Article
Genetics & Heredity
Dave J. Baker, Alp Aydin, Thanh Le-Viet, Gemma L. Kay, Steven Rudder, Leonardo de Oliveira Martins, Ana P. Tedim, Anastasia Kolyva, Maria Diaz, Nabil-Fareed Alikhan, Lizzie Meadows, Andrew Bell, Ana Victoria Gutierrez, Alexander J. Trotter, Nicholas M. Thomson, Rachel Gilroy, Luke Griffith, Evelien M. Adriaenssens, Rachael Stanley, Ian G. Charles, Ngozi Elumogo, John Wain, Reenesh Prakash, Emma Meader, Alison E. Mather, Mark A. Webber, Samir Dervisevic, Andrew J. Page, Justin O'Grady
Summary: CoronaHiT is a flexible sequencing method for SARS-CoV-2 genomes, suitable for rapid expansion of global sequencing efforts. In experiments, CoronaHiT demonstrated good performance on both nanopore and Illumina platforms.
Article
Immunology
Lauren M. Walker, Andrea R. Shiakolas, Rohit Venkat, Zhaojing Ariel Liu, Steven Wall, Nagarajan Raju, Kelsey A. Pilewski, Ian Setliff, Amyn A. Murji, Rebecca Gillespie, Nigel A. Makoah, Masaru Kanekiyo, Mark Connors, Lynn Morris, Ivelin S. Georgiev
Summary: The development of novel technologies for discovering human monoclonal antibodies has been extremely valuable in combating infectious diseases. LIBRA-seq with epitope mapping is a next-generation sequencing technology that can determine residue-level epitopes for thousands of single B cells simultaneously, making it an efficient tool for high-throughput identification of antibodies against specific antigen epitopes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Virology
Tomoyuki Nabeshima, Junya Abe
Summary: Vitis coignetiae samples from northern Japan were found to be infected with multiple RNA viruses, with three newly identified virus species assigned to different genera based on sequence identity and phylogenetic analysis.
Article
Immunology
Cristina Galli, Erika Ebranati, Laura Pellegrinelli, Martina Airoldi, Carla Veo, Carla Della Ventura, Arlinda Seiti, Sandro Binda, Massimo Galli, Gianguglielmo Zehender, Elena Pariani
Summary: The study successfully validated a rapid and reliable high-throughput sequencing protocol for obtaining the complete genome sequence of A(H3N2) influenza viruses directly from clinical specimens, providing important reference for influenza surveillance and outbreak investigation.
Article
Genetics & Heredity
Nasserdine Papa Mze, Idir Kacel, Mamadou Beye, Raphael Tola, Mariema Sarr, Leonardo Basco, Herve Bogreau, Philippe Colson, Pierre-Edouard Fournier
Summary: A rapid and cost-effective sequencing protocol is proposed to validate its reliability by comparing the SARS-CoV-2 genome sequences obtained using the modified Illumina COVIDSeq protocol with the standard protocol. The modified protocol saves time and costs, providing high-quality results comparable to the standard protocol.
Article
Biotechnology & Applied Microbiology
Panagiotis G. Adamopoulos, Panagiotis Tsiakanikas, Eleni E. Adam, Andreas Scorilas
Summary: Survivin, a member of the inhibitor of apoptosis protein family, is upregulated in malignant tumors and exists in multiple alternative splicing variants. A novel targeted DNA-seq assay identified fourteen new survivin alternative splice variants, shedding light on their expression profiles and potential biological functions. Further studies will be crucial in understanding how survivin isoforms regulate cell proliferation and apoptosis in cancer, offering new diagnostic and therapeutic opportunities.
Article
Fisheries
Yufeng Si, Jinxuan Wen, Yao Xu, Patarida Roengjit, Hao Wang
Summary: The 16S rRNA high throughput sequencing technology is increasingly used to discover pathogenic bacteria, with Edwardsiella identified as the main causative pathogen in the diseased turbot outbreak in China. This cost-effective and rapid technology helps in accurate pathogen identification and disease research.
