Evidence for positive selection on the E2 gene of bovine viral diarrhoea virus type 1

Abstract

Despite the growing interest in the molecular epidemiology of pestivirus, there have been few attempts to determine which regions of the pestivirus genome are subject to positive selection, although this may be a key indicator of the nature of the interaction between host and virus. By using likelihood-based methods for phylogenetic inference, the positive selection pressure of BVDV-1 E2 gene were assessed and a site-by-site analysis of the dN/dS ratio was performed, to identify specific codons undergoing diversifying positive selection. The overall omega was 0.20, indicating that most sites were subject to strong purifying selection and five positively selected sites (886, 888, 905, 944, and 946) were identified. It is surprising to find that all the potential positively selected sites fall within the C-terminal of E2, and out of the N-terminal of E2 which is thought to be surface-exposed and therefore prime targets for host antibody response. In conclusion, these results suggest that selection favoring avoidance of antibody recognition has not been a major factor in the history of BVDV-1. Further analysis is necessary to see if amino acid substitutions in the BVDV-1 positively selected sites can lead to change of host tropism or\and escape from epitope-specific CD8 T-cell response.

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

“…Herein, the E2 was the most variable gene and bearer of most sites evolving under a diversifying (positive) selection, reinforcing previous studies results on HoBiPeV. The positive sites observed in this study lies mainly in DA followed by DC, which corroborates with previous analysis based on the E2 of the HoBiPeV (Weber et al, 2017), BVDV‐1 and BVDV‐2 (Chernick et al, 2018; Lang et al, 2014; Tang & Zhang, 2007), and are a consequence of the DA being the target of most neutralizing antibodies. Some non‐structural genes (NS5A, p7, N pro ) also showed high amino acid variability at some sites and need to be further characterized alongside the role of these proteins.…”

Microbial Community Structure–Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities

“…LRT p -values from all tests were corrected by controlling at a FDR of 5%. If an OG had a corrected q -value < 0.05 under any of the three models, this gene group was considered to be under putative positive selection (e.g., as in Tang and Zhang, 2007 ).…”

Bovine viral diarrhea virus: An updated American College of Veterinary Internal Medicine consensus statement with focus on virus biology, hosts, immunosuppression, and vaccination

“…The outcomes of this diversification process are currently unknown. Considering the region of positive selection in the genome of BVDV, it seems unlikely that the avoidance of antibodies is the driver of diversification 37 . Other options are that genetic diversification enables host‐tropism changes which could play a role in the avoidance of either the CD8 T‐cell responses or the innate immune system 37 …”