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)
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)
Review
Biochemistry & Molecular Biology
Sujatha Thankeswaran Parvathy, Varatharajalu Udayasuriyan, Vijaipal Bhadana
Summary: Codon usage bias is a common phenomenon observed in bacteria, plants, and animals, with consistent and characteristic patterns across different species and genes. The formation of codon bias is influenced by factors such as genome composition, gene expression levels, and gene length. Understanding codon usage bias can provide insights into phylogenetic relationships and gene evolution among organisms.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Microbiology
Ayan Roy, Fucheng Guo, Bhupender Singh, Shelly Gupta, Karan Paul, Xiaoyuan Chen, Neeta Raj Sharma, Nishika Jaishee, David M. Irwin, Yongyi Shen
Summary: The study found that SARS-CoV-2 exhibits complex compositional features, including avoidance of certain codon pairs and strict avoidance of CpG dinucleotides, possibly to evade human immune responses.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Davide Arella, Maddalena Dilucca, Andrea Giansanti
Summary: This study investigated the relationship between codon usage bias, microbial lifestyles, and habitats in 615 microbial organisms. The results showed that species with similar phenotypic traits living in similar environmental conditions exhibit similar codon preferences and tRNA availability. Additionally, organisms able to live in multiple habitats have reduced translational efficiency.
MOLECULAR GENETICS AND GENOMICS
(2021)
Article
Virology
Anuj Tyagi, Vandan Nagar
Summary: The genome characteristics and codon usage patterns of 44 Aeromonas hydrophila phages were studied in this research. The findings showed variations in phage genome size and GC content, with all phages having lower GC content than the host. The study also revealed shared codon usage preferences between the phages and host, with more prominent codon usage bias in phages with smaller genomes.
Article
Infectious Diseases
Qi Peng, Xue Zhang, Jizong Li, Wenlong He, Baochao Fan, Yanxiu Ni, Maojun Liu, Bin Li
Summary: This study presents a comprehensive analysis of 54 representative PDCoV strains, revealing a certain codon usage bias in the S gene and a higher adaptation level of PDCoV to humans and chickens than to pigs. These findings contribute to our understanding of PDCoV's evolution, adaptability, and inter-species transmission.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Microbiology
Yuanzhi Liu, Anchun Cheng, Mingshu Wang, Sai Mao, Xumin Ou, Qiao Yang, Ying Wu, Qun Gao, Mafeng Liu, Shaqiu Zhang, Juan Huang, Renyong Jia, Dekang Zhu, Shun Chen, Xinxin Zhao, Yanling Yu, Yunya Liu, Ling Zhang, Bin Tian, Leichang Pan
Summary: DHAV-1 virus inhibits cellular translation in duck embryo fibroblasts by inducing eIF2 alpha phosphorylation.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Virology
Lang Qin, Shiwen Ding, Zhilei Wang, Runzhou Jiang, Zhen He
Summary: This study analyzed the compositional bias and codon usage of TuMV and found that there were changes in the genomic composition and codon usage choice. Statistical analysis showed that natural selection was the main factor affecting the codon usage patterns of TuMV. Additionally, the study revealed that TuMV genes were strongly adapted to Brassica oleracea and potentially preferred this host.
Article
Infectious Diseases
Zhipeng Zhang, Fucheng Guo, Ayan Roy, Jinjin Yang, Wen Luo, Xuejuan Shen, David M. Irwin, Rui-Ai Chen, Yongyi Shen
Summary: Thorough analysis of codon usage adaptation reveals that H3N2 is best adapted to the human cellular system, correlating with its highest epidemic intensity compared to other seasonal influenza viruses. Avoidance of CpG dinucleotide is strong among the seasonal influenza viruses, with a more restrained trend in influenza B viruses than in influenza A viruses, possibly reflecting the viral pathogens' strategy to evade human immune signals. The dynamic evolution in codon usage and elimination of CpG motif among the viruses, in line with their distinct host adaptation state, signifies the significant impact of selective force on viral genomes, aimed at efficient circulation, enhanced fitness, and successful infection in humans.
