotype evolution and recombinant form shifts Virus Evol. (IF 5.3) Pub Date : 2023-12-17 Zhenzhi Han, Fangming Wang, Jinbo Xiao, Hanhaoyu Fu, Yang Song, Mingli Jiang, Huanhuan Lu, Jichen Li, Yanpeng Xu, Runan Zhu, Yong Zhang, Linqing Zhao
Coxsackievirus A16 (CVA16) is a major pathogen that causes hand, foot, and mouth disease (HFMD). The recombination form (RF) shifts and global transmission dynamics of CVA16 remain unknown. In this retrospective study, global sequences of CVA16 were retrieved from the GenBank database and analyzed using comprehensive phylogenetic inference, RF surveys, and population structure. A total of 1663 sequences
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A new genus of alphasatellites associated with banana bunchy top virus in South-East Asia Virus Evol. (IF 5.3) Pub Date : 2023-12-13 Valentin Guyot, Tien-Dung Trieu, Oudomphone Insisiengmay, Ting Zhang, Marie-Line Iskra-Caruana, Mikhail M Pooggin
Autonomously-replicating alphasatellites (family Alphasatellitidae) are frequently associated with plant single-stranded (ss)DNA viruses of the families Geminiviridae, Metaxyviridae and Nanoviridae. Alphasatellites encode a single replication-initiator protein (Rep) similar to Rep proteins of helper viruses and depend on helper viruses for encapsidation, movement and transmission. Costs versus benefits
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Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster Virus Evol. (IF 5.3) Pub Date : 2023-12-12 Oscar M Lezcano, Lara Fuhrmann, Gayatri Ramakrishnan, Niko Beerenwinkel, Martijn A Huynen, Ronald P van Rij
Virus evolution is strongly affected by antagonistic co-evolution of virus and host. Host immunity positively selects for viruses that evade the immune response, which in turn may drive counter-adaptations in host immune genes. We investigated how host immune pressure shapes virus populations, using the fruit fly Drosophila melanogaster and its natural pathogen Drosophila C virus (DCV), as a model
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Coevolutionary phage training and Joint application delays the emergence of phage resistance in Pseudomonas aeruginosa Virus Evol. (IF 5.3) Pub Date : 2023-12-12 Mianzhi Wang, Jingyi Wei, Lei Jiang, Li Jiang, Junxuan Zhang, Xiaolu He, Yiwen Ren, Zixuan Wang, Yongxue Sun, Zhiqiang Wang
Antibiotic-resistant bacteria are current threats to available antibiotic therapies, and this has renewed interest in the therapeutic use of phage as an alternative. However, development of phage resistance has led to unsuccessful therapeutic outcomes. In the current study, we applied phage training to minimize bacterial phage resistance and to improve treatment outcome by adapting the phage to their
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Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021 Virus Evol. (IF 5.3) Pub Date : 2023-11-29 Ariane Weber, Sanni Översti, Denise Kühnert
Phylodynamic methods have lately played a key role in understanding the spread of infectious diseases. During the Coronavirus disease (COVID-19) pandemic, large scale genomic surveillance has further increased the potential of dynamic inference from viral genomes. With the continual emergence of novel severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, explicitly allowing transmission
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Optimizing ancestral trait reconstruction of large HIV Subtype C datasets through multiple-trait subsampling Virus Evol. (IF 5.3) Pub Date : 2023-11-22 Xingguang Li, Nídia S Trovão, Joel O Wertheim, Guy Baele, Adriano de Bernardi Schneider
Large datasets along with sampling bias represent a challenge for phylodynamic reconstructions, particularly when the study data are obtained from various heterogeneous sources and/or through convenience sampling. In this study, we evaluate the presence of unbalanced sampled distribution by collection date, location, and risk group of HIV-1 subtype C using a comprehensive subsampling strategy, and
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HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies Virus Evol. (IF 5.3) Pub Date : 2023-11-16 Hang Zhang, Rowena A Bull, Ahmed Abdul Quadeer, Matthew R McKay
The Hepatitis C virus (HCV) envelope glycoprotein E1 forms a noncovalent heterodimer with E2, the main target of neutralizing antibodies. How E1-E2 interactions influence viral fitness and contribute to resistance to E2-specific antibodies remains largely unknown. We investigate this problem using a combination of fitness landscape and evolutionary modelling. Our analysis indicates that E1 and E2 proteins
