Article
Immunology
Stephanie Bibert, Nicolas Guex, Joao Lourenco, Thomas Brahier, Matthaios Papadimitriou-Olivgeris, Lauro Damonti, Oriol Manuel, Robin Liechti, Lou Gotz, Jonathan Tschopp, Mathieu Quinodoz, Peter Vollenweider, Jean-Luc Pagani, Mauro Oddo, Olivier Hugli, Frederic Lamoth, Veronique Erard, Cathy Voide, Mauro Delorenzi, Nathalie Rufer, Fabio Candotti, Carlo Rivolta, Noemie Boillat-Blanco, Pierre-Yves Bochud
Summary: The dysregulated immunity in COVID-19 patients plays a key role in the severity of the disease, including defects in IFN responses, reduced toxicity-related molecules in NK cells, and increased neutrophil degranulation. Additionally, differences in gene expression patterns are also determinants of COVID-19 severity.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biology
Scott Burkholz, Michael Rubsamen, Luke Blankenberg, Richard T. Carback III, Daria Mochly-Rosen, Paul E. Harris
Summary: Analysis of next-generation sequencing data linked with clinical metadata reveals that Omicron reinfections occur at a higher frequency and within a shorter time interval compared to pre-Omicron variants. This suggests that a single infection may not generate the protective immunity required to defend against Omicron reinfections. Continued next-generation sequencing and inclusion of clinical metadata is necessary for effective surveillance, treatment, vaccine development, and public health recommendations.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Martin Hunt, Jeremy Swann, Bede Constantinides, Philip W. Fowler, Zamin Iqbal
Summary: The study developed a tool called ReadItAndKeep, which enables the removal of contaminating human reads from SARS-CoV-2 sequencing data on low-specification laptops. By excluding the polyA tail from the viral reference, the tool prevents the bleed-through of human reads.
Article
Biochemical Research Methods
Martin Hunt, Jeremy Swann, Bede Constantinides, Philip W. Fowler, Zamin Iqbal
Summary: The study introduces ReadItAndKeep, a tool developed to efficiently remove human reads from clinical samples in order to preserve SARS-CoV-2 sequencing data on low-specification devices. The tool has shown promising results with low RAM usage and short run-time, making it useful for viral sequencing data analysis.
Article
Cell Biology
Yu-Hang Zhang, Hao Li, Tao Zeng, Lei Chen, Zhandong Li, Tao Huang, Yu-Dong Cai
Summary: This study aimed to identify new transcriptomic signatures for clinical testing or therapeutic targets for vaccine design by integrating machine learning methods with upper airway tissue transcriptomics data. The findings could potentially help reveal the pathogenic mechanisms of COVID-19 and new vaccine targets.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Microbiology
Justin T. Landis, Razia Moorad, Linda J. Pluta, Carolina Caro-Vegas, Ryan P. McNamara, Anthony B. Eason, Aubrey Bailey, Femi Cleola S. Villamor, Angelica Juarez, Jason P. Wong, Brian Yang, Grant S. Broussard, Blossom Damania, Dirk P. Dittmer
Summary: Variants of concern (VOC) in SARS-CoV-2 are viruses with >= 3 single-nucleotide variants (SNVs) compared to the ancestor virus, with potential for higher transmissibility and/or worse clinical progression. Little is known about the frequency and circumstances of new viral variants emerging.
Article
Multidisciplinary Sciences
Muluneh Alene, Leltework Yismaw, Moges Agazhe Assemie, Daniel Bekele Ketema, Belayneh Mengist, Bekalu Kassie, Tilahun Yemanu Birhan
Summary: Asymptomatic SARS-CoV-2 infections are responsible for potentially significant transmission of COVID-19. A systematic review and meta-analysis of 28 studies with 6,071 cases found that the weighted pooled proportion of asymptomatic COVID-19 cases throughout the course of infection was 25%, suggesting the importance of scaling up testing for high risk populations to control the pandemic.
