Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fiocruz, 21040-360 Rio de Janeiro, Brazil.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, 4041 Durban, South Africa.
Viruses. 2021 Feb 23;13(2):349. doi: 10.3390/v13020349.
Intrahost genetic diversity is thought to facilitate arbovirus adaptation to changing environments and hosts, and it might also be linked to viral pathogenesis. Dengue virus serotype 2 (DENV-2) has circulated in Brazil since 1990 and is associated with severe disease and explosive outbreaks. Intending to shed light on the viral determinants for severe dengue pathogenesis, we sought to analyze the DENV-2 intrahost genetic diversity in 68 patient cases clinically classified as dengue fever ( = 31), dengue with warning signs ( = 19), and severe dengue ( = 18). Unlike previous DENV intrahost diversity studies whose approaches employed PCR, here we performed viral whole-genome deep sequencing from clinical samples with an amplicon-free approach, representing the real intrahost diversity scenario. Striking differences were detected in the viral population structure between the three clinical categories, which appear to be driven mainly by different infection times and selection pressures, rather than being linked with the clinical outcome itself. Diversity in the NS2B gene, however, showed to be constrained, irrespective of clinical outcome and infection time. Finally, 385 non-synonymous intrahost single-nucleotide variants located along the viral polyprotein, plus variants located in the untranslated regions, were consistently identified among the samples. Of them, 124 were exclusively or highly detected among cases with warning signs and among severe cases. However, there was no variant that by itself appeared to characterize the cases of greater severity, either due to its low intrahost frequency or the conservative effect on amino acid substitution. Although further studies are necessary to determine their real effect on viral proteins, this heightens the possibility of epistatic interactions. The present analysis represents an initial effort to correlate DENV-2 genetic diversity to its pathogenic potential and thus contribute to understanding the virus's dynamics within its human host.
宿主内遗传多样性被认为有助于虫媒病毒适应不断变化的环境和宿主，也可能与病毒发病机制有关。登革热病毒血清型 2（DENV-2）自 1990 年以来一直在巴西传播，与严重疾病和爆发性疫情有关。为了阐明严重登革热发病机制的病毒决定因素，我们试图分析 68 例临床分类为登革热（=31 例）、有警告症状的登革热（=19 例）和重症登革热（=18 例）患者的 DENV-2 宿主内遗传多样性。与以前采用 PCR 方法的 DENV 宿主内多样性研究不同，我们采用无扩增子的方法，对临床样本进行病毒全基因组深度测序，代表真实的宿主内多样性情况。在三个临床类别之间，病毒群体结构存在明显差异，这些差异似乎主要由不同的感染时间和选择压力驱动，而不是与临床结果本身有关。然而，NS2B 基因的多样性无论临床结果和感染时间如何都受到限制。最后，在病毒多蛋白沿线和非翻译区发现了 385 个非同义宿主内单核苷酸变异，这些变异在样本中始终存在。其中，有 124 个变异仅在有警告症状的病例和严重病例中被高度检测到。然而，没有一个变异本身能够描述更严重的病例，这要么是因为其在宿主内的频率较低，要么是因为对氨基酸取代的保守效应。尽管还需要进一步研究来确定它们对病毒蛋白的实际影响，但这增加了它们在病毒蛋白中存在上位性相互作用的可能性。本分析代表了将 DENV-2 遗传多样性与其致病潜力相关联的初步努力，从而有助于理解病毒在其人类宿主中的动态。