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Known phyla dominate the Tara Oceans RNA virome Virus Evol. (IF 5.3) Pub Date : 2023-11-10 Robert C Edgar
A recent study proposed five new RNA virus phyla, two of which, “Taraviricota” and “Arctiviricota”, were stated to be “dominant in the oceans”. However, the study’s assignments classify 28,353 putative RdRp-containing contigs to known phyla but only 886 (2.8%) to the five proposed new phyla combined. I re-mapped the reads to the contigs, finding that known phyla also account for a large majority (93
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Discovery and genome characterization of six new orthoparamyxoviruses in small Belgian mammals Virus Evol. (IF 5.3) Pub Date : 2023-11-10 Marie Horemans, Jessica Van Bets, Tibe Joly Maes, Piet Maes, Bert Vanmechelen
In the future, zoonotic spillover events are expected to happen more frequently. Consequences of such events have clearly been demonstrated by recent outbreaks of monkeypox, Ebola virus and the well-known SARS-CoV-2. Virus discovery has proven to be an important tool in the preparation against viral outbreaks, generating data concerning diversity, quantity and ecology of the vertebrate virome. Orthoparamyxoviruses
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Diving Deep into Fish Bornaviruses: Uncovering Hidden Diversity and Transcriptional Strategies through Comprehensive Data Mining Virus Evol. (IF 5.3) Pub Date : 2023-11-07 Mirette Eshak, Dennis Rubbenstroth, Martin Beer, Florian Pfaff
Recently, we discovered two novel orthobornaviruses in colubrid and viperid snakes using an in silico data mining approach. Here, we present the results of a screening of more than 100,000 nucleic acid sequence datasets of fish samples from the Sequence Read Archive (SRA) for potential bornaviral sequences. We discovered the potentially complete genomes of seven bornavirids in datasets from osteichthyans
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A 1.5 Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis Virus Evol. (IF 5.3) Pub Date : 2023-11-06 Hongda Zhao, Ruixuan Zhang, Junyi Wu, Lingjie Meng, Yusuke Okazaki, Hiroyuki Hikida, Hiroyuki Ogata
Most fungal viruses are RNA viruses and no double-stranded DNA virus that infects fungi is known to date. A recent study detected DNA polymerase genes that originated from large dsDNA viruses in the genomes of basal fungi, suggestive of the existence of dsDNA viruses capable of infecting fungi. In this study, we searched for viral infection signatures in chromosome-level genome assemblies of the arbuscular
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Divergent hepaciviruses, delta-like viruses and a chu-like virus in Australian marsupial carnivores (dasyurids) Virus Evol. (IF 5.3) Pub Date : 2023-10-14 Erin Harvey, Jonathon C.O Mifsud, Edward C Holmes, Jackie E Mahar
Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (Thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under
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Origin, genomic diversity and evolution of African swine fever virus in East Asia Virus Evol. (IF 5.3) Pub Date : 2023-10-07 Genyang Xin, Qiyuan Kuang, Shijia Le, Weichen Wu, Qi Gao, Han Gao, Zhiying Xu, Zezhong Zheng, Gang Lu, Lang Gong, Heng Wang, Guihong Zhang, Mang Shi, Yankuo Sun
Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries has caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated
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Viral community composition of hypersaline lakes. Virus Evol. (IF 5.3) Pub Date : 2023-08-30 Callum Le Lay,Joshua N Hamm,Timothy J Williams,Mang Shi,Ricardo Cavicchioli,Edward C Holmes
Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated the metatranscriptomes of hypersaline lakes that are a rich source of archaea. We sequenced RNA extracted
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Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens Virus Evol. (IF 5.3) Pub Date : 2023-08-24 Patricia Gil, Antoni Exbrayat, Etienne Loire, Ignace Rakotoarivony, Florian Charriat, Côme Morel, Thierry Baldet, Michel Boisseau, Albane Marie, Benoît Frances, Gregory L’Ambert, Mohamed Bessat, Yehia Otify, Maria Goffredo, Giuseppe Mancini, Núria Busquets-Martí, Lotty Birnberg, Sandra Talavera, Carlos Aranda, Emna Ayari, Selma Mejri, Soufien Sghaier, Amal Bennouna, Hicham El Rhaffouli, Thomas Balenghien