AQUACULTURE REPORTS
(2021)
Article
Microbiology
Eloiza May Galon, Adrian Miki Macalanda, Tatsuki Sugi, Kyoko Hayashida, Naoko Kawai, Taishi Kidaka, Rochelle Haidee Ybanez, Paul Franck Adjou Moumouni, Aaron Edmond Ringo, Hang Li, Shengwei Ji, Junya Yamagishi, Adrian Ybanez, Xuenan Xuan
Summary: Molecular assays and capillary electrophoresis sequencing were used to detect piroplasmid parasites infecting cattle in the Philippines. Targeted amplicon sequencing identified distinct amplicon sequence variants (ASVs) belonging to different genera, including Babesia, Theileria, Hepatozoon, and Sarcocystis. The results demonstrated the applicability of Ampliseq in detecting piroplasmid parasites in cattle.
Article
Virology
Meripet Polat Yamanaka, Susumu Saito, Kazuyoshi Hosomichi, Yoko Aida
Summary: A novel proviral DNA-capture sequencing method was developed to investigate the integration of bovine leukemia virus (BLV) in B-cell lymphoma lines. The method successfully detected the BLV proviral integration sites and provided comprehensive information on the proviral structure. This study contributes to the understanding of BLV-induced leukemogenesis and provides a potential tool for early screening of BLV-infected cattle.
Article
Microbiology
Caitriona Brennan, Rodolfo A. Salido, Pedro Belda-Ferre, MacKenzie Bryant, Charles Cowart, Maria D. Tiu, Antonio Gonzalez, Daniel McDonald, Caitlin Tribelhorn, Amir Zarrinpar, Rob Knight
Summary: High-throughput next generation sequencing (NGS) has made significant contributions to genomics, but there is room for further improvement. Uneven sequencing of samples in a multiplexed run leads to unexpected costs and low-quality data. To overcome this issue, a normalization method based on read counts is introduced, ensuring an even distribution of features of interest and improving the statistical power of data sets. This optimization method enhances the efficiency of NGS, which is already highly important in various biological areas.
Review
Pharmacology & Pharmacy
Charles Hadley S. King, Jonathon Keeney, Nuria Guimera, Souvik Das, Michiel Weber, Brian Fochtman, Mark O. Walderhaug, Sneh Talwar, Janisha A. Patel, Raja Mazumder, Eric F. Donaldson
Summary: This project demonstrates the use of the IEEE 2791-2020 Standard (BioCompute Objects [BCO]) to enable clear communication of NGS analysis results. It replicates a clinical trial and performs two independent analyses to validate the consistency of the results, showcasing how a template BCO enhances confidence in the regulatory submission process.
DRUG DISCOVERY TODAY
(2022)
Article
Microbiology
Martin Barbosa-Amezcua, Betzaida Cuevas-Cordoba, Cristobal Fresno, Joshua Haase-Hernandez, Karol Carrillo-Sanchez, Minerva Mata-Rocha, Marcela Munoz-Torrico, Claudia Backer, Vanessa Gonzalez-Covarrubias, Carmen Alaez-Verson, Xavier Soberon
Summary: The COVID-19 pandemic has had a negative impact on the diagnosis and treatment of Tuberculosis (TB) cases. In this study, a proof-of-concept protocol was developed to detect drug resistance and classify the phylogeny of Mycobacterium Tuberculosis (Mtb) from sputum samples. The results showed that the protocol could provide a complete drug resistance profile and phylogeny of Mtb, which could be useful for personalized and effective treatments.
MICROBIOLOGY SPECTRUM
(2022)
Article
Genetics & Heredity
Francois Bertucci, Anthony Goncalves, Arnaud Guille, Jose Adelaide, Severine Garnier, Nadine Carbuccia, Emilien Billon, Pascal Finetti, Patrick Sfumato, Audrey Monneur, Christophe Pecheux, Martin Khran, Serge Brunelle, Lenaig Mescam, Jeanne Thomassin-Piana, Flora Poizat, Emmanuelle Charafe-Jauffret, Olivier Turrini, Eric Lambaudie, Magali Provansal, Jean-Marc Extra, Anne Madroszyk, Marine Gilabert, Renaud Sabatier, Cecile Vicier, Emilie Mamessier, Christian Chabannon, Jihane Pakradouni, Patrice Viens, Fabrice Andre, Gwenaelle Gravis, Cornel Popovici, Daniel Birnbaum, Max Chaffanet
Summary: Extensive molecular profiling of newly biopsied tumor samples identified actionable genetic alterations (AGAs) in most cases, leading to matched therapy in 17% of screened patients, of which 36% showed clinical benefit. Whole-exome sequencing (WES) did not seem to improve these results.
