Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, 46556, Notre Dame, IN, USA.
BMC Microbiol. 2013 Feb 14;13:37. doi: 10.1186/1471-2180-13-37.
Dengue virus (DENV) infection represents a significant public health problem in many subtropical and tropical countries. Although genetically closely related, the four serotypes of DENV differ in antigenicity for which cross protection among serotypes is limited. It is also believed that both multi-serotype infection as well as the evolution of viral antigenicity may have confounding effects in increased dengue epidemics. Numerous studies have been performed that investigated genetic diversity of DENV, but the precise mechanism(s) of dengue virus evolution are not well understood.
We investigated genome-wide genetic diversity and nucleotide substitution patterns in the four serotypes among samples collected from different countries in Asia and Central and South America and sequenced as part of the Genome Sequencing Center for Infectious Diseases at the Broad Institute. We applied bioinformatics, statistical and coalescent simulation methods to investigate diversity of codon sequences of DENV samples representing the four serotypes. We show that fixation of nucleotide substitutions is more prominent among the inter-continental isolates (Asian and American) of serotypes 1, 2 and 3 compared to serotype 4 isolates (South and Central America) and are distributed in a non-random manner among the genes encoded by the virus. Nearly one third of the negatively selected sites are associated with fixed mutation sites within serotypes. Our results further show that of all the sites showing evidence of recombination, the majority (~84%) correspond to sites under purifying selection in the four serotypes. The analysis further shows that genetic recombination occurs within specific codons, albeit with low frequency (< 5% of all recombination sites) throughout the DENV genome of the four serotypes and reveals significant enrichment (p < 0.05) among sites under purifying selection in the virus.
The study provides the first evidence for intracodon recombination in DENV and suggests that within codons, genetic recombination has a significant role in maintaining extensive purifying selection of DENV in natural populations. Our study also suggests that fixation of beneficial mutations may lead to virus evolution via translational selection of specific sites in the DENV genome.
登革病毒（DENV）感染是许多亚热带和热带国家的一个重大公共卫生问题。尽管登革病毒在基因上密切相关，但四个血清型在抗原性方面存在差异，因此血清型之间的交叉保护作用有限。人们还认为，多血清型感染以及病毒抗原性的演变可能会对登革热流行的增加产生混杂影响。已经进行了许多研究来调查 DENV 的遗传多样性，但登革病毒进化的确切机制尚不清楚。
我们调查了在亚洲和中美洲和南美洲不同国家采集的样本中四个血清型的全基因组遗传多样性和核苷酸取代模式，并作为 Broad 研究所传染病基因组测序中心的一部分进行了测序。我们应用生物信息学、统计和合并模拟方法来研究代表四个血清型的 DENV 样本的密码子序列多样性。我们表明，与血清型 4 分离株（南美洲和中美洲）相比，1、2 和 3 型的跨大陆分离株（亚洲和美洲）中核苷酸取代的固定更为突出，并且在病毒编码的基因中呈非随机分布。近三分之一的负选择位点与血清型内的固定突变位点相关。我们的结果进一步表明，在所有显示重组证据的位点中，大多数（~84%）对应于四个血清型中纯化选择的位点。分析还表明，遗传重组发生在特定的密码子内，尽管在四个血清型的 DENV 基因组中重组频率较低（<所有重组位点的 5%），并且在病毒中纯化选择的位点中存在显著富集（p<0.05）。
该研究首次提供了 DENV 中内含子重组的证据，并表明在密码子内，遗传重组在维持 DENV 在自然种群中的广泛纯化选择中起着重要作用。我们的研究还表明，有益突变的固定可能通过 DENV 基因组中特定位点的翻译选择导致病毒进化。
