Article
Virology
Angelica Bravo, Leandro Fernandez-Garcia, Rodrigo Ibarra-Karmy, Gonzalo A. Mardones, Luis Mercado, Fernando J. Bustos, Robert J. Gifford, Gloria Arriagada
Summary: Endogenous viral elements (EVEs) are genomic DNA sequences derived from viruses and some of them can express proteins with physiological roles in their host. In this study, we found that DeRep, a protein encoded in an endogenous parvoviral element (EPV), demonstrated antiviral activity against an exogenous parvovirus in degu cells. This is the first time an EPV has been shown to have such activity.
Article
Immunology
Suparat Taengchaiyaphum, Phasini Buathongkam, Suchitraporn Sukthaworn, Prapatsorn Wongkhaluang, Kallaya Sritunyalucksana, Timothy William Flegel
Summary: This study reveals the existence of endogenous reverse transcriptase mechanisms in shrimp similar to those found in insects to inhibit viral replication. Extracted circular viral copy DNA from giant tiger shrimp significantly reduced the replication of infectious hypodermal and hematopoietic necrosis virus. The discovery that endogenous viral elements can give rise to cvcDNA provides a new pathway for using cvcDNA to enhance shrimp tolerance to viruses.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Virology
Samuel Cibulski, Diane Alves de Lima, Helton Fernandes dos Santos, Thais Fumaco Teixeira, Caroline Tochetto, Fabiana Quoos Mayer, Paulo Michel Roehe
Summary: A viral metagenomics study in meat from supermarkets in Southern Brazil revealed the presence of various viruses, including new species of gyroviruses and porcine parvoviruses. Although these viruses have not been transmitted to humans, consumption of these meats inevitably leads to intake of these viruses.
Article
Virology
Elliot W. Jackson, Roland C. Wilhelm, Mitchell R. Johnson, Holly L. Lutz, Isabelle Danforth, Joseph K. Gaydos, Michael W. Hart, Ian Hewson
Summary: Initial assumptions linking sea star wasting syndrome (SSWS) to a single densovirus were confounded by the discovery of a high diversity of densoviruses present in sea stars globally. It is now suggested that SSWS may not be solely caused by one virus, but rather by a combination of various densoviruses.
JOURNAL OF VIROLOGY
(2021)
Article
Microbiology
Satoshi Kawato, Reiko Nozaki, Hidehiro Kondo, Ikuo Hirono
Summary: In this study, the genomes of 27 endogenous nimaviruses were recovered from crustacean genome data. Phylogenetic analysis revealed different lineages and specific insertion preferences for each nimavirus species. These findings suggest that endogenous nimaviruses are giant transposable elements occupying different sequence niches.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
Paula Rozo-Lopez, William Brewer, Simon Kaefer, McKayla M. Martin, Benjamin J. Parker
Summary: Insects are an important reservoir of viral biodiversity, but the majority of insect-associated viruses remain undiscovered. This study used multiple sequencing methods to investigate the virome of the potato aphid and found insect-specific viruses, parasitoid virus, plant pathogenic virus, and phages. However, the analysis of the insect's genome assembly revealed that some of the "virome" could be attributed to endogenous viral elements.
Article
Virology
Miranda Barnes, Dana C. Price
Summary: The analysis of hard tick genome sequences reveals a diverse range of endogenous viral elements, with Rhabdoviridae being well-represented. Extensive integration of adintoviruses and presence of elements similar to known human and veterinary pathogens were also observed. These findings contribute to a better understanding of the viral fossils derived from ticks and can serve as a reference for quality control of tick-omics data.
Article
Biochemistry & Molecular Biology
Yahiro Mukai, Masayuki Horie, Shohei Kojima, Junna Kawasaki, Ken Maeda, Keizo Tomonaga
Summary: In this study, we revealed the existence of an EBLN that has been exapted as an RNA-binding protein in miniopterid bats, indicating its functional relationship with host RNA-binding proteins.