INFECTION GENETICS AND EVOLUTION
(2021)
Article
Biology
Meshal M. Almutairi
Summary: This study analyzed chromosome features in rice to predict gene expression through codon usage patterns. Results showed variations in codon adaptation index and guanine/cytosine content among different chromosomes, providing insights for future rice breeding and genetics projects.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Microbiology
Fusheng Si, Li Jiang, Ruisong Yu, Wenqiang Wei, Zhen Li
Summary: The study revealed a low codon usage bias in the PEDV genome, with natural selection being the dominant factor influencing codon usage bias. Genotype II PEDV strains showed the highest level of adaptation to Sus scrofa compared to other divergent clades. This comprehensive report provides insights into PEDV evolution, adaptation, and fitness towards their hosts.
FRONTIERS IN MICROBIOLOGY
(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
Biology
Meshal M. Almutairi, Abdullah A. Alrajhi
Summary: The study focused on analyzing gene features and codon usage patterns in spring wheat under drought stress, revealing higher codon adaptation index in wheat root and L-galactono-1, 4-lactone dehydrogenase. The research also identified high guanine and cytosine content in wheat root and explained a significant portion of variation in relative synonymous codon usage through principal component analysis. These findings have implications for genetic engineering, molecular evolution, and gene prediction in developing drought-tolerant wheat varieties.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Virology
Zhen He, Zhuozhuo Dong, Lang Qin, Haifeng Gan
Summary: Broad bean wilt virus 2 (BBWV-2) is an important pathogen that causes damage to economically important crops. Recombination and reassortment play a significant role in the genomic evolution of BBWV2, with natural selection shaping the codon usage pattern of the virus. The study provides insights into the phylodynamics, codon usage patterns, and adaptive evolution of BBWV2, aiding in the understanding of its origin.
Article
Immunology
Maria Isabel Costafreda, Silvia Sauleda, Angie Rico, Maria Piron, Marta Bes
Summary: This study found that nonenveloped HEV particles can be detected in the plasma of HEV-infected blood donors, which may pose an additional risk to blood safety. The study also observed a higher proportion of nonenveloped HEV in samples with HEV-positive serology and/or increased levels of liver injury markers.
JOURNAL OF INFECTIOUS DISEASES
(2022)
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)
Article
Biochemistry & Molecular Biology
Meritxell Llorens-Revull, Brenda Martinez-Gonzalez, Josep Quer, Juan Ignacio Esteban, Gonzalo Nunez-Moreno, Pablo Minguez, Idoia Burgui, Ricardo Ramos-Ruiz, Maria Eugenia Soria, Angie Rico, Mar Riveiro-Barciela, Silvia Sauleda, Maria Piron, Irene Corrales, Francesc E. Borras, Francisco Rodriguez-Frias, Ariadna Rando, Clara Ramirez-Serra, Silvia Camos, Esteban Domingo, Marta Bes, Celia Perales, Maria Isabel Costafreda
Summary: MicroRNAs (miRNAs) encapsulated in extracellular vesicles (EVs) have potential as diagnostic and prognostic biomarkers. This study aimed to find a reliable EV isolation method for miRNA sequencing, suitable for clinical applications. Results showed that SEC yielded the highest amount of EVs with good reproducibility, while GRAD and SEC+GRAD resulted in purer EV preparations. The NEBNext library exhibited the highest reproducibility in miRNA recovery and diversity. Therefore, combining GRAD EV isolation with NEBNext library preparation is suitable for miRNA detection using plasma samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Marta Bes, Maria Costafreda, Mar Riveiro-Barciela, Maria Piron, Angie Rico, Josep Quer, Lluis Puig, Silvia Sauleda
Summary: HEV is a major cause of acute viral hepatitis in several European countries, primarily acquired through consumption of contaminated pork and potentially through blood transfusion. A study in Catalonia, Spain found 151 HEV RNA-positive blood donations out of 4,341 screened, with infected donors commonly reporting consumption of pates and sausages. All infected donors cleared the infection spontaneously without neurologic symptoms or reinfections after 1 year of follow-up, highlighting the effectiveness of HEV screening in providing safer blood for recipients.
EMERGING INFECTIOUS DISEASES
(2022)
