Article
Virology
Yun Feng, Qin-yu Gou, Wei-hong Yang, Wei-chen Wu, Juan Wang, Edward C. Holmes, Guodong Liang, Mang Shi
Summary: This study used meta-transcriptomic sequencing to analyze mosquitoes collected from a bat-dwelling cave and a nearby village in Yunnan province, China. A total of 162 eukaryotic virus species were identified, with 101 being novel. Analysis of the virome showed differences in viral compositions and abundance levels between warmer and colder months, a strong host structure at the mosquito species level, and no significant differences between male and female mosquitoes. Some viruses were found to be ubiquitous throughout the year and across multiple mosquito species, while others were season and/or host specific.
Article
Virology
Fan Zhang, Zhihao Ren, Xiaomeng Guo, Yiting Wang, Fanzeng Meng, Weifeng Shi, Xinping Wang, Xuan Dong
Summary: Three novel RNA viruses and one nervous necrosis virus were identified in lined seahorse through meta-transcriptomic sequencing. The diversity and cross-species transmission of viruses pose a threat to this species.
Article
Virology
Vincenzo A. Costa, Jonathon C. O. Mifsud, Dean Gilligan, Jane E. Williamson, Edward C. Holmes, Jemma L. Geoghegan
Summary: Biological invasions pose significant threats to freshwater biodiversity, especially in the Murray-Darling Basin impacted by the introduction of common carp. Despite co-existing for over fifty years, there is limited virus transmission from common carp to native fish species, indicating a diverse array of viruses with deep evolutionary histories in fish.
Article
Virology
Vincenzo A. Costa, Jonathon C. O. Mifsud, Dean Gilligan, Jane E. Williamson, Edward C. Holmes, Jemma L. Geoghegan
Summary: This study investigated the viromes of freshwater fish in the Murray-Darling Basin to better understand the presence of viruses, particularly CyHV-3. While various vertebrate-associated and non-vertebrate-associated viruses were identified, CyHV-3 and related viruses were not detected. The study also revealed minimal virus transmission between invasive common carp and native fish species, indicating a lack of shared viruses despite co-existing for over fifty years.
Article
Genetics & Heredity
Ayda Susana Ortiz-Baez, Thomas G. T. Jaenson, Edward C. Holmes, John H. -O. Pettersson, Peter Wilhelmsson
Summary: Ticks, particularly the soft tick Carios vespertilionis, are carriers of a wide range of viruses and bacteria. In this study, we identified 16 novel viruses from 11 virus families in C. vespertilionis ticks collected from bats in Sweden. We also found abundant bacteria, including known tick-borne bacteria such as Coxiella spp. and Rickettsia spp. These findings highlight the importance of monitoring bat-associated ectoparasites for tracking viruses and bacteria circulating in bats and ticks.
MICROBIAL GENOMICS
(2023)
Article
Virology
Joanna C. A. Cobbin, Justine Charon, Erin Harvey, Edward C. Holmes, Jackie E. Mahar
Summary: Meta-transcriptomic next-generation sequencing has revolutionized virus discovery by expanding our knowledge of the virosphere, but faces challenges such as errors and limitations in viral sequences in public databases, as well as the lack of bioinformatic tools to identify novel viruses accurately.
CURRENT OPINION IN VIROLOGY
(2021)
Article
Microbiology
Qing Liu, Feng Cui, Xiang Liu, Yumei Fu, Wenjing Fang, Xun Kang, Hong Lu, Siping Li, Biao Liu, Wei Guo, Qianfeng Xia, Le Kang, Feng Jiang
Summary: This study analyzed RNA viromes of field-caught mosquitoes from Hainan Island, China, and found that virome composition is influenced by mosquito species and food sources. Most RNA viruses remained stable across three years and different locations, indicating species-specific viromes in Hainan Island. However, virome compositions of single mosquito species in different geographic regions worldwide were visibly distinct, consistent with differences in the widespread distribution of mosquito food sources.
Article
Virology
Ayda Susana Ortiz-Baez, Edward C. Holmes, Justine Charon, John H-O Pettersson, Jenny C. Hesson
Summary: This study analyzed the virus composition of mosquitoes and their parasitic mites, revealing a diverse range of RNA viruses in both hosts. The findings also suggest potential virus transfer between mosquitoes and mites during their symbiotic interaction.
