Phylogenetic and evolutionary analysis of HoBi‐like pestivirus: Insights into origin and dispersal

Abstract

The HoBi‐like pestivirus (HoBiPeV), currently classified as Pestivirus H species, is a pathogen associated with a broad spectrum of clinical manifestations in ruminants, particularly in cattle. Since HoBiPeV complete genome sequencing data is scarce, in the present study we described five nearly complete new Brazilian HoBiPeV genomes and further perform a more complete genetic and evolutionary characterization with all additional genome sequences available in the GenBank database. Entropy and selection pressure analysis showed the E2 gene, a surface glycoprotein, is the most variable gene, which also displays the greatest number of sites under positive selection. Phylogenetic and Bayesian inference based on complete genome and Npro gene, respectively, from all HoBiPeV sequences available so far, confirms the existence of three main clades (a, b, and c). The abovementioned analysis suggests that this pestivirus species probably emerged in Asia and spread to different regions including Brazil, where only strains belonging to specific genetic group ‘a’ have been found. The hypothesis of the HoBiPeV introduction in Brazil (between 1,890 and 1,962), formulated based on Bayesian inference, coincides with a period of intensive importation of water buffalo (Bubalus arnee) and indicine cattle (Bos taurus indicus) from Asia to Brazil, suggesting that this could be the origin of the current Brazilian HoBiPeV genetic group ‘a’.

Discovery of Flaviviridae-derived endogenous viral elements in shrew genomes provide novel insights into Pestivirus ancient history

“…There are only a handful of molecular dating estimates for pestiviruses and they mostly focus on viral species or clades that are associated with economic losses. Diversification of bovine viral diarrhea virus 1 (Pestivirus A) subtypes was estimated to have started about 363 years ago (Weber et al, 2021), and the divergence of HoBi-like pestivirus (Pestivirus H) was dated back to the 16 th century (Silveira et al, 2020). Our results provide the first robust ancient time node for pestiviruses based on the estimated EVEs integration date and suggest that pestiviruses were already circulating in mammals more than 10.8 million years ago.…”

Molecular characterization of recent HoBi‐like pestivirus isolates from cattle showing mucosal disease‐like signs in India reveals emergence of a novel genetic lineage

“…Although several regions of pestivirus genome have been used, phylogenetic analyses based on the entire N pro gene sequences or the combined datasets of 5′‐UTR and N pro sequences have been found useful in ascertaining the genotypes or clades within a pestivirus species as they provide increased statistical support (Becher et al., 1997; Liu et al., 2010; Liu, Xia, et al., 2009; Mishra et al., 2014; Silveira et al., 2020). Based on the 5′‐UTR sequences, four lineages or clades (a–d) of HoBiPeV have been reported, while based on complete N pro sequences, three clades (a, c and d) of HoBiPeV have been found thus far (Giammarioli et al., 2015; Mishra et al., 2014; Silveira et al., 2020).…”

“…Although several regions of pestivirus genome have been used, phylogenetic analyses based on the entire N pro gene sequences or the combined datasets of 5′‐UTR and N pro sequences have been found useful in ascertaining the genotypes or clades within a pestivirus species as they provide increased statistical support (Becher et al., 1997; Liu et al., 2010; Liu, Xia, et al., 2009; Mishra et al., 2014; Silveira et al., 2020). Based on the 5′‐UTR sequences, four lineages or clades (a–d) of HoBiPeV have been reported, while based on complete N pro sequences, three clades (a, c and d) of HoBiPeV have been found thus far (Giammarioli et al., 2015; Mishra et al., 2014; Silveira et al., 2020). Comparison of previously reported HoBiPeV sequences and the HoBiPeV sequences generated in this study revealed emergence of another novel lineage (proposed as HoBiPeV‐e) in India indicating that the currently circulating HoBiPeV strains around the world can be divided into five HoBiPeV lineages (a–e), based on 5′‐UTR sequences and into four lineages (a, c, d and e), on the basis of complete N pro sequences or combined 5′‐UTR‐N pro sequences.…”

“…On the contrary, when genetically highly divergent HoBiPeV strains of three distinct lineages were reported in cattle from Indian subcontinent (India and Bangladesh), it was hypothesized that HoBiPeV originated and evolved independently in Indian subcontinent and elsewhere (Giammarioli et al., 2015; Mishra et al., 2014). However, a recent study using Bayesian analysis of complete N pro gene of available HoBiPeV sequences has suggested that HoBiPeV probably emerged in Asia and spread to other continents and inferred that HoBiPeV‐d and c lineages diverged and evolved independently most likely in the 16th and 18th century, while the HoBiPeV‐a lineage diverged around the year 1856 (Silveira et al., 2020). Our phylogenetic analyses of all available HoBiPeV N pro sequences including the strains of new lineage HoBiPeV‐e showing Indian strains rooting the phylogenetic tree (ancestor) in this study support the theory of probable Indian origin of HoBiPeV (Silveira et al., 2020).…”

“…A moderate level of genetic diversity exists within HoBiPeV, and on the basis of phylogenetic analyses, HoBiPeV strains have been classified into four genetic lineages or clades (HoBiPeV‐a to HoBiPeV‐d) thus far (Giammarioli et al., 2015; Liu et al., 2009; Mishra et al., 2014; Silveira et al., 2020). The strains of HoBiPeV‐a clade are widely distributed and have been detected in infected cattle in Brazil, Italy, Turkey, Thailand and China or in contaminated FBS, either labelled as Brazilian origin or of unknown origin (Decaro et al., 2011; Kampa et al., 2009; Shi et al., 2020; Stahl et al., 2007; Xia et al., 2011).…”