A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens

Abstract

Anthrax is a zoonotic disease that occurs naturally in wild and domestic animals but has been used by both state-sponsored programs and terrorists as a biological weapon. A Soviet industrial production facility in Sverdlovsk, USSR, proved deficient in 1979 when a plume of spores was accidentally released and resulted in one of the largest known human anthrax outbreaks. In order to understand this outbreak and others, we generated a Bacillus anthracis population genetic database based upon whole-genome analysis to identify all single-nucleotide polymorphisms (SNPs) across a reference genome. Phylogenetic analysis has defined three major clades (A, B, and C), B and C being relatively rare compared to A. The A clade has numerous subclades, including a major polytomy named the trans-Eurasian (TEA) group. The TEA radiation is a dominant evolutionary feature of B. anthracis, with many contemporary populations having resulted from a large spatial dispersal of spores from a single source. Two autopsy specimens from the Sverdlovsk outbreak were deep sequenced to produce draft B. anthracis genomes. This allowed the phylogenetic placement of the Sverdlovsk strain into a clade with two Asian live vaccine strains, including the Russian Tsiankovskii strain. The genome was examined for evidence of drug resistance manipulation or other genetic engineering, but none was found. The Soviet Sverdlovsk strain genome is consistent with a wild-type strain from Russia that had no evidence of genetic manipulation during its industrial production. This work provides insights into the world’s largest biological weapons program and provides an extensive B. anthracis phylogenetic reference.

Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia

“…The two other Yakut strains, Ya3 and Ya4, belong to the Transeurasian radiation TEA 008/011 [32]. TEA 008/011 is a remarkable polytomy currently including seven lineages.…”

“…Figure 3 displays a minimum spanning tree based on the whole genome SNPs detected among the 75 strains assigned to TEA 008/011. The branches are named as previously proposed [32]. Distances from root to tips differ by a ratio of 11 among the different lineages.…”

“…The color coding reflects the lineages within the A.Br.008/011 polytomy using the previously defined classification [32]. Geographic origin is indicated when known.…”

“…The dating of nodes along the B. anthracis phylogeny is particularly difficult and challenging because of the irregularity of its evolution due to its ecology [28, 32, 39]. In contrast with other pathogens such as Mycobacterium tuberculosis [36, 52, 53], branch length does not correlate with time, as investigated and discussed in detail by [32]. Rather branch length most likely reflects the number of infection opportunities per year [28] or more rarely a mutator phenotype [54].…”

Genome Sequence of the Soviet/Russian Bacillus anthracis Vaccine Strain 55-VNIIVViM

“…The B.Br.003 canSNP allele state in the strain 55-VNIIVViM genome reported here (B.Br.003=G) differs from that reported by Afanas’ev et al (B.Br.003=A) (12). In addition, preliminary whole-genome comparisons suggest strain 55-VNIIViM falls within the newly identified STI group (13). The genome of strain 55-VNIIVViM has been made available for further cross-strain comparisons with other global representatives of B. anthracis .…”