Analysis of the codon usage of the ORF2 gene of feline calicivirus

Zang, Minghui; He, Wanting; Du, Fanshu; Wu, Gongjian; Wu, Bin; Zhou, Zhenlei

doi:10.1016/j.meegid.2017.06.013

Cited by 14 publications

(7 citation statements)

References 28 publications

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“…The strain in the present study did not had significant mutational changes in its nucleotide composition, which influenced the use of synonymous codons; however, in another study 21 , the feline CV, ORF2 gene codon use was influenced by mutational bias.…”

Section: Discussioncontrasting

confidence: 62%

First description of a whole genome of Bavovirus at the Amazonian Region, detected in a commercial chicken farm from Brazil

Castro

Siqueira

Chagas

et al. 2023

Revista Pan-Amazônica de Saúde

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OBJECTIVE: To investigate the presence of virus in fecal specimens of clinically normal chickens of the genus Gallus gallus, collected from a commercial farm located in the municipality of Benevides, in the metropolitan region of Belém City, capital of Pará State, Northern Brazil. MATERIALS AND METHODS: A whole genome was identified in a fecal pool of broiler chicken using high throughput sequencing and phylogenetic analysis. RESULTS: The complete genome was characterized as belonging to the genus Bavovirus within the family Caliciviridae. CONCLUSION: This is the first description of this genus in the Amazonian Region and one of the few in Brazil, highlighting the need to monitor this virus to better understand its epidemiology and zoonotic potential.

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Section: Discussioncontrasting

confidence: 62%

First description of a whole genome of Bavovirus at the Amazonian Region, detected in a commercial chicken farm from Brazil

Castro

Siqueira

Chagas

et al. 2023

Revista Pan-Amazônica de Saúde

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“…The host's cellular structure and metabolism are essential for viruses to efficiently replicate and establish an infection. Codon usage patterns of viruses reflect the adaptive changes which have allowed them to optimize their survival and fitness in the host cells (Su et al, 2017;Taylor et al, 2017;Zang et al, 2017;Rahman et al, 2018;Luo et al, 2019). The CAI and RCDI are indices that can be used efficiently to analyze the adaptation of a virus to the host microcellular environment (Carbone et al, 2003;Puigbò et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Host Adaptation and Evolutionary Analysis of Zaire ebolavirus: Insights From Codon Usage Based Investigations

et al. 2020

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Ebola virus (EBOV) has caused several outbreaks as the consequence of spillover events from zoonotic sources and has resulted in huge death tolls. In spite of considerable progress, a thorough know-how regarding EBOV adaptation in various host species and detailed information about the potential reservoirs of EBOV still remains obscure. The present study was executed to examine the patterns of codon usage and its associated influence in the adaptation of EBOV to potential hosts that dwell in Africa, the origin of the viral outbreaks. Correspondence analysis (CA) revealed that the codon usage signature in EBOV is a complex interplay of factors including compositional bias and natural selection, with the latter having a more pronounced impact. Low codon usage bias in EBOV indicates a flexibility of the viruses in adapting to diverse range of hosts with different codon usage architectures. EBOV adaptation in potential hosts, as estimated by codon adaptation index (CAI) and relative codon deoptimization index (RCDI), revealed that the viruses were relatively better adapted to African primates than other mammals examined, which might account for the high fatality rate of primates owing to EBOV infection. Bats have been speculated as natural reservoirs of EBOV. In the present analysis it was interesting to note that EBOV displayed lower degrees of adaptation, as estimated by CAI and RCDI, with bats in comparison to the primate hosts. Lower degrees of adaptation might contribute to long-term coexistence and circulation of the viral pathogens in bat populations. Codon usage patterns of EBOV isolates associated with different outbreaks varied significantly, with discrete patterns between the West and Central African isolates. Additional evolutionary analyses indicated that the West African Epidemic began with an initial spillover infection and there was more than one population of EBOV circulating in the natural reservoir in the Democratic Republic of the Congo. The present study yields valuable information regarding the possible circulation of EBOV in various African mammals.

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“…The ORF2 (2013 nt) encodes the capsid protein VP1 and is divided into six regions (A-F). The regions A, B, D, and F are relatively well conserved, whereas regions C and E are variable with significant sequence divergence levels [13]. Therefore, the VP1 gene is frequently used as a target in molecular epidemiological investigations [4,14,15].…”

Section: Introductionmentioning

confidence: 99%

Molecular Characterization and Cross-Reactivity of Feline Calicivirus Circulating in Southwestern China

Zhou

Liu

et al. 2021

Viruses

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Feline calicivirus (FCV) is an important pathogen of cats that has two genogroups (GI and GII). To investigate the prevalence and molecular characteristics of FCVs in southwestern China, 162 nasal swab samples were collected from cats in animal shelters and pet hospitals. In total, 38 of the clinical samples (23.46%) were identified as FCV positive using nested RT-PCR. Phylogenetic analyses using 10 capsid protein VP1 sequences revealed that 8 GI and 2 GII strains formed two independent clusters. Additionally, three separated FCVs that were not clustered phylogenetically (two GI and one GII strains) were successfully isolated from clinical samples and their full-length genomes were obtained. Phylogenetic and recombinant analyses of a GI FCV revealed genomic breakpoints in ORF1 and ORF2 regions with evidence for recombinant events between GI sub-genogroups, which is reported in China for the first time. Furthermore, sera obtained from mice immunized independently with the three FCV isolates and a commercial vaccine were used to evaluate the cross-reactivity of neutralizing antibodies. The three separate FCVs were neutralized by each other at a 1:19 to 1:775 titer range, whereas the triple-inactivated vaccine was at a titer of 1:16, which suggested that different genogroup/sub-genogroup FCV strains exhibit significantly different titers of neutralizing antibodies, including the commercial FCV vaccine. Thus, our study revealed the genetic diversity and complex cross-reactivity levels of FCVs in southwestern China, which provides new insights for application in vaccination strategies.

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Analysis of the codon usage of the ORF2 gene of feline calicivirus

Cited by 14 publications

References 28 publications

First description of a whole genome of Bavovirus at the Amazonian Region, detected in a commercial chicken farm from Brazil

First description of a whole genome of Bavovirus at the Amazonian Region, detected in a commercial chicken farm from Brazil

Host Adaptation and Evolutionary Analysis of Zaire ebolavirus: Insights From Codon Usage Based Investigations

Molecular Characterization and Cross-Reactivity of Feline Calicivirus Circulating in Southwestern China

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