Article
Biotechnology & Applied Microbiology
Suparat Taengchaiyaphum, Prapatsorn Wongkhaluang, Kanchana Sittikankaew, Nitsara Karoonuthaisiri, Timothy W. Flegel, Kallaya Sritunyalucksana
Summary: Shrimp have the ability to accommodate viruses in long term, persistent infections without signs of disease. EVE in shrimp genome may play a role in this process to dampen viral replication. Specificity of EVE clusters could be advantageous for genetic improvement in shrimp breeding.
Article
Biochemistry & Molecular Biology
Ioanna Kalvari, Eric P. Nawrocki, Nancy Ontiveros-Palacios, Joanna Argasinska, Kevin Lamkiewicz, Manja Marz, Sam Griffiths-Jones, Claire Toffano-Nioche, Daniel Gautheret, Zasha Weinberg, Elena Rivas, Sean R. Eddy, Robert D. Finn, Alex Bateman, Anton Petrov
Summary: Rfam is a database of RNA families with 3444 families, each represented by a multiple sequence alignment of known RNA sequences and a covariance model for searching additional members. Recent developments focused on improving data quality and coverage, adding new families like microRNAs, viral and bacterial RNAs through expert collaborations. The database saw significant growth with 759 new families added in Rfam 14, along with new features such as the Rfam Cloud family curation system.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Virology
Robert A. Lopez-Astacio, Oluwafemi F. Adu, Daniel J. Goetschius, Hyunwook Lee, Wendy S. Weichert, Brian R. Wasik, Simon P. Frueh, Brynn K. Alford, Ian E. H. Voorhees, Joseph F. Flint, Sarah Saddoris, Laura B. Goodman, Edward C. Holmes, Susan L. Hafenstein, Colin R. Parrish
Summary: Canine parvovirus (CPV) is a small DNA virus that causes serious diseases in dogs worldwide. In this study, in vitro selection and deep sequencing were used to investigate the escape mutations in CPV induced by two antibodies. The results provide insights into the selection of viral variants and the interactions between antibodies and receptors.
JOURNAL OF VIROLOGY
(2023)
Article
Multidisciplinary Sciences
Hai-Jian Huang, Yi-Yuan Li, Zhuang-Xin Ye, Li-Li Li, Qing-Ling Hu, Yu-Juan He, Yu-Hua Qi, Yan Zhang, Ting Li, Gang Lu, Qian-Zhuo Mao, Ji-Chong Zhuo, Jia-Bao Lu, Zhong-Tian Xu, Zong-Tao Sun, Fei Yan, Jian-Ping Chen, Chuan-Xi Zhang, Jun-Min Li
Summary: Non-retroviral endogenous viral elements (nrEVEs) are widely dispersed in eukaryotic genomes, with their functions largely unknown. In this study, researchers discovered that a ToEVE in planthoppers has been domesticated and plays essential roles in their development and reproduction. Analysis of arthropod genomes suggests that nrEVEs may contribute to the functional diversity of arthropod genes.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Clement Gilbert, Carole Belliardo
Summary: The study revealed the diversity of viral sequences integrated into insect genomes, which can be assigned to different families of RNA and single-stranded DNA viruses. Research on these endogenous viral elements has provided important insights into insect-virus interactions, highlighting the discovery of a new form of adaptive antiviral immunity. The diversity of insect EVE is expected to continue increasing with the sequencing of new insect genomes and exogenous viruses, making paleovirology a dynamic research field in the future.
CURRENT OPINION IN INSECT SCIENCE
(2022)
Review
Virology
Luca Nishimura, Naoko Fujito, Ryota Sugimoto, Ituro Inoue
Summary: The COVID-19 outbreak highlights the importance of studying viral evolution to understand complex viral changes and prevent future pandemics. Ancient viral genomes found in ancient remains, such as skeletons and mummified tissues, provide unique insights into viral evolution. With advancements in sequencing technologies, ancient viral DNA and RNA can be analyzed to reconstruct ancient pathogenic viral genomes and estimate past pandemics and evolutionary events. Recent studies have also discovered non-pathogenic viral genomes in ancient human bodies, providing information on their diet and lifestyles. This review summarizes past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the use of ancient viral genomes to understand long-term viral evolution.
