Article
Evolutionary Biology
Rosa M. Pinto, Albert Bosch
Summary: Codon bias, a common phenomenon in all organisms, is influenced by mutation, drift, and selection. While selection for translation efficiency and accuracy is well recognized, fewer studies have explored the impact of translation rate control on codon usage. Experimental molecular evolution using RNA virus populations is a powerful tool in understanding the mechanisms behind codon bias. Furthermore, experimental studies are encouraged to define the role of selection in codon evolution, as most studies on virus codon usage rely on computational analyses.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Bingzhe Li, Han Wu, Ziping Miao, Linjie Hu, Lu Zhou, Yihan Lu
Summary: This study characterized the codon usage bias of different genotypes of Hepatitis E virus (HEV), revealing significant differences in codon usage between human, zoonotic, and animal HEV genotypes. The study also found that HEV is influenced by translation selection, leading to a unique dinucleotide usage pattern. Natural selection was identified as the main driver of codon usage bias in HEV, although mutation pressure also played a role in certain genotypes.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Yi Liu, Qian Yang, Fangzhou Zhao
Summary: Codon usage bias affects gene expression levels and protein structures, influencing translation speed, accuracy, and the protein folding process. It also plays a key role in determining the proteome landscape. Furthermore, codon usage impacts mRNA levels through various effects on transcription and translation processes.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 90, 2021
(2021)
Article
Microbiology
Daniel Goncalves-Carneiro, Paul D. Bieniasz
Summary: The development of safe and effective vaccines against viruses is crucial for disease control. Recent advancements in DNA synthesis technology have fueled research efforts in generating attenuated viruses through synonymous mutations. Understanding the molecular mechanisms of attenuation by genetic recoding of viruses could provide insights for vaccine development.
Review
Microbiology
Judit Gimenez-Roig, Estela Nunez-Manchon, Ramon Alemany, Eneko Villanueva, Cristina Fillat
Summary: Vaccination is the most effective method to prevent viral diseases, with recombinant vaccines being one of the most efficient strategies. Recombinant vaccines use safe viral vectors and transgenes to induce an immune response, playing a crucial role in preventing infections.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Fangzhou Zhao, Zhipeng Zhou, Yunkun Dang, Hyunsoo Na, Catherine Adam, Anna Lipzen, Vivian Ng, Igor Grigoriev, Yi Liu
Summary: Codon usage bias plays a critical role in regulating gene expression levels, not only through translation but also through transcription in fungal and mammalian genes. In Neurospora, the correlation between codon usage and RNA levels is maintained both genome-wide and in the nucleus, suggesting a broad influence of codon usage on mRNA levels through transcription in a translation-independent manner. A large-scale genetic screen identified multiple chromatin regulators and transcription factors as mediators of the transcriptional effect of codon usage.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Nanoscience & Nanotechnology
Iris Seitz, Sharon Saarinen, Esa-Pekka Kumpula, Donna McNeale, Eduardo Anaya-Plaza, Vili Lampinen, Vesa P. Hytoenen, Frank Sainsbury, Jeroen J. L. M. Cornelissen, Veikko Linko, Juha T. Huiskonen, Mauri A. Kostiainen
Summary: DNA and RNA origami nanostructures can be used to control the size, shape, and topology of virus capsids, while also protecting encapsulated origami structures from degradation.