Article
Biochemistry & Molecular Biology
Cornelis A. M. Wagemaker, Liesje Mommer, Eric J. W. Visser, Alexandra Weigelt, Thomas P. van Gurp, Maarten Postuma, Annemiek E. Smit-Tiekstra, Hans de Kroon
Summary: Plant interactions belowground are important and difficult to quantify accurately. The msGBS method presented in this study allows for high taxonomic resolution and parallel quantification of multiple species in root samples. Compared to qPCR, msGBS offers similar results with advantages in revealing hidden belowground interactions.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Infectious Diseases
Slawomir Kubik, Ana Claudia Marques, Xiaobin Xing, Janine Silvery, Claire Bertelli, Flavio De Maio, Spyros Pournaras, Tom Burr, Yannis Duffourd, Helena Siemens, Chakib Alloui, Lin Song, Yvan Wenger, Alexandra Saitta, Morgane Macheret, Ewan W. Smith, Philippe Menu, Marion Brayer, Lars M. Steinmetz, Ali Si-Mohammed, Josiane Chuisseu, Richard Stevens, Pantelis Constantoulakis, Michela Sali, Gilbert Greub, Carsten Tiemann, Vicent Pelechano, Adrian Willig, Zhenyu Xu
Summary: This study aimed to establish clear and broadly applicable recommendations for reliable virus genotyping of SARS-CoV-2, finding that at least 1000 viral genomes are necessary to confidently detect variants in the genome. The broad applicability of the recommendations was validated in over 200 clinical samples, where genotype clustering by sampling location and period was observed.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Article
Microbiology
Willian P. Paim, Fabricio S. Campos, Samuel P. Cibulski, Camila M. Scheffer, Caroline Tochetto, Ana P. M. Varela, Dennis M. Junqueira, Fabiana Q. Mayer, Phyllis C. Romijn, Edviges M. Pituco, Ana C. Franco, Fernando R. Spilki, Paulo M. Roehe
Summary: In this study, we report the complete genome sequences of two subtype c strains of bovine alphaherpesvirus 5 isolated from cattle in southeast Brazil. Limited information is currently available on subtype c.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Genetics & Heredity
Andre Alberto Witt, Raquel Silva Alves, Juliana do Canto Olegario, Laura Junqueira de Camargo, Matheus Nunes Weber, Mariana Soares da Silva, Raissa Canova, Ana Cristina Sbaraini Mosena, Samuel Paulo Cibulski, Ana Paula Muterle Varela, Fabiana Quoos Mayer, Claudio Wageck Canal, Renata da Fontoura Budaszewski
Summary: This study aimed to expand the knowledge about the viral diversity associated with white-winged vampire bats by sampling and sequencing different organs of the bats. The results revealed various viruses closely related to different virus families. The findings are important for understanding the viral diversity of this bat species and for future comparisons of virus outbreaks.
Article
Infectious Diseases
Camila Pereira Silva, Celso Jose Bruno de Oliveira, Elma Lima Leite, Samuel Paulo Cibulski, Magda Fernandes, Priscylla Carvalho Vasconcelos, Larissa Maranhao Dias, Nubia Michelle Vieira da Silva, Felicio Garino Junior, Artur Cesar de Carvalho Fernandes
Summary: This study investigated the genetic context of expanded-spectrum 13-lactam resistance in a Klebsiella pneumoniae strain causing a hard-to-treat nasal infection in a domestic cat. The strain was found to carry multiple genes conferring resistance to various antimicrobial drugs. The results highlight the importance of horizontal gene transfer in the acquisition of antimicrobial resistance genes and emphasize the need for a One Health approach to understand the emergence and dissemination of antimicrobial resistance.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2022)
Article
Agriculture, Dairy & Animal Science
Elisa Rigo De Conti, Karine Ludwig Takeuti, Aparecida Tatiane Lino Fiuza, Laura Lopes de Almeida, David Emilio Santos Neves de Barcellos, Fernando Pandolfo Bortolozzo
Summary: This study evaluated the effect of mass vaccination with Mycoplasma hyopneumoniae on the humoral response of sows and their offspring. The results showed that mass vaccination resulted in a more robust serologic response in primiparous sows, which could be the main target for vaccination strategies in the breeding herd.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2022)
Article
Materials Science, Biomaterials
Samuel Cibulski, Thalisson Amorim de Souza, Joanda Paola Raimundo, Yuri Mangueira Nascimento, Lucas Silva Abreu, Norma Suarez, Iris Miraballes, Paulo Michael Roehe, Demetrius Antonio Machado de Araujo, Josean Fechine Tavares, Marcelo Sobral da Silva, Fernando Silveira
Summary: This study presents a protocol for formulating ISCOM-matrices using raw aqueous extract of Quillaja lancifolia leaves. The method is easier, more robust, cheaper, and environmentally friendly than traditional purification methods.
