Fix molecular clock based on literature search #38
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Lanciotti, et al, 1999. Origin of the West Nile virus responsible for an outbreak of encephalitis in the northeastern United States. Science, 286(5448), pp.2333-2337. https://www.science.org/doi/epdf/10.1126/science.286.5448.2333
Bakonyi, et al, 2006. Lineage 1 and 2 strains of encephalitic West Nile virus, central Europe. Emerging infectious diseases, 12(4), p.618. https://wwwnc.cdc.gov/eid/article/12/4/05-1379_article
Bakonyi, et al, 2005. Novel flavivirus or new lineage of West Nile virus, central Europe. Emerging infectious diseases, 11(2), p.225. https://wwwnc.cdc.gov/eid/article/11/2/04-1028_article
Chaintoutis, et al, 2013. West Nile virus lineage 2 strain in Greece, 2012. Emerging infectious diseases, 19(5), p.827. https://wwwnc.cdc.gov/eid/article/19/5/12-1418_article
Platonov, et al, 2001. Outbreak of West Nile virus infection, Volgograd Region, Russia, 1999. Emerging infectious diseases, 7(1), p.128. https://wwwnc.cdc.gov/eid/article/7/1/70-0128_article
From May et al, 2011 "Phylogeography of West Nile Virus: From the Cradle of Evolution in Africa to Eurasia, Australia, and the Americas" https://journals.asm.org/doi/10.1128/jvi.01963-10 "The mean rate of nucleotide substitution among all isolates of WNV is 7.55 x 10^-4 substitutions/site/year...This rate is comparable to that previously estimated for other flaviviruses...WNV show some heterogeneity among different genotypes, but all groups have various rates of between 2.24 x 10^-4 substitutions/site/year ... and 1.06 x 10^-3." Fixing the clock-rate at 0.00075 results in MRCA in auspice tree between 1600-1700 which matches the literature from Fall et al, 2017 "Biological and phylogenetic characteristics of West African lineages of West Nile virus" https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0006078 "The tMRCA of WNV is predicted to have originated in the late 16th/early 17th century (95%HPD: 1476–1765)"
From May et al, 2011 "Phylogeography of West Nile Virus: From the Cradle of Evolution in Africa to Eurasia, Australia, and the Americas" https://journals.asm.org/doi/10.1128/jvi.01963-10 Table 1, IS98-STD and North America 6.53E-04
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Consulted with @DOH-LMT2303 regarding the modifications. We compared our results to another repository that used a slightly different molecular clock rate (2e-4 instead of 7e-4). Despite this difference, both rates are of the same order of magnitude (10^-4) and represent an improvement over the original rate of 1.4e-5. Based on this discussion, we've decided to proceed with merging these changes, considering them an enhancement to the current setup. If needed, we can make additional refinements in future pull requests. |
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Description of proposed changes
For the West Nile Virus (WNV) global tree, the molecular clock estimates were too low. I searched the literature to find BEAST runs of the global WNV tree estimating average and lineage-based substitution rates per position per year to set the molecular clock in our global and Washington (WA) tree refinement steps. Literature sources are listed in the commit messages.
Before
View current WNV global tree: https://next.nextstrain.org/staging/WNV/genome
After
View fixed WNV global tree: https://next.nextstrain.org/staging/WNV/global
From this key commit: f34b755
I also used a literature search to set the clock rate on the Washington-focused build
View fixed Washington state tree: https://next.nextstrain.org/staging/WNV/WA?m=num_date
From this key commit: bf0ed7c
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