Version 1
: Received: 11 December 2020 / Approved: 14 December 2020 / Online: 14 December 2020 (09:21:34 CET)
How to cite:
Bergna, A.; Della Ventura, C.; Marzo, R.; Ciccozzi, M.; Galli, M.; Zehender, G.; Lai, A. Phylogeographical and Evolutionary History of Variola major Virus; A Question of Timescales?. Preprints2020, 2020120310. https://doi.org/10.20944/preprints202012.0310.v1
Bergna, A.; Della Ventura, C.; Marzo, R.; Ciccozzi, M.; Galli, M.; Zehender, G.; Lai, A. Phylogeographical and Evolutionary History of Variola major Virus; A Question of Timescales?. Preprints 2020, 2020120310. https://doi.org/10.20944/preprints202012.0310.v1
Bergna, A.; Della Ventura, C.; Marzo, R.; Ciccozzi, M.; Galli, M.; Zehender, G.; Lai, A. Phylogeographical and Evolutionary History of Variola major Virus; A Question of Timescales?. Preprints2020, 2020120310. https://doi.org/10.20944/preprints202012.0310.v1
APA Style
Bergna, A., Della Ventura, C., Marzo, R., Ciccozzi, M., Galli, M., Zehender, G., & Lai, A. (2020). Phylogeographical and Evolutionary History of <em>Variola major</em> Virus; A Question of Timescales?. Preprints. https://doi.org/10.20944/preprints202012.0310.v1
Chicago/Turabian Style
Bergna, A., Gianguglielmo Zehender and Alessia Lai. 2020 "Phylogeographical and Evolutionary History of <em>Variola major</em> Virus; A Question of Timescales?" Preprints. https://doi.org/10.20944/preprints202012.0310.v1
Abstract
In order to reconstruct the origin and pathways of variola virus (VARV) dispersion, we analyzed 47 VARV isolates available in public databases and their SNPs. The mean substitution rate of the whole genomes was 9.41x10-6 (95%HPD:8.5-11.3x10-6) substitutions/site/year. The time of the tree root was estimated to be a mean 68 years (95%HPD:60.5–75.9). The phylogeographical analysis showed that the Far East and India were the most probable locations of the tree root and of the inner nodes, respectively, whereas for the outer nodes it corresponded to the sampling locations. The Bayesian Skyline plot showed that the effective number of infections started to grow exponentially in 1915-1920, peaked in the 1940s, and then decreased to zero. Our results suggests that the VARV major strains circulating between 1940s-1970s probably shared a common ancestor originated in the Far East; subsequently moved to India, which became the center of its dispersion to eastern and southern Africa, and then to central Africa and the Middle East, probably following the movements of people between south-eastern Asia and the other places with a common colonial history. These findings may help to explain the controversial reconstructions of the history of VARV obtained using long- and short- term calibrations.
Keywords
Variola major; phylogeographical analysis; long-term calibrations; short- term calibrations
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Received:
22 December 2020
Commenter:
Dillon Adam
The commenter has declared there is no conflict of interests.
Comment:
Very interesting preprint, particularly the implementation of the Skyline Estimation.
I previously published on the phylogeography of Variola during my Ph.D. which would be worth citing and comparing to your results in any revised discussion.
Adam DC, Scotch M, MacIntyre CR. Bayesian phylogeography and pathogenic characterization of smallpox based on HA, ATI, and crMB genes. Molecular biology and evolution. 2018 Nov 1;35(11):2607-17.
We used a deeper timescale incorporating the Lithuanian strain which is why our root comes from Europe. But after that, you can see in Figure 4 our results that Southern Asia (India) and East Asia (Far East) are consistent with your analysis.
We also estimated a mean genome-wide evolutionary rate of 1.20 x 10-5 s/s/y (CI 1.12–1.28 × 10-5) seen in the Supplementary Results pdf which is very close and within your estimate and CI.
Commenter: Dillon Adam
The commenter has declared there is no conflict of interests.
I previously published on the phylogeography of Variola during my Ph.D. which would be worth citing and comparing to your results in any revised discussion.
Adam DC, Scotch M, MacIntyre CR. Bayesian phylogeography and pathogenic characterization of smallpox based on HA, ATI, and crMB genes. Molecular biology and evolution. 2018 Nov 1;35(11):2607-17.
https://academic.oup.com/mbe/article/35/11/2607/5067731
We used a deeper timescale incorporating the Lithuanian strain which is why our root comes from Europe. But after that, you can see in Figure 4 our results that Southern Asia (India) and East Asia (Far East) are consistent with your analysis.
We also estimated a mean genome-wide evolutionary rate of 1.20 x 10-5 s/s/y (CI 1.12–1.28 × 10-5) seen in the Supplementary Results pdf which is very close and within your estimate and CI.
Good luck with your peer-review.