Article
Virology
Ueric Jose Borges de Souza, Raissa Nunes dos Santos, Marta Giovanetti, Luiz Carlos Junior Alcantara, Jucimaria Dantas Galvao, Franciano Dias Pereira Cardoso, Feliph Cassio Sobrinho Brito, Ana Claudia Franco, Paulo Michel Roehe, Bergmann Morais Ribeiro, Fernando Rosado Spilki, Fabricio Souza Campos
Summary: This study investigates the genomic epidemiology of the CHIKV virus in Tocantins state, Brazil, and finds that the virus belongs to the ECSA lineage and is closely related to outbreaks in Northeast and Southeast Brazil. The study identifies several frequent non-synonymous mutations in the virus genome, indicating local transmission in the state. The findings highlight the importance of continued genomic surveillance for predicting new infections and improving public health services.
Article
Microbiology
Filipe Vieira Santos de Abreu, Kamila Lorene Soares Rocha, Ramon Silva-Oliveira, Mariana Viana Macedo, Thamires Gabriele Macedo Silva, Maria Eduarda Goncalves-Dos-Santos, Cirilo Henrique de Oliveira, Sandy Micaele Aquino-Teixeira, Vinicius de Oliveira Ottone, Alex Junio Jardim da Silva, Ronaldo Medeiros Dos Santos, Aline Tatila-Ferreira, Marco Antonio Barreto de Almeida, Edmilson Dos Santos, Jader da Cruz Cardoso, Aline Alves Scarpellini Campos, George Rego Albuquerque, Anaia da Paixao Seva, Bergmann Morais Ribeiro, Danilo Simonini Teixeira, Fabricio Souza Campos, Ana Claudia Franco, Paulo Michel Roehe, Giliane de Souza Trindade, Danilo Bretas de Oliveira
Summary: Evidence of Orthopoxvirus (OPXV) infection has been detected for the first time in neotropical free-living primates in southeast Brazil, indicating their previous exposure to the virus. This finding is significant for understanding the transmission and infection risks of OPXV in primates.
Article
Microbiology
Lina Violet-Lozano, Vanessa Haach, Camila Mosca Barboza, Juliana dos Santos, Bianca Ferreira Gomes, Tatiane de Cassia Pardo de Souza, Pedro Carnieli Junior, Clarice Weis Arns, Helena Beatriz de Carvalho Ruthner Batista, Paulo Michel Roehe, Ana Claudia Franco
Summary: This study aimed to evaluate the presence of influenza A virus and coronavirus in non-hematophagous bats in Brazil. However, all samples analyzed were negative, suggesting that virus circulation in bats in the wild often occurs at low viral loads.
BRAZILIAN JOURNAL OF MICROBIOLOGY
(2023)
Article
Microbiology
Camila Mengue Scheffer, Ana Paula Muterle Varela, Thais Fumaco Teixeira, Candice Schmidt, Samuel Paulo Cibulski, Helton Fernandes dos Santos, Phelipe Magalhaes Duarte, Fabricio Souza Campos, Ana Claudia Franco, Paulo Michel Roehe
Summary: Water buffaloes have been introduced as a source of animal protein, but little is known about infectious diseases of them. This study investigated the neutralizing antibodies to alphaherpesviruses in bubaline sera, and found that 46.9% of the samples neutralized at least one of the viruses tested.