Our knowledge on the diversity of eukaryotic viruses has recently undergone a massive expansion. This diversity could influence host physiology through yet unknown phenomena of potential interest to the fields of health and food production. However, the assembly processes of this diversity remain elusive in the eukaryotic viromes of terrestrial animals. This situation hinders hypothesis-driven tests
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Going beyond consensus genome sequences: an innovative SNP-based methodology reconstructs different Uganda cassava brown streak virus haplotypes at a nationwide scale in Rwanda. Virus Evol. (IF 5.3) Pub Date : 2023-08-22 Chantal Nyirakanani, Lucie Tamisier, Jean Pierre Bizimana, Johan Rollin, Athanase Nduwumuremyi, Vincent de Paul Bigirimana, Ilhem Selmi, Ludivine Lasois, Hervé Vanderschuren, Sébastien Massart
Cassava Brown Streak Disease (CBSD), which is caused by cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), represents one of the most devastating threats to cassava production in Africa, including in Rwanda where a dramatic epidemic in 2014 dropped cassava yield from 3.3 million to 900,000 tonnes (1). Studying viral genetic diversity at the genome level is essential in
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Dynamics of the rice yellow mottle disease in western Burkina Faso: epidemic monitoring, spatio-temporal variation of viral diversity and pathogenicity in a disease hotspot Virus Evol. (IF 5.3) Pub Date : 2023-08-21 Estelle Billard, Mariam Barro, Drissa Sérémé, Martine Bangratz, Issa Wonni, Moustapha Koala, Abalo Itolou Kassankogno, Eugénie Hébrard, Gaël Thébaud, Christophe Brugidou, Nils Poulicard, Charlotte Tollenaere
The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at local scale remain scarce, in spite of potential implications for crop protection. Here we describe a five-years (2015-2019)
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Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype. Virus Evol. (IF 5.3) Pub Date : 2023-08-18 Wan-Ting He,Dongyan Li,Guy Baele,Jin Zhao,Zhiwen Jiang,Xiang Ji,Michael Veit,Marc A Suchard,Edward C Holmes,Philippe Lemey,Maciej F Boni,Shuo Su
Swine pathogens have a long history of zoonotic transmission to humans, occasionally leading to sustained outbreaks or pandemics. Through a retrospective epidemiological study of swine populations in China, we describe novel lineages of porcine hemagglutinating encephalomyelitis virus (PHEV) complex coronaviruses (CoVs) that cause exclusively respiratory symptoms with no signs of the neurological symptoms
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Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda Virus Evol. (IF 5.3) Pub Date : 2023-08-03 Edward Nelson Kankaka, Andrew D Redd, Amjad Khan, Steven J Reynolds, Sharada Saraf, Charles Kirby, Briana Lynch, Jada Hackman, Stephen Tomusange, Taddeo Kityamuweesi, Samiri Jamiru, Aggrey Anok, Paul Buule, Daniel Bruno, Craig Martens, Larry W Chang, Thomas C Quinn, Jessica L Prodger, Art Poon
The timing of the establishment of the HIV latent viral reservoir (LVR) is of particular interest, as there is evidence that proviruses are preferentially archived at the time of antiretroviral therapy (ART) initiation. Quantitative viral outgrowth assays (QVOAs) were performed using Peripheral Blood Mononuclear Cells (PBMC) collected from Ugandans living with HIV who were virally suppressed on ART
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Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes Virus Evol. (IF 5.3) Pub Date : 2023-08-02 Brenda Delamonica, Liliana Davalos, Mani Larijani, Simon J Anthony, Jia Liu, Thomas MacCarthy
APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational “hotspots,” can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outbreak has shown a high frequency of C>T mutations at
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Continuous presence of genetically diverse rustrela virus lineages in yellow-necked field mouse reservoir populations in northeastern Germany Virus Evol. (IF 5.3) Pub Date : 2023-07-28 Sina Nippert, Dennis Rubbenstroth, Jessica Anna Geers, Arnt Ebinger, Donata Hoffmann, Angele Breithaupt, Claudia Wylezich, Xuejing Wang, Viola Haring, Philip Starcky, Paola Fruci, Christoph Langner, Christin Trapp, Heiko Schulz, Wilko Stubbe, Christian Imholt, Gerald Heckel, Martin Beer, Florian Pfaff, Rainer G Ulrich
