Estimate How Many More Viruses We Can Expect To Discover
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8.8 years ago
Whetting ★ 1.5k

Hi boys and girls,
I am writing a review about the evolution of a specific virus family. I though it would be informative to try to estimate the diversity within this family of viruses. To date the community has isolated ~250 unique viral types. A unique type is defined as having <90% sequence identity across a certain ORF.
Does anyone know of any tools (I though about rarefaction curves) I could use to estimate the diversity? Calculating the effective population size may be a possibility? However, it requires one to know (or estimate) the viral evolutionary rate.
Any help would be greatly appreciated

metagenomics • 1.5k views
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Entering edit mode
8.8 years ago
Josh Herr 5.7k

That's a really difficult question to answer which has come up a bunch at meetings I have been to and also in the literature. You accented the problems already: sequence diversity, sampling, etc. It's similar to a question I am working on for microbial Eukaryotes -- I'm currently trying to address diversity by looking at how many species are not represented in databases, using BLAST hits and sequence homology. There are problems addressing this completely in a review; you should do a full and complex analysis and publish that.

Here's some papers I have bookmarked in this area that I have found useful: Delwart Review, Bexfield & Kellam Review, Schoenfeld Review, Roossinck Review, Steward & Preston Paper.

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thanks Josh. Those papers do look informative. The main issue with my dataset is that it is not a random sample. It may not be feasible...

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Entering edit mode

I have been having the same issue, but have tired to supplement my dataset with public data to try to solve this. It might be a problem with the lack of viral sequences from the environment? Some of the above reviews address how to capture more viral diversity. Best of luck.

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