Article
Biochemistry & Molecular Biology
Yeonhwa Jo, Hoseong Choi, Jeong Hun Lee, Sang Hyun Moh, Won Kyong Cho
Summary: This study provides a comprehensive overview of viromes in 15 major pepper cultivars through RNA sequencing. Bean broad wilt virus 2 (BBWV2) and cucumber mosaic virus (CMV) were identified as the major viruses infecting pepper plants, with different cultivars showing variations in virus infection and symptoms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Marko Melnick, Patrick Gonzales, Thomas J. LaRocca, Yuping Song, Joanne Wuu, Michael Benatar, Bjorn Oskarsson, Leonard Petrucelli, Robin D. Dowell, Christopher D. Link, Mercedes Prudencio
Summary: This study developed a bioinformatic pipeline to identify potential etiological agents in RNA-seq data, successfully confirming the presence of known and novel viral sequences through testing and application in practical cases.
G3-GENES GENOMES GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Stephanie LaHaye, James R. Fitch, Kyle J. Voytovich, Adam C. Herman, Benjamin J. Kelly, Grant E. Lammi, Jeremy A. Arbesfeld, Saranga Wijeratne, Samuel J. Franklin, Kathleen M. Schieffer, Natalie Bir, Sean D. McGrath, Anthony R. Miller, Amy Wetzel, Katherine E. Miller, Tracy A. Bedrosian, Kristen Leraas, Elizabeth A. Varga, Kristy Lee, Ajay Gupta, Bhuvana Setty, Daniel R. Boue, Jeffrey R. Leonard, Jonathan L. Finlay, Mohamed S. Abdelbaki, Diana S. Osorio, Selene C. Koo, Daniel C. Koboldt, Alex H. Wagner, Ann-Kathrin Eisfeld, Krzysztof Mrozek, Vincent Magrini, Catherine E. Cottrell, Elaine R. Mardis, Richard K. Wilson, Peter White
Summary: The EnFusion pipeline utilizes seven fusion calling algorithms to increase the accuracy of identifying clinically relevant fusions in pediatric cancer. By combining ensemble fusion-calling pipeline with a knowledge-based filtering strategy, it accurately identifies driver fusions in pediatric cancer, contributing evidence to diagnosis and guiding targeted therapies where appropriate.
Article
Genetics & Heredity
V. Kavi Sidharthan, N. S. Kalaivanan, V. K. Baranwal
Summary: Using a combination of bioinformatic analyses and Next Generation Sequencing, nine putative novel viruses were discovered in public domain transcriptome datasets of endangered plant species. This methodology can be useful for identifying new viruses in plant species with limited genomic information.
Article
Virology
Xin-Xin Chen, Wei-Chen Wu, Mang Shi
Summary: A previous study identified a wide viral diversity of RNA viruses in lower vertebrate hosts, but the diversity of DNA and retro-transcribing viruses remained uncharacterized. This study utilized metatranscriptomics sequencing to reveal complete genome sets of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray-finned fishes, and amphibians, shedding light on the evolutionary relationships within these virus groups.
Article
Biotechnology & Applied Microbiology
Ayda Susana Ortiz-Baez, Mang Shi, Ary A. Hoffmann, Edward C. Holmes
Summary: This study investigates the potential virus protective effect of the wAu strain of Wolbachia on individual wild-caught flies, finding no significant variation in virus composition and abundance between Wolbachia-infected and uninfected flies. It remains unclear if wAu affects viral infection by increasing tolerance rather than inducing complete resistance. The study also uncovers the natural virome diversity of D. simulans, identifying known RNA viruses and discovering five novel viruses.
JOURNAL OF GENERAL VIROLOGY
(2021)
Article
Microbiology
Xiaojing Yang, Shiyu Qin, Xiong Liu, Na Zhang, Jiali Chen, Meiling Jin, Fangni Liu, Yong Wang, Jinpeng Guo, Hua Shi, Changjun Wang, Yong Chen
Summary: The composition of viromes in mosquitoes and Culicoides on Zhoushan Island varied widely and was related to the host species, with many unknown viruses present. Monitoring their viromes is crucial for evaluating the risk of disease transmission.
MICROBIOLOGY SPECTRUM
(2023)
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
Article
Virology
Naiqing Xu, Xinen Tang, Xin Wang, Miao Cai, Xiaowen Liu, Xiaolong Lu, Shunlin Hu, Min Gu, Jiao Hu, Ruyi Gao, Kaituo Liu, Yu Chen, Xiufan Liu, Xiaoquan Wang
Summary: This study found that the H9N2 subtype avian influenza virus has a high airborne transmissibility, while the H7N9 virus does not. The Hemagglutinin protein of the H9N2 virus was found to play a key role in replication, stability, and airborne transmission.