NATURE NANOTECHNOLOGY
(2023)
Article
Virology
Elisson N. Lopes, Vagner Fonseca, Diego Frias, Stephane Tosta, Alvaro Salgado, Ricardo Assuncao Vialle, Toscano S. Paulo Eduardo, Fernanda K. Barreto, Vasco Ariston de Azevedo, Michele Guarino, Silvia Angeletti, Massimo Ciccozzi, Luiz C. Junior Alcantara, Marta Giovanetti
Summary: The COVID-19 pandemic caused by SARS-CoV-2 has become a major global health issue, with vaccine rollouts bringing hope of herd immunity. However, concerns arise with the emergence of virus variants that may possess enhanced virulence. Codon usage analysis helps elucidate viral evolution and potential variants, highlighting the importance of genomic monitoring to prevent and mitigate the pandemic.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Janaina Lima de Oliveira, Atahualpa Castillo Morales, Laurence D. Hurst, Araxi O. Urrutia, Christopher R. L. Thompson, Jason B. Wolf
Summary: Studies have found that synonymous codons are used at different frequencies due to the effects of neutral and selective forces. Selection in highly expressed genes remains to be extensively studied, with some evidence suggesting that certain factors do not impact codon preference.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Zhaleh Ghaemi, Martin Gruebele, Emad Tajkhorshid
Summary: The disassembly process of HBV capsid involves structurally heterogeneous cracks mainly within hexameric sites, with only a small subset of capsid protein monomers engaged in each instance of disassembly. Specific residues at interfaces between dimers within hexamers, such as R127, I139, Y132, N136, A137, and V149, are identified as hot spots for disassembly by avoiding overstabilization of capsids, and are evolutionarily conserved.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Rekha Khandia, Azmat Ali Khan, Noushad Karuvantevida, Pankaj Gurjar, Igor Vladimirovich Rzhepakovsky, Isabel Legaz
Summary: This study found that codon usage bias in HCV is dependent upon the nucleotide composition, with CTC-CTG being a preferred codon pair. The primary host of HCV was identified as chimpanzees, providing a theoretical basis for generating a safe and effective vaccine.
Article
Multidisciplinary Sciences
Jonathan J. Knowlton, Daniel Gestaut, Boxue Ma, Gwen Taylor, Alpay Burak Seven, Alexander Leitner, Gregory J. Wilson, Sreejesh Shanker, Nathan A. Yates, B. V. Venkataram Prasad, Ruedi Aebersold, Wah Chiu, Judith Frydman, Terence S. Dermody
Summary: The TRiC chaperonin plays a crucial role in folding and assembly of the reovirus sigma 3 capsid protein, interacting with a network of chaperones including prefoldin. This study sheds light on the molecular dynamics of sigma 3 folding and establishes a biological function for TRiC in virus assembly, while also providing structural and functional insights into how TRiC and prefoldin participate in protein complex assembly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Veterinary Sciences
Xianglong Yu, Kuipeng Gao, Molin Pi, Huizi Li, Wenxia Zhong, Baojian Li, Zhangyong Ning
Summary: PCV3, a highly contagious virus causing severe dermatitis and nephropathy syndrome, has a worldwide distribution and significant economic impact on the swine industry. The phylogenetic analysis showed dispersed Rep genes in PCV3a and clustered Cap genes into distinct clades by genotypes. The study revealed a bias in codon usage and suggested natural selection as the main force influencing the pattern in PCV3.
VETERINARY RESEARCH COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Ping Song, Fan Yang, Hongchuan Jin, Xian Wang
Summary: In addition to gene regulation and post-translational modifications, abnormal translation from mRNAs to proteins is essential in cancer pathogenesis. Targeting mRNA translation presents a potential strategy for cancer treatment. Modulation of protein translation involves factors such as initiation factors, RNA-binding proteins, mRNA modifications like m(6)A, and noncoding RNAs like microRNAs and long noncoding RNAs. This review highlights the interplay between mRNA modifications and ncRNAs in regulating protein translation, offering insights for precision therapy in human cancers.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2021)
Article
Biochemistry & Molecular Biology
Gabriel Wright, Anabel Rodriguez, Jun Li, Tijana Milenkovic, Scott J. Emrich, Patricia L. Clark
Summary: Research has shown that synonymous codon usage can affect various mechanisms related to protein production, especially in co-translational protein folding. Conservation of synonymous codon usage patterns across evolution highlights the potential benefits of matching codon usage patterns from the original organism in heterologous gene expression.
Article
Biotechnology & Applied Microbiology
Gemma Chavarria-Miro, Eduard Anfruns-Estrada, Adan Martinez-Velazquez, Mario Vazquez-Portero, Susana Guix, Miquel Paraira, Belen Galofre, Gloria Sanchez, Rosa M. Pinto, Albert Bosch
Summary: The study showed that monitoring SARS-CoV-2 in wastewater in Barcelona helped anticipate the COVID-19 pandemic situation, demonstrating the usefulness of water-based epidemiology as a tool for tracking virus circulation and aiding health authorities in taking timely measures.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Virology
Ignacio Parron, Elsa Plasencia, Thais Cornejo-Sanchez, Mireia Jane, Cristina Perez, Conchita Izquierdo, Susana Guix, Angela Dominguez
Summary: This study investigated an outbreak of acute gastroenteritis caused by human astrovirus in a daycare center, identifying a higher attack rate among household contacts of affected attenders and asymptomatic infections among daycare attendees. The transmission of HAstV extended to household contacts of both affected and non-affected attenders during the outbreak.