Article
Veterinary Sciences
Shixing Yang, Yumin He, Xu Chen, Ullah Kalim, Yan Wang, Shuyu Yang, Haifeng Qi, Hengzheng Cheng, Xiang Lu, Xiaochun Wang, Quan Shen, Wen Zhang
Summary: Raccoon dogs, as an ancient species of Canidae, carry various viruses, some of which have been detected from recent development in raccoon dog breeding. A study on the virome in raccoon dog feces from a farm in Jilin Province, China, identified DNA or RNA viruses mainly from seven families. This research contributes to a better understanding of the virome in raccoon dogs and provides valuable information for viral disease monitoring, prevention, and treatment in these animals.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Virology
Marcilio Jorge Fumagalli, Carlos Fabiano Capato, Luiza Antunes de Castro-Jorge, William Marciel de Souza, Eurico Arruda, Luiz Tadeu Moraes Figueiredo
Summary: This study found differences in the stability of different viruses under various conditions, such as reduced thermal stability of coxsackievirus B5 at 45 degrees Celsius and residual infectivity of SARS-CoV-2 at 55 degrees Celsius; UV light exposure was an efficient means of viral inactivation, but less effective for non-enveloped viruses; rhinovirus A16 and respiratory syncytial virus showed extreme sensitivity to acid conditions.
ARCHIVES OF VIROLOGY
(2022)
Article
Virology
Marcilio Jorge Fumagalli, Luiza Antunes Castro-Jorge, William Marciel de Souza, Patrick Orestes de Azevedo, Alana Witt Hansen, Ricardo Tostes Gazzinelli, Benedito Antonio Lopes da Fonseca, Fernando Rosado Spilki, Luiz Tadeu Moraes Figueiredo
Summary: The emergence of the Delta variant of SARS-CoV-2 has raised concerns about vaccine effectiveness. However, this study found that the Delta variant is still neutralized effectively by antibodies produced from CoronaVac or ChAdOx1 vaccination, indicating the importance of vaccination even for individuals previously infected by the Gamma variant.
Article
Biochemistry & Molecular Biology
Andrea Brizzi, Charles Whittaker, Luciana M. S. Servo, Iwona Hawryluk, Carlos A. Prete Jr, William M. de Souza, Renato S. Aguiar, Leonardo J. T. Araujo, Leonardo S. Bastos, Alexandra Blenkinsop, Lewis F. Buss, Darlan Candido, Marcia C. Castro, Silvia F. Costa, Julio Croda, Andreza Aruska de Souza Santos, Christopher Dye, Seth Flaxman, Paula L. C. Fonseca, Victor E. V. Geddes, Bernardo Gutierrez, Philippe Lemey, Anna S. Levin, Thomas Mellan, Diego M. Bonfim, Xenia Miscouridou, Swapnil Mishra, Melodie Monod, Filipe R. R. Moreira, Bruce Nelson, Rafael H. M. Pereira, Otavio Ranzani, Ricardo P. Schnekenberg, Elizaveta Semenova, Raphael Sonnabend, Renan P. Souza, Xiaoyue Xi, Ester C. Sabino, Nuno R. Faria, Samir Bhatt, Oliver Ratmann
Summary: Analysis of individual-level patient records from Brazil reveals that COVID-19 mortality rates are significantly influenced by pre-pandemic geographic inequities and healthcare capacity during the pandemic. The study also documents the temporary shocks in hospital fatality rates following the spread of the Gamma variant in 14 state capitals, where more than half of hospitalized patients aged 70 years and older died. The fluctuations in Brazil's COVID-19 in-hospital fatality rates were primarily associated with geographic inequities and shortages in healthcare capacity. Approximately half of the COVID-19 deaths in hospitals in the 14 cities could have been avoided without pre-pandemic geographic inequities and healthcare pressure. Investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize the impact of highly transmissible and deadly pathogens like SARS-CoV-2, especially in low- and middle-income countries.