Article
Virology
Samar S. Ewies, Sabry M. Tamam, Ahmed S. Abdel-Moneim, Sherin R. Rouby
Summary: Contagious ecthyma (CE) is a highly contagious viral disease of sheep and goats worldwide. The study provided a clinical description of CE and screened for genetic variation in the B2L gene. Infected sheep exhibited anorexia and oral lesions, while inoculated chicken embryos showed pock lesions. The B2L gene was successfully amplified and found to be highly conserved.
Article
Virology
Yigal Farnoushi, Dan Heller, Avishai Lublin
Summary: In recent years, new variants of avian reovirus (ARV) have caused a variety of symptoms in chickens worldwide, including viral arthritis/tenosynovitis. This study analyzed emerging ARV variants in Israel and found significant genetic diversity. Most ARV isolates in Israel belonged to genotypic cluster 5 (GC5). The study suggests that Israel has not experienced the emergence of new ARV variants since the introduction of the live vaccine (ISR-7585), but ongoing monitoring is needed due to the continuous emergence of ARV variants.
Article
Virology
Shigeru Tajima, Michiyo Kataoka, Yuki Takamatsu, Hideki Ebihara, Chang-Kweng Lim
Summary: Yokose virus (YOKV), a bat-associated flavivirus, was found to replicate at a slower rate in mosquito cells compared to other mosquito-borne flaviviruses. Specific nucleotide mutations in the virus were identified to enhance its proliferation ability in mosquito cells.
Article
Virology
Alejandra Borjabad, Baojun Dong, Wei Chao, David J. Volsky, Mary Jane Potash
Summary: This study investigated HIV brain disease using a mouse model, and found that poly I:C can reverse associated cognitive impairment and reduce virus burden. The results also revealed transcriptional changes related to neuronal function and innate immune responses.
Article
Virology
Ching-Hung Lin, Feng-Cheng Hsieh, Meilin Wang, Chieh Hsu, Hsuan-Wei Hsu, Chun-Chun Yang, Cheng-Yao Yang, Hung-Yi Wu
Summary: This study demonstrates that the synthesis of coronavirus subgenomic mRNA is not solely determined by the sequence homology between the leader TRS and TRS-B, but also by the disassociation of the coronavirus polymerase from the viral genome. This finding provides a new insight into the transcription mechanism of coronaviruses.
Article
Virology
Nicholas S. Kron, Benjamin W. Neuman, Sathish Kumar, Patricia L. Blackwelder, Dayana Vidal, Delphina Z. Walker-Phelan, Patrick D. I. Gibbs, Lynne A. Fieber, Michael C. Schmale
Summary: Two recent studies documented the genome of a novel virus in marine animals, finding that the virus is widespread in apparently healthy animals but not highly expressed in neurons. The studies also identified viral replication factories and high levels of defective genomes in chronically infected animals.
Article
Virology
Andrew M. Ramey, Laura C. Scott, Christina A. Ahlstrom, Evan J. Buck, Alison R. Williams, Mia Kim Torchetti, David E. Stallknecht, Rebecca L. Poulson
Summary: We successfully detected and characterized highly pathogenic avian influenza viruses in hunter-harvested wild waterfowl samples from western Alaska. Genomic analysis revealed three independent viral introductions into Alaska. Our findings demonstrate the utility and potential limitations of using molecular processing approaches directly on original swab samples for viral research and monitoring.
Article
Virology
Ting Gong, Dongdong Wu, Yongzhi Feng, Xing Liu, Qi Gao, Xiaoyu Zheng, Zebu Song, Heng Wang, Guihong Zhang, Lang Gong
Summary: This study discovered that quercetin can inhibit PEDV replication both in vivo and in vitro, and alleviate the clinical symptoms and intestinal injury caused by the virus. This provides a new direction for the development of PED antiviral drugs.
Article
Virology
Min Zhu, Hao Zeng, Jianqiao He, Yaohui Zhu, Pingping Wang, Jianing Guo, Jinfan Guo, Huabo Zhou, Yifeng Qin, Kang Ouyang, Zuzhang Wei, Weijian Huang, Ying Chen
Summary: The reassortment between avian H9N2 and Eurasian avian-like (EA) H1N1 viruses may have potentially changed from avian-to-mammals adaptation. This study found that the introduction of EA H1N1 internal genes into H9N2 virus restored the replication capability and resulted in extreme virulence in some cases. This raises new concerns for public health due to the possible coexistence of H9N2 and EA H1N1 viruses in dogs.