Article
Multidisciplinary Sciences
Ki Wook Kim, Ira W. Deveson, Chi Nam I. Pang, Malinna Yeang, Zin Naing, Thiruni Adikari, Jillian M. Hammond, Igor Stevanovski, Alicia G. Beukers, Andrey Verich, Simon Yin, David McFarlane, Marc R. Wilkins, Sacha Stelzer-Braid, Rowena A. Bull, Maria E. Craig, Sebastiaan J. van Hal, William D. Rawlinson
Summary: There is a high prevalence of viral co-infections among SARS-CoV-2 patients, which may worsen the clinical outcome of COVID-19. Studies in Australia show the importance of assessing all pathogens in symptomatic patients, and the dual-functionality of Twist hybrid-capture for SARS-CoV-2 whole-genome sequencing and simultaneous identification of viral co-infections.
SCIENTIFIC REPORTS
(2021)
Article
Virology
Yi Wang, Xiaoxia Wang, Laurence Don Wai Luu, Jieqiong Li, Xiaodai Cui, Hailan Yao, Shaojin Chen, Jin Fu, Licheng Wang, Chongzhen Wang, Rui Yuan, Qingguo Cai, Xiaolan Huang, Junfei Huang, Zhenjun Li, Shijun Li, Xiong Zhu, Jun Tai
Summary: This study compared the immune responses of individuals immunized with CoronaVac and COVID-19 infected patients using single-cell RNA sequencing. Both the inactivated vaccine and SARS-CoV-2 infection altered immune cell proportions, activated B cells, and induced antibody-related gene expression in the plasma. However, the immune responses were more pronounced in COVID-19 patients, especially those with severe disease. The study also identified distinct gene expression and cell phenotypes between CoronaVac immunization and SARS-CoV-2 infection.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Biochemical Research Methods
Mengya Chai, Yajuan Guo, Liu Yang, Jianhui Li, Shuo Liu, Lei Chen, Yuelei Shen, Yi Yang, Youchun Wang, Lida Xu, Changyuan Yu
Summary: Our study focused on neutralizing antibodies targeting the S2 subunit of SARS-CoV-2 and SARS-CoV. Using high-throughput single-cell sequencing technology, we identified 215 antibodies with binding affinities. Plasmablasts and GC-dependent memory B-cells were considered the main cell types involved in producing virus-specific antibodies.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Immunology
Umberto Molini, Lauren M. Coetzee, Tanya Engelbrecht, Lourens de Villiers, Mari de Villiers, Iolanda Mangone, Valentina Curini, Siegfried Khaiseb, Massimo Ancora, Cesare Camma, Alessio Lorusso, Giovanni Franzo
Summary: The COVID-19 pandemic has brought attention to the role of the human-animal-environment interface in disease emergence. A study in Namibia found a 1% prevalence of SARS-CoV-2 in dogs, but there was no clear evidence of pet-to-pet transmission. However, it is recommended to conduct further investigations on companion animal populations.
Article
Microbiology
Blanca Borras-Bermejo, Maria Pinana, Cristina Andres, Ricardo Zules, Alejandra Gonzalez-Sanchez, Juliana Esperalba, Oleguer Pares-Badell, Damir Garcia-Cehic, Ariadna Rando, Carolina Campos, Maria Gema Codina, Maria Carmen Martin, Carla Castillo, Karen Garcia-Comunas, Rodrigo Vasquez-Mercado, Reginald Martins-Martins, Sergi Colomer-Castell, Tomas Pumarola, Magda Campins, Josep Quer, Andres Anton
Summary: This study describes the clinical and molecular characteristics of 24 confirmed cases of SARS-CoV-2 reinfection in Barcelona over a one-year period. The study finds that reinfections can occur in a relatively short time and mainly affect immunocompetent patients. Reinfection episodes are often asymptomatic and less severe than primary infections.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Nicholas G. Davies, Christopher I. Jarvis, W. John Edmunds, Nicholas P. Jewell, Karla Diaz-Ordaz, Ruth H. Keogh
Summary: Studies have shown that the SARS-CoV-2 B.1.1.7 lineage is more transmissible and may cause more severe illness compared to pre-existing variants.