Article
Virology
Monica Carol, Victor Guadalupe-Fernandez, Cristina Rius, Nuria Soldevila, Efren Razquin, Susana Guix, Angela Dominguez
Summary: An outbreak of acute gastroenteritis occurred among schoolchildren at a holiday camp in Catalonia in February 2017, with a total of 41 cases identified among 174 individuals. Water consumption was found to be the main factor associated with the outbreak. Detection of Norovirus and other pathogens in fecal and water samples highlighted the potential risks of untreated water from natural fountains.
Article
Virology
Eduard Anfruns-Estrada, Sara Sabate, Efren Razquin, Thais Cornejo Sanchez, Rosa Bartolome, Nuria Torner, Conchita Izquierdo, Nuria Soldevila, Lorena Coronas, Angela Dominguez, Cristina Fuentes, Rosa M. Pinto, Albert Bosch, Susana Guix
Summary: The study aimed to describe the genetic diversity and epidemiology of human norovirus (HuNoV) outbreaks in Catalonia, Spain between 2017 and 2019. The predominant genotypes were GII, particularly GII.4 Sydney 2012. Foodborne outbreaks had higher attack rates and shorter duration compared to person-to-person transmitted outbreaks. The prevalence of genotypes differed between different settings, with GII.4 Sydney 2012 outbreaks significantly associated with nursing homes.
Article
Microbiology
Ignacio Parron, Irene Barrabeig, Nuria Soldevila, Rosa Bartolome, Susana Guix, Cristina Rius, Thais Cornejo-Sanchez, Conchita Izquierdo, Angela Dominguez
Summary: We studied outbreaks of acute gastroenteritis due to norovirus in schools and summer camps during 2017-2019 in Catalonia (Spain). The overall attack rate was higher in summer camps than in schools, and outbreaks were more common in cold months. There was a correlation between the delay in reporting and the duration of outbreaks. In outbreaks with person-to-person transmission, the risk increased with longer delay in reporting.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Meriem Bekliz, Kenneth Adea, Olha Puhach, Francisco Perez-Rodriguez, Stefane Marques Melancia, Stephanie Baggio, Anna-Rita Corvaglia, Frederique Jacquerioz, Catia Alvarez, Manel Essaidi-Laziosi, Camille Escadafal, Laurent Kaiser, Isabella Eckerle
Summary: The sensitivity for detecting Omicron-BA.1 varies among different Ag-RDTs, highlighting the need for careful consideration when using these tests. Analytical and retrospective testing demonstrated variable sensitivity for both Omicron-BA.1 and Delta, but all seven Ag-RDTs showed comparable sensitivities in the retrospective study.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Josep Gregori, Sergi Colomer-Castell, Carolina Campos, Marta Ibanez-Lligona, Damir Garcia-Cehic, Ariadna Rando-Segura, Caroline Melanie Adombie, Rosa Pinto, Susanna Guix, Albert Bosch, Esteban Domingo, Isabel Gallego, Celia Perales, Maria Francesca Cortese, David Tabernero, Maria Buti, Mar Riveiro-Barciela, Juan Ignacio Esteban, Francisco Rodriguez-Frias, Josep Quer
Summary: This study presents a method to partition quasispecies haplotypes into four fractions based on their fitness and uses diversity indices to analyze the molecular changes in the composition of a quasispecies over time. The results suggest that mutagenic antiviral treatment can lead to the selection of a diverse set of synonymous haplotypes, while a prevalent master phenotype is observed at the protein level. This observation may have implications for mutagenic antiviral treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Maria Costafreda, Silvia Sauleda, Mar Riveiro-Barciela, Angie Rico, Meritxell Llorens-Revull, Susana Guix, Rosa M. Pinto, Albert Bosch, Francisco Rodriguez-Frias, Ariadna Rando, Maria Piron, Marta Bes
Summary: Different outcomes of HEV infection are associated with specific dysregulation of microRNAs, which can serve as biomarkers for HEV infection outcomes and contribute to improving the clinical management of hepatitis E patients. This study provides new insights into HEV pathogenesis and potential targets for antiviral treatments.
