Article
Biotechnology & Applied Microbiology
Julien Martinez, Perran A. Ross, Xinyue Gu, Thomas H. Ant, Shivan M. Murdochy, Lily Tong, Ana da Silva Filipe, Ary A. Hoffmann, Steven P. Sinkins
Summary: Dengue, a viral disease transmitted by Aedes mosquitoes, poses a threat to half of the world's population. Recent advances in dengue control involve introducing Wolbachia bacterial symbionts into mosquito populations, which can greatly reduce disease incidence. This study reveals the existence of two variants of a Wolbachia strain being released in natural populations of Aedes aegypti mosquitoes. These variants differ in genome architecture and gene content, affecting their density and tolerance to heat stress. The findings suggest that different variants may be more suitable for field deployment depending on local environmental conditions.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Tanya N. Phung, Timothy H. Webster, Elizabeth Lenkiewicz, Smriti Malasi, Mariacarla Andreozzi, Ann E. McCullough, Karen S. Anderson, Barbara A. Pockaj, Melissa A. Wilson, Michael T. Barrett
Summary: Breast cancers show intratumoral heterogeneity, with genomic analysis helping to identify different populations within the tumors, which can aid in understanding disease progression and treatment resistance.
SCIENTIFIC REPORTS
(2021)
Article
Ecology
Nikos Patias, Francisco Rowe, Stefano Cavazzi, Dani Arribas-Bel
Summary: Current planning strategies promoting suburbanisation and low built-up density areas tend to increase the environmental footprint of cities, while international and local government plans are increasingly targeted at making urban areas more sustainable. Urban structure plays a crucial role in guiding urban smart growth policies that promote sustainable urban environments and improve neighbourhood social cohesion.
LANDSCAPE AND URBAN PLANNING
(2021)
Article
Microbiology
Ternenge Thaddaeus Apaa, Harriet Mcfadzean, Sara Gandy, Kayleigh Hansford, Jolyon Medlock, Nicholas Johnson
Summary: This study examined the presence of A. phagocytophilum in livestock and wildlife in Great Britain, with a focus on cattle. The results showed the presence of ecotype I in cattle, sheep, red deer, and Ixodes ricinus ticks, and ecotype II in roe deer and I. ricinus removed from deer carcasses. However, only ecotype I was detected in cattle in this study.
Article
Multidisciplinary Sciences
Jianzhen Lin, Xinxin Peng, Kun Dong, Junyu Long, Xuejiao Guo, Hongyue Li, Yi Bai, Xu Yang, Dongxu Wang, Xin Lu, Yilei Mao, Xinting Sang, Xuwo Ji, Haitao Zhao, Han Liang
Summary: This study uses genomics to analyze the progression from biliary tract intraepithelial neoplasia (BilIN) to gallbladder carcinoma (GBC), revealing two distinct evolutionary paths for GBC development.
NATURE COMMUNICATIONS
(2021)
Article
Environmental Sciences
Han Wang, Yunqing Xuan
Summary: This paper analyzes the temporal variation of annual maximum daily rainfall (AMDR) in Great Britain and Australia, considering the spatial properties of location, size, and shape. The study finds that most regions show an increasing trend in AMDR over time, and larger-sized regions tend to have lower AMDR values. However, the temporal variation of AMDR does not have a consistent relationship with the size of the region. The impact of climate change on extreme rainfall is higher for rounded shapes, although the shape of the region is not as significant as the other two spatial properties. Additionally, conventional stationary models underestimate AMDR in regions where a nonstationary (i.e., time-varying) model is preferred. The findings suggest the need for a comprehensive overhaul of storm design procedures to account for the impact of climate change and spatial variation in natural processes.
