Chabi-Jesus Camila, Ramos-González Pedro L, Postclam-Barro Matheus, Fontenele Rafaela Salgado, Harakava Ricardo, Bassanezi Renato B, Moreira Alecio S, Kitajima Elliot W, Varsani Arvind, Freitas-Astúa Juliana
Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, São Paulo, Brazil.
Instituto Biológico/IB, São Paulo, Brazil.
Front Microbiol. 2021 Apr 29;12:641252. doi: 10.3389/fmicb.2021.641252. eCollection 2021.
Despite the importance of viral strains/variants as agents of emerging diseases, genetic and evolutionary processes affecting their ecology are not fully understood. To get insight into this topic, we assessed the population and spatial dynamic parameters of citrus leprosis virus C (CiLV-C, genus , family ). CiLV-C is the etiological agent of citrus leprosis disease, a non-systemic infection considered the main viral disorder affecting citrus orchards in Brazil. Overall, we obtained 18 complete or near-complete viral genomes, 123 complete nucleotide sequences of the open reading frame (ORF) encoding the putative coat protein, and 204 partial nucleotide sequences of the ORF encoding the movement protein, from 430 infected spp. samples collected between 1932 and 2020. A thorough examination of the collected dataset suggested that the CiLV-C population consists of the major lineages CRD and SJP, unevenly distributed, plus a third one called ASU identified in this work, which is represented by a single isolate found in an herbarium sample collected in Asuncion, Paraguay, in 1937. Viruses from the three lineages share about 85% nucleotide sequence identity and show signs of inter-clade recombination events. Members of the lineage CRD were identified both in commercial and non-commercial citrus orchards. However, those of the lineages SJP were exclusively detected in samples collected in the citrus belt of São Paulo and Minas Gerais, the leading Brazilian citrus production region, after 2015. The most recent common ancestor of viruses of the three lineages dates back to, at least, ∼1500 years ago. Since citrus plants were introduced in the Americas by the Portuguese around the 1520s, the Bayesian phylodynamic analysis suggested that the ancestors of the main CiLV-C lineages likely originated in contact with native vegetation of South America. The intensive expansion of CRD and SJP lineages in Brazil started probably linked to the beginning of the local citrus industry. The high prevalence of CiLV-C in the citrus belt of Brazil likely ensues from the intensive connectivity between orchards, which represents a potential risk toward pathogen saturation across the region.
尽管病毒株/变体作为新兴疾病的病原体很重要，但影响其生态的遗传和进化过程尚未完全明了。为深入了解这一主题，我们评估了柑橘麻风病毒C（CiLV - C，属，科）的种群和空间动态参数。CiLV - C是柑橘麻风病的病原体，这是一种非系统性感染，被认为是影响巴西柑橘园的主要病毒病害。总体而言，我们从1932年至2020年间收集的430份受感染的 spp. 样本中，获得了18个完整或近乎完整的病毒基因组、123个编码假定外壳蛋白的开放阅读框（ORF）的完整核苷酸序列，以及204个编码运动蛋白的ORF的部分核苷酸序列。对收集到的数据集进行全面检查表明，CiLV - C种群由分布不均的主要谱系CRD和SJP组成，外加本研究中鉴定出的第三个谱系ASU，它由1937年在巴拉圭亚松森采集的一份标本样本中发现的单个分离株代表。来自这三个谱系的病毒共享约85%的核苷酸序列同一性，并显示出跨分支重组事件的迹象。CRD谱系的成员在商业和非商业柑橘园中均有发现。然而，SJP谱系的成员仅在2015年后于巴西主要柑橘产区圣保罗和米纳斯吉拉斯的柑橘带采集的样本中被检测到。这三个谱系病毒的最近共同祖先至少可追溯到约1500年前。由于柑橘植物于16世纪20年代左右由葡萄牙人引入美洲，贝叶斯系统发育动力学分析表明，主要CiLV - C谱系的祖先可能起源于与南美洲本土植被的接触。CRD和SJP谱系在巴西的密集扩张可能始于当地柑橘产业的开端。CiLV - C在巴西柑橘带的高流行率可能源于果园之间的密集连通性，这对该地区病原体饱和构成潜在风险。