Rustrela virus (RusV; species Rubivirus strelense, family Matonaviridae) was discovered in different zoo animal species affected by fatal encephalitis. Simultaneous RusV RNA detection in multiple yellow-necked field mice (Apodemus flavicollis) suggested this rodent as a reservoir of RusV. Here we investigated 1,264 yellow-necked field mice and sympatric other small mammals from different regions in
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Longitudinal anellome dynamics in the upper respiratory tract of children with acute respiratory tract infections Virus Evol. (IF 5.3) Pub Date : 2023-07-13 Le Cao, Yingying Ma, Zhenzhou Wan, Bing Li, Weimin Tian, Chiyu Zhang, Yanpeng Li
Anelloviruses (AVs) are ubiquitous in humans and are the most abundant components of the commensal virome. Previous studies on the diversity, transmission and persistence of AVs mainly focused on the blood or transplanted tissues from adults; however, the profile of the anellome in the respiratory tract in children are barely known. We investigated the anellome profile and their dynamics in the upper
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From Vaccine to Pathogen: Modeling Sabin 2 Vaccine Virus Reversion and Evolutionary Epidemiology in Matlab, Bangladesh Virus Evol. (IF 5.3) Pub Date : 2023-07-08 Wesley Wong, Jillian Gauld, Michael Famulare
The oral poliovirus vaccines (OPV) are one of most effective disease eradication tools in public health. However, the oral poliovirus vaccine strains are genetically unstable and can cause outbreaks of circulating, vaccine-derived poliovirus (cVDPV2) that are clinically indistinguishable from wild poliovirus (WPV). Here, we developed a Sabin 2 reversion model that simulates the reversion of Sabin 2
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Metagenomics reveals the structure of Mastrevirus-host interaction network within an agro-ecosystem Virus Evol. (IF 5.3) Pub Date : 2023-07-06 Sohini Claverie, Murielle Hoareau, Sélim Ben Chéhida, Denis Filloux, Arvind Varsani, Philippe Roumagnac, Darren P Martin, Jean-Michel Lett, Pierre Lefeuvre
As highly pervasive parasites that sometimes cause disease, viruses are likely major components of all natural ecosystems. An important step towards both understanding the precise ecological roles of viruses and determining how natural communities of viral species are assembled and evolve, is obtaining full descriptions of viral diversity and distributions at ecosystem scales. Here we focused on obtaining
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Genome analyses of species A rotavirus isolated from various mammalian hosts in Northern Ireland during 2013-2016. Virus Evol. (IF 5.3) Pub Date : 2023-07-04 Paula Lagan,Mark H Mooney,Ken Lemon
Rotavirus group A (RVA) is the most important cause of acute diarrhoea and severe dehydration in young mammals. Infection in livestock is associated with significant mortality and economic losses and, together with wildlife reservoirs, acts as a potential source of zoonotic transmission. Therefore, molecular surveillance of circulating RVA strains in animal species is necessary to assess the risks
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Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants Virus Evol. (IF 5.3) Pub Date : 2023-06-29 Anže Božič, Rudolf Podgornik
The spike protein of SARS-CoV-2 is responsible for target recognition, cellular entry, and endosomal escape of the virus. At the same time, it is the part of the virus which exhibits the greatest sequence variation across the many variants which have emerged during its evolution. Recent studies have indicated that with progressive lineage emergence, the positive charge on the spike protein has been
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The hidden diversity of ancient bornaviral sequences from X and P genes in vertebrate genomes Virus Evol. (IF 5.3) Pub Date : 2023-06-09 Bea Clarise B Garcia, Yahiro Mukai, Keizo Tomonaga, Masayuki Horie
Endogenous bornavirus-like elements (EBLs) are heritable sequences derived from bornaviruses in vertebrate genomes that originate from transcripts of ancient bornaviruses. EBLs have been detected using sequence similarity searches such as tBLASTn, whose technical limitations may hinder the detection of EBLs derived from small and/or rapidly evolving viral X and P genes. Indeed, no EBLs derived from