MICROBIOLOGY SPECTRUM
(2023)
Article
Engineering, Environmental
Ines Giron-Guzman, Azahara Diaz-Reolid, Pilar Truchado, Albert Carcereny, David Garcia-Pedemonte, Bruno Hernaez, Albert Bosch, Rosa Maria Pinto, Susana Guix, Ana Allende, Antonio Alcami, Alba Perez-Cataluna, Gloria Sanchez
Summary: Monkeypox virus (MPXV) DNA was detected in various samples including saliva, semen, urine, and fecal samples besides nasopharyngeal swabs. The study analyzed the presence of MPXV DNA in wastewater collected from different areas of Spain using a surveillance network. The results showed that MPXV DNA could be consistently detected in longitudinal wastewater samples from different treatment plants, indicating the possibility of underestimated cases and frequent asymptomatic infections.
Article
Microbiology
Manel Essaidi-Laziosi, Lena Royston, Bernadett Boda, Francisco Javier Perez-Rodriguez, Isabelle Piuz, Nicolas Hulo, Laurent Kaiser, Sophie Clement, Song Huang, Samuel Constant, Caroline Tapparel
Summary: By comparing infections of in vitro reconstituted airway epithelia from asthmatic and healthy donors, we found that tissues from asthmatic donors were more susceptible to respiratory viruses and had higher viral replication levels. In addition, viral infections led to alterations in gene expression, affecting cilia structure and motility, mucociliary clearance, and mucus secretion. These findings shed light on the mechanisms of asthma exacerbations and provide potential therapeutic targets.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
M. T. Ngo Nsoga, F. J. Perez-Rodriguez, A. Mamin, A. G. L'Huillier, A. Cherkaoui, L. Kaiser, M. Schibler
Summary: Microbiological testing is often excessive in the diagnosis of central nervous system (CNS) infections, leading to unnecessary laboratory work and costs. The modified Reller criteria have been developed to reduce unnecessary testing for herpes simplex virus 1 (HSV-1) in the cerebrospinal fluid (CSF) when suspecting encephalitis. This retrospective study demonstrates that applying the modified Reller criteria could safely reduce unnecessary microbiological testing in the diagnosis of CNS infections.
MICROBIOLOGY SPECTRUM
(2023)
Article
Engineering, Environmental
Mattia Mattei, Rosa M. Pinto, Susana Guix, Albert Bosch, Alex Arenas
Summary: We analyzed SARS-CoV-2 genome copies in Catalonia's wastewater and developed a mathematical model to estimate the number of infections and the temporal relationship between reported and unreported cases. Samples from 16 wastewater treatment plants were used in an epidemiological model, showing a strong correlation between genome copies and reported cases with a delay of 8.8 days. The model estimated a higher infection rate (53%) compared to the reported cases (19%), indicating under-reporting in November and December 2021. The maximum genome copies shed in feces by an infected individual ranged from 1.4 x 108 gc/g to 4.4 x 108 gc/g. This study highlights the potential of using wastewater data as an early indicator for new infections and provides a framework for integrating such data into epidemiological models.
Article
Medicine, General & Internal
Pierre Van Damme, Rosa M. Pinto, Zongdi Feng, Fuqiang Cui, Angela Gentile, Daniel Shouval
Summary: Hepatitis A is a vaccine-preventable infection caused by the hepatitis A virus (HAV). It leads to an acute inflammatory reaction in the liver, but usually resolves without chronic sequelae. Factors such as immunological status, age, pregnancy, and underlying hepatic diseases can affect the severity of the disease. Vaccination and natural immunity can provide long-term protection against re-infection. The WHO recommends vaccination for high-risk individuals in low endemicity countries and universal childhood vaccination in intermediate endemicity countries.
NATURE REVIEWS DISEASE PRIMERS
(2023)
Review
Immunology
Rosa M. Pinto, Francisco-Javier Perez-Rodriguez, Maria-Isabel Costafreda, Gemma Chavarria-Miro, Susana Guix, Enric Ribes, Albert Bosch
Summary: Hepatitis A is an acute liver infection that is mostly asymptomatic in children but becomes more severe with age. While most patients recover completely, some may experience prolonged, relapsed, or fulminant forms. The severity of the infection is believed to be determined by host factors such as immunological status, age, and underlying liver diseases, with possible contributions from virus traits.