Article
Biochemistry & Molecular Biology
Nnaemeka Ndodo, Jonathan Ashcroft, Kuiama Lewandowski, Adesola Yinka-Ogunleye, Chimaobi Chukwu, Adama Ahmad, David King, Afolabi Akinpelu, Carlos Maluquer de Motes, Paolo Ribeca, Rebecca P. Sumner, Andrew Rambaut, Michael Chester, Tom Maishman, Oluwafemi Bamidele, Nwando Mba, Olajumoke Babatunde, Olusola Aruna, Steven T. Pullan, Benedict Gannon, Colin S. Brown, Chikwe Ihekweazu, Ifedayo Adetifa, David O. Ulaeto
Summary: The 2022 global mpox outbreak raises questions about its human-to-human transmission and adaptation. Analysis of monkeypox virus isolates in Nigeria before the outbreak sheds light on the virus diversification that led to the 2022 lineage, revealing the coexistence of multiple lineages and progressive mutations over time.
Article
Biochemistry & Molecular Biology
Hang-Yu Zhou, Ye-Xiao Cheng, Lin Xu, Jia-Ying Li, Chen-Yue Tao, Cheng-Yang Ji, Na Han, Rong Yang, Hui Wu, Yaling Li, Aiping Wu
Summary: This study proposes a method called Cov2Coinfect, which can accurately determine co-infected SARS-CoV-2 variants from deep sequencing data. Results from two independent projects show a co-infection rate of 0.3-0.5% in SARS-CoV-2 positive samples. The co-infected variants are highly consistent with the co-circulating SARS-CoV-2 lineages in the regional epidemiology.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Virology
Jasper Goetting, Claas Baier, Victoria Panagiota, Britta Maecker-Kolhoff, Akshay Dhingra, Albert Heim
Summary: The study on the molecular phylogeny of HAdV-A31 revealed that the virus evolved slowly with six co-circulating lineages, emphasizing the high genetic stability of HAdV-A31 over almost six decades. Surprisingly, regions of higher diversity were found in gene regions coding for non-structural and minor capsid proteins, suggesting ongoing evolution within the virus. The analysis also indicated the presence of different sublineages causing simultaneous nosocomial outbreaks.
Article
Multidisciplinary Sciences
Olayinka Sunday Okoh, Nicholas Israel Nii-Trebi, Abdulrokeeb Jakkari, Tosin Titus Olaniran, Tosin Yetunde Senbadejo, Anna Aba Kafintu-kwashie, Emmanuel Oluwatobi Dairo, Tajudeen Oladunni Ganiyu, Ifiokakaninyene Ekpo Akaninyene, Louis Odinakaose Ezediuno, Idowu Jesulayomi Adeosun, Michael Asebake Ockiya, Esther Moradeyo Jimah, David J. Spiro, Elijah Kolawole Oladipo, Nidia S. Trovao
Summary: This study investigates the epidemiology and genetic diversity of COVID-19 in Africa, revealing the circulating viral lineages and trends in cases and deaths. Results show that African viruses are more closely related to those from Europe, highlighting the need for expanded surveillance efforts and better public health measures in Africa.
Article
Biotechnology & Applied Microbiology
Yezhi Fu, Nkuchia M. M'ikanatha, Edward G. Dudley
Summary: Passerine-associated S. Typhimurium strains have been linked to human salmonellosis outbreaks in recent years. Here, we investigated the phylogenetic relationship of globally distributed passerine isolates and profiled their genomic similarity and diversity. Our study reveals two passerine-associated S. Typhimurium lineages circulating in Europe, Oceania, and North America. Isolates from the two lineages presented phylogenetic and genetic signatures that were distinct from those of isolates from other hosts. The findings shed light on the host adaptation of S. Typhimurium in passerines and are important for source attribution of S. Typhimurium strains to avian hosts. Further, we found that S. Typhimurium definitive phage type 160 (DT160) from passerines, which caused decades-long human salmonellosis outbreaks in New Zealand and Australia, formed a sublineage of the US passerine lineage, suggesting that DT160 might have originated from passerines outside Oceania. Our study demonstrates the importance of whole-genome sequencing and genomic analysis of historical microbial collections to modern epidemiologic surveillance.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kevin Weitemier, Brooke E. Penaluna, Laura L. Hauck, Lucas J. Longway, Tiffany Garcia, Richard Cronn
Summary: Genetic diversity is crucial for species conservation and management, and this study analyzed mitochondrial genetic diversity in four Oncorhynchus species using multigene metabarcode sequences. Variations in genetic diversity were found among species, with unique haplotypes present in certain regions. Characterizing genetic diversity at multiple loci provides essential information for conservation efforts and genetic management.