Article
Immunology
Jennifer T. Grier, Brock A. Arivett, Maria S. Ramirez, Renee J. Chosed, Jessica A. Bigner, Emily J. Ohneck, Maeva L. Metz, Cecily R. Wood, Sergio Arce, Andrea Tartaro, Ryan F. Relich, Luis A. Actis, Steven E. Fiester
Summary: This study analyzed XDR isolates of A. baumannii in a case of necrotizing fasciitis, revealing genetic differences that could lead to distinct phenotypic characteristics at the cellular level.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Environmental Sciences
Jennifer L. Williamson, Andrew Tye, Dan J. Lapworth, Don Monteith, Richard Sanders, Daniel J. Mayor, Chris Barry, Mike Bowes, Michael Bowes, Annette Burden, Nathan Callaghan, Gareth Farr, Stacey Felgate, Alice Fitch, Stuart Gibb, Pete Gilbert, Geoff Hargreaves, Patrick Keenan, Vassilis Kitidis, Monika Juergens, Adrian Martin, Ian Mounteney, Philip D. Nightingale, M. Gloria Pereira, Justyna Olszewska, Amy Pickard, Andrew P. Rees, Bryan Spears, Mark Stinchcombe, Debbie White, Peter Williams, Fred Worrall, Chris Evans
Summary: This study provides a comprehensive assessment of riverine dissolved organic carbon (DOC) export in Great Britain, revealing that smaller river systems draining peat-rich areas are underestimated in global syntheses. The study also highlights the significant influence of upland conifer plantation forestry on the spatial distribution of DOC exports. These findings have implications for future assessments of CO2 sequestration potential and climate change mitigation strategies.
Article
Multidisciplinary Sciences
Gayatri Shankar Chilambi, Hayley R. Nordstrom, Daniel R. Evans, Regis P. Kowalski, Deepinder K. Dhaliwal, Vishal Jhanji, Robert M. Q. Shanks, Daria Van Tyne
Summary: This study reveals the genomic and phenotypic variability among E. faecalis causing endophthalmitis, including antibiotic resistance genes and virulence factors. Additionally, possible adaptive mechanisms were identified, shedding light on the reasons behind bacterial persistence during recurrent ocular infection.
Article
Virology
Peter J. Kerr, Isabella M. Cattadori, Derek Sim, June Liu, Edward C. Holmes, Andrew F. Read
Summary: This study investigated the virulence and disease phenotypes of recent isolates of myxoma virus in Australian rabbits. The viruses showed different levels of virulence, causing acute death with minimal signs of myxomatosis and bacterial invasions, but no inflammatory response. Some rabbits developed an amyxomatous phenotype. It was also found that certain laboratory rabbits had innate resistance to myxomatosis. The alterations in disease pathogenesis and bacterial invasions suggest that the virulence grades of modern viruses cannot be directly compared with earlier studies.
JOURNAL OF VIROLOGY
(2022)
Article
Genetics & Heredity
Josine L. Min, Gibran Hemani, Eilis Hannon, Koen F. Dekkers, Juan Castillo-Fernandez, Rene Luijk, Elena Carnero-Montoro, Daniel J. Lawson, Kimberley Burrows, Matthew Suderman, Andrew D. Bretherick, Tom G. Richardson, Johanna Klughammer, Valentina Iotchkova, Gemma Sharp, Ahmad Al Khleifat, Aleksey Shatunov, Alfredo Iacoangeli, Wendy L. McArdle, Karen M. Ho, Ashish Kumar, Cilia Soderhall, Carolina Soriano-Tarraga, Eva Giralt-Steinhauer, Nabila Kazmi, Dan Mason, Allan F. McRae, David L. Corcoran, Karen Sugden, Silva Kasela, Alexia Cardona, Felix R. Day, Giovanni Cugliari, Clara Viberti, Simonetta Guarrera, Michael Lerro, Richa Gupta, Sailalitha Bollepalli, Pooja Mandaviya, Yanni Zeng, Toni-Kim Clarke, Rosie M. Walker, Vanessa Schmoll, Darina Czamara, Carlos Ruiz-Arenas, Faisal Rezwan, Riccardo E. Marioni, Tian Lin, Yvonne Awaloff, Marine Germain, Dylan Aissi, Ramona Zwamborn, Kristel van Eijk, Annelot Dekker, Jenny van Dongen, Jouke-Jan Hottenga, Gonneke Willemsen, Cheng-Jian Xu, Guillermo Barturen, Francesc Catala-Moll, Martin Kerick, Carol Wang, Phillip Melton, Hannah R. Elliott, Jean Shin, Manon Bernard, Idil Yet, Melissa