Genomic stratification and differential natural selection signatures among human norovirus genogroup II isolates

Kakakhel, Sehrish; Khan, Hizbullah; Nigar, Kiran; Khan, Asifullah

doi:10.1007/s00705-022-05396-9

Cited by 5 publications

(4 citation statements)

References 67 publications

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“…The comprehensive G -gene-based population genetic analyses were performed to infer the genetic diversity and evolutionary distinction across the VHSV samples. The methodological approach employed in the current study has previously been adopted for other viruses, including Begomovirus ( Prasanna et al, 2010 ), coxsackievirus ( Khan and Khan, 2021 ), Lassa Mammarenavirus ( Forni and Sironi, 2020 ), rhinovirus ( Waman et al, 2014 ), and human norovirus ( Kakakhel et al, 2022 ). The analyses speculate that spatiotemporal and selection pressure events possibly contribute toward the diversification of the VHSV isolate samples deposited in the public database.…”

Section: Discussionmentioning

confidence: 99%

Population genetic analyses unveiled genetic stratification and differential natural selection signatures across the G-gene of viral hemorrhagic septicemia virus

et al. 2022

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Introduction: Viral hemorrhagic septicemia virus (VHSV) is the most lethal pathogen in aquaculture, infecting more than 140 fish species in marine, estuarine, and freshwater environments. Viral hemorrhagic septicemia virus is an enveloped RNA virus that belongs to the family Rhabdoviridae and the genus Novirhabdovirus. The current study is designed to infer the worldwide Viral hemorrhagic septicemia virus isolates’ genetic diversity and evolutionary dynamics based on G-gene sequences.Methods: The complete G-gene sequences of viral hemorrhagic septicemia virus were retrieved from the public repositories with known timing and geography details. Pairwise statistical analysis was performed using Arlequin. The Bayesian model-based approach implemented in STRUCTURE software was used to investigate the population genetic structure, and the phylogenetic tree was constructed using MEGA X and IQ-TREE. The natural selection analysis was assessed using different statistical approaches, including IFEL, MEME, and SLAC.Results and Discussion: The global Viral hemorrhagic septicemia virus samples are stratified into five genetically distinct subpopulations. The STRUCTURE analysis unveiled spatial clustering of genotype Ia into two distinct clusters at K = 3. However, at K = 5, the genotype Ia samples, deposited from Denmark, showed temporal distribution into two groups. The analyses unveiled that the genotype Ia samples stratified into subpopulations possibly based on spatiotemporal distribution. Several viral hemorrhagic septicemia virus samples are characterized as genetically admixed or recombinant. In addition, differential or subpopulation cluster-specific natural selection signatures were identified across the G-gene codon sites among the viral hemorrhagic septicemia virus isolates. Evidence of low recombination events elucidates that genetic mutations and positive selection events have possibly driven the observed genetic stratification of viral hemorrhagic septicemia virus samples.

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Section: Discussionmentioning

confidence: 99%

Population genetic analyses unveiled genetic stratification and differential natural selection signatures across the G-gene of viral hemorrhagic septicemia virus

et al. 2022

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“…Several pandemic GII.4 variations have been identified, including GII.4 US95/96, GII.4 Farmington Hills2002, GII.4 Hunter2004, GII.4 Yerseke2006a, GII.4 Den Haag2006b, GII.4 New Orleans2009, and GII.4 Sydney2012 [ 21 , 73 ]. Recently, non-GII.4 genotypes, including the GII.17 variant and the GII.2[P16] recombinant strain, have also been reported to cause epidemics [ 74 , 75 ]. The GII.17 variant caused norovirus outbreaks in some Asian countries, replacing the GII.4 Sydney2012 [ 74 ].…”

Section: N - and O -Glycosylationmentioning

confidence: 99%

“…Recently, non-GII.4 genotypes, including the GII.17 variant and the GII.2[P16] recombinant strain, have also been reported to cause epidemics [ 74 , 75 ]. The GII.17 variant caused norovirus outbreaks in some Asian countries, replacing the GII.4 Sydney2012 [ 74 ]. Moreover, the GII.2[P16] recombinant strain is reported to have swept through Japan, China, and Germany [ 75 , 76 , 77 ].…”

Section: N - and O -Glycosylationmentioning

confidence: 99%

Elucidating the Implications of Norovirus N- and O-Glycosylation, O-GlcNAcylation, and Phosphorylation

Ченг

Chu

et al. 2023

Viruses

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Norovirus is the most common cause of foodborne gastroenteritis, affecting millions of people worldwide annually. Among the ten genotypes (GI–GX) of norovirus, only GI, GII, GIV, GVIII, and GIX infect humans. Some genotypes reportedly exhibit post-translational modifications (PTMs), including N- and O-glycosylation, O-GlcNAcylation, and phosphorylation, in their viral antigens. PTMs have been linked to increased viral genome replication, viral particle release, and virulence. Owing to breakthroughs in mass spectrometry (MS) technologies, more PTMs have been discovered in recent years and have contributed significantly to preventing and treating infectious diseases. However, the mechanisms by which PTMs act on noroviruses remain poorly understood. In this section, we outline the current knowledge of the three common types of PTM and investigate their impact on norovirus pathogenesis. Moreover, we summarize the strategies and techniques for the identification of PTMs.

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“…We randomly checked 12 reports published in 2022 which employed 9−538 (median = 43 < 50) sequences for estimating the selection pressure on sites in protein-encoding genes of viruses using the ω approach [26][27][28][29][30][31][32][33][34][35][36][37] . Therefore, as per the above data calculated with 50 sequences using the MEME and FEL methods, at least half of these 12 reports could underestimate SPSs and SNgSs by more than 60.8% and 37.0%, respectively, in the relevant viral genes.…”

Section: The First Mechanism For Underestimating Selectionmentioning

confidence: 99%

Natural selection and neutral mutations through the lens of viruses

Chen

Gong

et al. 2022

Preprint

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The Neutral Theory and the Modern Synthesis, a modified version of Darwin's theory, have been arguing for decades about the influence of natural selection on molecular evolution. Here we elucidate through the lens of viruses that a frequently used method employing the ratio of nonsynonymous versus synonymous substitution rates has dramatically underestimated the influence of natural selection on molecular evolution. We also find novel evidence from viral sequences to support the co-existence of the crucial role of natural selection in molecular evolution and the ubiquity of neutral mutations. The co-existence has perplexed biologists for decades. We then elucidate for the first time the causality between natural selection and the ubiquity of neutral mutations with a novel interpretation of natural selection. This novel interpretation incorporates biochemistry, genetics, epigenetics, physiology, and dynamics. It holds that natural selection acts directly on the overall phenotypic performance of organisms and indirectly on each genomic site or phenotypic trait. It highlights not only restrictions and competitions but also freedom and diversity, besides the overall harmonious development of organisms and human societies. Therefore, this novel interpretation could have far-reaching implications in the natural and social sciences.

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Genomic stratification and differential natural selection signatures among human norovirus genogroup II isolates

Cited by 5 publications

References 67 publications

Population genetic analyses unveiled genetic stratification and differential natural selection signatures across the G-gene of viral hemorrhagic septicemia virus

Population genetic analyses unveiled genetic stratification and differential natural selection signatures across the G-gene of viral hemorrhagic septicemia virus

Elucidating the Implications of Norovirus N- and O-Glycosylation, O-GlcNAcylation, and Phosphorylation

Natural selection and neutral mutations through the lens of viruses

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