Article
Biotechnology & Applied Microbiology
Josiah O. Kuja, Bernard N. Kanoi, Renzo F. Balboa, Clement Shiluli, Michael Maina, Harrison Waweru, Kimita Gathii, Mary Mungai, Moses Masika, Omu Anzala, Matilu Mwau, Taane G. Clark, John Waitumbi, Jesse Gitaka
Summary: Genomic surveillance is crucial for understanding the diversity and lineages of SARS-CoV-2. A study in Kenya revealed that B.1.1.7 and B.1 were predominant lineages, with multiple introductions from different countries.
Article
Environmental Sciences
Caroline Graham, Evgeny A. Pakhomov, Brian P. V. Hunt
Summary: The study examined spatial patterns in diet, trophic niche width, and niche overlap of chum, pink, and sockeye salmon across the North Pacific. Different species showed variations in diet preference in different regions, with higher niche width and overlap in areas of high prey availability. Chum salmon demonstrated greater diet specialization compared to other species, especially in areas with abundant prey.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Agronomy
Felix Moran, Ester Marco-Noales, Elena Landeras, Montserrat Rosello, Adela Abelleira, Ana J. Gonzalez, Maria M. Lopez
Summary: The cultivation of kiwifruit in the European Union has attracted great economic interest due to high consumer demand and good production potential and fruit quality. A study identified a new group of Pseudomonas syringae that affects kiwifruit plants, which is different from the previously described lineages, demonstrating the diversity found in P. syringae species affecting kiwifruit plants.
Article
Biochemistry & Molecular Biology
Yi Zeng, Benjamin J. Fair, Huilin Zeng, Aiswarya Krishnamohan, Yichen Hou, Johnathon M. Hall, Alexander J. Ruthenburg, Yang Li, Jonathan P. Staley
Summary: Previous studies suggested that most vertebrate genes require exon definition for splicing, where spliceosome assembly occurs on exons rather than introns. However, our research found that 90% of introns, including long introns, can splice before the transcription of a downstream exon, indicating that exon definition is not necessary for most human introns. Additionally, splicing timing varies greatly among introns and is influenced by various genetic elements.
Article
Microbiology
Sara Ceballos, Carmen Lozano, Carmen Aspiroz, Laura Ruiz-Ripa, Paula Eguizabal, Allelen Campana-Burguet, Emilia Cercenado, Ana Isabel Lopez-Calleja, Javier Castillo, Jose Manuel Azcona-Gutierrez, Luis Torres, Jorge Calvo, Carmen Martin, Maria Navarro, Myriam Zarazaga, Carmen Torres
Summary: This study characterises a collection of 95 Tet(R)-MRSA isolates to detect MRSA clonal complexes associated with the Tet(R) marker. The isolates belong to various clonal complexes, including CC1, CC5, CC8, and CC45. The isolates show multidrug resistance and the presence of important virulence factors, suggesting a potential association with livestock or humans.
Article
Infectious Diseases
Suwarak Wannaratana, Wikanda Tunterak, Duangduean Prakairungnamthip, Jiroj Sasipreeyajan, Aunyaratana Thontiravong
Summary: The study investigated the geographic distribution and genetic characteristics of MDV-1 field strains circulating in chickens in Thailand between 2013 and 2021, revealing extensive distribution of MDV-1 field strains in major chicken raising areas, with cluster 1 being predominant. The findings suggested that most of the Thai MDV-1 field strains were potentially highly virulent.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Genetics & Heredity
John P. Fellers, Sharadha Sakthikumar, Fei He, Katie McRell, Guus Bakkeren, Christina A. Cuomo, James A. Kolmer
Summary: This study analyzed whole-genome sequences of 121 P. triticina isolates to gain insight into race evolution. The isolates were clustered into 11 major lineages based on genetic variants, with high ratios of nonsynonymous to synonymous mutations and nonsense to readthrough mutations in gene-coding regions. Variants were distributed across the entire genome, suggesting that recurrent mutation and selection play a major role in differentiation within the clonal lineages.
G3-GENES GENOMES GENETICS
(2021)
Article
Infectious Diseases
Vanessa Silva, Claudia Alfarela, Manuela Canica, Vera Manageiro, Miguel Novoa, Belen Leiva, Maria Kress, Jose Luis Capelo, Patricia Poeta, Gilberto Igrejas
Summary: Donkeys in Europe are declining, with an increased association of staphylococci carriage among animals and handlers. Resistance to multiple antibiotics was found in CoNS isolates from donkeys, while S. aureus isolates exhibited resistance to penicillin, aminoglycosides, and tetracycline. Molecular typing showed different genetic lineages of S. aureus between donkeys and handlers, indicating limited transmission between the two groups.