Article
Biotechnology & Applied Microbiology
Oscar Gonzalez-Recio, Monica Gutierrez-Rivas, Ramon Peiro-Pastor, Pilar Aguilera-Sepulveda, Cristina Cano-Gomez, Miguel angel Jimenez-Clavero, Jovita Fernandez-Pinero
Summary: The study compared the sequencing of the SARS-CoV-2 genome using R9 vs R10 flow cells and a Rapid Barcoding Kit (RBK) vs a Ligation Sequencing Kit (LSK). Results showed that the R9 chemistry had a lower error rate and the LSK provided longer DNA fragments, contributing to a better assembly of SARS-CoV-2 despite potential impacts on variant detection in a R10 flow cell. The study suggests that nanopore sequencing could be valuable in the epidemiological surveillance of SARS-CoV-2.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Engineering, Environmental
G. La Rosa, P. Mancini, G. Bonanno Ferraro, C. Veneri, M. Iaconelli, L. Lucentini, L. Bonadonna, S. Brusaferro, D. Brandtner, A. Fasanella, L. Pace, A. Parisi, D. Galante, E. Suffredini
Summary: A nested RT-PCR assay was developed to detect key mutations of SARS-CoV-2 variants, showing potential for rapid screening of clinical samples and detection of variants in sewage. The study highlights the importance of wastewater surveillance in exploring SARS-CoV-2 diversity and distribution.
Article
Ecology
Sarah C. Hill, Sarah Francois, Julien Theze, Adrian L. Smith, Peter Simmonds, Christopher M. Perrins, Lia van der Hoek, Oliver G. Pybus
Summary: Wildlife carries pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. Changes in wildlife population age-structures and age-stratified behaviors can alter the level of pathogen detection within a species and the risk of spillover to other species. By using a metagenomic approach, this study characterized viral and prokaryotic carriage in a healthy wild bird population and identified novel virus species and the core prokaryotic microbiome. The findings suggest that perturbations in wildlife population age-structures could impact the circulation dynamics and spillover risk of microbes, potentially including pathogens.
Article
Biochemistry & Molecular Biology
Guogang Zhang, Bingying Li, Jayna Raghwani, Bram Vrancken, Ru Jia, Sarah C. Hill, Guillaume Fournie, Yanchao Cheng, Qiqi Yang, Yuxin Wang, Zengmiao Wang, Lu Dong, Oliver G. Pybus, Huaiyu Tian
Summary: Migratory birds have played a crucial role in the rapid dissemination of highly pathogenic avian influenza (HPAI) H5N8 virus clade 2.3.4.4 across Eurasia. This study investigated the seasonal transmission dynamics of HPAI H5N8 viruses using new genomic data obtained from surveying wild birds in China and tracking the migratory patterns of bird species across China since 2006. The findings reveal the association between the introductions of HPAI H5N8 viruses in different Eurasian regions and the seasonal migration of wild birds, and highlight Europe's role as both a source and a sink in the global HPAI virus transmission network.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Michelle Wille, Simeon Lisovski, David Roshier, Marta Ferenczi, Bethany J. J. Hoye, Trent Leen, Simone Warner, Ron A. M. Fouchier, Aeron C. C. Hurt, Edward C. C. Holmes, Marcel Klaassen
Summary: Host susceptibility to LPAIV is influenced by factors such as genetics, ecology, age, and season. This study analyzed data from wild birds in Australia over 11 years and found that host phylogeny is a key driver in determining host range. The study provides insights into the evolutionary ecology of LPAIV in its avian reservoir community and expands our global understanding of LPAIV.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Virology
Janelle R. Wierenga, Kerri J. Morgan, Stuart Hunter, Harry S. Taylor, Lisa S. Argilla, Trudi Webster, Jeremy Dubrulle, Fatima Jorge, Mihnea Bostina, Laura Burga, Edward C. Holmes, Kate McInnes, Jemma L. Geoghegan
Summary: Yellow-eyed penguins in New Zealand are at risk of extinction due to infectious diseases, with respiratory distress syndrome (RDS) causing high mortality in young chicks. A novel and highly abundant gyrovirus belonging to the Anelloviridae family has been identified in 80% of tissue samples from dead chicks. This gyrovirus is closely related to a diseased seabird virus and is likely associated with RDS in yellow-eyed penguin chicks.