Smarts, Tyler Gorrie-Stone, Chris Shaw, Ammar Al Chalabi, Susan M. Ring, Goran Pershagen, Erik Melen, Jordi Jimenez-Conde, Jaume Roquer, Deborah A. Lawlor, John Wright, Nicholas G. Martin, Grant W. Montgomery, Terrie E. Moffitt, Richie Poulton, Tonu Esko, Lili Milani, Andres Metspalu, John R. B. Perry, Ken K. Ong, Nicholas J. Wareham, Giuseppe Matullo, Carlotta Sacerdote, Salvatore Panico, Avshalom Caspi, Louise Arseneault, France Gagnon, Miina Ollikainen, Jaakko Kaprio, Janine F. Felix, Fernando Rivadeneira, Henning Tiemeier, Marinus H. van IJzendoorn, Andre G. Uitterlinden, Vincent W. V. Jaddoe, Chris Hale, Andrew M. McIntosh, Kathryn L. Evans, Alison Murray, Katri Raikkonen, Jari Lahti, Ellen A. Nohr, Thorkild I. A. Sorensen, Torben Hansen, Camilla S. Morgen, Elisabeth B. Binder, Susanne Lucae, Juan Ramon Gonzalez, Mariona Bustamante, Jordi Sunyer, John W. Holloway, Wilfried Karmaus, Hongmei Zhang, Ian J. Deary, Naomi R. Wray, John M. Starr, Marian Beekman, Diana VanHeemst, P. Eline Slagboom, Pierre-Emmanuel Morange, David-Alexandre Tregouet, Jan H. Veldink, Gareth E. Davies, Eco J. C. de Geus, Dorret Boomsma, Judith M. Vonk, Bert Brunekreef, Gerard H. Koppelman, Marta E. Alarcon-Riquelme, Rae-Chi Huang, Craig E. Pennell, Joyce van Meurs, M. Arfan Ikram, Alun D. Hughes, Therese Tillin, Nish Chaturvedi, Zdenka Pausova, Tomas Paus, Timothy D. Spector, Meena Kumari, Leonard C. Schalkwyk, Peter M. Visscher, George Davey Smith, Christoph Bock, Tom R. Gaunt, Jordana T. Bell, Bastiaan T. Heijmans, Jonathan Mill, Caroline L. Relton
Summary: In this study, DNA methylation quantitative trait locus (mQTL) analyses were conducted on 32,851 participants, revealing genetic variants associated with DNA methylation at 420,509 sites in blood and generating a database of over 270,000 independent mQTLs. The genetic architecture of DNA methylation levels was shown to be highly polygenic, with some genetic variants linked to both DNA methylation levels and complex diseases, indicating a complex genotype-phenotype map.
Article
Genetics & Heredity
Salma Shickh, Agnes H. Sebastian, Marc Clausen, Chloe Mighton, Christine F. Elser, Andrea Eisen, Larissa Waldman, Seema Panchal, Thomas Ward, June E. Carroll, Emily Glogowski, Kasmintan Schrader, Jordan A. Lerner-Ellis, Raymond Kim, Kevin E. Thorpe, Yvonne Bombard
Summary: This study aimed to understand patient preferences and factors influencing preferences for secondary findings from genomic sequencing. The majority of adult cancer patients in the trial expressed interest in receiving various types of secondary findings, even those without immediate medical actionability. Older participants were more interested in early-onset neurological diseases, and those with lower decisional conflict were more likely to select all categories. The results emphasize the importance of incorporating patient preferences into guidelines on secondary findings.
Article
Engineering, Civil
Andrew M. Tye, Jennifer L. Williamson, Helen P. Jarvie, Nancy B. Dise, Dan J. Lapworth, Don Monteith, Richard Sanders, Daniel J. Mayor, Michael J. Bowes, Michael Bowes, Annette Burden, Nathan Callaghan, Gareth Farr, Stacey L. Felgate, Stuart Gibb, Pete J. Gilbert, Geoff Hargreaves, Patrick Keenan, Vassilis Kitidis, Monika D. Jurgens, Adrian Martin, Ian Mounteney, Philip D. Nightingale, M. Gloria Pereira, Justyna Olszewska, Amy Pickard, Andrew P. Rees, Bryan Spears, Mark Stinchcombe, Debbie White, Peter Williams, Fred Worrall, Chris D. Evans
Summary: This study investigated the DIC and free CO2 concentrations in waters of 41 catchments in Great Britain. The study found that dissolved inorganic carbon dominates in coastal waters, while free CO2 concentrations are strongly linked to catchment macronutrient status. The findings provide a basis for developing management strategies to reduce free CO2 concentrations in rivers and mitigate its evasion to the atmosphere.
