scholarly journals Genome Variability and Capsid Structural Constraints of Hepatitis A Virus

2003 ◽  
Vol 77 (1) ◽  
pp. 452-459 ◽  
Author(s):  
Glòria Sánchez ◽  
Albert Bosch ◽  
Rosa M. Pintó
Keyword(s):  
Codon Usage ◽  
Rna Structure ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Foot And Mouth Disease ◽  
Structural Constraints ◽  
Translation Speed ◽  
Synonymous Mutations ◽  
Rare Codons ◽  
Mouth Disease Virus

ABSTRACT The number of synonymous mutations per synonymous site (Ks ), the number of nonsynonymous mutations per nonsynonymous site (Ka ), and the codon usage statistic (Nc ) were calculated for several hepatitis A virus (HAV) isolates. While Ks was similar to those of poliovirus (PV) and foot-and-mouth disease virus (FMDV), Ka was 1 order of magnitude lower. The Nc parameter provides information on codon usage bias and decreases when bias increases. The Nc value in HAV was about 38, while in PV and FMDV, it was about 53. The emergence of 22 rare codons in front of 8 in PV and 7 in FMDV was detected. Most of the conserved rare codons of the P1 region were strategically located at the carboxy borders of β barrels and α helices, their potential function being the assurance of proper folding of the capsid proteins through a decrease in the translation speed. This strategic location was not observed for amino acids encoded by the conserved rare codons of the 3D region. The percentage of bases with low pairing number values was higher in the latter region, suggesting a role of the conserved rare codons in the maintenance of RNA structure. Many of the rare codons in HAV are among the most frequent in humans, unlike in PV or in FMDV. This fact may be explained by the lack of cellular shutoff in HAV. One hypothesis is that HAV has evolved in order to avoid competition with its host for cellular tRNAs.

scholarly journals The Critical Role of Codon Composition on the Translation Efficiency Robustness of the Hepatitis A Virus Capsid

2019 ◽  
Vol 11 (9) ◽  
pp. 2439-2456 ◽  
Author(s):  
Lucía D’Andrea ◽  
Francisco-Javier Pérez-Rodríguez ◽  
Montserrat de Castellarnau ◽  
Susana Guix ◽  
Enric Ribes ◽  
...  
Keyword(s):  
Codon Usage ◽  
Sequence Space ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Critical Role ◽  
Translation Efficiency ◽  
Rare Codons ◽  
Codon Composition ◽  
Cellular Genome

AbstractHepatoviruses show an intriguing deviated codon usage, suggesting an evolutionary signature. Abundant and rare codons in the cellular genome are scarce in the human hepatitis A virus (HAV) genome, while intermediately abundant host codons are abundant in the virus. Genotype–phenotype maps, or fitness landscapes, are a means of representing a genotype position in sequence space and uncovering how genotype relates to phenotype and fitness. Using genotype–phenotype maps of the translation efficiency, we have shown the critical role of the HAV capsid codon composition in regulating translation and determining its robustness. Adaptation to an environmental perturbation such as the artificial induction of cellular shutoff—not naturally occurring in HAV infection—involved movements in the sequence space and dramatic changes of the translation efficiency. Capsid rare codons, including abundant and rare codons of the cellular genome, slowed down the translation efficiency in conditions of no cellular shutoff. In contrast, rare capsid codons that are abundant in the cellular genome were efficiently translated in conditions of shutoff. Capsid regions very rich in slowly translated codons adapt to shutoff through sequence space movements from positions with highly robust translation to others with diminished translation robustness. These movements paralleled decreases of the capsid physical and biological robustness, and resulted in the diversification of capsid phenotypes. The deviated codon usage of extant hepatoviruses compared with that of their hosts may suggest the occurrence of a virus ancestor with an optimized codon usage with respect to an unknown ancient host.

scholarly journals New possibilities for egg white lysozyme: heat-denatured lysozyme partially inactivates select foot-and-mouth disease virus strains

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Katsuhiko Fukai ◽  
Kazuyuki Inoue ◽  
Akira Takeuchi ◽  
Makoto Yamakawa
Keyword(s):  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Foot And Mouth Disease ◽  
Egg White ◽  
Mouth Disease ◽  
Egg White Lysozyme ◽  
Contagious Diseases ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Virus Strains

AbstractFoot-and-mouth disease (FMD) is one of the most contagious diseases of cloven-hoofed animals. Disinfectants are used to inactivate FMD virus (FMDV) in Japan. Reports that heat-denatured lysozyme inactivates bacteria as well as viruses, such as norovirus and hepatitis A virus, led us to determine its effects on FMDV. We show here that heat-denatured lysozyme partially inhibited the infectivity of FMDV O/JPN/2010-1/14C but of FMDVs A/TAI/46-1/2015 and Asia1/Shamir (ISR/3/89). Further, heat-denatured lysozyme variably reduced RNA loads of FMDVs O/JPN/2010-1/14C, O/MOG/2/Ca/BU/2017, O/Taiwan/1997, Asia1/Shamir (ISR/3/89), Asia1/TUR/49/2011, SAT1/KEN/117/2009, SAT2/SAU/6/2000 and SAT3/ZIM/3/83 but could not those of O/JPN/2000, A/TAI/46-1/2015, A22/IRQ/24/64, A15/TAI/1/60 and C/PHI/7/84. These findings indicate that heat-denatured lysozyme may serve as a new disinfectant against FMDV.

