Aedes aegypti from Amazon Basin Harbor High Diversity of Novel Viral Species

Abstract

Viruses are the most diverse and abundant microorganisms on earth, highly adaptive to a wide range of hosts. Viral diversity within invertebrate hosts has gained notoriety in recent years in public health as several such viruses have been of medical importance. Aedes aegypti serves as a vector for several viruses that have caused epidemics within the last year throughout Brazil; including Dengue, Zika and Chikungunya. This study aimed to identify new viral agents within Aedes aegypti mosquito in a city of the Amazonian region, where it is highly endemic. Metagenomic investigation was performed on 60 mosquito pools and viral RNA sequences present in their microbiota were characterized using genomic and phylogenetic tools. In total, we identified five putative novel virus species related to the Sobemovirus genus, Iflavirus genus and Permutatetraviridae family. These findings indicate a diverse taxonomy of viruses present in the mosquito microbiota of the Amazon, the region with the greatest invertebrate diversity in the world.

Keywords: Aedes aegypti; Amazon; NGS; insect-virus; microbiota; mosquito; viral diversity.

Figure 1

Luteo-sobemo-related viruses genomes map and phylogeny. (a) Open read-frame organization of closest related virus to Aedes sobemo-like virus and Guadeloupe mosquito virus. (b) Nucleotide maximum likelihood tree based on segment 1 for Sobemo-like viruses and Luteovirus and Sobemovirus genus. Aedes sobemo-like virus and Guadeloupe mosquito virus sequenced in this study are highlighted in orange and green, respectively. The diagram in the base of the tree is the likelihood map of the nucleotide alignment of genomes of Luteo-sobemo-related viruses. The likelihood quartet mapping is a method that allows to visualize the tree-likeness of all quartets in a single graph and provide a direct measure of the phylogenetic signal in an alignment. The triangle shows the location of all quartets calculated with the alignment used to infer the ML tree. Values in the center of the triangle represent the percentage of unresolved quartet trees (star-like trees), values in the vertices represent the percentage of fully resolved trees and values in the intermediate areas (between vertices) are the percentage of conflicting trees. The analysis was performed using GTR+ gamma correction model as is implemented in the tree puzzle software v 5.3 (http://www.tree-puzzle.de).

Figure 2

Iflavi-related contigs position in Yongsan picorna-like virus genome. (a) Contigs position of Aedes Iflavi-like virus and structure-based alignment with relative closest virus, Yongsan picorna-like virus. (b) Maximum likelihood tree (ML) for RdRp protein of Aedes Iflavi-like virus (orange) with Iflavirus genus (indicated in a blue area) and Iflavi-like sequences related to Aedes Iflavi-like virus by Blastp search. Sequences from the current study are colored in red. The diagram in the base of the tree is the likelihood map of the nucleotide alignment of genomes of Iflavi-related viruses. The likelihood quartet mapping is a method that allows to visualize the tree-likeness of all quartets in a single graph and provide a direct measure of the phylogenetic signal in an alignment. The triangle shows the location of all quartets calculated with the alignment used to infer the ML tree. Values in the center of the triangle represent the percentage of unresolved quartet trees (star-like trees), values in the vertices represent the percentage of fully resolved trees and values in the intermediate areas (between vertices) are the percentage of conflicting trees. The analysis was performed using JTT model as is implemented in the tree puzzle software v 5.3 (http://www.tree-puzzle.de).

Figure 3

Permutotetra-related contigs position in most related viruses genomes. (a) Schematic representation of Culex Daeseongdong-like virus, Aedes permutetra-like virus 1, (b) Sarawak virus and Aedes permutetra-like virus 2. (c) Maximum likelihood phylogenetic tree for RdRp protein and (d) maximum likelihood phylogenetic tree for capsid protein. Viruses originally found in mosquitoes are marked by orange. Sequences from this study are indicated in red. * Indicate the location in the RdRp tree of the reference viruses used to construct the capsid tree. The diagram in the base of the tree is the likelihood map. The likelihood quartet mapping is a method that allows to visualize the tree-likeness of all quartets in a single graph and provide a direct measure of the phylogenetic signal in an alignment. The triangle shows the location of all quartets calculated with the alignment used to infer the ML tree. Values in the center of the triangle represent the percentage of unresolved quartet trees (star-like trees), values in the vertices represent the percentage of fully resolved trees and values in the intermediate areas (between vertices) are the percentage of conflicting trees. The analysis was performed using JTT+gamma correction model as is implemented in the tree puzzle software v 5.3 (http://www.tree-puzzle.de).