Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host

Kattoor, Jobin Jose; Malik, Yashpal Singh; Sasidharan, Aravind; Rajan, Vishnuraj Mangalathu; Dhama, Kuldeep; Ghosh, Souvik; Bányai, Krisztiàn; Kobayashi, Nobumichi; Singh, Raj Kumar

doi:10.1016/j.meegid.2015.06.018

Cited by 25 publications

(20 citation statements)

References 39 publications

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“…Consistent with previous studies [13, 16, 18, 47–49], we found a clearly separated and independent evolution of RVA and RVD strains (Figs. 1, 2 and 3) and a high proportion of RVA/RVD co-infections.…”

Section: Discussionsupporting

confidence: 93%

“…However, virus-host coevolution remains the major evolutionary pattern reported for RVs [16] and reassortment events mainly occur between strains of the same RV group [17, 18]. Nevertheless, some natural reassortants show characteristics suggestive of mixed host species origins [19] and a potential for cross-group reassortment was revealed for RVA and RVD [20].…”

Section: Introductionmentioning

confidence: 99%

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Molecular epidemiology of Avian Rotaviruses Group A and D shed by different bird species in Nigeria

Pauly

Oni

Sausy

et al. 2017

Virol J

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BackgroundAvian rotaviruses (RVs) cause gastrointestinal diseases of birds worldwide. However, prevalence, diversity, epidemiology and phylogeny of RVs remain largely under-investigated in Africa.MethodsFecal samples from 349 birds (158 symptomatic, 107 asymptomatic and 84 birds without recorded health status) were screened by reverse transcription PCR to detect RV groups A and D (RVA and RVD). Partial gene sequences of VP4, VP6, VP7 and NSP4 for RVA, and of VP6 and VP7 for RVD were obtained and analyzed to infer phylogenetic relationship. Fisher’s exact test and logistic regression were applied to identify factors potentially influencing virus shedding in chickens.ResultsA high prevalence of RVA (36.1%; 126/349) and RVD (31.8%; 111/349) shedding was revealed in birds. In chickens, RV shedding was age-dependent and highest RVD shedding rates were found in commercial farms. No negative health effect could be shown, and RVA and RVD shedding was significantly more likely in asymptomatic chickens: RVA/RVD were detected in 51.9/48.1% of the asymptomatic chickens, compared to 18.9/29.7% of the symptomatic chickens (p < 0.001/p = 0.01). First RVA sequences were obtained from mallard ducks (Anas platyrhynchos) and guinea fowls (Numida meleagris). Phylogenetic analyses illustrated the high genetic diversity of RVA and RVD in Nigerian birds and suggested cross-species transmission of RVA, especially at live bird markets. Indeed, RVA strains highly similar to a recently published fox rotavirus (RVA/Fox-tc/ITA/288356/2011/G18P[17]) and distantly related to other avian RVs were detected in different bird species, including pigeons, ducks, guinea fowls, quails and chickens.ConclusionThis study provides new insights into epidemiology, diversity and classification of avian RVA and RVD in Nigeria. We show that cross-species transmission of host permissive RV strains occurs when different bird species are mixed.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-017-0778-5) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Molecular epidemiology of Avian Rotaviruses Group A and D shed by different bird species in Nigeria

Pauly

Oni

Sausy

et al. 2017

Virol J

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“…Studies have shown that the higher the gene expression level is, the stronger is the preferred use of codon [1][2][3]6,15,16,49,[55][56][57][58][59][60]. In our study, the codon usage bias results of all cotton species were shown in S1 Table. The correlation between the parameters of 4 cotton species and 4 subgenomes had the same rule, except the correlation between G3s and C3s.…”

Section: Correlation Analysis Between Codon Usage Bias Indicesmentioning

confidence: 73%

Genome-wide analysis of codon usage bias in four sequenced cotton species

et al. 2018

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Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.

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“…In zika virus and tembusu virus codon usage was driven by the mutation bias (Cristina et al, 2015;Zhou et al, 2015) while in Parvoviridae and pedCoV it was dominated by selection pressure (Shi et al, 2013;Chen et al, 2014b). Some of the viruses observed with the codon bias related to their hosts during their adaptation (Chantawannakul and Cutler, 2008;Bahir et al, 2009;Cheng et al, 2012;Kattoor et al, 2015;Ma et al, 2015;Nasrullah et al, 2015). Studies directed at the conserved regions of viral proteins are useful for developing diagnostic reagents and probes for detecting a range of viruses and isolates in one test and for vaccine development (Du et al, 2010;Johnson et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design

Sheikh

Al‐Taher

Al‐Nazawi

et al. 2020

Journal of Virological Methods

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The nucleocapsid (N) protein of a coronavirus plays a crucial role in virus assembly and in its RNA transcription. It is important to characterize a virus at the nucleotide level to discover the virus's genomic sequence variations and similarities relative to other viruses that could have an impact on the functions of its genes and proteins. This entails a comprehensive and comparative analysis of the viral genomes of interest for preferred nucleotides, codon bias, nucleotide changes at the 3 rd position (NT3s), synonymous codon usage and relative synonymous codon usage. In this study, the variations in the N proteins among 13 different coronaviruses (CoVs) were analysed at the nucleotide and amino acid levels in an attempt to reveal how these viruses adapt to their hosts relative to their preferred codon usage in the N genes. The results revealed that, overall, eighteen amino acids had different preferred codons and eight of these were over-biased. The N genes had a higher AT% over GC% and the values of their effective number of codons ranged from 40.43 to 53.85, indicating a slight codon bias. Neutrality plots and correlation analyses showed a very high level of GC3s/GC correlation in porcine epidemic diarrhea CoV (pedCoV), followed by Middle East respiratory syndrome-CoV (MERS CoV), porcine delta CoV (dCoV), bat CoV (bCoV) and feline CoV (fCoV) with r values 0.81, 0.68, -0.47, 0.98 and 0.58, respectively. These data implied a high rate of evolution of the CoV genomes and a strong influence of mutation on evolutionary selection in the CoV N genes. This type of genetic analysis would be useful for evaluating a virus's host adaptation, evolution and is thus of value to vaccine design strategies.

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Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host

Cited by 25 publications

References 39 publications

Molecular epidemiology of Avian Rotaviruses Group A and D shed by different bird species in Nigeria

Molecular epidemiology of Avian Rotaviruses Group A and D shed by different bird species in Nigeria

Genome-wide analysis of codon usage bias in four sequenced cotton species

Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design

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