scholarly journals Mapping codon usage in sequence regions flanking cleavage positions in the hepatitis A virus polyprotein

2013 ◽  
Vol 12 (3) ◽  
pp. 2306-2319 ◽  
Author(s):  
X.-X. Ma ◽  
Y.-P. Feng ◽  
L. Chen ◽  
Y.-Q. Zhao ◽  
J.-L. Liu ◽  
...  
Keyword(s):  
Codon Usage ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Virus Polyprotein

scholarly journals Application of Median Lethal Concentration (LC50) of Pathogenic Microorganisms and Their Antigens in Vaccine Development

2020 ◽  
Author(s):  
Saganuwan Alhaji Saganuwan
Keyword(s):  
Staphylococcus Aureus ◽  
Disease Virus ◽  
Vaccine Development ◽  
Hepatitis A Virus ◽  
Lethal Dose ◽  
Vaccine Dose ◽  
Foot And Mouth Disease ◽  
Bacterial Colony ◽  
Mouth Disease Virus

Abstract Objective: Lack of ideal mathematical models to qualify and quantify both pathogenicity, and virulence is a dreadful setback in development of new antimicrobials and vaccines against resistance pathogenic microorganisms.Hence, the modified arithmetical formula of Reed and Muenchhas been integrated with other formulas and used to determine bacterial colony forming unit/ viral concentration, virulence and immunogenicity from LC50s established in the laboratories. Results: Microorganisms’antigens tested are Staphylococcus aureus, Streptococcuspneumonia, Pseudomonas aeruginosa in mice and rat, Edwardsiellaictaluri, Aeromonashydrophila, Aeromonasveronii in fish, New Castle Disease virus in chicken, Sheep Pox Virus, Foot-and-Mouth Disease Virus and Hepatitis A virus in vitro, respectively. The LC50s for the pathogens using different routes of administrations are 1.93 x 103(sheep poxvirus) and 1.75 x 1010 for Staphylococcus aureus (ATCC29213) in rat respectively. Titre index (TI) equals N log10 LC50 and provides protection against lethal dose in graded fashion which translates to protection index. N is the number of vaccine dose that could neutralize the LC50. Hence, parasite inoculum of 103 to 1011could be used as basis for determination of median lethal dose(LD50), LC50 and median bacterial concentrations (BC50)determination, pathogenic dose for immune stimulation should be sought at concentrations less than LC10.

scholarly journals Determination of Median Lethal Concentrations (Lc50) of Pathogenic Antigens and Their Applications in Vaccine Development

2020 ◽  
Author(s):  
Saganuwan Alhaji Saganuwan
Keyword(s):  
Staphylococcus Aureus ◽  
Disease Virus ◽  
Vaccine Development ◽  
Hepatitis A Virus ◽  
Lethal Dose ◽  
Vaccine Dose ◽  
Foot And Mouth Disease ◽  
Mouth Disease Virus

Abstract Objective: Lack of ideal mathematical models to qualify and quantify both pathogenicity, and virulence is a dreadful setback in development of new antimicrobials and vaccines against resistance pathogenic microorganisms. Hence, the modified arithmetical formula of Reed and Muench has been integrated with other formulas and used for determination of antigen concentration and parasites inoculums that would kill 50% of test animals (LC50).Results: Microorganisms’ antigens tested are Staphylococcus aureus, Streptococcus pneumonia, Pseudomonas aeruginosa in mice and rat, Edwardsiella ictaluri, Aeromonas hydrophila, Aeromonas veronii in fish, New Castle Disease virus in chicken, Sheep Pox Virus, Foot-and-Mouth Disease Virus and Hepatitis A virus in vitro, respectively. The LC50s for the pathogens using different routes of administrations are 1.93 x 103 (sheep poxvirus) and 1.75 x 1010 for Staphylococcus aureus (ATCC29213) in rat respectively. N is the number of vaccine dose that could neutralize the LC50.Titre index (TI) equals N log10 LC50 and provides protection against lethal dose in graded fashion which translates to protection index. Hence, parasite inoculum of 103 to 1011 could be used as basis for median lethal dose (LD50), LC50 and median bacterial concentrations (BC50) determination, pathogenic dose for immune stimulation should be sought at concentrations less than LC10.

scholarly journals Hepatitis A Virus Codon Usage: Implications for Translation Kinetics and Capsid Folding

2018 ◽  
Vol 8 (10) ◽  
pp. a031781 ◽  
Author(s):  
Rosa M. Pintó ◽  
Francisco-Javier Pérez-Rodríguez ◽  
Lucia D’Andrea ◽  
Montserrat de Castellarnau ◽  
Susana Guix ◽  
...  
Keyword(s):  
Codon Usage ◽  
Hepatitis A ◽  
Hepatitis A Virus

Characteristics of codon usage bias in two regions downstream of the initiation codons of foot-and-mouth disease virus

Biosystems ◽  
2010 ◽  
Vol 101 (1) ◽  
pp. 20-28 ◽  
Author(s):  
Jian-hua Zhou ◽  
Jie Zhang ◽  
Yao-zhong Ding ◽  
Hao-tai Chen ◽  
Li-na Ma ◽  
...  
Keyword(s):  
Codon Usage ◽  
Disease Virus ◽  
Codon Usage Bias ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Mouth Disease Virus ◽  
Foot And Mouth
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