Article
Microbiology
Kathryn Campbell, Robert J. Gifford, Joshua Singer, Verity Hill, Aine O'Toole, Andrew Rambaut, Katie Hampson, Kirstyn Brunker
Summary: The availability of pathogen sequence data and the use of genomic surveillance are increasing rapidly. In this study, the researchers propose an updated genomic tool and classification system for better understanding the dynamics of rabies virus and improving disease control. By implementing this tool, they were able to define 96 total lineages within the globally distributed Cosmopolitan Glade of rabies virus, which is a significant increase from the previously reported 22 lineages. The integration of this tool with a new rabies virus sequence data resource enables rapid application and provides insights into the control and elimination of dog-mediated rabies.
Correction
Biochemistry & Molecular Biology
Andrea Brizzi, Charles Whittaker, Luciana M. S. Servo, Iwona Hawryluk, Carlos A. Prete, William M. de Souza, Renato S. Aguiar, Leonardo J. T. Araujo, Leonardo S. Bastos, Alexandra Blenkinsop, Lewis F. Buss, Darlan Candido, Marcia C. Castro, Silvia F. Costa, Julio Croda, Andreza Aruska de Souza Santos, Christopher Dye, Seth Flaxman, Paula L. C. Fonseca, Victor E. V. Geddes, Bernardo Gutierrez, Philippe Lemey, Anna S. Levin, Thomas Mellan, Diego M. Bonfim, Xenia Miscouridou, Swapnil Mishra, Melodie Monod, Filipe R. R. Moreira, Bruce Nelson, Rafael H. M. Pereira, Otavio Ranzani, Ricardo P. Schnekenberg, Elizaveta Semenova, Raphael Sonabend, Renan P. Souza, Xiaoyue Xi, Ester C. Sabino, Nuno R. Faria, Samir Bhatt, Oliver Ratmann
Article
Microbiology
Christian Shema Mugisha, Tung Dinh, Abhishek Kumar, Kasyap Tenneti, Jenna E. Eschbach, Keanu Davis, Robert Gifford, Mamuka Kvaratskhelia, Sebla B. Kutluay
Summary: In addition to its catalytic function, HIV-1 integrase (IN) binds to the viral RNA genome (gRNA) through positively charged residues (i.e., R262, R263, R269, K273) within its C-terminal domain (CTD) and regulates proper virion maturation. Mutation of these residues results in the formation of morphologically aberrant viruses blocked at an early reverse transcription stage in cells.
Article
Public, Environmental & Occupational Health
Ana Catharina Nastri, Amaro Nunes Duarte-Neto, Luciana Vilas Boas Casadio, William Marciel de Souza, Ingra M. Claro, Erika R. Manuli, Gloria Selegatto, Matias C. Saloma, Gabriel Fialkovitz, Mariane Taborda, Bianca Leal de Almeida, Marcello C. Magri, Ana Rubia Guedes, Laura Vieira Perdigao Neto, Fatima Mitie Sataki, Thais Guimaraes, Maria Cassia Mendes-Correa, Tania R. Tozetto-Mendoza, Marcilio Jorge Fumagalli, Yeh-Li Ho, Camila ALves Maia da Silva, Thais M. Coletti, Jacqueline Goes de Jesus, Camila M. Romano, Sarah C. Hill, Oliver Pybus, Joao Renato Rebello Pinho, Felipe Lourenco Ledesma, Yuri R. Casal, Cristina Kanamura, Leonardo Jose Tadeu de Araujo, Camila Santos da Silva Ferreira, Juliana Mariotti Guerra, Luiz Tadeu Moraes Figueiredo, Marisa Dolhnikoff, Nuno R. Faria, Ester C. Sabino, Venacio Avancini, Ferreira Alves, Anna S. Levin
Summary: This study reports two cases of Brazilian Sabi virus infection diagnosed using metagenomics. The patients presented with hepatitis, bleeding, and neurological alterations, leading to death. No nosocomial transmission was found in the contact tracing.
TRAVEL MEDICINE AND INFECTIOUS DISEASE
(2022)
Article
Multidisciplinary Sciences
Liane P. Fernandes, Rocio Enriquez-Gasca, Poppy A. Gould, James H. Holt, Lucia Conde, Gabriela Ecco, Javier Herrero, Robert Gifford, Didier Trono, George Kassiotis, Helen M. Rowe
Summary: Research has found that the regulation of cell fate can be influenced by ZFP819, which targets a satellite DNA array called ZP3AR. The depletion of ZFP819 leads to a transition from a pluripotent state to a 2-cell-like state in cells. This transition is accompanied by changes in chromatin structure and the inactivation of master transcription factor genes.
