A detailed comparative analysis on the overall codon usage patterns in West Nile virus

Moratorio, Gonzalo; Iriarte, Andrés; Moreno, Pilar; Musto, Héctor; Cristina, Juan

doi:10.1016/j.meegid.2013.01.001

Cited by 68 publications

(52 citation statements)

References 42 publications

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“…The synonymous codon usage among TMUV CDSs was relatively low (ENC=53.287, S.D.=0.149), in agreement with previous results for RNA virus genomes, including West Nile virus (ENC=53.81)(Moratorio et al, 2013), Hepatitis C virus (ENC=52.62)(Hu et al, 2011), Newcastle disease virus(ENC= 56.15)…”

supporting

confidence: 90%

“…To date, analyses of Flavivirus codon usage are fragmentary, and such studies have primarily focused on particular virus species, as previously described (Hu et al, 2011;Moratorio et al, 2013;Zhou et al, 2013). Conversely, the evolutionary characteristics and genetic relationships of codon usage bias in the TMUV genome have not been systematically studied; indeed, only a few genomic sequences of TMUV have been sequenced to date, with many studies only recently performed.…”

Section: Discussionmentioning

confidence: 99%

“…For viruses, little information exists regarding the extent and origin of synonymous codon variation. Recent efforts to elucidate codon usage biases in Flaviviridae have concentrated mainly on Dengue virus (DGV) (Zhou et al, 2013), West Nile virus (WNV) (Moratorio et al, 2013), and Hepatitis C virus (HCV) (Hu et al, 2011). In contrast, investigations of TMUV have primarily focused on viral isolation and identification Tang et al, 2013a), the establishment and application of diagnostic methods (Li et al, 2012b;Yun et al, 2012), and genetic analyses of complete genome sequences Wan et al, 2012;Zhu et al, 2012), whereas information regarding codon usage patterns is not available.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Evolutionary characterization of Tembusu virus infection through identification of codon usage patterns

Zhou

Yan

Chen

et al. 2015

Infection, Genetics and Evolution

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supporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Evolutionary characterization of Tembusu virus infection through identification of codon usage patterns

Zhou

Yan

Chen

et al. 2015

Infection, Genetics and Evolution

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“…CAI:eCAI ratios were for the vertebrates were borderline for significance (0.99) and so it was difficult to be conclusive in that case, but may indicate a codon preference with vertebrates. This result compares with a recent study looking at codon preferences in 449 WNV strains with a clear codon preference towards human usage [23]. The inability to find a clear codon preference in our data may be due to sequence differences between global WNV strains, and WNV KUN strains circulating in Australia.…”

Section: Resultscontrasting

confidence: 59%

Archival Isolates Confirm a Single Topotype of West Nile Virus in Australia

et al. 2016

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West Nile virus is globally wide-spread and causes significant disease in humans and animals. The evolution of West Nile virus Kunjin subtype in Australia (WNVKUN) was investigated using archival samples collected over a period of 50 years. Based on the pattern of fixed amino acid substitutions and time-stamped molecular clock analyses, a single long-term lineage (or topotype) was inferred. This implies that a bottleneck exists such that regional strains eventually die out and are replaced with strains from a single source. This was consistent with current hypotheses regarding the distribution of WNVKUN, whereby the virus is enzootic in northern Australia and is disseminated to southern states by water-birds or mosquitoes after flooding associated with above average rainfall. In addition, two previous amino acid changes associated with pathogenicity, an N-Y-S glycosylation motif in the envelope protein and a phenylalanine at amino acid 653 in the RNA polymerase, were both detected in all isolates collected since the 1980s. Changes primarily occurred due to stochastic drift. One fixed substitution each in NS3 and NS5, subtly changed the chemical environment of important functional groups, and may be involved in fine-tuning RNA synthesis. Understanding these evolutionary changes will help us to better understand events such as the emergence of the virulent strain in 2011.

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“…In this pretext, it has been suggested that viral robustness, survival and evasion of host's immune signals and responses largely depend on the interplay of codon usage patterns of the concerned virus and its respective host (Shackelton et al, 2006; Moratorio et al, 2013). Here, we have considered the similarity index to understand the influence of host genome on the adaptability of virus genome inside the host.…”

Section: Methodsmentioning

confidence: 99%

HIV Progression Depends on Codon and Amino Acid Usage Profile of Envelope Protein and Associated Host-Genetic Influence

2017

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Acquired immune deficiency syndrome (AIDS) is a spectrum of conditions caused by infection with the human immunodeficiency virus (HIV). Two types of HIV have been characterized: HIV-1 and HIV-2. The present study investigated whether evolutionary selection pressure differs between rapid progressor (RP), slow progressor (SP), and long-term non-progressor (LTNP) of HIV-I infected individuals. An unexpected association between the evolutionary rate of substitution in envelope (env) gene and disease progression is observed. Our present study suggests that env genes of LTNP are subject to unusually strong functional constraint with respect to RP. We also observed that the three categories of env genes i.e., RP, SP, and LTNP, had their own characteristic pattern of amino acid usage and SP and LTNP sequences shared similar patterns of amino acid usage different from RP sequences and evolutionary rate significantly influenced the amino acid usage pattern of the three different types of env gene sequences. It was also noted that the evolutionary rate for the glycosylation sites of LTNP and SP sequences were even significantly less than the RP sequences. Comparative analysis on the influence of human host on the three categories of env genes are well correlated with the rates of disease progression suggesting the adaptive strategies of the viruses for successful residence and infection. Host associated selective constraints appeared most relaxed on the RP sequences and strongest in LTNP sequences. The present study clearly portrays how evolutionary selection pressure differs between three categories of env genes i.e., RP, SP, and LTNP. The env genes, coding for the env glycoproteins, experience severe selection constraints from the host due to their constant exposure to the host immune system. In this perspective it might be suggested that env gene evolution occurs mainly by negative selection with the occurrence of mutation that might not reach fixation in the viral population. This work also confers a deeper insight into the crucial effects of host factors that govern the overall progression of HIV infection.

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A detailed comparative analysis on the overall codon usage patterns in West Nile virus

Cited by 68 publications

References 42 publications

Evolutionary characterization of Tembusu virus infection through identification of codon usage patterns

Evolutionary characterization of Tembusu virus infection through identification of codon usage patterns

Archival Isolates Confirm a Single Topotype of West Nile Virus in Australia

HIV Progression Depends on Codon and Amino Acid Usage Profile of Envelope Protein and Associated Host-Genetic Influence

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