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
Virology
Lei Lei, Huan Qin, Jin Luo, Yiluo Tan, Jie Yang, Zishu Pan
Summary: This study demonstrates that VLPs containing antigenic peptides of F protein combined with a CTL epitope of M2 may represent a promising RSV subunit vaccine candidate.
Article
Immunology
Florence Abravanel, Florence Nicot, Sebastien Lhomme, Michele Cazabat, Thomas Drumel, Aurelie Velay, Justine Latour, Julie Belliere, Pascal Cintas, Nassim Kamar, Jacques Izopet
Summary: In this study, HEV quasispecies in the blood and cerebrospinal fluid of five patients with neurological symptoms were investigated. There was no virus compartmentalization in the acute-phase patients, but evidence of HEV quasispecies compartmentalization was found in the CSF of patients with chronic infection.
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
Immunology
Junyu Lin, Jing Li, Peilin Xie, Yue Han, Demin Yu, Jia Chen, Xinxin Zhang
Summary: The mutation or deletion of HBV middle surface antigen (MHBs) can promote the persistence of specific HBV variants in a mouse model, while the re-expression of MHBs can facilitate the rapid clearance of HBV. Clearance of HBV is associated with an increase in cytokines such as CXCL1, CXCL2, IL-6, and IL-33.
Article
Infectious Diseases
Bingzhe Li, Han Wu, Ziping Miao, Yihan Lu
Summary: This study explored potential animal hosts for hepatitis E virus (HEV) through codon usage analysis. The results showed that all HEV genotypes exhibited a preference for guanine/cytosine in the third position of synonymous codons. Animals in close contact with humans, such as cattle, dogs, rats, cats, and swine, showed a high preference for HEV.
INFECTION GENETICS AND EVOLUTION
(2022)
Article
Pharmacology & Pharmacy
Xia Tang, Wenxun Huang, Juan Kang, Keyue Ding
Summary: Telbivudine treatment in chronic HBV patients led to significant differences in viral quasispecies, with a reduced dN/dS ratio indicating selective constraints from antiviral therapy. Evolution patterns and resistant mutations in the quasispecies varied over a short-term treatment course.
ANTIVIRAL RESEARCH
(2021)
Article
Pharmacology & Pharmacy
Steve Leumi, Mingzhe Guo, Jie Lu, Zhaoning Wang, Tianyu Gan, Lin Han, Jackline Ngari, Yimin Tong, Xiaogang Xiang, Qing Xie, Lanfeng Wang, Jin Zhong
Summary: Despite the excellent antiviral potency of direct-acting antivirals (DAAs) against hepatitis C virus (HCV), drug-resistant viral mutations remain a potential challenge. This study identified the combination of two NS5B mutations, S282T and K74R, as a novel resistance-associated substitution (RAS) that confers substantial resistance to SOF while retaining the HCV replication capacity.
ANTIVIRAL RESEARCH
(2022)
Article
Evolutionary Biology
Christine Mordstein, Laura Cano, Atahualpa Castillo Morales, Bethan Young, Alexander T. Ho, Alan M. Rice, Michael Liss, Laurence D. Hurst, Grzegorz Kudla
Summary: The codon usage of viruses is influenced by various selective and mutational pressures, including GC content, dinucleotide content, and sequence motifs related to gene regulation. The effects of these factors on gene expression vary depending on whether the genetic material is DNA or RNA, how it is transcribed, and where transcription occurs.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Virology
Bornali Deb, Arif Uddin, Supriyo Chakraborty
Summary: In this study, codon usage strategies and base distribution of Horseshoe bat hepatitis B virus (HBHBV) were analyzed and compared with its host Rhinolophus sinicus, revealing low synonymous codon usage bias with a higher proportion of base C in both virus and host. Commonly used, less frequently used, and underrepresented codons were found to be similar in both sequences, indicating a potential viral adaptation to its host. Neutrality plot analysis showed a greater role of natural selection in evolution for HBHBV and R. sinicus.
Article
Microbiology
Xin Wang, Jing Sun, Yueyan Zheng, Fuqiang Xie
Summary: This study analyzed the synonymous codon usage of hepatitis E virus (HEV) genomes and found different usage patterns in HEV from different hosts. The genomes from ruminants showed the most stable synonymous codon usage patterns, while those from pigs had more concentrated codons. Human-derived HEV showed a distinct overall codon usage pattern. The synonymous codon usage patterns differed among the ORF regions of the HEV genome. Overall, stable codon usage in ORF1 may help sustain infection, while varied usage patterns in ORF3 may facilitate cross-species infection and host range expansion.
JOURNAL OF BASIC MICROBIOLOGY
(2022)
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
Immunology
Ya Fu, Fengling Fang, Hongyan Guo, Xialin Xiao, Yuhai Hu, Yongbin Zeng, Tianbin Chen, Songhang Wu, Ni Lin, Jinlan Huang, Ling Jiang, Qishui Ou, Can Liu
Summary: This study investigates the evolutionary characteristics of HBV X gene in the hepatocellular carcinoma microenvironment, and finds lower heterogeneity in tumor tissues and a location bias in X gene mutations. Additionally, the study reveals that HBx harboring mutation T81P/S101P/L123S promotes cell proliferation and increases genomic instability.
EMERGING MICROBES & INFECTIONS
(2022)
Article
Microbiology
Zhengwu Chang, Xiaoyu Dong, Zhao Guan, Kejia Lu, Xi Chen, Xi Wei, Hanwei Guo, Ruyi Dang, Juan Wang, Xinglong Wang, Sa Xiao, Zengqi Yang, Haijin Liu
Summary: Vaccines are widely used to prevent Newcastle disease virus. A study found that epitope mutations in the virus may decrease the effectiveness of the vaccine, but their contribution to antigenic mutation and immune escape is still controversial. The study also showed that a matched vaccine, generated through modification of the virus protein, was more effective in inhibiting viral shedding and tissue damage compared to an unmatched vaccine. However, both vaccines induced similar levels of neutralizing antibodies in vaccinated chickens.
VETERINARY MICROBIOLOGY
(2023)
Article
Virology
Irene Hoxie, John J. Dennehy
Summary: The reassortment of Rotavirus A (RVA) may generate new genome constellations with different segments showing varying degrees of co-segregation and host-species associations. The genetic diversity of all segments decreased dramatically around 2007, coinciding with the introduction of RVA vaccines. Additionally, codon usage patterns varied among segments, with some exhibiting higher adaptation to host genomes.
Article
Microbiology
Cristina Fuentes, Francisco J. Perez-Rodriguez, Aurora Sabria, Nerea Beguiristain, Rosa M. Pinto, Susana Guix, Albert Bosch
Summary: The study evaluated the effect of heat treatment on clams experimentally contaminated with HuNoV, using PMA-viability RTqPCR assay to minimize measurement of non-infectious viruses. Results showed a significant reduction in infectious HAV and a better correlation with risk reduction for GII using PMA-RTqPCR assay.
FRONTIERS IN 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
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
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)