JOURNAL OF HYDROLOGY
(2022)
Article
Infectious Diseases
Shukho Kim, Hyesoon Song, Jong Sook Jin, Weon Ju Lee, Jungmin Kim
Summary: In this study, we isolated 15 phages specific to Cutibacterium acnes from clinical samples and sequenced the genomes of three phages. Bioinformatic analysis revealed the hydrophobic nature of the capsid and tape measure proteins. Additionally, we found that the phage particles can be efficiently solubilized in an SMT2 buffer containing Tween 20.
Article
Biochemistry & Molecular Biology
Jorge Botas, Alvaro Rodriguez del Rio, Joaquin Giner-Lamia, Jaime Huerta-Cepas
Summary: GeCoViz is an online resource that provides fast and interactive visualization of custom genomic regions, allowing for easy investigation of the functional and evolutionary interpretation of prokaryotic genes.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Biochemistry & Molecular Biology
Mary E. Petrone, Edward C. Holmes, Erin Harvey
Summary: To mitigate the emergence of new pathogenic viruses, public health strategies should conduct long-term surveillance of ecosystems experiencing changes in biodiversity using metagenomic techniques to identify generalist viruses.
Article
Virology
Soufien Sghaier, Corinne Sailleau, Maurilia Marcacci, Sarah Thabet, Valentina Curini, Thameur Ben Hassine, Liana Teodori, Ottavio Portanti, Salah Hammami, Lucija Jurisic, Massimo Spedicato, Lydie Postic, Ines Gazani, Raja Ben Osman, Stephan Zientara, Emmanuel Breard, Paolo Calistri, Jurgen A. Richt, Edward C. Holmes, Giovanni Savini, Francesca Di Giallonardo, Alessio Lorusso
Summary: Epizootic haemorrhagic disease (EHD) is a viral disease transmitted by Culicoides and affects domestic and wild ruminants, particularly white-tailed deer and cattle. Recent outbreaks of EHDV-8 have been reported in cattle farms in central/western Tunisia, spreading rapidly throughout the country with more than 200 confirmed cases. This study emphasizes the need for vaccines targeting various serotypes of EHDV.
Article
Microbiology
Nannan Li, Cixiu Li, Tao Hu, Juan Li, Hong Zhou, Jingkai Ji, Jiangli Wu, Weipeng Kang, Edward C. Holmes, Weifeng Shi, Shufa Xu
Summary: Through meta-transcriptomic sequencing of nearly 2000 samples collected across China, researchers have revealed the diversity and prevalence of honeybee viruses, as well as the existence of novel genetic variants associated with China. The study highlights the widespread distribution and genetic diversity of honeybee viruses, suggesting the importance of understanding and mitigating viral infectious diseases in honeybees.
Article
Virology
Vincenzo A. Costa, David R. Bellwood, Jonathon C. O. Mifsud, Kate Van Brussel, Jemma L. Geoghegan, Edward C. Holmes, Erin Harvey
Summary: The Great Barrier Reef is the largest coral reef ecosystem in the world, supporting over 1,200 fish species with high potential for virus transmission. However, our understanding of virus diversity and connectivity in tropical reef fishes remains poor. The reef has also faced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet.
Editorial Material
Biochemistry & Molecular Biology
Meng Lu, Wan -Ting He, John H. -O. Pettersson, Guy Baele, Mang Shi, Edward C. Holmes, Na He, Shuo Su
Article
Biochemistry & Molecular Biology
Katherine Eaton, Ravneet K. Sidhu, Jennifer Klunk, Julia A. Gamble, Jesper L. Boldsen, Ann G. Carmichael, Nukhet Varlik, Sebastian Duchene, Leo Featherstone, Vaughan Grimes, Brian Golding, Sharon N. DeWitte, Edward C. Holmes, Hendrik N. Poinar
Summary: By investigating 13 archaeological sites in Denmark, a study found that the plague appeared and evolved continuously in the region from the 14th to the 17th century, with cross-interactions with other European countries, rather than long-term local persistence. This research provides epidemiological links between the plague and the unknown pestilence in medieval and early modern Europe, and demonstrates how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology, paving the way for the next generation of historical disease research.