BRAZILIAN JOURNAL OF MICROBIOLOGY
(2023)
Article
Virology
Cirilo H. de Oliveira, Miguel S. Andrade, Fabricio S. Campos, Jader da C. Cardoso, Maria Eduarda Goncalves-dos-Santos, Ramon Silva Oliveira, Sandy Micaele Aquino-Teixeira, Aline A. S. Campos, Marco A. B. Almeida, Danilo Simonini-Teixeira, Anaia da P. Seva, Andrea Oliveira Dias Temponi, Fernando Maria Magalhaes, Agna Soares da Silva Menezes, Bartolomeu Teixeira Lopes, Hermes P. Almeida, Ana Lucia Pedroso, Giovani Pontel Goncalves, Danielle Costa Capistrano Chaves, Givaldo Gomes de Menezes, Sofia Bernal-Valle, Nicolas F. D. Mueller, Luis Janssen, Edmilson dos Santos, Maria A. Mares-Guia, George R. Albuquerque, Alessandro P. M. Romano, Ana C. Franco, Bergmann M. Ribeiro, Paulo M. Roehe, Ricardo Lourenco-de-Oliveira, Filipe Vieira Santos de Abreu
Summary: In a survey conducted in the Cerrado areas of Minas Gerais, Brazil, it was found that mosquitoes of the Sabethes genus, particularly Sabethes chloropterus, were the primary vectors involved in maintaining the yellow fever virus (YFV) in semi-arid environments. The high number of YFV RNA copies and relative abundance in Sa. chloropterus indicate its importance as a vector, while Sa. albiprivus, despite being naturally infected with YFV, had fewer viral RNA copies and a lower infection rate.
Article
Immunology
Fernando Silveira, Mariana Rivera-Patron, Nikita Deshpande, Soledad Sienra, Jackeline Checa, Maria Moreno, Jose A. Chabalgoity, Samuel P. Cibulski, Mariana Baz
Summary: We demonstrate that adjuvanting a seasonal trivalent influenza vaccine with Quillaja brasiliensis saponin-based nanoparticles significantly improves immune responses and provides full protection against influenza virus challenge. The adjuvanted vaccine elicited high levels of neutralizing antibodies, a mixed Th1/Th2 cytokine response, and effector T cell-mediated immune responses. The viral titers in the lungs of animals receiving the adjuvanted vaccine were significantly lower, and there was no mortality observed in mice vaccinated with the adjuvanted vaccine.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Veterinary Sciences
Camila Mengue Scheffer, Sylio Alfredo Petzhold, Ana Paula Muterle Varela, Willian Pinto Paim, Phelipe Magalhaes Duarte, Marcia Regina Loiko, Cristine Cerva, Candice Schmidt, Adrieli Wendlant, Samuel Paulo Cibulski, Diane Alves de Lima, Caroline Tochetto, Anne Caroline Ramos dos Santos, Juliana Ines Herpich, Thais Fumaco Teixeira, Helton Fernandes dos Santos, Fabricio Souza Campos, Ana Claudia Franco, Paulo Michel Roehe
Summary: A highly sensitive and specific multi-antigen ELISA method has been developed for detecting antibodies to Bovine alphaherpesviruses type 1, type 5, and bubaline herpesvirus type 1. The sensitivity and specificity of this method are comparable to serum neutralization tests.
VETERINARY SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Tatiana R. Vieira, Esther F. Cavinatto de Oliveira, Samuel P. Cibulski, Nubia M. V. Silva, Mauro R. Borba, Celso J. B. Oliveira, Marisa Cardoso
Summary: This study investigated the microbial composition, abundance of antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs) in retail chicken carcasses from different production systems. Although there were no differences in microbial diversity, certain taxa, including spoilage-associated organisms, showed significant differences across the groups. The co-resistome comprised 29 shared ARGs, and their abundance was lower in chicken carcasses from certified antimicrobial-free intensive production systems (AF) and certified organic production systems with restricted antimicrobial use (OR) compared to conventional intensive production systems (CO). Transposases were the most abundant MGEs, with a higher abundance in CO compared to OR.
Article
Agriculture, Multidisciplinary
Tatiana Regina Vieira, Esther Cavinatto de Oliveira, Samuel Paulo Cibulski, Mauro Riegert Borba, Marisa Cardoso
Summary: This study assessed the antimicrobial resistance profiles of Escherichia coli isolated from whole chickens originating from farming systems with and without restrictions on the use of antimicrobials. The results showed that the chicken meat from farming systems with restrictions on antimicrobial use had lower resistance to antibiotics, indicating lower selection pressure for antimicrobial resistance.
SEMINA-CIENCIAS AGRARIAS
(2022)
