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静态与不断演变的诺如病毒基因型:对流行病学和免疫的影响

Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity.

作者信息

Parra Gabriel I, Squires R Burke, Karangwa Consolee K, Johnson Jordan A, Lepore Cara J, Sosnovtsev Stanislav V, Green Kim Y

机构信息

Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America.

Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America.

出版信息

PLoS Pathog. 2017 Jan 19;13(1):e1006136. doi: 10.1371/journal.ppat.1006136. eCollection 2017 Jan.

Abstract

Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII.4. The non-GII.4 genotypes were comprised of one or more intra-genotypic variants, with each variant containing strains that differed by only a few residues over several decades (remaining "static") and that have co-circulated with no clear epidemiologic pattern. In contrast, the GII.4 genotype presented the largest number of variants (>10) that have evolved over time with a clear pattern of periodic variant replacement. To expand our understanding of these two patterns of diversification ("static" versus "evolving"), we analyzed using NGS the nearly full-length norovirus genome in healthy individuals infected with GII.4, GII.6 or GII.17 viruses in different outbreak settings. The GII.4 viruses accumulated mutations rapidly within and between hosts, while the GII.6 and GII.17 viruses remained relatively stable, consistent with their diversification patterns. Further analysis of genetic relationships and natural history patterns identified groupings of certain genotypes into larger related clusters designated here as "immunotypes". We propose that "immunotypes" and their evolutionary patterns influence the prevalence of a particular norovirus genotype in the human population.

摘要

诺如病毒是全球范围内与急性肠胃炎相关的主要病原体。它们的RNA基因组具有多样性,有两个主要的基因群(GI和GII),由至少28种与人类疾病相关的基因型组成。为了阐明诺如病毒多样性和进化的潜在机制,我们采用大规模基因组学方法分析人类诺如病毒序列。对代表大多数已知感染人类的GI和GII基因型的2000多个近乎全长的ORF2序列进行比较,结果显示除了GII.4之外,每个基因型内不同的基因型内变体数量有限(≤5个)。非GII.4基因型由一个或多个基因型内变体组成,每个变体包含在几十年间仅相差几个残基的毒株(保持“静态”),并且它们共同传播,没有明确的流行病学模式。相比之下,GII.4基因型呈现出数量最多(>10个)的变体,这些变体随着时间的推移以明显的周期性变体替换模式进化。为了扩展我们对这两种多样化模式(“静态”与“进化”)的理解,我们使用二代测序(NGS)分析了在不同暴发环境中感染GII.4、GII.6或GII.17病毒的健康个体中的近乎全长诺如病毒基因组。GII.4病毒在宿主内部和宿主之间迅速积累突变,而GII.6和GII.17病毒则保持相对稳定,这与它们的多样化模式一致。对遗传关系和自然史模式的进一步分析确定了某些基因型可分为更大的相关簇,在此指定为“免疫型”。我们提出“免疫型”及其进化模式会影响特定诺如病毒基因型在人群中的流行率。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a889/5283768/6bad33187778/ppat.1006136.g001.jpg

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