Article
Microbiology
Arno Thibau, Katharina Hipp, Diana J. Vaca, Sounak Chowdhury, Johan Malmstroem, Athanasios Saragliadis, Wibke Ballhorn, Dirk Linke, Volkhard A. J. Kempf
Summary: Bartonella henselae, the causative agent of cat scratch disease, displays genomic and phenotypic differences related to the expression of outer membrane proteins. The trimeric autotransporter adhesin, BadA, is a major virulence factor and crucial for initial host binding. A conserved genome was found among eight B. henselae isolates, but a variable genomic badA island with highly repetitive genes was identified. The variations in BadA proteins might contribute to host immune evasion and efficient colonization in different host environments, potentially facilitated by active recombination mechanisms. It is important to consistently check for BadA surface expression during experimental infection procedures.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Debes H. Christiansen, Alastair J. A. McBeath, Maria Aamelfot, Iveta Matejusova, Mickael Fourrier, Patricia White, Petra E. Petersen, Knut Falk
JOURNAL OF GENERAL VIROLOGY
(2017)
Article
Parasitology
Simon Chioma Weli, Ole Bendik Dale, Haakon Hansen, Mona Cecilie Gjessing, Liv Birte Ronneberg, Knut Falk
PARASITES & VECTORS
(2017)
Article
Fisheries
G. Kurath, J. R. Winton, O. B. Dale, M. K. Purcell, K. Falk, R. A. Busch
JOURNAL OF FISH DISEASES
(2016)
Article
Fisheries
M. Aamelfot, O. B. Dale, A. McBeath, K. Falk
JOURNAL OF FISH DISEASES
(2015)
Article
Fisheries
A. Dalum, R. Tangen, K. Falk, I. Hordvik, G. Rosenlund, B. Torstensen, E. O. Koppang
JOURNAL OF FISH DISEASES
(2016)
Article
Fisheries
A. McBeath, M. Aamelfot, D. H. Christiansen, I. Matejusova, T. Markussen, M. Kaldhusdal, O. B. Dale, S. C. Weli, K. Falk
JOURNAL OF FISH DISEASES
(2015)
Review
Fisheries
M. Aamelfot, O. B. Dale, K. Falk
JOURNAL OF FISH DISEASES
(2014)
Article
Biotechnology & Applied Microbiology
Mickael Fourrier, Katherine Lester, Even Thoen, Aase Mikalsen, Oystein Evensen, Knut Falk, Bertrand Collet, Alastair McBeath
JOURNAL OF GENERAL VIROLOGY
(2014)
Article
Immunology
Ida Bergva Aas, Lars Austbo, Melanie Koenig, Mohasina Syed, Knut Falk, Ivar Hordvik, Erling O. Koppang
JOURNAL OF IMMUNOLOGY
(2014)
Article
Multidisciplinary Sciences
Mickael Fourrier, Katherine Lester, Turhan Markussen, Knut Falk, Christopher J. Secombes, Alastair McBeath, Bertrand Collet
Article
Multidisciplinary Sciences
Maria Aamelfot, Debes H. Christiansen, Ole Bendik Dale, Alastair McBeath, Sylvie L. Benestad, Knut Falk
Article
Multidisciplinary Sciences
Michael D. Gallagher, Iveta Matejusova, Lien Nguyen, Neil M. Ruane, Knut Falk, Daniel J. Macqueen
SCIENTIFIC REPORTS
(2018)
Article
Microbiology
Maria Aamelfot, Johanna Hol Fosse, Hildegunn Viljugrein, Frieda Betty Ploss, Sylvie L. Benestad, Alastair McBeath, Debes Hammershaimb Christiansen, Kyle Garver, Knut Falk
Summary: Infection with ISAV leads to the destruction of the viral vascular surface receptor, resulting in interference with subsequent ISAV attachment. This study provides insights into the kinetics of viral receptor destruction and the potential role of vascular surface modulation in the pathogenesis of infectious salmon anaemia.
Article
Fisheries
Ida Bergva Aas, Lars Austbo, Knut Falk, Ivar Hordvik, Erling Olaf Koppang
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2017)
Article
Veterinary Sciences
Maria Aamelfot, Alastair McBeath, Debes H. Christiansen, Iveta Matejusova, Knut Falk
VETERINARY RESEARCH
(2015)