Re-Assembly and Analysis of an Ancient Variola Virus Genome

Abstract

We report a major improvement to the assembly of published short read sequencing data from an ancient variola virus (VARV) genome by the removal of contig-capping sequencing tags and manual searches for gap-spanning reads. The new assembly, together with camelpox and taterapox genomes, permitted new dates to be calculated for the last common ancestor of all VARV genomes. The analysis of recently sequenced VARV-like cowpox virus genomes showed that single nucleotide polymorphisms (SNPs) and amino acid changes in the vaccinia virus (VACV)-Cop-O1L ortholog, predicted to be associated with VARV host specificity and virulence, were introduced into the lineage before the divergence of these viruses. A comparison of the ancient and modern VARV genome sequences also revealed a measurable drift towards adenine + thymine (A + T) richness.

Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

“…[ 37 ] Smithson et al . [ 39 ] mean tMRC 95% HPD mean tMRCA 95% HPD mean tMRCA mean tMRCA 95% HPD split VD21/P328/modern VARV 1651 1639–1662 1617 1588–1645 1350 1517 1470–1563 split P328/modern VARV 1701 1687–1714 na na na na na split P-I/P-II 1809 1797–1820 1764 1734–1793 1695 1623 1579–1667 split P-I internal 1911 1908–1915 1910 1902–1917 1887 1881 1861–1897 split P-II internal 1886 1877–1893 1870 1855–1885 1808 1794 1754–1828 …”

“…[ 36 ]. Bayesian analysis assuming a strict molecular clock and constant population size suggests a common ancestor between 1639 and 1662 AD for all VARV strains included in this study [ 37 , 39 , 70 – 72 ]. This is consistent with the common ancestor suggested between modern strains and VD21, dated to between 1588 and 1645 AD [ 36 ], and clearly younger than the common ancestor dated to 1350 AD suggested by Pajer et al .…”

“…Of the four historic strains included in our study, the younger V563 and V1588 [ 37 ] fall within the diversity of modern VARV strains, clustering in the P-I and P-II clades, respectively. By contrast, the seventeenth century VD21 [ 36 , 39 ] and the eighteenth century P328 both form their own sister groups to the twentieth century strains. This observation is consistent with modern VARV strains not being representative of past viral diversity and agrees with the scenario that selective pressure from increasing levels of vaccination caused several VARV lineages to disappear [ 3 , 36 ].…”

Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum

“…In sum, we suggest that the rates of nucleotide substitution and time-scale of VARV proposed by Duggan et al [ 2 ] are still the best evolutionary description of this historically important human pathogen, with no compelling evidence that available strains of VARV share a common ancestor as early as ~1350 AD. Given the highly variable branch lengths between VARV and other mammalian poxviruses, which likely result from very different rates of evolutionary change, we also believe it is unwise to use molecular clock methods to date the divergence between VARV and its closest animal relatives [ 3 ].…”

“…This is older than the time to common ancestry (1588–1645) previously determined by Duggan et al [ 2 ] following the description of a complete VARV genome (VD21) from a 17th century Lithuanian mummy, and implies that smallpox has greater antiquity in Europe. Herein we query the estimated ages of V1588 and V563 and hence the time-scale of smallpox evolution presented by Pajer et al [ 1 ], particularly as more recent studies have also utilized V1588 and V563 to date the antiquity of VARV [ 3 ].…”