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

Abstract

The complete genome sequences of two strains of variola virus (VARV) sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show that the two Czech strains exhibit anomalous branch lengths given their proposed age, and by assuming a constant rate of evolutionary change across the rest of the VARV phylogeny estimate that their true age in fact lies between 1918 and 1937. We therefore suggest that the age of the common ancestor of currently available VARV genomes most likely dates to late 16th and early 17th centuries and not ~1350 AD.

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

“…As there are discrepancies about the dating of samples V563 and V1588 [ 37 , 38 ], we used the Bayesian framework BEAST 2.5.2 [ 81 ] to estimate the tip dates for the historic genomes based on the time intervals given in the electronic supplementary material, table S2. These intervals cover the years from the original publication [ 37 ] and the corresponding comment [ 38 ]. We used uniform distributions for P328 (1760–1793 AD) and VD21 (1643–1665 AD) and normal distributions for V563 (mean: 1925, s.d.…”

Bayesian Phylogeography and Pathogenic Characterization of Smallpox Based onHA,ATI, andCrmBGenes

“…2016 ; Pajer et al. 2017 ; Porter et al. 2017 ) totalling 51 WG isolates ( supplementary table S1 , Supplementary Material online).…”

“…2010 ). We set the sampling year for the three WG isolates sampled from historic remains (BK010317, LT706528, and LT706529) to 1654, 1929, and 1925 respectively based on previous work ( Porter et al. 2017 ).…”

“…For final models, we specified the same substitution model under a strict molecular clocks and a constant coalescent tree prior based on model testing and previously published results ( Duggan et al. 2016 ; Porter et al. 2017 ).…”

Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation

“…Tracing back the environmental origins of ancient malarial strains, perhaps from preserved mosquitos or unique environmental samples, would also be important to better trace is distribution in the ancient past. Despite the exciting new questions that can be approaches using aDNA, it is also clear that strict aDNA methodologies must be performed during ancient viral and eukaryotic studies, as in bacterial studies, as the reliability of several ancient viral studies has already been questioned in the literature (Porter et al, 2017;Duchêne and Holmes, 2018).…”