2014年在日本流行的本土1型登革热病毒株的分类

4open Pub Date : 2019-01-01 DOI:10.1051/FOPEN/2019018
M. Cordeiro, J. E. García, V. González-López, Sergio L. M. londono
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引用次数: 2

摘要

在本文中,我们通过代表性对与2014年日本爆发相对应的登革热病毒1型(DENV-1)的一组完整基因组序列的元素进行了分类。这套套装来自千叶、兵库县、静冈县和东京四个地区。我们认为这个集合是由来自有限阶和有限字母的马尔可夫过程的独立样本组成的。在假定存在至少在该集合的50%的样本中普遍存在的定律的情况下,我们确定了受主导定律支配的序列(见[1,2])。分类规则基于样本间的局部度量,当我们比较具有相同规律的序列时,该度量趋向于零,当我们比较具有不同规律的序列时,该度量趋向于无穷大。我们发现,代表性的顺序,从高到低,按照序列的起源是:东京,千叶,兵库县和静冈县。当将日本的序列与亚洲的同期序列进行比较时,我们发现代表性较差的序列(来自静冈县)位于与日本其他地区的序列相当远的群体中,这为假设日本的疫情可能由多种DENV-1型引起提供了证据。
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Classification of autochthonous dengue virus type 1 strains circulating in Japan in 2014
In this paper, we classify by representativeness the elements of a set of complete genomic sequences of Dengue Virus Type 1 (DENV-1), corresponding to the outbreak in Japan during 2014. The set is coming from four regions: Chiba, Hyogo, Shizuoka and Tokyo. We consider this set as composed of independent samples coming from Markovian processes of finite order and finite alphabet. Under the assumption of the existence of a law that prevails in at least 50% of the samples of the set, we identify the sequences governed by the predominant law (see [1, 2]). The rule of classification is based on a local metric between samples, which tends to zero when we compare sequences of identical law and tends to infinity when comparing sequences with different laws. We found that the order of representativeness, from highest to lowest and according to the origin of the sequences is: Tokyo, Chiba, Hyogo, and Shizuoka. When comparing the Japanese sequences with their contemporaries from Asia, we find that the less representative sequence (from Shizuoka) is positioned in groups considerably far away from that which includes the sequences from the other regions in Japan, this offers evidence to suppose that the outbreak in Japan could be produced by more than one type of DENV-1.
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