Genomic Analysis of the Vaccinia Virus Strain Variants Found in Dryvax Vaccine

Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, 6020 Katz Group Centre, Edmonton, AB T6G 2H7, Canada.
Journal of Virology (Impact Factor: 4.44). 12/2011; 85(24):13049-60. DOI: 10.1128/JVI.05779-11
Source: PubMed


Smallpox was eradicated using variant forms of vaccinia virus-based vaccines. One of these was Dryvax, a calf lymph vaccine derived from the New York City Board of Health strain. We used genome-sequencing technology to examine the genetic diversity of the population of viruses present in a sample of Dryvax. These studies show that the conserved cores of these viruses exhibit a lower level of sequence variation than do the telomeres. However, even though the ends of orthopoxviruses are more genetically plastic than the cores, there are still many telomeric genes that are conserved as intact open reading frames in the 11 genomes that we, and 4 genomes that others, have sequenced. Most of these genes likely modulate inflammation. Our sequencing also detected an evolving pattern of mutation, with some genes being highly fragmented by randomly assorting mutations (e.g., M1L), while other genes are intact in most viruses but have been disrupted in individual strains (e.g., I4L in strain DPP17). Over 85% of insertion and deletion mutations are associated with repeats, and a rare new isolate bearing a large deletion in the right telomere was identified. All of these strains cluster in dendrograms consistent with their origin but which also surprisingly incorporate horsepox virus. However, these viruses also exhibit a "patchy" pattern of polymorphic sites characteristic of recombinants. There is more genetic diversity detected within a vial of Dryvax than between variola virus major and minor strains, and our study highlights how propagation methods affect the genetics of orthopoxvirus populations.

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    • "YMTV, tanapox virus (TPV; [15], [33]) and yaba-like disease virus (YLDV; [16], [17], [34]) are poxviruses, which have limited host range and infect primates, including humans; YMTV produces a large localized tumor-like lesion, where as YLDV infections have been reported to resemble a mild form of smallpox. The fact that 3 of 23 MYXV genomes have truncated versions of the O1L ortholog is intriguing because 2 of these viruses are also described as very attenuated in wild rabbit populations [18]–[20], [31]. Of the 3 genes annotated in CRV (062, 063, 064), CRV-062 is the most likely to be a functional O1L ortholog. "
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    ABSTRACT: Variola virus, the agent of smallpox, has a severely restricted host range (humans) but a devastatingly high mortality rate. Although smallpox has been eradicated by a World Health Organization vaccination program, knowledge of the evolutionary processes by which human super-pathogens such as variola virus arise is important. By analyzing the evolution of variola and other closely related poxviruses at the level of single nucleotide polymorphisms we detected a hotspot of genome variation within the smallpox ortholog of the vaccinia virus O1L gene, which is known to be necessary for efficient replication of vaccinia virus in human cells. These mutations in the variola virus ortholog and the subsequent loss of the functional gene from camelpox virus and taterapox virus, the two closest relatives of variola virus, strongly suggest that changes within this region of the genome may have played a key role in the switch to humans as a host for the ancestral virus and the subsequent host-range restriction that must have occurred to create the phenotype exhibited by smallpox.
    Full-text · Article · Mar 2014 · PLoS ONE
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    • ", we refer to the original TianTan virus sequence (AF095689) as " TT00 " throughout this communication. Genome assemblies were prepared using CLC Genomics Workbench (v4.6) and annotated using GATU (Tcherepanov et al., 2006), also as described previously (Qin et al., 2011). Bioinformatic analyses were performed using Viral Genome Organizer (Lefkowitz et al., 2005; Upton et al., 2000) and Poxvirus Orthologous Clusters (Ehlers et al., 2002). "
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    ABSTRACT: Vaccinia virus (VACV) strain TianTan was used for much of China's modern history to vaccinate against smallpox, however the only genome sequence contains errors. We have sequenced additional examples of TianTan to obtain a better picture of this important virus. We detected two different subclones. One (TP03) encodes large deletions in the terminal repeats that extend into both VEGF genes and create a small plaque variant. The second clone (TP05) encodes a nearly intact complement of genes in the terminal repeats, except for an insertion of sequences resembling the telomeric 69bp repeats. The TP05 genome spans 196,260bp and encodes 219 genes. The revised sequence documents the integrity of all the genes in the conserved virus core. Phylogenetic methods show that TianTan belongs to a unique clade of VACV, but probably also share a common origin with strains belonging to the Copenhagen/Lister lineage and distinct from the Wyeth/Dryvax lineage.
    Full-text · Article · Apr 2013 · Virology
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    • "TT clones were isolated from TT (752-1) by plaque-purifications at terminal dilutions. Seven viral plaques were isolated and amplified by sequential four rounds of passages to produce enough material for sequencing [13]. Plaque images (Fig. S1) were processed with ImageJ (National Institutes of Health) [22]. "
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    ABSTRACT: Despite the worldwide eradication of smallpox in 1979, the potential bioterrorism threat from variola virus and the ongoing use of vaccinia virus (VACV) as a vector for vaccine development argue for continued research on VACV. In China, the VACV Tiantan strain (TT) was used in the smallpox eradication campaign. Its progeny strain is currently being used to develop a human immunodeficiency virus (HIV) vaccine. Here we sequenced the full genomes of five TT clones isolated by plaque purification from the TT (752-1) viral stock. Phylogenetic analysis with other commonly used VACV strains showed that TT (752-1) and its clones clustered and exhibited higher sequence diversity than that found in Dryvax clones. The ∼190 kbp genomes of TT appeared to encode 273 open reading frames (ORFs). ORFs located in the middle of the genome were more conserved than those located at the two termini, where many virulence and immunomodulation associated genes reside. Several patterns of nucleotide changes including point mutations, insertions and deletions were identified. The polymorphisms in seven virulence-associated proteins and six immunomodulation-related proteins were analyzed. We also investigated the neuro- and skin- virulence of TT clones in mice and rabbits, respectively. The TT clones exhibited significantly less virulence than the New York City Board of Health (NYCBH) strain, as evidenced by less extensive weight loss and morbidity in mice as well as produced smaller skin lesions and lower incidence of putrescence in rabbits. The complete genome sequences, ORF annotations, and phenotypic diversity yielded from this study aid our understanding of the Chinese historic TT strain and are useful for HIV vaccine projects employing TT as a vector.
    Full-text · Article · Apr 2013 · PLoS ONE
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