Pirahy virus: Identification of a new and potential emerging arbovirus in South Brazil

Abstract

Genomic and epidemiological surveillance are paramount for the discovery of new viruses with the potential to cross species barriers. Here, we present a new member of the genus Alphavirus found in Trichoprosopon and Wyeomia mosquitoes, tentatively named Pirahy virus (PIRAV). PIRAV was isolated from mosquitoe pools collected in a rural area of Piraí do Sul, South Brazil. In vitro assays revealed that PIRAV replicates and causes cytopathic effects in vertebrate cell lines such as Vero E6, SH-SY5Y, BHK-21 and UMNSAH/DF-1. Genomic signature analysis supports these results showing a dinucleotide and codon usage balance compatible with several hosts. Phylogenetic analyses placed PIRAV basal to the Venezuelan equine encephalitis complex. Genome analyses, electron microscopy, and biological characterization show findings that may alert for the emergence of a new arbovirus in South America.

Arbovirus surveillance in mosquitoes: Historical methods, emerging technologies, and challenges ahead

“…67 New arboviruses have been characterized and evaluated for vertebrate infectivity using cell culture inoculation. 74 Molecular techniques: PCR is a molecular technique that allows for the amplification and detection of viral nucleic acid in a sample. This technique has revolutionized viral detection and diagnosis because it is highly sensitive and can detect a single positive mosquito in a pool of hundreds or thousands.…”

“…67 New arboviruses have been characterized and evaluated for vertebrate infectivity using cell culture inoculation. 74…”

Analyzing the Evolution and Host Adaptation of the Rabies Virus from the Perspective of Codon Usage Bias

“…The codon adaption index (CAI) is supposed to investigate the codon usage bias of viral genome or gene across different species, with a range from 0 to 1. Theoretically, a high-CAI value means that the codon usage pattern of a virus is adapted to that of its host [50,51]. The relative codon deoptimization index (RCDI) is used to compare the similarity of codon usage between virus and host.…”

Predicting novel mosquito-associated viruses from metatranscriptomic dark matter

“…Classifying mosquito-associated viruses as arboviruses or MSVs relies on viral isolation and subsequent inoculation experiments in vertebrate and mosquito cell lines ( 20 ). In silico classification depends on taxonomy analysis and phylogenetic inference to assess the evolutionary distance between a novel virus and a well-described antigenic complex ( 21 ). Since exogenous viruses should carry a protein to replicate their genome, most phylogenetic analyses of newly discovered mosquito-associated viruses focus on the RNA-dependent RNA polymerase (RdRp) protein domain ( 17 , 22 ).…”

“…These signatures may uncover the genomic compositional signals shaped by natural selection, resulting in adaptation of mosquito-associated viruses with diverse genomic and taxonomic structures to a common host range ( 26 ). Previous studies have described genome-level mutations between dual-host and single-host viruses, especially variations in the relative frequencies of dinucleotide composition and codon adaptation index, which is a measure associated with codon usage bias ( 21 , 26 , 27 ). However, employing these features for classifying mosquito-associated viruses faces substantial challenges, as they are primarily documented for Flaviviridae and might not apply universally across novel viruses from distant families.…”