Article
Evolutionary Biology
Mary E. Petrone, Carolina Lucas, Bridget Menasche, Mallery Breban, Inci Yildirim, Melissa Campbell, Saad B. Omer, Edward C. Holmes, Albert Ko, Nathan D. Grubaugh, Akiko Iwasaki, Craig B. Wilen, Chantal B. F. Vogels, Joseph R. Fauver
Summary: Developing a timely and effective response to emerging SARS-CoV-2 variants of concern is crucial for public health. Global health surveillance relies not only on genomic data but also on methods that utilize genomic data to estimate the epidemiological dynamics of emerging lineages. In this study, the differences in reporting delays among SARS-CoV-2 VOCs were analyzed, indicating that these delays may have delayed the global response to the Mu variant. The nonsystematic biases in the reporting of genomic data could impede the assessment of future emerging variants.
GENOME BIOLOGY AND EVOLUTION
(2023)
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
Virology
Peiwen Chen, Ziying Jin, Liuxia Peng, Zuoyi Zheng, Yiu-Man Cheung, Jing Guan, Liming Chen, Yiteng Huang, Xiaohui Fan, Zengfeng Zhang, Dongmei Shi, Jin Xie, Rirong Chen, Boheng Xiao, Chun Hung Yip, David K. Smith, Wenshan Hong, Yongmei Liu, Lifeng Li, Jia Wang, Edward C. Holmes, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan
Summary: A novel H3N8 virus with zoonotic potential has emerged in chickens in China through reassortment with avian H3 and N8 viruses and enzootic H9N2 viruses. This H3N8 virus has independent gene lineages but exchanges internal genes with other H9N2 viruses. Experimental studies show that it is transmissible in ferrets, and serological data suggest a lack of immunological protection in humans.
JOURNAL OF VIROLOGY
(2023)
Article
Virology
Rachel L. Tulloch, Karan Kim, Chisha Sikazwe, Alice Michie, Rebecca Burrell, Edward C. Holmes, Dominic E. Dwyer, Philip N. Britton, Jen Kok, John-Sebastian Eden
Summary: The RAPIDprep assay is a simple and fast protocol for diagnosing infections within 24 hours of sample collection by sequencing ribosomal RNA-depleted total RNA. It effectively depletes human and microbial rRNA and amplifies genomic yield without the need for nucleic acid quantification or quality assessment. This assay can detect known and undiagnosed pathogens, providing valuable information for molecular epidemiological investigations and vaccine design.
Article
Virology
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
Summary: Through retrospective epidemiological study, new lineages of porcine hemagglutinating encephalomyelitis virus (PHEV) complex coronaviruses (CoVs) were discovered in swine populations in China. These novel lineages cause respiratory symptoms without neurological symptoms typically associated with classical PHEV infection. The novel lineages have been circulating in at least eight provinces in southeastern China.
Article
Virology
Callum Le Lay, Joshua N. Hamm, Timothy J. Williams, Mang Shi, Ricardo Cavicchioli, Edward C. Holmes
Summary: Despite the presence of DNA viruses infecting archaea, no RNA viruses associated with archaea have been identified. In this study, researchers investigated the metatranscriptomes of hypersaline lakes to search for highly divergent RNA viruses. They identified several candidate sequences, but couldn't provide definitive evidence of RNA viruses in archaea.
Article
Virology
Erin Harvey, Jonathon C. O. Mifsud, Edward C. Holmes, Jackie E. Mahar
Summary: This study identified the viral diversity in four Dasyuromorph species using publicly available RNA-seq data. Fifteen new virus sequences were discovered, including five DNA virus families and three RNA virus taxa. Particularly noteworthy was the discovery of a marsupial-specific clade of delta-like viruses and a highly divergent hepacivirus. Understanding the virome of these species is crucial for preventing virus transmission to naive populations, as they are currently being used in translocation efforts.
Article
Virology
Brian R. Wasik, Evin Rothschild, Ian E. H. Voorhees, Stephanie E. Reedy, Pablo R. Murcia, Nicola Pusterla, Thomas M. Chambers, Laura B. Goodman, Edward C. Holmes, James C. Kile, Colin R. Parrish
Summary: This study compares the canine influenza virus (CIV) in dogs and the equine influenza virus (EIV) in horses to reveal their host-specific evolution, determine the sources and connections between outbreaks, and gain insight into the factors controlling their evolutionary fates.
Letter
Virology
Lin Xu, Wei Liu, Mengyu Bie, Tao Hu, Dong Yan, Zhishu Xiao, Edward C. Holmes, Weifeng Shi