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

Abstract

Smallpox was declared eradicated in 1980 after an intensive vaccination program using different strains of vaccinia virus (VACV; Poxviridae). VACV strain IOC (VACV-IOC) was the seed strain of the smallpox vaccine manufactured by the major vaccine producer in Brazil during the smallpox eradication program. However, little is known about the biological and immunological features as well as the phylogenetic relationships of this first-generation vaccine. In this work, we present a comprehensive characterization of two clones of VACV-IOC. Both clones had low virulence in infected mice and induced a protective immune response against a lethal infection comparable to the response of the licensed vaccine ACAM2000 and the parental strain VACV-IOC. Full-genome sequencing revealed the presence of several fragmented virulence genes that probably are nonfunctional, e.g., F1L, B13R, C10L, K3L, and C3L. Most notably, phylogenetic inference supported by the structural analysis of the genome ends provides evidence of a novel, independent cluster in VACV phylogeny formed by VACV-IOC, the Brazilian field strains Cantagalo (CTGV) and Serro 2 viruses, and horsepox virus, a VACV-like virus supposedly related to an ancestor of the VACV lineage. Our data strongly support the hypothesis that CTGV-like viruses represent feral VACV that evolved in parallel with VACV-IOC after splitting from a most recent common ancestor, probably an ancient smallpox vaccine strain related to horsepox virus. Our data, together with an interesting historical investigation, revisit the origins of VACV and propose new evolutionary relationships between ancient and extant VACV strains, mainly horsepox virus, VACV-IOC/CTGV-like viruses, and Dryvax strain. IMPORTANCEFirst-generation vaccines used to eradicate smallpox had rates of adverse effects that are not acceptable by current health care standards. Moreover, these vaccines are genetically heterogeneous and consist of a pool of quasispecies of VACV. Therefore, the search for new-generation smallpox vaccines that combine low pathogenicity, immune protection, and genetic homogeneity is extremely important. In addition, the phylogenetic relationships and origins of VACV strains are quite nebulous. We show the characterization of two clones of VACV-IOC, a unique smallpox vaccine strain that contributed to smallpox eradication in Brazil. The immunogenicity and reduced virulence make the IOC clones good options for alternative second-generation smallpox vaccines. More importantly, this study reveals the phylogenetic relationship between VACV-IOC, feral VACV established in nature, and the ancestor-like horsepox virus. Our data expand the discussion on the origins and evolutionary connections of VACV lineages. S mallpox, caused by variola virus (genus Orthopoxvirus, family Poxviridae), accounted for millions of deaths throughout human history. The disease was declared eradicated in 1980 after a worldwide program implemented by the WHO involving strict surveillance and intensive vaccination using vaccinia vi...

Serro 2 Virus Highlights the Fundamental Genomic and Biological Features of a Natural Vaccinia Virus Infecting Humans

“…As described previously, the BVV strains grouped into two well-defined clades which do not appear as each other’s closest relatives [19,20]. A recent study, using a genome-wide approach, grouped S2V a Brazilian VACV lineage with Cantagalo virus (CTGV) and the vaccine strain IOC [82]. However, the lack of additional genome sequences of Brazilian feral samples hampers a conclusive statement about their origins.…”

“…As a result, vaccine escape has been hypothesized to account for the origin of the Brazilian VACV (BVV) [8,18,19,20]. A recent study presented a close phylogenetic relationship between S2V, VACV-IOC (a smallpox vaccine strain used in Brazil) and the presumed ancestor-like horsepox virus (HSPV) [21]. …”

“…However, genetic comparison of the limited DNA sequence data collected thus far has been unable to sustain this hypothesis with regard to members of the more virulent group of BVV (group 2), suggesting that multifactorial events may best explain the genetic diversity present among the strains now circulating [19,20,21]. In vivo studies have shown that different BVV strains are quite different regarding virulence on intranasal infection in BALB/c mice [22].…”

Genome Sequence of Vaccinia virus Strain Lister-Butantan, a Lister Vaccine Variant Used during a Smallpox Eradication Campaign in Brazil

“…Due to this, several different strains were generated in different countries, leading ultimately to a slightly divergent variants of the Lister Elstree original strain (LO) ( 2 , 3 ). In Brazil, some laboratories received financial support for the development of freeze-dried vaccine production during earlier years of the national smallpox eradication campaign ( 1 , 4 ). In this work, we report the genome sequence of vaccine Vaccinia virus strain Lister-Butantan (LBT), a strain largely used during the national smallpox eradication campaign in Brazil.…”

Dairy production practices and associated risks for bovine vaccinia exposure in cattle, Brazil

“…Speculation about the origin and emergence of VACV strains has pointed towards either the escape of so-called feral smallpox vaccine strains [3] , [20] or the emergence of resident ancestral strains [6] , [7] , [14] , [21] , [22] . Neither hypothesis has been wholly successful at explaining the range of lineages observed, some with genetic similarities to historic smallpox vaccine strains and others without these similarities.…”