A Wide Extent of Inter-Strain Diversity in Virulent and Vaccine Strains of Alphaherpesviruses

Abstract

Alphaherpesviruses are widespread in the human population, and include herpes simplex virus 1 (HSV-1) and 2, and varicella zoster virus (VZV). These viral pathogens cause epithelial lesions, and then infect the nervous system to cause lifelong latency, reactivation, and spread. A related veterinary herpesvirus, pseudorabies (PRV), causes similar disease in livestock that result in significant economic losses. Vaccines developed for VZV and PRV serve as useful models for the development of an HSV-1 vaccine. We present full genome sequence comparisons of the PRV vaccine strain Bartha, and two virulent PRV isolates, Kaplan and Becker. These genome sequences were determined by high-throughput sequencing and assembly, and present new insights into the attenuation of a mammalian alphaherpesvirus vaccine strain. We find many previously unknown coding differences between PRV Bartha and the virulent strains, including changes to the fusion proteins gH and gB, and over forty other viral proteins. Inter-strain variation in PRV protein sequences is much closer to levels previously observed for HSV-1 than for the highly stable VZV proteome. Almost 20% of the PRV genome contains tandem short sequence repeats (SSRs), a class of nucleic acids motifs whose length-variation has been associated with changes in DNA binding site efficiency, transcriptional regulation, and protein interactions. We find SSRs throughout the herpesvirus family, and provide the first global characterization of SSRs in viruses, both within and between strains. We find SSR length variation between different isolates of PRV and HSV-1, which may provide a new mechanism for phenotypic variation between strains. Finally, we detected a small number of polymorphic bases within each plaque-purified PRV strain, and we characterize the effect of passage and plaque-purification on these polymorphisms. These data add to growing evidence that even plaque-purified stocks of stable DNA viruses exhibit limited sequence heterogeneity, which likely seeds future strain evolution.

Molecular cloning and characterization of the pseudorabies virus US1 gene

“…Thus, viral evolution can be discussed at the molecular level. Our analysis revealed that the nucleotide sequence similarity of US1 of PRV Becker to Kaplan and Bartha was 92 and 89% ( Figures 2A and 3A); the aa sequence similarities were up to 92 and 88%, respectively, consistent with a previous report (Szpara et al, 2011). Meanwhile, it may be that this evolutionary difference produces the variable virulence of distinct PRV strains.…”

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

“…High‐throughput genome sequencing has provided evidence of recombination between strains in other herpesviruses, namely HSV‐2, VZV, Marek's disease virus, HSV‐1, pseudorabies virus, human cytomegalovirus and infectious laryngotracheitis virus (Hughes & Rivailler, 2007; Kolb, Larsen, Cuellar, & Brandt, 2015; Lee et al., 2013; Norberg et al., 2011, 2015; Sijmons et al., 2015; Szpara et al., 2014; Szpara, Tafuri, et al., 2011; Zell et al., 2012). In the present study, network analysis suggested that recombination has also occurred between EHV‐1 strains.…”

Glycoproteins gE and gI Are Required for Efficient KIF1A-Dependent Anterograde Axonal Transport of Alphaherpesvirus Particles in Neurons

“…While Us9 is necessary for directly or indirectly interacting with KIF1A and recruiting the motor complex to transport vesicles, at least one additional viral protein that is missing or mutated in PRV Bartha is required for this interaction (6). The genome sequences of wild-type PRV Becker and Bartha have been completed (28). Compared to the 67 wild-type protein-coding regions, PRV Bartha has missense or silent mutations in at least 46 proteins as well as a deletion in the unique short region of the PRV genome that removes the coding sequences for gI (Us7), gE (Us8), Us9, and Us2.…”

“…KIF1A is necessary for anterograde axonal movement of viral particles, but at least one additional viral protein is required to facilitate or stabilize its interaction with Us9; this protein (or proteins) is not expressed by the attenuated PRV strain Bartha (6). The PRV Bartha genome contains multiple mutations compared to virulent PRV, including a deletion in the coding region for gI, gE, Us9, and Us2 (28). Since deletion of gE or gI severely reduces but does not completely disrupt the anterograde spread capacity of PRV in vitro (24), we hypothesized that these two proteins may be involved in the Us9-KIF1A interaction to promote virion transport.…”