Article
Virology
Roziah Kambol, Anna Gatseva, Robert J. Gifford
Summary: This study reports a previously unknown endogenous lentivirus lineage in the genome of the South African springhare, revealing that the host range of lentiviruses has historically extended to rodents. Through comparative and phylogenetic analysis of virus and host genomes, the long-term evolutionary history of the genus is further understood by considering biogeographic and ecological characteristics of host species.
Article
Biochemistry & Molecular Biology
Matthew A. Campbell, Shannon Loncar, Robert M. Kotin, Robert J. Gifford
Summary: In this study, a comprehensive analysis of endogenous parvoviral elements (EPVs) in 752 published vertebrate genomes was conducted, revealing the ecology and evolution of individual parvovirus genera. The findings show long-term evolution of different parvovirus genera and their interaction with hosts, providing a theoretical foundation for developing parvoviruses as therapeutic tools.
Article
Virology
Maria-Luisa Carrozza, Anna-Maria Niewiadomska, Maurizio Mazzei, Mounir R. Abi-Said, Stephane Hue, Joseph Hughes, Anna Gatseva, Robert J. Gifford
Summary: Small ruminant lentiviruses (SRLVs) cause chronic, persistent infections in domestic sheep and goats worldwide. Phylogenetic analysis reveals that the global diversity of SRLVs can be traced back to ancient splits into Eastern and Western lineages during the Neolithic period, and the emergence of SRLV-A is linked to the international export of Central Asian Karakul sheep in the early 20th century.
Article
Cell Biology
Rocio Enriquez-Gasca, Poppy A. Gould, Hale Tunbak, Lucia Conde, Javier Herrero, Alexandra Chittka, Christine R. Beck, Robert Gifford, Helen M. Rowe
Summary: Endogenous retroviruses (ERVs) have reconfigured host gene networks. Using an active murine ERV (IAPEz) and an ESC-NPC differentiation model, the origins of co-option were explored. Transcriptional silencing via TRIM28 was found to be mediated by a 190 bp sequence encoding the IAP signal peptide, which is responsible for retrotransposition. Escapee IAPs, in contrast, evade repression in both cell types, resulting in their transcriptional derepression, particularly in NPCs. It was shown that the enhancer function of a 47 bp sequence within the U3 region of the LTR is validated, and escapee IAPs have an activating effect on nearby neural genes.
Article
Virology
Angelica Bravo, Leandro Fernandez-Garcia, Rodrigo Ibarra-Karmy, Gonzalo A. Mardones, Luis Mercado, Fernando J. Bustos, Robert J. Gifford, Gloria Arriagada
Summary: Endogenous viral elements (EVEs) are genomic DNA sequences derived from viruses and some of them can express proteins with physiological roles in their host. In this study, we found that DeRep, a protein encoded in an endogenous parvoviral element (EPV), demonstrated antiviral activity against an exogenous parvovirus in degu cells. This is the first time an EPV has been shown to have such activity.
Article
Biochemistry & Molecular Biology
Michael R. Oliver, Kamilla J. Toon, Charlotte B. Lewis, Stephen Devlin, Robert J. Gifford, Joe Grove
Summary: The structures of E1E2 glycoproteins from 60 viral species in the Hepacivirus, Pegivirus, and Pestivirus genera were predicted using systematic genome annotation and AlphaFold modelling, revealing that while E2 varied widely, E1 exhibited a consistent fold across different viruses, indicating a common and novel membrane fusion mechanism. Comparison of E1E2 models from various species also provided insights into the evolution of membrane fusion in these viral genera.
Article
Virology
Connor G. G. Bamford, William M. de Souza, Rhys Parry, Robert J. Gifford
Summary: Flavivirids, a family of RNA viruses, have been found to be over 100 million years old and have evolved in early animals, co-diverging with major animal phyla. The study also reveals that some classical flaviviruses initially evolved in hematophagous arachnids and later acquired the ability to be transmitted by insects.