Surveillance and Genomic Evolution of Infectious Precocity Virus (IPV) from 2011 to 2024

Abstract

Infectious precocity virus (IPV) poses a significant economic threat to the aquaculture industry by causing sexual precocity and slow growth in Macrobrachium rosenbergii. In this study, we conducted an in-depth investigation into the genetic evolution of IPV from 2011 to 2024 by collecting 31 IPV variants through epidemiological surveys and public databases, including 29 variants with complete genomic sequences. The phylogenetic analysis revealed that these complete genomic sequences clustered into two distinct phylogenetic clades as follows: the Southeast Asian clade and the Chinese clade. Nucleotide and protein variation analyses demonstrated a high degree of similarity, with nucleotide identity ranging from 98.5% to 100% and protein identity from 99.4% to 100%. Further analysis of protein variations within the putative coding region identified two distinct variation patterns. The average dN/dS ratio of 0.12 highlights the strong purifying selection acting on IPV, particularly on structural proteins. In conclusion, this study significantly expands the genomic database of IPV and provides valuable insights into its genetic evolution. These findings offer critical scientific evidence to enhance detection protocols and support sustainable M. rosenbergii aquaculture practices.

Keywords: Flaviviridae; IPV; Macrobrachium rosenbergii; phylogenetic analysis.

Figure 1

Phylogenetic analyses of 29 infectious precocity virus (IPV) variants. The analysis was conducted using the complete sequences of the 29 variants with IQ-TREE2 v2.3.5, which determined TN+F+I as the best-fit model. The scale bar indicates the number of nucleotide substitutions per site. Only bootstrap support values greater than 70% are displayed. The red font highlights the two variants from Southeast Asia, and the red triangles represent the four IPV variants currently available in NCBI with GenBank accessions MT084113.1, ON382579.1, MT648663.1, and MT648664.1.

Figure 2

Overview of genetic variance of the 29 IPV variants. (A) Nucleotide similarity among the 29 variants, with the genomic structure and similarity measured relative to variant “MR2018” (12,630 nt). (B) Amino acid conservation among the 29 variants. The highlighted bars indicate the percentage of variants sharing the same amino acid at each position with variant “MR2018”. The bars represent 100% similarity and are downplayed for clarity. Colored boxes denote protein domains.

Figure 3

Phylogenetic tree of the 29 IPV variants based on 48 polymorphic sites. The left side shows a phylogenetic tree based on 48 polymorphic sites, while the right side presents the corresponding amino acid polymorphism information. The MR2018 sequence is used as the reference, with identical amino acids represented by “.”, and polymorphic sites highlighted with colored backgrounds. Variant names are labeled on the left side of the phylogenetic tree and the polymorphism chart, while amino acid positions are indicated below the polymorphism chart.

Figure 4

Selection pressure in the 29 IPV variants. Maximum likelihood estimates of synonymous (α) and non-synonymous rates (β) at each site. Estimates above 10 are censored at this value. p-values are also shown. Kernel density estimates of site-level rate estimates. The means are expressed by red rules.