Evolution of and Evolutionary Relationships between Extant Vaccinia Virus Strains

Abstract

Although vaccinia virus (VACV) was once used as a vaccine to eradicate smallpox on a worldwide scale, the biological origins of VACV are uncertain, as are the historical relationships between the different strains once used as smallpox vaccines. Here, we sequenced additional VACV strains that either represent relatively pristine examples of old vaccines (e.g., Dryvax, Lister, and Tashkent) or have been subjected to additional laboratory passage (e.g., IHD-W and WR). These genome sequences were compared with those previously reported for other VACVs as well as other orthopoxviruses. These extant VACVs do not always cluster in simple phylogenetic trees that are aligned with the known historical relationships between these strains. Rather, the pattern of deletions suggests that all existing strains likely come from a complex stock of viruses that has been passaged, distributed, and randomly sampled over time, thus obscuring simple historical or geographic links. We examined surviving nonclonal vaccine stocks, like Dryvax, which continue to harbor larger and now rare variants, including one that we have designated "clone DPP25." DPP25 encodes genes not found in most VACV strains, including an ankyrin-F-box protein, a homolog of the variola virus (Bangladesh) B18R gene which we show can be deleted without affecting virulence in mice. We propose a simple common mechanism by which recombination of a larger and hypothetical DPP25-like ancestral strain, combined with selection for retention of critically important genes near the terminal inverted repeat boundaries (vaccinia virus growth factor gene and an interferon alpha/beta receptor homolog), could produce all known VACV variants. IMPORTANCE Smallpox was eradicated by using a combination of intensive disease surveillance and vaccination using vaccinia virus (VACV).Interestingly, little is known about the historical relationships between different strains of VACV and how these viruses may have evolved from a common ancestral strain. To understand these relationships, additional strains were sequenced and compared to existing strains of VACV as well as other orthopoxviruses by using whole-genome sequence alignments. Extant strains of VACV did not always cluster in simple phylogenetic trees based on known historical relationships between these strains. Based on these findings, it is possible that all existing strains of VACV are derived from a single complex stock of viruses that has been passaged, distributed, and sampled over time.

Genomic Analysis, Phenotype, and Virulence of the Historical Brazilian Smallpox Vaccine Strain IOC: Implications for the Origins and Evolutionary Relationships of Vaccinia Virus

“…Despite that, both CTGV and Serro 2 virus have smaller genomes than the IOC clones, indicating a greater loss of genetic information during their divergence and coevolution over time. On the other hand, and more importantly, IOC-B141, CTGV, and Serro 2 virus share the same junction site of the 3= ITR, which has been suggested to be a genetic feature of VACV lineages (13). Together, these phenotypic and genotypic features support the close phylogenetic relatedness of VACV-IOC and CTGV-like viruses.…”

“…ACAM2000 induces immune responses and protection similar to that of the parental strain and was selected in parallel to the neurovirulent clone 3 (CL-3), also isolated from the Dryvax vaccine (4,9). Work involving additional clonal selection further confirmed the genotypic diversity of Dryvax (11,13).…”

“…9B) with some exceptions, notably the 10.7-kb stretch of HSPV ORFs (HSPV007-HSPV015b), which in fact is absent from all known VACV strains (13,37). IOC clones and CTGV-like viruses have distinct deletion patterns in the 5= end not found in the genomes of other VACV strains included in the analysis, especially the Dryvax-derived viruses DPP17, Duke, ACAM2000, and CL-3.…”

“…9C). Interestingly, Qin et al (13) suggested that the junction site of the 3= ITR is a common genetic feature of VACV strains belonging to the same lineage. Accordingly, clone B141, CTGV, and Serro 2 virus have the same 3= ITR junction site located at the end of genes IOC_235, CTGV_205, and Serro2_201 (VACV-Cop B20R), respectively (Fig.…”

“…Nevertheless, recent reports have shown that the structural analysis of the variable genome ends of VACV also can provide relevant information about virus relationships (10,13). Therefore, we aligned ϳ20 kb of the 5= (Fig.…”