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.
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
Evolutionary Biology
Marina Escalera-Zamudio, Sergei L. Kosakovsky Pond, Natalia Martinez de la Vina, Bernardo Gutierrez, Rhys P. D. Inward, Julien Theze, Lucy van Dorp, Hugo G. Castelan-Sanchez, Thomas A. Bowden, Oliver G. Pybus, Ruben J. G. Hulswit
Summary: Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, although the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Xianghui Liang, Xiaoyuan Chen, Junqiong Zhai, Xiaobing Li, Xu Zhang, Zhipeng Zhang, Ping Zhang, Xiao Wang, Xinyuan Cui, Hai Wang, Niu Zhou, Zu-Jin Chen, Renwei Su, Fuqing Zhou, Edward C. Holmes, David M. Irwin, Rui-Ai Chen, Qian He, Ya-Jiang Wu, Chen Wang, Xue-Qing Du, Shi-Ming Peng, Wei-Jun Xie, Fen Shan, Wan-Ping Li, Jun-Wei Dai, Xuejuan Shen, Yaoyu Feng, Lihua Xiao, Wu Chen, Yongyi Shen
Summary: Using CT scans, histological examination, blood gas tests, and transcriptome analysis, this study reveals the pathogenicity and tissue tropism of SARSr-CoV-2 in Malayan pangolins. The virus infects multiple organs, with the lungs being the major target. The study also provides initial evidence for vertical transmission of the virus in pangolin fetuses.
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
Microbiology
Cixiu Li, Shuqi Liu, Hong Zhou, Wei Zhu, Mingxue Cui, Juan Li, Jiao Wang, Jiangyun Liu, Jin Zhu, Weiping Li, Yuhai Bi, Michael J. Carr, Edward C. Holmes, Weifeng Shi
Summary: This study revealed the great capacity of mosquitoes to host a diverse range of RNA viruses, with notable differences in viromic structure between mosquito genera and species. The genetic diversity and abundance of the endosymbiont bacteria Wolbachia also varied between mosquito populations. Mosquitoes play a significant role in shaping the virome's composition and understanding these differences is important.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Jing Wang, Yuan-fei Pan, Li-fen Yang, Wei-hong Yang, Kexin Lv, Chu-ming Luo, Juan Wang, Guo-peng Kuang, Wei-chen Wu, Qin-yu Gou, Gen-yang Xin, Bo Li, Huan-le Luo, Shoudeng Chen, Yue-long Shu, Deyin Guo, Zi-Hou Gao, Guodong Liang, Jun Li, Yao-qing Chen, Edward C. Holmes, Yun Feng, Mang Shi
Summary: The diversity and abundance of viruses in bats are not fully understood. This study analyzes individual bat viromes and reveals a high frequency of co-infection and spillover among bats. It also identifies viruses with the potential to infect humans or livestock.
NATURE COMMUNICATIONS
(2023)
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.
Letter
Virology
Lin Xu, Wei Liu, Mengyu Bie, Tao Hu, Dong Yan, Zhishu Xiao, Edward C. Holmes, Weifeng Shi
