From transmission to adaptive evolution: genomic surveillance of Getah virus

Abstract

Getah virus (GETV) is a member of the Alphavirus of the Togaviridae. It is a single-stranded positive-RNA virus that is mainly transmitted by mosquitoes. In recent years, the spread of GETV has become increasingly serious, causing serious losses to the animal economy and posing a potential threat to public health. GETV infected animals extend from traditional domestic animals such as horses and pigs to cattle, foxes and other animals. Especially in China, the virus has been detected in many provinces in recent years. In addition, GETV-specific antibodies were detected in healthy humans. However, the threat posed by GETV in China has not received enough attention. In this study, we downloaded all available GETV genome-wide serials (82 serials in total) from the NCBI as of December 2023. We integrate multiple bioinformatics approaches to understand the characteristics of GETV from the perspectives of epidemiology, virus-host co-evolution, and viral adaptation analysis. The results of this study show that GETV is rapidly expanding its host range and geographical distribution at high evolutionary rates due to the lack of commercially available vaccines. Second, we clearly reveal the cross-species transmission of GETV. Finally, we identified important adaptive and active selection sites. GETV and its media are widely distributed in China, and new host infections continue to appear. Therefore, strengthening surveillance and prevention to avoid serious losses to the pandemic is an important task we face today.

Keywords: Getah virus; adaptive evolution; cross-species; epidemiological situation; host range.

Figure 1

Distribution of GETV. (A) Distribution of GETV in Asia. Different color blocks represent different countries. (B) Distribution of GETV in China. The left chart shows the distribution of two different genotypes of GETV across 15 provinces in China, with both Fujian and Yunnan provinces containing two genotypes of GETV. The right chart shows the number of sequences uploaded from the 15 provinces. The X-axis represents the number of virus sequences, and the Y-axis represents the name of the province in China.

Figure 2

Source and genotypes of GETV. (A) Sources of GETV(Asia). The horizontal axis represents the source countries, the vertical axis represents the number of sequences, and different countries are represented by different color blocks. The X-axis represents the country and the Y-axis represents the number of viral sequences (B) Genotypes of GETV. The horizontal axis represents the different genotypes of GETV, the vertical axis represents the number of sequences, and Group III is the dominant genotype of GETV. The X-axis represents the four different groupings of GETV, and the Y-axis represents the number of viral sequences.

Figure 3

Susceptible host types and distribution. (A) Susceptible host types of GETV at the family level (Asia). The X-axis represents the two family levels, and the Y-axis represents the number of viral sequences. (B) Distribution of GETV among susceptible hosts in China. Different colors on the map represent different genotypes. (BI) The color blocks on the map indicate the host classification, and the circles indicate the specific host species (BII) The X-axis represents the number of virus sequences, and the Y-axis represents the provinces of China. (BIII) The X-axis represents the provinces of China, and the Y-axis represents the number of virus sequences.

Figure 4

Complete genome phylogenetic analysis and entanglement relationship between GETV and hosts. (A) The squares represent the groupings, and the circles represent the country of origin. (B) A phylogenetic tree was constructed using 82 full-genome sequences of GETV, with the best model selection being GTR+G+I. Additionally, 10 different host mitochondrial DNA sequences were used for tree construction, with the best model selection being TPM2u+F+R3. Branches and associations are colored according to host types. Tree scale 1 represents the unit in which each unit length corresponds to 1 nucleotide or amino acid substitution; Tree Scale 10 represents the unit in which each unit length corresponds to 10 nucleotide or amino acid substitutions.

Figure 5

Vector transmission of GETV. The vector transmission of GETV occurs through three main modes: horizontal transmission between vertebrate hosts and vectors, vertical transmission from infected female mosquitoes to their offspring, and sexual transmission from infected female mosquitoes to male mosquitoes and vice versa.

Figure 6

Evolution of amino acid adaptive sites in GETV. Single nucleotide variants in each gene of GETV strains obtained from NCBI. Amino acid variation in polyproteins is distributed along the genome. The 82 GETV complete genome sequences downloaded from the NCBI database show only mutations that appear in more than 10 serial lines. NSP1–4 represents non-structural proteins, C, E3, E2, 6K, E1 represent structural proteins, and UTR represents untranslated regions.

Figure 7

Analysis of amino acid variations in GETV. Visualization analysis of the amino acid positive selection sites detected in Table 1 , with the horizontal axis representing the positions of amino acids.